commit c94456cbdd26b2a5aab01f9df897edc719e4a5d6
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Mon May 1 15:21:58 2023 -0400
add chemical potential to problem namespace (#2434)
Exec/science/subchandra/_prob_params
commit 3b36e5d3a3378af2d02dd8e16120d8d1454cb49a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 10:50:13 2023 -0400
update changes
CHANGES.md
commit 8bbd3cfe29f6331b7f6ddf6d2e95de122b8a27b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 10:47:37 2023 -0400
update to 23.05
external/Microphysics
external/amrex
commit 93f66e4fddf52fd6e9bdeb91b81e5204709c1e6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 08:45:29 2023 -0400
fix radiation compile due to merge conflict (#2432)
this is from #2428 and #2415 changing the same code
Source/radiation/RadPlotvar.cpp
commit 8dd673cd719858c3c1f3f28d49179016afa21062
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 08:00:17 2023 -0400
sync up with Microphysics removal of abort_on_failure (#2431)
we rely on the retry or if retry is off, then Castro to abort
Source/driver/Castro_setup.cpp
commit 81e05558ca1d0da41252fd6c4ead937686cfaeef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 28 21:44:12 2023 -0400
add a codespell CI action (#2430)
.codespell-ignore-words
.codespellrc
.github/workflows/codespell.yml
Docs/source/rad.rst.old
Exec/radiation_tests/RadSphere/inputs
Exec/science/convective_flame/initial_model.H
Exec/science/flame/inputs.H_He
Exec/science/flame/problem_initialize.H
Source/hydro/outline.txt
requirements.txt
commit 631491b7425556df0dd7cb9932eeadc7271e35b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 28 21:43:39 2023 -0400
Fix indexing in plotfile radiation lab/COM flux (#2415)
This looks like it was an error in the port from Fortran in #1700. This should address the issue in #2413.
Source/radiation/RadPlotvar.cpp
commit 2affa95203f703868c8fb147c2b4afea18f9cbb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 28 20:45:52 2023 -0400
remove the old Fortran checker script (#2425)
Util/code_checker/fortran_checker.py
commit 48b37c46ba313dbfb4d67ef8bcd3e74489d0c25c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 28 20:42:29 2023 -0400
update / fix the diffusion docs (#2429)
they were still referring to the Fortran way
Docs/source/diffusion.rst
Docs/source/refs.bib
commit ccc2333e5f0c21c9534aac663d5f6e9fb52282ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 28 20:38:39 2023 -0400
more spelling fixes (#2427)
CHANGES.md
Diagnostics/DustCollapse/main.cpp
Diagnostics/Radiation/README.md
Diagnostics/Sedov/README.md
Exec/gravity_tests/StarGrav/problem_initialize_mhd_data.H
Exec/gravity_tests/hse_convergence/README.md
Exec/gravity_tests/hse_convergence/initial_model.H
Exec/gravity_tests/hse_convergence_general/initial_model.H
Exec/mhd_tests/Alfven/README
Exec/mhd_tests/MagnetosonicWaves/README
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/Rad2Tshock/python/Analytical-Test.py
Exec/radiation_tests/RadBlastWave/inputs.1d
Exec/radiation_tests/RadBlastWave/inputs.2d
Exec/radiation_tests/RadBlastWave/inputs.3d
Exec/radiation_tests/RadBlastWave/inputs.3d.test
Exec/radiation_tests/RadBlastWave/inputs.kp
Exec/radiation_tests/RadBlastWave/inputs.kp.2d
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/inputs.1d.test
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadSphere/Tools/fradsphere.f90
Exec/radiation_tests/RadSuOlson/inputs
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadThermalWave/inputs.1d
Exec/radiation_tests/RadThermalWave/inputs.1d.test
Exec/radiation_tests/RadThermalWave/inputs.2d
Exec/radiation_tests/RadThermalWave/inputs.2d.test
Exec/radiation_tests/RadThermalWave/inputs.3d
Exec/radiation_tests/RadThermalWave/inputs.3d.test
Exec/reacting_tests/bubble_convergence/initial_model.H
Exec/science/Detonation/nse_runs/README.md
Exec/science/Detonation/nse_runs/setup_runs.py
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
Exec/science/flame_wave/initial_model.H
Exec/science/nova/problem_initialize.H
Exec/science/planet/HotJupiter.cpp
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/inputs
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/unit_tests/diffusion_test/README.md
Source/driver/set_variables.py
Source/radiation/HypreMultiABec.H
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/trace_ppm_rad.cpp
Source/sdc/Castro_sdc_util.H
Util/exact_riemann/riemann_support.H
commit 74750db38b6680773bff73d309823db25754c086
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 28 20:37:23 2023 -0400
move some more radiation parameters to _cpp_parameters (#2428)
Source/driver/_cpp_parameters
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
commit 56573d78a37c2069bb17bd07fbb201516ae05e34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 28 20:36:44 2023 -0400
fix misspelled parameter names (#2426)
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
commit f9272dfba91336244b5b7285e6688f3ee5604afa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 26 16:42:11 2023 -0400
some codespell fixes (#2424)
Docs/source/AMR.rst
Docs/source/FlowChart.rst
Docs/source/Verification.rst
Docs/source/build_system.rst
Docs/source/creating_a_problem.rst
Docs/source/faq.rst
Docs/source/io.rst
Docs/source/mpi_plus_x.rst
Docs/source/radiation.rst
Docs/source/rotation.rst
Docs/source/software.rst
Docs/source/timestepping.rst
Exec/Make.Castro
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/_cpp_parameters
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/fourth_order.cpp
Source/hydro/riemann_solvers.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/mhd/Castro_mhd.cpp
Source/mhd/ct_upwind.cpp
commit b19bc86260dc3f075604585cda1e4ffd934f3df0
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Mon Apr 17 19:56:08 2023 -0400
Fix clang-tidy warnings from flame_wave (#2422)
.clang-tidy
Source/diffusion/Diffusion.H
Source/driver/Castro.H
Source/driver/parse_castro_params.py
Source/driver/set_variables.py
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/sources/Castro_sources.H
Util/scripts/write_probdata.py
commit 519fc54577195b1774e559343b4ce6984344a239
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 16 14:11:34 2023 -0400
remove some unused vars in massive_star (#2418)
Exec/science/massive_star/problem_initialize_state_data.H
commit d609468a9f7798b0942667a8831ec8d7c1dcdbfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 16 14:11:09 2023 -0400
we already have ql_arr / qr_arr, so don't redo .array() (#2419)
Source/hydro/Castro_ctu_hydro.cpp
commit b6d6fbd03d123017f6e0d2c7799e2ccea56ed31b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 16 14:10:48 2023 -0400
add some frontier scaling numbers (#2411)
Exec/science/flame_wave/scaling/frontier/frontier-scaling-2023-04-06.txt
Exec/science/flame_wave/scaling/frontier/frontier_flame_wave_scaling.png
Exec/science/flame_wave/scaling/frontier/frontier_flame_wave_scaling_by_gpus.png
Exec/science/flame_wave/scaling/frontier/frontier_scaling.py
Exec/science/flame_wave/scaling/summit/scaling_20230407.txt
commit 27602695d1fe4a0f50c6be02c645db580ef54aa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 16 11:11:40 2023 -0400
put the im2, im1, i0, ... indices into a namespace (#2420)
this is safer, and also makes it easier to adapt
Source/hydro/Castro_mol.cpp
Source/hydro/ppm.H
Source/hydro/reconstruction.H
Source/hydro/slope.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
commit dc5a63a14c85d780a495412d57021131520dc8e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 13 18:31:55 2023 -0400
update the mailmap (#2417)
.mailmap
commit ea050c895695b98064ba527bebfc7db0da7dad29
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 13 18:16:38 2023 -0400
MHD clang tidy (#2401)
.clang-tidy
Exec/mhd_tests/BrioWu/problem_initialize.H
Exec/mhd_tests/BrioWu/problem_initialize_mhd_data.H
Exec/mhd_tests/BrioWu/problem_initialize_state_data.H
Source/driver/Castro.cpp
Source/driver/sum_integrated_quantities.cpp
Source/driver/timestep.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Make.package
Source/hydro/advection_util.cpp
Source/hydro/flatten.cpp
Source/mhd/Castro_mhd.cpp
Source/mhd/hlld.cpp
Source/problems/Castro_problem_source.cpp
Source/sources/Castro_geom.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_thermo.cpp
commit 1c684935ae8f1c8767b8e8f18288cdb7e3e83cdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 13 15:40:13 2023 -0400
make functions static (#2414)
this was done automatically via clang-tidy
Co-authored-by: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Source/gravity/Gravity.H
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util.cpp
Source/reactions/Castro_react.H
Source/sources/Castro_sources.H
Source/sources/Castro_thermo.cpp
commit 8aa9bad61b5f85214af1c891bfce1180951588ce
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Thu Apr 13 13:50:19 2023 -0400
Remove some erroneous includes of Castro_hydro.H (#2416)
This header should only be included from within the Castro class in
Castro.H.
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_rad.cpp
Source/hydro/edge_util.cpp
commit 4402e6bb6fdb1c6c18d9fd053b59f57a4192ff09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 11 15:24:52 2023 -0400
add CLANG_TIDY_CONFIG_FILE (#2397)
this allows us to use the AMReX GNU Make clang-tidy build
.clang-tidy
Docs/source/debugging.rst
Exec/Make.Castro
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/sum_utils.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/hydro/riemann.H
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/problems/problem_checkpoint.H
Source/problems/problem_restart.H
Source/sources/Castro_sources.H
Util/model_parser_cxx/model_parser.H
commit c2542242ec00a4bab44e82ebdbde40c3b8f8aaef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 8 20:21:01 2023 -0400
remove the "experimental" note for HIP (#2412)
Docs/source/mpi_plus_x.rst
commit 063c27faf5de399a19621682d34c931c21844fcb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 8 20:20:39 2023 -0400
don't do limit_hydro_fluxes_on_small_dens with MHD (#2402)
This would not have been an issue until we added multilevel to MHD, but better fix it now
Source/driver/Castro.cpp
commit c4f7b300a0d77147015193eeb1557d4fd22a5eff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 7 14:29:37 2023 -0400
remove derived in_nse plot var and rename new one to in_nse (#2409)
We switched from deriving whether we are in NSE for the plotfiles and instead
using the NSE state stored in the Reactions_Type StateData. This change eliminates
the duplicated derived in_nse plot variable and renames the new Reactions_Type
plot variable to in_nse. This makes our scripts compatible with the way of computing
it without needing to change them.
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
commit 91ac2674479443e4b9ef3c78c6d4886a6e62a1cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 7 07:48:51 2023 -0400
disable Jacobian caching for the massive star (#2410)
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
commit abeccccb9055c86f95a6003756895bafade12168
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 4 13:36:27 2023 -0400
add a script to automate massivestar vis on OLCF Andes (#2406)
Exec/science/massive_star/analysis/andes-slice.submit
Exec/science/massive_star/analysis/massive_star_multi.py
commit 68c92753d363077f662332f23e66e741895d5fd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 3 16:10:13 2023 -0400
add a link check to the docs (#2408)
this will fail if any of the external links cannot be resolved
.github/workflows/docs-test.yml
Docs/source/AMR.rst
Docs/source/Preface.rst
Docs/source/conf.py
Docs/source/refs.bib
commit 7ba21e2cac7a885cd329ebc28c7ec2e38a734ca4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 1 09:37:47 2023 -0400
update to 23.04
CHANGES.md
external/Microphysics
external/amrex
commit f4ff573dd0b55027e7c7a7f11a55c7db8f740e70
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Thu Mar 30 22:32:55 2023 -0400
Make sure generated code is identical between make runs (#2407)
This fixes cache misses when using ccache.
Source/driver/parse_castro_params.py
Source/driver/set_variables.py
commit 1be2962ce60e162f104c7c821bc7c492eceff571
Author: Khanak Bhargava <56127611+khanakbhargava@users.noreply.github.com>
Date: Wed Mar 29 07:56:28 2023 -0400
Added output file parameter in sphinx (#2404)
Docs/source/io.rst
commit f84bee6a26e053054469540be289c48edf130e68
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Tue Mar 28 16:25:33 2023 -0400
initialize ye for SDC (#2403)
Need to initialize ye for simplified-SDC to avoid uninitialized errors for NSE_NET.
Did the same for Strang.
Source/reactions/Castro_react.cpp
commit ff559716a43013351c375c28c95551bdd14e14df
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Tue Mar 28 14:58:03 2023 -0400
add nse status of burn_t to reactions_type (#2390)
this allows us to capture whether we are in NSE directly from the burn, which works better for the cases where we bail out of integration and into NSE
Source/driver/Castro_setup.cpp
Source/reactions/Castro_react.cpp
commit 8309823c4341c1236d48aed35ea8fea3b456d168
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 24 14:39:20 2023 -0400
we don't need mhd_sizes.H in Castro.H (#2400)
Source/driver/Castro.H
commit 7e0f49884c9429b7fc7a2dc9817c2c682398596f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 16:34:41 2023 -0400
fix wrong comment and indentation in nse_test problem init (#2399)
Exec/reacting_tests/nse_test/problem_initialize_state_data.H
commit a5407e248a5bdd61b81b129a532804c8b5c728e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 09:28:58 2023 -0400
update the scripts for nse_test with vel (#2398)
they had the wrong plotfile numbers
Exec/reacting_tests/nse_test/convergence_simplified_sdc_w_vel.sh
Exec/reacting_tests/nse_test/convergence_strang_w_vel.sh
commit 2ceb4ee920a155f5ed977e22a32935de0967108c
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Wed Mar 22 08:29:57 2023 -0400
add NSE_NET compatibility for the detonation problem (#2369)
Exec/science/Detonation/GNUmakefile
Exec/science/Detonation/_prob_params
Exec/science/Detonation/inputs-det-x.nse_net
Exec/science/Detonation/problem_initialize_state_data.H
commit 3402d3973243a9b02000f803507211a09da9ef01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 08:29:26 2023 -0400
fix some issues with the flux limiting docs (#2394)
Docs/source/Hydrodynamics.rst
commit 2433cabb33d40779ad690a5fb9b9c286f4384c09
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Tue Mar 21 09:12:47 2023 -0400
add sphinx_rtd_theme to extensions (#2396)
Docs/source/conf.py
commit e8cab45ef3e66f0e338f679eef295092f1bdb3e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 16 07:45:52 2023 -0400
sync xrb_mixed up with the MAESTROeX version (#2371)
Exec/science/xrb_mixed/inputs_2d
Exec/science/xrb_mixed/problem_initialize.H
Exec/science/xrb_mixed/toy_xrb.hi_dens.hse.tanh.delta_12.000cm.dx_6.000cm.CNO
Exec/science/xrb_mixed/toy_xrb.hi_dens.hse.tanh.delta_12cm.dx_6cm
commit 17ee5df0a5ab0c6425d204b4021a0124f0c987a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 08:49:37 2023 -0400
Even more clang tidy fixes (#2392)
.clang-tidy
Exec/science/flame_wave/problem_initialize.H
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/CastroBld.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_util.H
Source/driver/main.cpp
Source/driver/sum_integrated_quantities.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.cpp
Source/hydro/ppm.H
Source/problems/hse_fill.cpp
Source/scf/scf_relax.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
commit 4e534c06a1bfc154dc7edcf2adbf0d267c78cfab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 19:16:26 2023 -0400
add more 3-d flame_wave plotting scripts (#2388)
Exec/science/flame_wave/analysis/vis_3d/andes-slice.submit
Exec/science/flame_wave/analysis/vis_3d/andes.submit
Exec/science/flame_wave/analysis/vis_3d/slice_vertical.py
Exec/science/flame_wave/analysis/vis_3d/vol-xrb-abar.py
Exec/science/flame_wave/analysis/vis_3d/vol-xrb-enuc.py
commit 1c0509d5d2c1c4ea96e2597255ac9fdc9fce8728
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 19:09:20 2023 -0400
add code of conduct (#2393)
code_of_conduct.md
commit 025cf7b58f0bf83bf8a24a5410ccbac177e009c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 18:34:40 2023 -0400
update the massive_star inputs (#2383)
remove the 1- and 3-d cases -- these are not kept up to date switch to cubic NSE interpolation
make the NSE density consistent with the table
switch to analytic Jacobian
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_1d.nse.sdc
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
Exec/science/massive_star/inputs_3d.nse
commit c5d832a60028d9c43f2b376c0a63724078092193
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Tue Mar 14 18:32:05 2023 -0400
Cleaning unused nova files (#2387)
Exec/science/nova/glasner_T51600.hse
Exec/science/nova/glasner_T9_1e+04cm.hse
Exec/science/nova/glasner_enriched1600.hse
commit abadb9176382e41a2b0774778a1d2e70fb5cfcbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 07:36:11 2023 -0400
More tidy fixes (#2380)
.github/workflows/c-linter.yml
Exec/science/flame_wave/problem_initialize.H
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/main.cpp
Source/driver/runtime_parameters.H
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_util.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/riemann_solvers.H
Source/hydro/trace_ppm.cpp
Source/problems/Castro_problem_source.cpp
Source/rotation/Castro_rotation.cpp
Source/scf/scf_relax.cpp
Source/sources/Castro_geom.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
Util/model_parser_cxx/model_parser.H
commit 0304294be5a7220e4583d3c2286dca9eae683b92
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Wed Mar 8 19:16:27 2023 -0500
add files for compling subchandra with NSE_NET (#2391)
add input files to compile subchandra with NSE_NET.
Neutron is added to the new model file for the ase network.
Exec/science/subchandra/GNUmakefile.nse_net
Exec/science/subchandra/inputs_2d.N14_NSE
Exec/science/subchandra/problem_initialize_state_data.H
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.CO.N14.N.10.00km
commit 11cc0c2dea39930e2b8a72d2ba82b95b5e970798
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 2 18:59:49 2023 -0500
test on empty strings instead of comparing to "" (#2386)
this makes clang-tidy happier
Exec/gravity_tests/hse_convergence_general/problem_initialize.H
Exec/reacting_tests/reacting_convergence/problem_initialize.H
commit f11295fa353cb7bf11a2aa4336df3b403153c12e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 13:50:40 2023 -0500
update changes
CHANGES.md
commit 0ce23795c4176fe41009823a899b9d7497a6cec6
Merge: d38883281 650457e02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 13:48:55 2023 -0500
Merge branch 'development'
commit 650457e02eb4344c48725cc63b5eb4d7f943614f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 13:48:37 2023 -0500
update to 23.03
external/Microphysics
external/amrex
commit 9d50cb1a94cfa617c04e4a8543cc47638ba9f0ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 13:36:42 2023 -0500
address some clang-tidy issues (#2379)
mostly narrowing and nullptrs
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Castro_util.H
Source/driver/main.cpp
Source/gravity/Gravity.cpp
Source/hydro/trans.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.cpp
commit 85a50fad458d01277aeda001ca1066bd0bd83afd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 07:35:44 2023 -0500
add a plot script for the nova problem (#2378)
Exec/science/nova/analysis/nova_slice.py
commit 64dea9509306be32551c9549dd8c2d5802f8864a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 07:35:04 2023 -0500
disable a few more clang-tidy checks (#2385)
.clang-tidy
commit 97cf489854f9d3ff9643c70053b5115faaebdc26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 28 08:23:52 2023 -0500
add a new CI action on SDC Detonation (#2376)
this tests 1-d as well as simplified SDC
.github/workflows/detonation-sdc-compare.yml
Exec/science/Detonation/ci-benchmarks/sdc_det_plt00040_extrema.out
commit 0ea215c63ccdd533ad305d19303c870af875d8b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 27 16:03:27 2023 -0500
for nse_test use cubic interp if we are using the NSE table (#2384)
Exec/reacting_tests/nse_test/inputs.128
Exec/reacting_tests/nse_test/inputs.256
Exec/reacting_tests/nse_test/inputs.256.test
Exec/reacting_tests/nse_test/inputs.512
Exec/reacting_tests/nse_test/inputs.64
commit 45975047f0e46baaea97539358424e7ba3a03145
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 27 14:45:27 2023 -0500
use a .clang-tidy file for the CI action (#2381)
.clang-tidy
.github/workflows/c-linter.yml
commit 89201c02d59af0787f6b17545475adac6261c87e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 08:12:34 2023 -0500
remove an #ifdef GRAVITY nested in #ifdef GRAVITY (#2382)
Source/driver/Castro.cpp
commit 91f954a0006b88b79cede0ce3972781dcf57bb52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 24 08:24:33 2023 -0500
add CI on GCC compiler warnings (#2373)
.github/workflows/compiler-warnings.yml
Exec/science/Detonation/problem_initialize_state_data.H
Exec/science/Detonation/problem_source.H
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/problem_source.H
Exec/science/wdmerger/wdmerger_util.H
Exec/science/wdmerger/wdmerger_util.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_util.H
Source/driver/timestep.cpp
Source/gravity/binary.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/advection_util.cpp
Source/hydro/trans.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
commit 76337b0828491bdace68261702ced25bc424a17b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 18:53:30 2023 -0500
provisionally define CASTRO_HOME for wdmerger (#2374)
Exec/science/wdmerger/GNUmakefile
commit a618d3bfa9a0321250489d39128482b74cab2ee9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 14:30:19 2023 -0500
check HSE after reading in the model (#2377)
Exec/science/nova/problem_initialize.H
commit 42e281783d95c230892cb64867f5be4a294d3a95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 22 14:41:27 2023 -0500
silence more compiler warnings (#2360)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Castro_util.H
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/driver/timestep.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_util.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol.cpp
Source/hydro/advection_util.H
Source/hydro/advection_util.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/problems/Castro_problem_source.cpp
Source/problems/ambient_fill.cpp
Source/problems/hse_fill.cpp
Source/problems/problem_bc_fill.H
Source/problems/problem_checkpoint.H
Source/problems/problem_restart.H
Source/problems/problem_source.H
Source/problems/problem_tagging.H
Source/reactions/Castro_react.cpp
Source/sources/Castro_geom.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit 3b4bb12a31c91ed3d7bda9cb01629469b0f931ea
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Wed Feb 22 11:23:12 2023 -0500
Adding Difussion to nova (#2372)
Exec/science/nova/GNUmakefile
Exec/science/nova/glasner_T7_1e+04cm.hse
Exec/science/nova/inputs_nova_t7
commit 5a867ca5c04f38c47aa9dd4db709abbdb2455ba7
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Sat Feb 18 11:29:45 2023 -0500
Extending the T7 initial model crust inward keeping hse (T=constant) (#2368)
Exec/science/nova/glasner_T7_1e+04cm.hse
commit ed328a8dbccaa79aa0ddf21048b6cf70e6d919c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 17 16:58:46 2023 -0500
improve the default inputs file (#2367)
remove unused inputs
Exec/science/Detonation/README.md
Exec/science/Detonation/analysis/compare_plot.py
Exec/science/Detonation/analysis/profiles.py
Exec/science/Detonation/analysis/shock_speed.py
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.nse
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc2
commit fc251492d99f716cd1973e5866164833f08f69fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 12 17:01:12 2023 -0500
only add Ye if we are reacting (#2365)
Source/driver/Castro_setup.cpp
commit a99a2ce48bffbbbf3d122de911c4a8eca1d2c469
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 11 20:27:14 2023 -0500
fix the indexing of a derive (#2364)
it was using the old names
Exec/gravity_tests/hydrostatic_adjust/Problem_Derives.H
commit 2beeb7491225dbc8e50ea6424541d96e4fb068a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 11 15:29:48 2023 -0500
Merge main 23.02 (#2363)
We never merged main back into development after tagging 23.02
Docs/source/FlowChart.rst
external/Microphysics
external/amrex
commit d40ca41b259cd130cfb5a3e872fc4a84658296b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 11 12:36:42 2023 -0500
remove the old Castro state indices (#2362)
these have long been replaced by the versions from _variables
Source/driver/Castro.H
commit a853402c7e30539f480fc6b227b8fa0b8471bb76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 10 13:37:37 2023 -0500
add Ye as a derived variable (#2361)
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
commit 4522d745494b4657eec33417849102c23bc3f462
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 9 13:55:03 2023 -0500
silence some compiler warnings (#2358)
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_util.H
Source/hydro/advection_util.cpp
commit ffc7a30560eada2d69756d07cf05697a3221b534
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Thu Feb 9 12:38:02 2023 -0500
add tolerance for NSE_NET in nse_test (#2359)
Adds a tolerance for NSE_NET in nse_test. Changed tolerance to 100 instead of 0.1 (default value) to ensure we're always in NSE since in this unit test we primarily test for nse_burn.
Exec/reacting_tests/nse_test/_prob_params
Exec/reacting_tests/nse_test/inputs.128
Exec/reacting_tests/nse_test/inputs.256
Exec/reacting_tests/nse_test/inputs.512
Exec/reacting_tests/nse_test/inputs.64
Exec/reacting_tests/nse_test/problem_initialize_state_data.H
commit 09845e315367cc41e49f494b8a656b0fc56c9e11
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Wed Feb 8 12:36:51 2023 -0500
Add chemical potential to State_Type (#2354)
Add chemical potential to State_Type for the NSE solver initial guess
Addresses Issue #2347
Exec/reacting_tests/nse_test/problem_initialize_state_data.H
Source/driver/Castro_setup.cpp
Source/driver/Derive.cpp
Source/driver/_variables
Source/driver/timestep.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/riemann.H
Source/hydro/riemann_solvers.H
Source/hydro/riemann_util.cpp
Source/reactions/Castro_react.cpp
commit babec27eb989a9d9d61e7444d12f2093e205056b
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Mon Feb 6 18:59:09 2023 -0500
fix typo (#2357)
Source/hydro/Castro_mol_hydro.cpp
commit d38883281e7b4b86cbd526ccaca06cda89c74c11
Merge: dec21f515 d6813142f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 1 12:48:00 2023 -0500
Merge branch 'development'
commit d6813142f750f3484ed42f6bfc64e06f8e123a47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 1 12:47:11 2023 -0500
update to 23.02
external/Microphysics
external/amrex
commit 39382f3e8a99ba0df4f3180e9837d389b9ac8ed4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 1 12:22:50 2023 -0500
add an action to check the ifdefs (#2356)
this makes sure that we don't mistype a define
Co-authored-by: Eric T. Johnson <yut23@users.noreply.github.com>
.github/workflows/check-ifdefs.yml
.github/workflows/check_ifdefs.py
.github/workflows/good_defines.txt
commit 5599e7ccadb4b0be9052c252dd7370eb80b4e78a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 31 16:09:01 2023 -0500
use different conditions for nse_test (#2353)
This is hotter, denser, and also ensures that we don't end with a single tiny step
at the end (which destroys convergence). To converge well, tricubic interpolation
of NSE is needed.
Exec/reacting_tests/nse_test/convergence_simplified_sdc.sh
Exec/reacting_tests/nse_test/convergence_strang.sh
Exec/reacting_tests/nse_test/inputs.128
Exec/reacting_tests/nse_test/inputs.256
Exec/reacting_tests/nse_test/inputs.512
Exec/reacting_tests/nse_test/inputs.64
commit ea6c85cf3d9371a475e28e2315addadf0f559f94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 31 15:49:28 2023 -0500
update massive_star to use burn_t version of in_nse (#2355)
Exec/science/massive_star/problem_initialize_state_data.H
commit 165eb8c7543b59a038e3ee71a29ac1e1607e8061
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 30 20:12:25 2023 -0500
change the in_nse() check in timestep to work on burn_t (#2348)
this will allow us eventually to remove the in_nse(eos_t) specialization
Source/driver/Derive.cpp
Source/driver/timestep.cpp
commit a2fda2438d080d70deddbb85edd2071b2311e9dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 30 07:21:09 2023 -0500
update flame analysis to use hint="castro" for yt.load (#2351)
also some linting
Exec/science/flame/analysis/flame_speed.py
Exec/science/flame/analysis/flame_speed_convergence.py
Exec/science/flame/analysis/profile_start_finish.py
Exec/science/flame/analysis/profiles.py
Exec/science/flame/analysis/profiles_zoom.py
commit 69c1508041bad683666bcefc42cad2540861f0e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 29 16:57:29 2023 -0500
update the flowchart based on some recent changes (#2343)
Docs/source/FlowChart.rst
Docs/source/refs.bib
commit 91c91fcdf4b663dbe0e46c1c439235be4d160acd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 26 08:33:42 2023 -0500
for Strang burn or NSE, set T_fixed (#2345)
this is needed for drive_initial_convection to ensure that the
energy of the cell is not computed based on T_fixed
Source/reactions/Castro_react.cpp
commit 08651568d0f96a6cf65294c07d733f24095f1125
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Wed Jan 25 14:59:05 2023 -0500
modifying the blocking factor parameter (#2349)
Exec/science/nova/inputs_nova_t7
commit 3fdf87713e30518958f31cbf8dfa7e22959f563e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 24 11:23:12 2023 -0500
allow for an ambient velocity field in the nse_test problem (#2346)
Exec/reacting_tests/nse_test/_prob_params
Exec/reacting_tests/nse_test/convergence_simplified_sdc_w_vel.sh
Exec/reacting_tests/nse_test/convergence_strang_w_vel.sh
Exec/reacting_tests/nse_test/problem_initialize_state_data.H
commit bb2758482bcab1b989b8efb555a66369898ed25a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 20 10:34:07 2023 -0500
fix NAUX -> NAUX_NET (#2341)
The preprocessor define is NAUX_NET
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive.cpp
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.cpp
Exec/reacting_tests/reacting_bubble/Problem_Derive.cpp
commit 111d2fb9500ca522f3461ee9c73ea8a321421cf8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 19 09:49:41 2023 -0500
fix an AMREX_SPACEDIM (#2340)
Source/driver/timestep.cpp
commit abbd8430b4173437e9b5d53a4e99aee9c87d9442
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 19 09:39:59 2023 -0500
simplify some ifdefs to make our checking easier (#2339)
Exec/reacting_tests/nse_test/problem_initialize.H
Source/driver/Castro.cpp
commit d760f9747e31caa51e02e130a20936e59d7d8df4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 18 13:22:28 2023 -0500
fix #ifdef REACTION -> #ifdef REACTIONS (#2338)
Source/driver/sum_integrated_quantities.cpp
commit 78178b78e92deb5277bc67349123ce54c8cc7e78
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Wed Jan 11 21:08:47 2023 -0500
update nse make option (#2335)
Update tabulated nse make option with Microphysics.
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/nse_test/problem_initialize.H
Exec/science/Detonation/GNUmakefile.nse
Exec/science/massive_star/GNUmakefile
commit dec21f515b0e6c61978f87f69162000cfe8ba398
Author: Y.Liu <55120383+Tom-Y-Liu@users.noreply.github.com>
Date: Tue Jan 10 15:10:38 2023 -0500
Update FlowChart.rst (#2334)
Corrected one possible typo. "Single Step Flowchat" -> "Single Step Flowchart"
Docs/source/FlowChart.rst
commit c82f2cb993e76bade14e2fe6a72de3d49732eb10
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Tue Jan 10 10:35:00 2023 -0500
updating resolution of the finest level with the init_model one (#2333)
Exec/science/nova/inputs_nova_t7
commit 63195e409ceb7829858d35e2a9dab4ff0367e830
Merge: 45d01ffe1 48c33b84a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 13:10:56 2023 -0500
Merge branch 'main' into development
commit 48c33b84a9f42e12deedc2b53e114ab1387a0714
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 13:10:33 2023 -0500
update for 23.01
CHANGES.md
commit 37029bd23736568847b84bb56a8f7ecb948d5fce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 13:08:41 2023 -0500
update for 23.01
external/Microphysics
external/amrex
commit 45d01ffe1d4e4ad80e453bac8b0f2a679f9653fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 24 19:53:50 2022 -0500
get the Sedov diagnostic tools building again (#2297)
this converts the Sedov diagnostic tool to C++ and now it builds again. I compared the 3-d spherical and 2-d spherical and cylindrical Sedov explosions to the old Fortran script and the output agrees to roundoff
Diagnostics/Sedov/GNUmakefile
Diagnostics/Sedov/Make.package
Diagnostics/Sedov/Sedov_F.H
Diagnostics/Sedov/main.cpp
Diagnostics/Sedov/sedov_util.f90
commit 5f3dd2aaaf39aa347d498acbbbc2e7e674b0bc13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 23 10:51:38 2022 -0500
get nse_test working with self-consistent NSE (#2331)
this way we can run without the table
Exec/reacting_tests/nse_test/problem_initialize.H
Exec/reacting_tests/nse_test/problem_initialize_state_data.H
commit 8b131d1862fd2fa0945265fb9ef2dc1bfdc4c3bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 22 08:42:02 2022 -0500
add a new nse_test inputs (#2329)
this gives a better comparison for the changes in T/Ye
also add a plotting script
Exec/reacting_tests/nse_test/analysis/slice_multi.py
Exec/reacting_tests/nse_test/inputs.256.test
commit 84be662677d0368f5ed15ab0a92fafda8c19bdfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 22 08:41:41 2022 -0500
clean up wht nse_test convergence script (#2328)
this now gives nicer output with `--simple`
Exec/reacting_tests/nse_test/create_pretty_tables.py
commit 8978569ca1c17c9b551b7f3c81092e4bd0af6522
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 22 08:41:18 2022 -0500
remove the timestep limiter diag tool (#2332)
we now report where the timestep limit is set as Castro is run
and the runtime version supports all of the limiters
Diagnostics/timestep_limiter/GNUmakefile
Diagnostics/timestep_limiter/Limiter_F.H
Diagnostics/timestep_limiter/Make.package
Diagnostics/timestep_limiter/limiter_util.F90
Diagnostics/timestep_limiter/main.cpp
Diagnostics/timestep_limiter/probin
commit 4bbdf33fad611ec8550097153a52c8b5bd2f6128
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 20 18:23:51 2022 -0500
fix compilation of the massive star problem (#2330)
Exec/science/massive_star/problem_initialize_state_data.H
commit 3ad2ef0c0724c9e3150a5390787b85fafa595208
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Wed Dec 14 19:57:01 2022 -0500
Convert science/flame to new problem diagnostics scheme (#2327)
The code is the same as toy_flame (see #1458)
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame/inputs.1d
Exec/science/flame/inputs.1d.aprox13
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame/inputs.H_He
Exec/science/flame/problem_diagnostics.H
Exec/science/flame/problem_initialize.H
Exec/science/flame/sum_integrated_quantities.cpp
commit e473a3c5d4573834323623bf6791e3d28b60ca9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 20:24:24 2022 -0500
set the aux state in Detonation problem_initialize (#2326)
this is needed if we are doing AUX_THERMO
Exec/science/Detonation/problem_initialize.H
commit debbe0b7862c4aa17fc9f9dd920c83a1ddecac57
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 4 13:33:33 2022 -0500
Don't subtract initial energy in burn (#2310)
This will allow us to update Microphysics so that burn_state.e is always the real internal energy.
Exec/Make.auto_source
Exec/science/flame_wave/ci-benchmarks/grid_diag.out
Exec/science/flame_wave/ci-benchmarks/species_diag.out
Source/reactions/Castro_react.cpp
Source/reactions/_parameters
commit f621d71b636e445fccf9a2ea859f1b0bf668f084
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 13:32:59 2022 -0500
add a script to parse Castro's stdout (#2323)
this will look for VODE errors and tell you what step, level, and sdc
iteration they happened at
Util/scripts/parse_stdout.py
commit 72b1adb4a7e361a5f9326ef05ad150533ed14376
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 13:32:10 2022 -0500
Add dx to burn_t (#2324)
Source/driver/timestep.cpp
Source/reactions/Castro_react.cpp
external/Microphysics
commit 383004adb68497198027c0cf11b11c415f7809be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 11:52:37 2022 -0500
update external modules to 22.12
external/Microphysics
external/amrex
commit 093c32c9603a5ba6f025f85e03ee181188d7f4cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 15:54:11 2022 -0500
remove USE_FORT_MICROPHYSICS (#2319)
this is no longer part of Microphysics
Exec/Make.Castro
Exec/hydro_tests/Sedov/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/massive_star/GNUmakefile
commit 8906bb3a55e0a39e538710a4980c9f19b22d4fac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 14:38:47 2022 -0500
fix compilation of true SDC (#2318)
this syncs up with the VODE interface changes
Source/sdc/vode_rhs_true_sdc.H
commit 49ca139a0b7e7d2705e4ef0793d1e2aaf84e547e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 24 07:54:44 2022 -0500
Minor interface change in wdmerger (#2315)
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/wdmerger_util.H
commit 8a860d631cb5c251fb77199e066c387b0d847631
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Thu Nov 24 07:53:17 2022 -0500
add sol to invalid mass fraction (#2317)
Adds solution to the invalid mass fraction error in FAQ
Docs/source/faq.rst
commit f382ff54667db96718c635ce35d3b829e9f68ddd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 24 07:52:22 2022 -0500
Add safety checks on new interpolation scheme (#2316)
Source/driver/Castro.cpp
commit 129e2797fadcd683ad8e6668b0cd76bea18673b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 22 18:25:21 2022 -0500
Move binary.H to Source/gravity (#2314)
Exec/science/wdmerger/Make.package
Source/gravity/Make.package
Source/gravity/binary.H
commit a00eb1604cce5e76ee66a71ef481f8e57ca28fdd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 14:52:45 2022 -0500
fix compilation of true SDC (#2311)
Source/sdc/Castro_sdc_util.H
commit 3b5735e85a6b355ffc88688bae8afc81b5ff97d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 15 11:48:11 2022 -0500
remove self_heat burn parameter (#2308)
this no longer does anything
Diagnostics/timestep_limiter/limiter_util.F90
Source/driver/timestep.cpp
Source/reactions/Castro_react_util.H
commit cd7cb4550e4a84c156e00ea1fa642bfdafb4223a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 14 13:02:50 2022 -0500
Add new extremum- and linear combination-preserving interpolater (#2306)
Implements the new interpolater MFCellConsLinMinmaxLimitInterp from AMReX-Codes/amrex#3020.
CHANGES.md
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
external/amrex
commit 10bc66746fbdbea55c9f88de4afc32090ec5c721
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Mon Nov 14 13:01:13 2022 -0500
solving negative density retry issue (#2307)
required changes to run our T7 model. It is important to mention that:
Our T7 model supports up to 5 levels of refinement, with a max resolution of ~0.14km .
The model is now running within all the levels for further post-processing.
We plan to apply the same changes to the remaining models.
Exec/science/nova/inputs_nova_t7
commit 4f06edda5fabe5075d1865804f67eeb77fd87924
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 12 08:56:00 2022 -0500
add contours of compression to subch_sequence script (#2304)
Exec/science/subchandra/analysis/subch_sequence.py
commit 1e17e1958e5987cc3c6a65970005aeaeb2eeafca
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 11 16:40:07 2022 -0500
Create new function that saves data for a retry (#2305)
Simple refactor for the purposes of additional profiling data.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
commit 14ecd000ba420324cfe755c72fc626baaf8ca5b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 10 10:25:50 2022 -0500
add a HIP compilation test (#2295)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
.github/workflows/dependencies_hip.sh
.github/workflows/hip.yml
commit df7325d29124806690b751426ff7726346ef3bc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 10 10:15:40 2022 -0500
add an exact Riemann solver CI test (#2298)
.github/workflows/exact_riemann.yml
Util/exact_riemann/ci-benchmarks/test1-riemann.out
commit 7a1fb63092b8ccfc10b0784c2fdffcc2189b5dab
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Thu Nov 10 10:13:11 2022 -0500
deleting outdate initial models (#2302)
Exec/science/nova/glasner_T71600.hse
Exec/science/nova/glasner_T91600.hse
commit d343b2c997a88bfd50bb0560b1472bee4a805231
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Wed Nov 9 12:42:39 2022 -0500
Extending the y domain to include the buffer (#2301)
this also changes the name of the initial models, and fixes the t9 run
Exec/science/nova/glasner_T7_1e+04cm.hse
Exec/science/nova/glasner_T9_1e+04cm.hse
Exec/science/nova/inputs_nova_t7
Exec/science/nova/inputs_nova_t9
commit 71af3f92dc19044bc03c221b7640035b72e8b40a
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Mon Nov 7 08:14:07 2022 -0500
correcting number of points in initial model (#2300)
In this PR, I correct the number of points that our T7 and T9 initial model needs to finally support up to 5 levels of refinement. This is equivalent to a resolution of 0.1 km in the last level.
Exec/science/nova/glasner_T73800.hse
Exec/science/nova/glasner_T74096.hse
Exec/science/nova/glasner_T93800.hse
Exec/science/nova/glasner_T94096.hse
Exec/science/nova/inputs_nova_t7
Exec/science/nova/inputs_nova_t9
commit 167e7429b8cd231dc3882e943c4b284f98759364
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Sun Nov 6 18:34:18 2022 -0500
Inputs nova t9 changes (#2299)
In this pull request, I modify the glasner et.al T9 initial model to be consistent with a resolution of 0.1km and five levels of refinement
Exec/science/nova/glasner_T93800.hse
Exec/science/nova/inputs_nova_t9
commit b27642d867d762dea0d154ec5ef504e2787f2afe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 14:16:28 2022 -0400
no longer need CXX_REACTIONS (#2292)
this does nothing in Microphysics anymore
Exec/Make.Castro
commit 928996e6d78e76f6a35b68ade78d2898bdc8213a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 12:16:45 2022 -0400
update changes
CHANGES.md
commit 523865bea4164d1e817f55359b1bcfbb0f0874b4
Merge: 388d150d8 a35798916
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 12:14:42 2022 -0400
Merge branch 'development'
commit a35798916d0967184e369f1f0812cf389adc3f23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 31 22:41:55 2022 -0400
add a docs build CI (#2291)
.github/workflows/docs-test.yml
commit 8bcc50b8c1352cda72c1a4c4674eaf7cf6dc23c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 31 18:45:18 2022 -0400
use new AUX_THERMO directive and interfaces (#2289)
Exec/reacting_tests/nse_test/problem_initialize.H
Exec/reacting_tests/reacting_convergence/problem_initialize.H
Exec/reacting_tests/reacting_convergence/problem_initialize_state_data.H
Exec/science/Detonation/problem_initialize.H
Exec/science/Detonation/problem_initialize_state_data.H
Exec/science/celldet/problem_initialize.H
Exec/science/celldet/problem_initialize_state_data.H
Exec/science/massive_star/problem_initialize.H
Exec/science/massive_star/problem_initialize_state_data.H
Exec/science/xrb_mixed/problem_initialize.H
Source/driver/Castro_setup.cpp
commit b8a024a511c1150a7229efe3c613a93d6b3cf70b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 31 12:49:26 2022 -0400
add a flame_wave CI test (#2290)
this adds: 2d, diffusion, reactions, constant gravity to the testing
.github/workflows/flame_wave-compare.yml
Exec/science/flame_wave/ci-benchmarks/grid_diag.out
Exec/science/flame_wave/ci-benchmarks/species_diag.out
commit 4d18c91ff7ad6ead9ccad7b883cf8d3b13ea0689
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Sun Oct 30 20:55:52 2022 -0400
updating bc and the intial model of t7 (#2281)
Co-authored-by: Alexander Smith Clark <asclark@login3.summit.olcf.ornl.gov>
Exec/science/nova/glasner_T73800.hse
Exec/science/nova/inputs_nova_t7
commit 643f3be3238a4d6e310b5dab6167d80962feaa2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 30 11:17:35 2022 -0400
output the location where the timestep is set (#2273)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/timestep.cpp
external/Microphysics
external/amrex
commit 005715a46af2b2cd09bd1cf3297c3243c01c0253
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 28 10:05:30 2022 -0400
remove an unused inputs (#2286)
update the "coarse" inputs file to something that seems to work well
(runs past the C detonation ignition)
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/inputs_2d.N14.coarse
commit b268a9470f105958de05cc74a2424d9bb7a890a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 27 21:49:29 2022 -0400
Remove CFL violation check for MHD CTU advance (#2284)
This follows the same logic as #1873. We are already implicitly checking for CFL violations at the beginning and end of the timestep, so an additional check inside the CTU update is unnecessary.
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/mhd_util.cpp
commit 7c221cf2fe4a2a306b023b8969777c47c6653ca1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 27 21:40:22 2022 -0400
Update mass fluxes at end of timestep with full timestep's worth (#2147)
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit 388d150d813c141a96b15588578c0a5439bfef7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 26 10:43:42 2022 -0400
move the check on OMP + GPU to after USE_GPU is set (#2282)
Exec/Make.Castro
commit 41697201cbf513ed847497f897c497f2bf50e010
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 26 07:59:11 2022 -0400
update the versions of the github actions (#2280)
.github/workflows/c-linter.yml
.github/workflows/create_release.yml
.github/workflows/gh-pages.yml
.github/workflows/gpu_action.yml
.github/workflows/sedov-compare.yml
commit eb5c4b665218128d33cbb094716134f2cf69b714
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Tue Oct 25 12:15:17 2022 -0400
Updating last nova t7 running inputs (#2279)
Exec/science/nova/GNUmakefile
Exec/science/nova/glasner_T5_Gconst_Snone.hse
Exec/science/nova/inputs_2d
Exec/science/nova/inputs_nova_t7
Exec/science/nova/model_hse1600
commit 49747ea6216918d2b35e3e1c4da0f80a52d79d9e
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Thu Oct 6 15:08:52 2022 -0400
latest modifications to the inputs (#2277)
Exec/science/nova/GNUmakefile
Exec/science/nova/inputs_nova_t9
commit 99a0d3367a479c5b33d0f87cd46a21f75fbef8e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 1 09:18:01 2022 -0400
update to 22.10
external/Microphysics
external/amrex
commit 65b273ad07ab0179fefcfa4d505fcca6186c7e7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 19:06:41 2022 -0400
update AMReX submodule to get cublas fix (#2275)
external/amrex
commit 999607e001a558bf5446493108e01376ff18cfea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 1 11:23:32 2022 -0400
update to 22.09
external/Microphysics
external/amrex
commit a978fcf88117778f0fe5a5cc9872af1a2811c47f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 10:21:06 2022 -0400
tweak the subchandra initial models (#2261)
this used tighter tolerances to get the masses more accurate
also fixed an issue with the resolution
finally, there is now a model without N14
Exec/science/subchandra/inputs_2d.N14
Exec/science/subchandra/inputs_3d.N14
Exec/science/subchandra/sub_chandra.M_WD-1.1.M_He-0.051.hse.CO.N14.10km
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.N14.5.000km
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.CO.10.00km
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.CO.N14.10.00km
commit 31f088979a0b3084407384c3f0de5f8d428b9f9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 10:18:34 2022 -0400
update flame_wave He inputs (#2267)
in particular, the 2-d version should use 1/2 the x size, since
it is axisymmetric. Also fix the BCs for the pslope case in 3-d
this also adds an inputs with non-square zones
I did a 2-d XRB with this and it looked really good.
This is cooler than the hottest model we've used before, which
helps keep the flame structure clean.
Exec/science/flame_wave/inputs_He/inputs.He.25cm.static.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.static.1000Hz.pslope
Exec/science/flame_wave/inputs_He/inputs.He.nonsquare.static.1000Hz.pslope.cool
commit 064129943dd0a6326a80fd7d6680f337a675f32e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 10:17:41 2022 -0400
move Schlieren plot into main routine (#2270)
also do it as a derived field
Exec/science/subchandra/analysis/schlieren.py
Exec/science/subchandra/analysis/subch_sequence.py
commit 2409a13d71d664e28080f15958db60823b724ea3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 19:16:58 2022 -0400
update apt before an install (#2265)
this seems to be needed on ubuntu-latest
see: https://docs.github.com/en/actions/using-github-hosted-runners/customizing-github-hosted-runners#installing-software-on-ubuntu-runners
.github/workflows/gh-pages.yml
commit 3000c3954aea22b63ce8e86ce7c0fd553c5dc8af
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Tue Aug 9 17:30:51 2022 -0400
adding more inputs modifications (#2264)
Exec/science/nova/_prob_params
Exec/science/nova/inputs_nova_en
Exec/science/nova/inputs_nova_t5
Exec/science/nova/inputs_nova_t7
Exec/science/nova/inputs_nova_t9
Exec/science/nova/problem_initialize_state_data.H
commit 2aa2c77ae6db868da308211ce3516c3386b89f5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 18:14:20 2022 -0400
refine more smarter for subchandra (#2257)
Exec/science/subchandra/inputs_2d.N14.coarse
commit e21ba0e9d2732dfc93839e86644b6b68c1af0d28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 16:13:35 2022 -0400
document derefinement tagging (#2259)
Docs/source/AMR.rst
commit f2e4d6894f0fb48873b65cddd6fec02335831893
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 16:13:12 2022 -0400
add option castro.allow_non_unit_aspect_zones (#2256)
this will allow the code to run with dx != dy without aborting.
Most of the solvers should work fine with non-unit aspect zones, but this
has not been rigorously tested
CHANGES.md
Exec/hydro_tests/acoustic_pulse/analysis/acoustic_aspect_test.ipynb
Exec/hydro_tests/acoustic_pulse/inputs.128.aspect_x
Exec/hydro_tests/acoustic_pulse/inputs.128.aspect_y
Exec/unit_tests/diffusion_test/analysis/diffusion_aspect_test.ipynb
Exec/unit_tests/diffusion_test/inputs.2d.aspect_x
Exec/unit_tests/diffusion_test/inputs.2d.aspect_y
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
commit d8626868070286be014877e902c40f944ee8d8d0
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Sun Aug 7 10:09:28 2022 -0400
Add updated H/He flame_wave inputs file (#2260)
Exec/science/flame_wave/inputs_H_He/inputs.H_He.20cm.1000Hz.pslope
commit c80b53e95af7f19f6ae753dcfa90a6ada722a927
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Fri Aug 5 08:33:20 2022 -0400
Adding temperature perturbation setup in the nova problem (#2258)
I have added here a temperature perturbation setup for the nova problem. The parameters are:
problem.amplitude : The intensity of perturbation.
problem.width : The spatial allocation of the perturbation across the y-axis.
problem.num_vortices : The number of valleys and hills across the x-axis.
Exec/science/nova/GNUmakefile
Exec/science/nova/_prob_params
Exec/science/nova/inputs_nova_t7
Exec/science/nova/problem_initialize.H
Exec/science/nova/problem_initialize_state_data.H
commit 4c16aad670925e6509c8d22d149bf35208179958
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 07:50:59 2022 -0400
update the flame_wave volume rendering scripts (#2255)
this runs on Andes, and works with the latest version of yt
that fixed sigma_clip
Exec/science/flame_wave/analysis/volume_rendering/andes.submit
Exec/science/flame_wave/analysis/volume_rendering/vol-xrb-abar.py
Exec/science/flame_wave/analysis/volume_rendering/vol-xrb-enuc.py
commit f11aed88a0bfdb6a98f0d290fad756a93264f72a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 19:29:23 2022 -0400
update changes
CHANGES.md
commit 41495a0e6e31d573f4e52b8bddab3d0e3d02ea2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 19:26:48 2022 -0400
update submodules
external/Microphysics
external/amrex
commit a2a554e52487b1c2997cb670bb83ff0c2cc407dc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 30 13:51:30 2022 -0400
Only access old data when needed in GetCrsePhi (#2253)
On a restart, if castro.dump_old is not set to 1, there will not be old time data saved, including for PhiGrav_Type. But the code was attempting to access the old data on the multilevel Poisson solve after a restart in the linear interpolation in GetCrsePhi. This is unnecessary because in this solve after a restart, all levels are at the same time, so we can skip the interpolation and copy directly from the new-time state (using the same logic found in make_radial_gravity). So this works around the issue.
Source/gravity/Gravity.cpp
commit 4177c4b3022bb5c60893e8fefb0cc16837b59aa6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 20:01:13 2022 -0400
turn on USE_SIMPLIFIED_SDC by default for subchandra (#2248)
this is the preferred way to run this problem
Exec/science/subchandra/GNUmakefile
commit 2cddab3851fe537e63b7f7fce7f1dc5b0f460543
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 20:00:50 2022 -0400
fix the source term corrector with SDC (#2252)
for iterations after the first, we need to use the "new time" source,
since there is no swap between iterations.
Source/driver/Castro.cpp
commit 1827d920d889ff906c9bbe0fa69b5e06a39fb7bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 20:00:30 2022 -0400
enable castro.store_omegadot (#2249)
this is required for the flame diagnostics
Exec/reacting_tests/toy_flame/inputs.1d
Exec/reacting_tests/toy_flame/inputs.1d.testsuite
Exec/science/flame/inputs.1d
Exec/science/flame/inputs.1d.aprox13
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame/inputs.H_He
commit f80c3f7eb4dbe0ffb9832ae1797f93da0741be96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 15:46:08 2022 -0400
remove the electric field from the plotfile (#2246)
we cannot derive E_x, E_y, E_z because we need to mix
face-centered and cell-centered data and AMReX doesn't support this.
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
commit 2aedb848ff7a2f2c17b1ef3d3c781c3935126fbd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 13:49:53 2022 -0400
use a bigger domain to allow for expansion (#2244)
Exec/science/subchandra/analysis/schlieren.py
Exec/science/subchandra/analysis/subch_sequence.py
Exec/science/subchandra/analysis/subch_slice.py
Exec/science/subchandra/inputs_2d.N14
commit 45516643d8bf1abe64782478d30fc85ff1c7e50d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 18:44:05 2022 -0400
some cleaning of the embiggener (#2243)
Util/ConvertCheckpoint/Embiggen.cpp
Util/ConvertCheckpoint/GNUmakefile
Util/ConvertCheckpoint/probinit.f90
commit 2748a6a7e759ca6a98cf95cd8af210b3e3427761
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 19 10:06:18 2022 -0400
Enable opting into new AMRErrorTag derefinement (#2238)
This allows the user to take advantage of the new functionality in AMReX-Codes/amrex#2875.
Source/driver/Castro.cpp
external/amrex
commit 8dff7e76c8be73093b0946e6222162c5fdf0daa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 10:06:55 2022 -0400
update the default subchandra network to subch_approx (#2242)
Exec/science/subchandra/GNUmakefile
commit 8855157b6344baf075d554368600b5b7d545a2d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 15:08:01 2022 -0400
this is the set of inputs to run for the science sims (#2241)
Exec/science/subchandra/inputs_2d.N14
Exec/science/subchandra/inputs_3d.N14
commit 31cce7d5aefe23f2bd63a7e731cd4747aa1d5fd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 13:47:10 2022 -0400
add a schlieren plot (#2240)
Exec/science/subchandra/analysis/schlieren.py
commit edf563b3ef070bc8794b2b76d7ca2914f752253b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 10:17:30 2022 -0400
tweak the sequence script (#2239)
it now spills to 2 rows if there are a lot of plotfiles
Exec/science/subchandra/analysis/subch_sequence.py
commit b650c4446748356c8786240ccf4eb6830313b70c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 9 09:59:38 2022 -0400
update Microphysics submodule (#2237)
we need the screening name for development to compile
external/Microphysics
commit 2377b4709ea29844b9e3f8137e6cdfc62fbb0669
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 11:40:33 2022 -0400
add the screening method to the job_info file (#2236)
Source/driver/Castro_io.cpp
commit 6801988d4bf9d422322e074be362f2f32600dbe7
Merge: f724cd959 d68821af9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 14:56:08 2022 -0400
Merge branch 'development'
commit f724cd959956ad57552b1cba70054d7a640a3bd5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 14:55:19 2022 -0400
update to 22.07
external/Microphysics
external/amrex
commit d68821af9cecb650705e2a2758b5180cfcfe5752
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 09:58:30 2022 -0400
don't allocate memory in prim state q for passives (#2179)
We can create the primitive variable passives as needed in the tracing routines
from the conserved state, saying on memory (with ghost cells) in the primitive
variable array q
Source/driver/_variables
Source/driver/set_variables.py
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.H
Source/hydro/advection_util.cpp
Source/hydro/reconstruction.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/mhd/Castro_mhd.cpp
Source/radiation/trace_ppm_rad.cpp
Source/reactions/Castro_react.cpp
commit da0f2312bc0d770a7c2f94aa25707a3906c22850
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 30 14:13:16 2022 -0400
update the subchandra volume rendering scripts (#2232)
+ sigma_clip works now
Exec/science/subchandra/analysis/andes.submit
Exec/science/subchandra/analysis/vol-abar-subch.py
Exec/science/subchandra/analysis/vol-enuc-pos-subch.py
Exec/science/subchandra/analysis/vol-enuc-subch.py
commit ec8d8a9574f786883c61eb4e8f5c9833b2cd2e43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 30 14:12:35 2022 -0400
update the subch inputs (#2233)
this now uses Poisson gravity and does better refinement tagging
add an analysis that shows a time sequence
sync up 3D inputs
Exec/science/subchandra/analysis/subch_sequence.py
Exec/science/subchandra/inputs_2d.N14
Exec/science/subchandra/inputs_3d.N14
commit 556652b03f9e84c916357f0a916faf70bcf6abbd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 11:32:32 2022 -0400
t = 0.0 should be std::fixed in diags (#2230)
Exec/hydro_tests/Sedov/ci-benchmarks/grid_diag.out
Source/driver/sum_integrated_quantities.cpp
commit ef6a933cb00105fe9c3f53421b9728dbdf1c4f9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 11:31:27 2022 -0400
Updated flame wave scaling (#2180)
This removes some of the old scaling tests that we have not kept up with and
focuses on the main 3-d scaling test. Results for the past 3 years are here
and the inputs / submission scripts are updated to the latest versions.
Exec/science/flame_wave/scaling/1lev/scaling-2019-11-18.txt
Exec/science/flame_wave/scaling/2lev/scaling-2020-02-19.txt
Exec/science/flame_wave/scaling/2lev/scaling-2020-03-08.txt
Exec/science/flame_wave/scaling/2lev/scaling-2020-03-17.txt
Exec/science/flame_wave/scaling/3d_science/avg_time.sh
Exec/science/flame_wave/scaling/3d_science/inputs.He.25cm.static.1000Hz
Exec/science/flame_wave/scaling/3d_science/inputs.noboost.25cm.1000Hz.3d
Exec/science/flame_wave/scaling/3d_science/summit_gpu_1366.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_171.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_192.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_256.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_342.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_512.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_683.submit
Exec/science/flame_wave/scaling/3d_science/summit_gpu_768.submit
Exec/science/flame_wave/scaling/3lev/scaling-2020-03-18.txt
Exec/science/flame_wave/scaling/3lev/scaling-2020-03-21.txt
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/flame_wave/scaling/submit_flame.sh
Exec/science/flame_wave/scaling/submit_flame_384.sh
Exec/science/flame_wave/scaling/submit_flame_576.sh
Exec/science/flame_wave/scaling/summit/flame_wave_scaling.py
Exec/science/flame_wave/scaling/summit/flame_wave_summary.py
Exec/science/flame_wave/scaling/summit/scaling_20200613.txt
Exec/science/flame_wave/scaling/summit/scaling_20210606.txt
Exec/science/flame_wave/scaling/summit/scaling_20220430.txt
commit bc2a3f464c03e6b28491f84815aa4fff553ace20
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Thu Jun 9 11:19:20 2022 -0400
adding new inputs (#2229)
Exec/science/nova/inputs_nova_en
Exec/science/nova/inputs_nova_t5
Exec/science/nova/inputs_nova_t7
Exec/science/nova/inputs_nova_t9
commit 26873b1cc5b155295ebc3d823234c6c3c2d0fd75
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 8 20:45:10 2022 -0400
Disable transverse correction if it causes invalid X (#2227)
Source/hydro/trans.cpp
commit 57e916fbd7864caa014b8d880894dfca30f79427
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 8 18:06:43 2022 -0400
Add maximum subcycle count to amr_diag.out (#2226)
This is the maximum over all levels. If this value is greater than 1, that means a retry occurred on at least one level. Addresses the request in #1995.
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/sum_integrated_quantities.cpp
commit 014ddc814f2bb93b047148df6de85e3844ac4fa6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 19:51:23 2022 -0700
Fix test for pre-advance timestep check (#2225)
This should run on everything but the very first fine timestep in a given coarse step.
Also, #2222 missed that estTimeStep always operated on the new-time state, so all of the estdt interfaces are updated to accept an is_new parameter and use the old-time state if it is set to zero. The pre-advance check then uses the old-time state as intended.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/timestep.cpp
commit 5d93b318f71a415df2d7c9d2ccc39e890c0a42cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 14:39:35 2022 -0700
Improve robustness of hydro flux limiter (#2223)
The flux coming into this limiter can be zero in some zones during the reflux, so we want to avoid situations like divide-by-zero.
Source/hydro/advection_util.cpp
commit 8fe32c1664740b2ea56671dc703a35ef931df9a7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 08:48:15 2022 -0700
Check validity of dt prior to advance (#2222)
This helps catch issues with subcycling where the AMR advance dt drifts very far away from the current local stable timestep.
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit fbc287aee2b4c92ffc0293647d83a73cb383afa8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 17:32:45 2022 -0700
Move to edge-based strategy for invalid X check in reflux (#2220)
Source/driver/Castro.cpp
commit 213a0763f762f095e438dd5ee8c446d94903b825
Merge: 979150baa 9af379e6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 10:14:10 2022 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 979150baa718bb042bdebea0f98e9aaed864fda7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 12:33:57 2022 -0700
Use hydro limiter on negative density in reflux (#2219)
Source/driver/Castro.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
commit 9af379e6cecff5f9393f3032c8b0ff016b59cc78
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 12:33:57 2022 -0700
Use hydro limiter on negative density in reflux (#2219)
Source/driver/Castro.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
commit 5fd5c69491986e504cc6ccd7ade8126397a628d5
Merge: a30f95ac5 3e6f5a67b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 1 13:50:54 2022 -0400
Merge branch 'development'
commit 3e6f5a67be26cfe0c66da91e21ad8c4dfa9721df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 1 13:50:29 2022 -0400
update to 22.06
external/Microphysics
external/amrex
commit 04a5f031611ece433abcc5e331815c4e07bc7a29
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 31 18:41:15 2022 -0400
fix the Sedov action (#2217)
.github/workflows/sedov-compare.rst
.github/workflows/sedov-compare.yml
commit 4d1edf1fe18bac39ff0eb909a4a4670887c85de1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 31 18:40:55 2022 -0400
add some volume rendering to subchandra problem (#2215)
also tweak the 3-d plotfiling
Exec/science/subchandra/analysis/andes.submit
Exec/science/subchandra/analysis/vol-subch.py
Exec/science/subchandra/inputs_3d.N14
commit ebf8c4c442ab4362e76bb0eb84724d9c24f10e09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 31 18:40:36 2022 -0400
fix PPM use_pslope at the top of an atmosphere (#2214)
This fixes the reconstruction at the top of the atmosphere where p_hse might go negative. It also adds an inputs file
for flame_wave that runs with this change and reflecting BCs.
Exec/science/flame_wave/inputs_He/inputs.He.25cm.static.1000Hz.pslope
Source/hydro/ppm.H
Source/hydro/trace_ppm.cpp
commit dc175b6b9d1d2b9355e16378df5f2f7aa3cad556
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 31 12:44:13 2022 -0400
update some problem setup paper refs (#2216)
Docs/source/problem_setups.rst
Docs/source/refs.bib
commit a30f95ac5f5e40f04706cc3aef4f3d71cf53c238
Author: AMReX-Fusion <97451237+AMReX-Fusion@users.noreply.github.com>
Date: Tue May 31 14:31:46 2022 +0200
fixed wrong variable names (#2218)
Docs/source/Hydrodynamics.rst
commit 67ce1b31abf883040c07a45e89c91774ad1b1e6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 30 19:48:55 2022 -0400
add Sedov run github action
this compares the grid_diag.out to a stored benchmark
.github/workflows/sedov-compare.rst
Exec/hydro_tests/Sedov/ci-benchmarks/grid_diag.out
commit 9203058b8fd677cf4eea7a9ad5b6b609f6e5b9ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 25 15:15:54 2022 -0400
add a 3-d subch inputs (#2213)
Exec/science/subchandra/inputs_3d.N14
commit 1070f4487b94a5650cf7aa79322be5ed69ad2bb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 16:24:26 2022 -0400
PPM well-balanced (#2202)
this extends use_pslope to PPM reconstruction
CHANGES.md
Docs/source/hse.rst
Source/hydro/ppm.H
Source/hydro/trace_ppm.cpp
commit 40781911655dfd852858e320c19d437136e7183a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 13:28:03 2022 -0400
sync up some flame_wave fixes (#2212)
this adds the retry bypass on density and abundances at small density
it also switches the HSE BC to use a fixed temperature equal to the
star temperature
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.dynamic.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.static.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
commit d5011e1de647e7fca542e2365862c74470bdaf43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 13:27:52 2022 -0400
some more docs on retry (#2211)
Docs/source/timestepping.rst
commit f507f242f387c1b5582d51089442b0b85a48e187
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 20 15:19:02 2022 -0400
Add support for early stopping based on exceeding some threshold value (#2209)
This was originally developed for wdmerger and Detonation, but now all applications should be able to use it.
amr.message_int is overridden to be 1 by default to support this.
CHANGES.md
Docs/source/faq.rst
Exec/gravity_tests/advecting_white_dwarf/inputs
Exec/science/Detonation/Prob.cpp
Exec/science/Detonation/Problem.H
Exec/science/Detonation/_prob_params
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/wdmerger/inputs
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/main.cpp
commit dd4cbd13f56963f07ca89f84c35552dea7abb217
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 19 10:41:37 2022 -0400
generalize the interface state reflection logic to all reconstruction (#2203)
also simplify some logic in MOL to use the load_stencil() routine
Docs/source/hse.rst
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol.cpp
Source/hydro/advection_util.cpp
commit c5aaa019d954eaabe7c71f118160affa4917f470
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 19 08:57:00 2022 -0400
turn off use_pslope by default (#2205)
this only affects ppm_type = 0, but we will soon extend its functionality
to PPM as well. Disabling it by default means that the behavior of most
problems will not change. For the inputs files that use gravity and have
ppm_type = 0 currently, I've explicitly re-enabled it.
CHANGES.md
Exec/gravity_tests/evrard_collapse/inputs
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/gravity_tests/hse_convergence/convergence_plm.sh
Exec/gravity_tests/hse_convergence/convergence_sdc.sh
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Source/driver/_cpp_parameters
commit c63c961b1accbc701e8ea59b8f70dd75759cf314
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 19 08:55:15 2022 -0400
update the retry docs a bit (#2206)
Docs/source/timestepping.rst
commit 360eefcc40f0b90c2fffbd842c29ae6d5143e12d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 19 08:35:42 2022 -0400
Add assertion on MAX_LEV (#2208)
Source/diffusion/Diffusion.cpp
Source/gravity/Gravity.cpp
commit 1b7bd38a3a0325cb56486b56e80c0dcb9d58221d
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Wed May 18 19:33:19 2022 -0400
change abundance tolerance to fix mass fraction not summing up to 1 (#2207)
change the abundance failure tolerance in the input file to 0.1 for the flame wave problem to fix the invalid mass fraction error (mass fraction not summing up to 1).
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
commit fe7cbdba00ac58a7373090f7e1f33dd043a54b6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 18 10:37:19 2022 -0400
start of docs on HSE (#2200)
Docs/source/hse.rst
Docs/source/index.rst
Docs/source/refs.bib
commit 2d25c3ccb912e9f8fdd2e6496a7666c70e051750
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 17 12:41:17 2022 -0400
HSE BCs: don't reflect the transverse velocity in the ghost cells (#2201)
I don't think we ever intended to do this -- this looks like a simple bug.
Source/problems/hse_fill.cpp
commit d98f2bb40d95ee1c960adada6872643ec0c2c52f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 16 12:31:42 2022 -0400
Query for volume weighting in AMRErrorTag (#2198)
Source/driver/Castro.cpp
external/amrex
commit 664df1cd7eb02ca7b08937f5107b4f1b1e769392
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 16 12:15:36 2022 -0400
add a new initial model that has a C/O core (#2196)
Exec/science/subchandra/sub_chandra.M_WD-1.1.M_He-0.051.hse.CO.N14.10km
commit b73328b6b49a11b4b576aa0b804e8998a8c43d41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 16 12:15:19 2022 -0400
updated subchandra scripts (#2199)
These are the versions of the vis scripts used for the SDC paper
Exec/science/subchandra/analysis/nrhs_slice.py
Exec/science/subchandra/analysis/subch_mass_fraction_slice.py
Exec/science/subchandra/analysis/subch_slice.py
Exec/science/subchandra/analysis/summary_plot.py
commit 847c0dc94dd092da992f738aad595ceb52925493
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 13 19:04:59 2022 -0500
Add a parameter for whether to check dt validity after advance (#2197)
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit 551249f3f7f7e16c8a5d41dde8a82fa126412618
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 13 09:46:03 2022 -0500
Inline get_react_source_prim (#2174)
Fixes #2156
Source/driver/Castro_advance_ctu.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
commit cd83f56f0e5918092497729c1d04097026271213
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Thu May 12 10:07:32 2022 -0400
Adding High Temperature and Enriched Nova Initial Models (#2193)
I have enforced HSE, in the Glasner et.al (2007) enriched, T5 and T7 models.
Exec/science/nova/glasner_T51600.hse
Exec/science/nova/glasner_T71600.hse
Exec/science/nova/glasner_T91600.hse
Exec/science/nova/glasner_enriched1600.hse
Exec/science/nova/inputs_nova_en
Exec/science/nova/inputs_nova_t5
Exec/science/nova/inputs_nova_t7
Exec/science/nova/inputs_nova_t9
commit d639bc4237c2b5dc3cba279cad702de6f3b23455
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 12 09:07:02 2022 -0500
Store rotation period in the checkpoint file (#2194)
This is upstreamed from wdmerger. For most problems it will have no effect, because most problems don't update the rotation period from the value in the inputs.
Exec/science/wdmerger/problem_checkpoint.H
Exec/science/wdmerger/problem_restart.H
Source/driver/Castro_io.cpp
commit 587b076f422846092f52e69ff88d0b91d0cb4833
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 11 10:58:33 2022 -0400
update the subch inputs file (#2190)
this is in line with what we ran for the SDC paper
Exec/science/subchandra/inputs_2d.N14
commit f77d5f5113b12000adf140c07d79a3c6b767ef6c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 11 08:58:14 2022 -0600
The advecting WD problem can use a small network (#2191)
Also, fix species indexing.
Exec/gravity_tests/advecting_white_dwarf/GNUmakefile
Exec/gravity_tests/advecting_white_dwarf/problem_initialize.H
commit b79cf46247463cafe0f2f8ab31636e1c1698ded5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 8 13:04:26 2022 -0700
Move extrema diagnostics from wdmerger into main code (#2188)
This also deletes the wdmerger custom stopping criterion which has not been recently needed.
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/inputs
Exec/science/wdmerger/problem_checkpoint.H
Exec/science/wdmerger/problem_restart.H
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_data.H
Exec/science/wdmerger/wdmerger_data.cpp
Source/driver/sum_integrated_quantities.cpp
commit b985d1be32350228b9c69c7162680198196c2fc4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 6 10:33:17 2022 -0700
Fix how multiple faces are accounted for in density flux limiter (#2186)
As noted in #2182, the way we account for multiple faces is incorrect. We are currently increasing the floor by a factor of 6 (or 4 or 2, in 2D and 1D respectively). But instead we need to check on whether the flux multiplied by a factor of 6 would violate the floor. This is more aggressive and may result in some unnecessary limiting; in a future PR we can potentially be more sophisticated by considering the relative magnitude of the fluxes on the various faces.
Source/hydro/advection_util.cpp
commit 5caf4517fee1a6e0967175ffd6b6a7a9c6fc989d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 5 09:55:25 2022 -0400
use the load_stencil for ppm radiation (#2184)
Source/radiation/trace_ppm_rad.cpp
commit f85dde19e5aaa5ce3610b83b379baa9d1906faf3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 4 06:09:39 2022 -0400
remove PRIM_SPECIES_HAVE_SOURCES -- it is unused (#2181)
* remove PRIM_SPECIES_HAVE_SOURCES -- it is unused
* fix none
Docs/source/FlowChart.rst
Source/driver/_variables
Source/hydro/advection_util.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/radiation/trace_ppm_rad.cpp
commit f5a7de0a10fcce62d244a91516385bc7b54729bf
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 3 09:57:39 2022 -0700
Add some ifdef guards for simplified SDC (#2178)
Source/hydro/Castro_ctu_hydro.cpp
commit 73bd5a423c27eed9f41f7a6b1f41d05e032b5a29
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 3 09:08:48 2022 -0700
Add new advecting white dwarf problem setup (#2168)
In this problem setup, a white dwarf is placed on a grid at a uniform translation velocity along the x-axis. The purpose of the problem is to study how well HSE is maintained in the advecting star, and also to understand the numerical issues at the edges of the star when it is moving at non-trivial speed relative to the domain. This is similar to the problem posed in Section 4.3.2 of Katz et al. (2016), which at the time was implemented as a variant of the wdmerger problem setup.
Exec/gravity_tests/advecting_white_dwarf/GNUmakefile
Exec/gravity_tests/advecting_white_dwarf/Make.package
Exec/gravity_tests/advecting_white_dwarf/_prob_params
Exec/gravity_tests/advecting_white_dwarf/inputs
Exec/gravity_tests/advecting_white_dwarf/problem_initialize.H
Exec/gravity_tests/advecting_white_dwarf/problem_initialize_state_data.H
commit 67ad0c6d955e28c5a5edbdfe91f31997c4095e02
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 3 08:29:28 2022 -0700
Remove castro.show_center_of_mass (#2176)
The center of mass is now calculated and displayed by default if we're already doing sums. The additional marginal cost of this sum is not high, so we should just simplify the code.
CHANGES.md
Docs/source/Hydrodynamics.rst
Exec/science/flame/sum_integrated_quantities.cpp
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/_cpp_parameters
Source/driver/sum_integrated_quantities.cpp
commit 5e901d4cb525ce841789b66ff886a3b5e0bfb6a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 3 07:56:47 2022 -0700
Move cons_to_prim implementation to a header function (#2173)
Source/hydro/advection_util.H
Source/hydro/advection_util.cpp
commit f29a2dba768ed1ae62d28d7539859386aa836339
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 3 05:48:45 2022 -0700
Fix GPU implementation of moving_center (#2175)
Some of the data is accessed on the CPU as well as the GPU.
Source/driver/Castro.cpp
commit 9521c359de82c616a67df9e51cd22b4c1004ac3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 3 05:48:05 2022 -0700
Add missing volume weighting in locWgtSum (#2177)
This caused the center of mass to be off by a factor of the domain volume. This was correctly observed as a bug by Lupe in #800, but I misunderstood the issue and did not address it at the time.
Source/driver/sum_utils.cpp
commit 1289ecab737d0ea13a0b5155bc88f761d5aaaac1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 12:54:27 2022 -0700
Remove state_in_rotating_frame parameter (#2172)
This was an interesting experiment but ultimately did not seem to help too much.
CHANGES.md
Docs/source/rotation.rst
Exec/hydro_tests/rotating_torus/problem_initialize_state_data.H
Exec/science/wdmerger/inputs
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/problem_source.H
Exec/science/wdmerger/tests/wdmerger_relaxation/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/timestep.cpp
Source/hydro/advection_util.cpp
Source/hydro/hybrid.H
Source/rotation/Rotation.H
Source/rotation/rotation_sources.cpp
commit 750d39702aa7ae7c89ea959d14b6029c774b0990
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 11:50:07 2022 -0700
Move some radiation parameters to _cpp_parameters (#2171)
Source/driver/_cpp_parameters
Source/hydro/Castro_ctu_rad.cpp
Source/hydro/advection_util.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/hydro/trans.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/RadPlotvar.cpp
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
Source/radiation/fluxlimiter.H
Source/radiation/rad_util.H
commit e16fef1bb4e2c2d5c6719f970102f23481b0f745
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 2 13:46:23 2022 -0400
update to 22.05
external/Microphysics
external/amrex
commit 724564bd59a1bbca1c3d5d4879c0b058192f14cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 09:23:13 2022 -0700
Revert to managed memory for radiation builds (#2170)
The GPU build of radiation isn't ready to avoid managed memory yet (there are still some Fab operations which explicitly run on the host).
Source/driver/main.cpp
commit 83e21ff25fcbc1569434372ad48af12b01af4cbe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 09:09:12 2022 -0700
Inline make_sdc_hydro_plus_sources (#2167)
There is not a need for a separate MultiFab when we can just compute this locally on a zone-per-zone basis.
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
commit a5f2bd1285567ef2f067660904785aefc96452f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 08:59:00 2022 -0700
Update example Hypre build on Summit (#2169)
Docs/source/radiation.rst
commit dd7643ce98d4cc60346054c60c77d4168607447e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 1 14:42:04 2022 -0400
if we are using use_retry don't abort in the burner (#2151)
if abort is set, then we warn and disable it.
Source/driver/Castro_setup.cpp
commit 479b4af54679a903e9fd3350c6dbadef7d6a20d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 1 11:38:56 2022 -0700
Remove some unused quantities in wdmerger (#2166)
These are all computed in sum_integrated_quantities.cpp now.
Exec/science/wdmerger/Prob.cpp
commit f4e4ea945127defa1a40f315b70a82a8817dbd30
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 1 11:32:42 2022 -0700
Improve efficiency of the gwstrain calculation (#2165)
#2029 is addressed by avoiding unnecessary Derive calls (and by doing the mask calculation inline), which speeds up this calculation by a factor of 2x at small scale (and probably more at scale). Also, the reduction is now done using ReduceOps rather than with atomics, which speeds up the kernel by another factor of 10x on A100. (This may now be slower in the CPU OpenMP build.)
Source/driver/sum_utils.cpp
commit 647fd47a632966e1aafa0c5f2c828ab612c0af89
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 1 09:20:55 2022 -0700
Avoid use of Derive in wdmerger post_timestep (#2163)
Exec/science/wdmerger/Prob.cpp
commit 9c986cbfe841f8fb47a98fcb06a4142d031f961c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 1 08:33:38 2022 -0700
Add sum_utils variants that operate on MultiFab (#2164)
This allows us to avoid calling Derive() in cases where that's unnecessary because the data is already in StateData.
Also, volWgtSquaredSum is removed since that appeared to be unused.
Source/driver/Castro.H
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
commit 4a1a7a92bef24b1a4a00354731a515ec6e24102b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 1 06:01:53 2022 -0700
Move wdmerger stellar mask logic into a header function (#2162)
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/wdmerger_util.H
commit 3340f7ee224130c522d60c28388a129d72343951
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 30 17:00:53 2022 -0700
Apply mask factor inline in sum_utils (#2158)
Source/driver/sum_utils.cpp
commit 80932fbb028375678264fa39bacd6b5b0f19d6ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 30 16:45:07 2022 -0700
Remove some unused variables (#2161)
Source/driver/Castro.cpp
commit 34808b43df67d8c9c6b8688101f6acb86fe98dda
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 30 18:28:54 2022 -0400
update the GPU running docs a bit (#2160)
Docs/source/mpi_plus_x.rst
commit d6b0e5ec1b76f0d97b55137bcd654e761d71482b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 30 15:04:25 2022 -0700
Fix CUDA build of gw_dist (#2159)
This is more fallout from #1632.
Source/driver/sum_utils.cpp
commit 268342bd984d4dfb7e62bd6c1637a9a283f91ce5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 30 15:03:44 2022 -0700
Apply mask factor inline in wdmerger (#2157)
Exec/science/wdmerger/Prob.cpp
commit 910da6ab7db14af3e940f0d4caa2ad5050e0c5d6
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Fri Apr 29 17:06:49 2022 -0400
Fix GPU compilation action (#2155)
.github/workflows/gpu_action.yml
commit 4855a27e5880342e768ee9714b8a17c024b9cb9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 29 14:06:21 2022 -0700
Add parameter for controlling GPU memory footprint (#2153)
The CTU hydro allocates a lot of temporary Fab data for its computation. This can result in a memory footprint on GPU builds that is significantly higher than the memory of the StateData itself. A new option, castro.hydro_memory_footprint_ratio, is added which can help limit the amount of temporary Fab data active at any one time.
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/hydro/Castro_ctu_hydro.cpp
commit 1914c3477ebddc840e3b1a8c5e9dafa00f5901c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 29 10:32:25 2022 -0400
use the ambient condition outflow boundary for nova (#2148)
this syncs it up with how flame_wave works. This will now initialize
the ghost cells at the top of the domain with the conditions from the
initial model. This makes things better behaved over long times.
Exec/science/nova/inputs_nova
Exec/science/nova/problem_initialize.H
commit 79b2157686244afd511bcc7305541b6917d7e59f
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Fri Apr 29 10:16:46 2022 -0400
Adding new nova inputs settings (#2152)
I reset all the input options and input files to the ones currently in use.
Exec/science/nova/glasner_T51600.hse
Exec/science/nova/inputs_nova
commit ef991073e8c9541546f1564015ecbcfe7786501e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 28 15:23:53 2022 -0700
Convert remainder of CTU to use per-zone flattening (#2149)
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/radiation/trace_ppm_rad.cpp
commit 08ace7d9fbee2a5249d54c4ecd5d078fc40d8bc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 17:54:59 2022 -0400
update docs on retry (#2150)
Docs/source/timestepping.rst
commit 174a584bcc0c76ab91aa0b08064aa5f6b9386a56
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 28 10:25:32 2022 -0700
Add a per-zone flattening implementation and use it in PPM (#2143)
This PR adds a header implementation of the flattening routine implemented on a per-zone basis (the existing flattening routine is done on a per-box basis). This new version of the function is used in the hydro instead of the flatn array.
This aligns with a goal of limiting the total number of temporary Fabs created in the hydro. At the moment, we don't actually get rid of the flatn and flatg arrays, because they will still be needed for PLM, so for the moment we will have duplicative work and redundant memory. (This helps keep the PR short and readable.) But if this PR is valid and merged, we can then do the same thing in PLM in a second PR, and then after that remove the temporary array and the call to uflatten.
In general, our strategy should be to only have temporary Fab data for things that are either (a) used more than once and/or (b) involve accesses to multiple zones in the same array in a stencil-like operation, so that the cost of accessing the data is amortized. As currently implemented the flattening satisfies neither of these properties, it's only used once and the PPM update for a zone only needs the flattening coefficient at that zone.
Source/hydro/Make.package
Source/hydro/flatten.H
Source/hydro/trace_ppm.cpp
commit 4551a6c467b0719afa2fdd392378aafcf4ae2a0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 28 10:24:07 2022 -0700
Do src_to_prim on a per-zone basis (#2145)
src_to_prim is now called within a ParallelFor on a per-zone basis, and is moved to a header.
This permits a future change that merges the src_to_prim call inline within a separate parallel loop, potentially avoiding an explicit Fab construction.
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.H
Source/mhd/Castro_mhd.cpp
commit 4475bf77e1307ca20f1b7e3060ca3e54637d6ac9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 28 06:20:10 2022 -0700
Fix multipole BCs now that Fabs default to the device arena (#2142)
When CUDA-aware MPI is not enabled, we need to stage device data through the host.
Source/gravity/Gravity.cpp
commit cf0d74ed7d11feda0399fa468b7d41665f7fbe2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 28 05:13:54 2022 -0700
Fix typo in the hydro (#2144)
Source/hydro/Castro_ctu_hydro.cpp
commit 98386115fa1269753c5c46340b59af496910ce38
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 28 05:13:29 2022 -0700
Add some more BL_PROFILES to Castro.cpp (#2146)
Source/driver/Castro.cpp
commit b93839ec1442c0c64c51f3314b0d8ecdef50a713
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Wed Apr 27 11:48:22 2022 -0400
updates to nova (#2141)
this now automatically detects where the base of the fuel layer is and uses a better initial model
Exec/science/nova/_prob_params
Exec/science/nova/glasner_T51600.hse
Exec/science/nova/inputs_nova
Exec/science/nova/problem_initialize.H
Exec/science/nova/problem_initialize_state_data.H
commit fc892eddf5004e96bd5d573bee6503e8f78b5723
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 27 08:44:29 2022 -0700
Use device memory instead of managed memory (#1632)
The arena used for Fab allocations will now be device memory instead of managed memory. Managed memory was extremely convenient during our initial GPU port, but now causes a lot of problems with people inadvertently overfilling GPU memory and running extremely slowly when they should probably abort and change their setup. Managed memory can still be opted into in the inputs file with amrex.the_arena_is_managed = 1 for people who really want to oversubscribe, but it is non-recommended.
Source/driver/main.cpp
commit 196dbf43b28c62c8b62495ca6a111d107a686277
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 27 07:13:41 2022 -0700
wdmerger stopping criteria params should be queried (#2140)
Exec/science/wdmerger/_prob_params
commit 0fc977232c902d579fb9484c8c86a0e8f2992781
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 27 04:18:44 2022 -0700
Remove old parameter in wdmerger (#2139)
This should have been removed in #2132
Exec/science/wdmerger/inputs
commit ef71a3e034eda63f028125fb0f7c053cb5d216a7
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 27 04:18:20 2022 -0700
Don't use show_center_of_mass in wdmerger (#2138)
Exec/science/wdmerger/inputs
commit 3e7bcd3b65c9ade60f525b08ab90781a1161208b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 26 17:58:56 2022 -0700
Clamp ambient temperature in wdmerger (#2137)
Exec/science/wdmerger/inputs
commit e62fa6becd2240844fdfcd75b9aef43f8c11f5bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 26 08:11:49 2022 -0700
Update CHANGES (#2135)
CHANGES.md
commit 569d56a8c4a7e74f25e7c8465c3350529a2275d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 26 06:41:06 2022 -0700
Simplify the density flux limiter algorithm (#2134)
The flux limiter that prevents small densities uses an algorithm that blends the second order flux with a first order flux which guarantees positivity of density (under certain conditions). However, this blending causes some undesirable behavior when it comes to multi-fluid advection, for example with the species fluxes potentially not moving in the same direction as the density flux which they are supposed to be passively following. So this change simplifies the algorithm to a simple linear scaling of the fluxes (which we had been doing anyway, and which I suspect this algorithm was simplifying to much of the time).
Source/hydro/advection_util.cpp
commit 01919e129982f460c5e92bc04ec9273074b31269
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 26 06:37:46 2022 -0700
Add option to avoid abort for invalid X (#2124)
Exec/science/wdmerger/inputs
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit 7e86dbe56fc5cc4b10758963e539113a55554168
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 24 20:23:33 2022 -0400
fix the yt syntax (#2133)
Exec/gravity_tests/hse_convergence_general/hse.py
Exec/gravity_tests/hse_convergence_general/profile.py
commit e56cbb6422944ac49def5b14db9cc38d7d60767d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 15:35:09 2022 -0700
Remove flux limiter on large velocities (#2132)
This was added in #712 but ended up not being that useful.
CHANGES.md
Source/driver/_cpp_parameters
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/advection_util.cpp
commit d899a58bff15b9da4672dc7904b2f1ade64bc6df
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 11:22:13 2022 -0700
Move abundance failure tolerance into the runtime parameters (#2131)
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit cff9b2143785ca3f74d46ccffb98068983683d9d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 09:19:15 2022 -0700
Upstream wdmerger's max_tagging_radius (#2127)
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/inputs
Exec/science/wdmerger/problem_tagging.H
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
commit e1da1c15647fa99777430e6ef0b96f0b24cf7e3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 09:18:41 2022 -0700
Remove bulk velocity functionality from wdmerger (#2130)
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/inputs
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_util.H
Exec/science/wdmerger/wdmerger_util.cpp
commit f1043ba59e270f460e4364983c74447d2acf69b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 08:53:36 2022 -0700
Migrate some wdmerger parameters to _prob_params (#2128)
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/inputs
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_data.H
Exec/science/wdmerger/wdmerger_data.cpp
commit fe6c0c3248313efea47876e49ea59ba10d5dd905
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 08:49:39 2022 -0700
Remove old do_constant_volume_burn from inputs (#2129)
Exec/science/wdmerger/inputs
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/xrb_mixed/inputs_2d
commit 003769418f30810d24b7e0ece1dc69d642088179
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 07:55:29 2022 -0700
Switch wdmerger density tagging to refinement_indicators (#2126)
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/inputs
Exec/science/wdmerger/problem_tagging.H
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_relaxation/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit de349f69475ca00d874baecc3a78c7799a3c69b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 07:31:09 2022 -0700
Turn off flux correction if it would cause X < 0 or X > 1 (#2123)
The reflux currently zeros out any flux corrections that would cause a negative or small density. A check is added to this that also turns off flux corrections if they would cause X > 1 or X < 0 (within some tolerance). Since it is possible that multiple flux corrections at the same zone center could conspire together to cause this, the only general way to do this is to loop over zone centers and consider all adjacent fluxes simultaneously, so this code is switched to a zone center loop instead of a zone face loop (and the same logic is now applied to the density check, which should also make it more accurate).
Source/driver/Castro.cpp
commit ba7d54c6abc7b47162773fb37751336b3c3ec187
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 24 06:44:52 2022 -0700
Switch wdmerger temperature tagging to refinement_indicators scheme (#2125)
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/inputs
Exec/science/wdmerger/problem_tagging.H
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit 8e4d617f77f502692eb5a208bf6b012510b7220c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 23 16:54:53 2022 -0700
Fix check on small_dens in reflux (#2122)
The flux is already scaled by dt when it is added to the flux register, so this multiply by dt was unnecessary and wrong.
Source/driver/Castro.cpp
commit 73a6bfab1377322f2b7e92c041c0b260bdd47e1b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 23 15:59:30 2022 -0700
Issue a retry when X is invalid after a hydro update (#2121)
(rho X) can be negative after a hydro update even if rho itself is not, for example due to transverse terms being applied near sharp composition gradients. We should retry with a smaller timestep in that scenario.
Source/driver/Castro_advance_ctu.cpp
commit a08241dd2ad6be0deeddbb35a409ee9ef36d2b4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 23 12:17:25 2022 -0700
Reset composition on a density reset in trans (#2120)
Source/hydro/trans.cpp
commit 6bb504c9f537ad31e1615d633c98a3eca901563f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 22 10:21:53 2022 -0700
Only do update_max_rhs if do_grav = 1 (#2117)
Source/driver/Castro_advance.cpp
commit fb46aec8cca1eb65cec88c7e0599d687f01d7a7c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 22 05:54:30 2022 -0700
Radsolve default values should be set before overrides (#2113)
As originally written, this change unintentionally overrode the level_solver_flag in 1D, leading to diffs for inputs files that were not using Hypre SMG (radsolve.level_solver_flag = 0). To simplify the code and avoid the regression test diff, this override has been removed; there is already an abort later in this routine that covers the unsupported case radsolve.level_solver_flag = 1.
Source/radiation/RadSolve.cpp
commit e738d8fe179f513991ea6a9b5d661aafaba52bc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 20 14:05:37 2022 -0400
add a diag for subchandra (#2104)
add a diag for subch that reports that average, L2-norm, and max of burn weights
this works only on the finest level and only for zones with non-zero weights
Exec/science/subchandra/analysis/GNUmakefile
Exec/science/subchandra/analysis/Make.package
Exec/science/subchandra/analysis/fburn_weight_avg.cpp
commit 78961ce2c140ce84c9d41328d6661455a77f251f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 18 15:00:37 2022 -0400
update an action to some later versions (#2116)
.github/workflows/gh-pages.yml
commit 21d524f768f88a1f5cd8c6050797de62e7c2151e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 18 14:59:31 2022 -0400
add density to the normalize_species error message (#2115)
this can help with context
Source/driver/Castro.cpp
commit 99f854a06b14ff0215ea8132f61ca95e90005d48
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 18 07:56:31 2022 -0700
Fix box bounds in update_dcf (#2114)
Tiling was originally added to update_dcf in commit c54638f. However, I think there was a bug in this commit. The dcf array has a single ghost zone, but not all of the source arrays filling it do, and the original Fortran looped from dcf_lo+1 to dcf_hi-1, which would have been only the valid domain. But this commit used a growntilebox() for the MFIter loop, which is a change from the Fortran and one that will not make sense unless all of the source MultiFabs have a ghost zone too.
Source/radiation/Radiation.cpp
commit 765ae0c56c776c84624ce0eb5dc882940c2963b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 15 18:27:20 2022 -0400
remove support for Fortran from _variables and python scripts (#2111)
Exec/Make.auto_source
Source/driver/_variables
Source/driver/set_variables.py
Util/scripts/write_probdata.py
commit 3d383424800b87b1adc82c761b22a68b5d2b66f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 15 13:41:49 2022 -0400
retry_burn no longer exists (#2112)
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/inputs-det-x.nse
Exec/science/Detonation/inputs-det-x.simplified_sdc
Exec/science/Detonation/nse_runs/inputs.template.simple_sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/nse_runs/inputs.template.true_sdc
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.dynamic.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.static.1000Hz
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_1d.nse.sdc
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
Exec/science/massive_star/inputs_3d.nse
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/inputs_2d.N14
Exec/science/wdmerger/inputs
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit e155ea40fe8d6ce3919fef215af9040c77f53a37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 15 12:00:00 2022 -0400
change subchandra to use relative T gradient for tagging (#2110)
we were tagging too much
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/inputs_2d.N14
commit b265ab832466398883c3e30d771e37897239319e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 15 10:57:56 2022 -0500
Improve lambda capture of dx in estimate_gamrPr (#2108)
The capture of dx in this ParallelFor may not work as desired, so explicit local copies of the dx variables are made instead.
Source/radiation/MGFLD.cpp
commit 56e025faeb38172e47c1dd9412fa081d527030ef
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 15 07:49:27 2022 -0500
Enable NaN check in the GPU build (#2106)
The Fab and MultiFab contains_nan methods are GPU safe, we just want to avoid the bit that iterates through the memory and prints out the zone value because that's not safe for non-managed-memory (though we could add that back for managed memory builds if needed).
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
commit cc7674a9c52d1890db7815442c65f89ce2b41c96
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 15 07:12:55 2022 -0500
Add GPU synchronizes to avoid race conditions in Hypre solve (#2107)
This routine is not async-safe presently, which is why many of the operations have synchronizes already, but these two were missed, and could result in race conditions.
Source/radiation/HypreABec.cpp
commit e187d3d559fa742a8d26ecaf4f405a88b868f371
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 15 06:10:15 2022 -0500
Fix argument passing in ca_init_fort_constants (#2105)
Source/radiation/Rad_nd.F90
commit b747836025c263dff630c6027c7361650b081509
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Wed Apr 6 13:08:22 2022 -0400
Updating inputs (#2103)
We consider instead of glasner_T5.hse, our new model model_hse1600 constructed by imposing HSE equilibrium over the T5 Solar Model in nova. With these new changes the code runs smoothly, but a correct initial perturbation should be set up, to produce mixing.
Exec/science/nova/glasner_T5.hse
Exec/science/nova/inputs_nova
Exec/science/nova/model_hse1600
commit abf8dcbcc0bd195a249a21ba29596ac5519ac2ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 4 14:41:25 2022 -0400
subchandra: adjust integration tols and retry params (#2101)
Exec/science/subchandra/inputs_2d.N14
commit fe02ff4a25a49b6fccb03112651a258e1a6dba32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 1 11:41:44 2022 -0400
update changes
CHANGES.md
commit aad54d3afe8ca744fab7816444d8ea4004213ecb
Merge: 58ae16308 10f3bd6b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 1 11:40:47 2022 -0400
Merge branch 'development'
commit 10f3bd6b52c223aeba34fffaf4a2e150320037f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 1 11:40:27 2022 -0400
update to 22.04
external/Microphysics
external/amrex
commit a92ac477d94458d560ccb65c71cb12189403e000
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 27 14:26:51 2022 -0700
Abort on invalid species in GPU build (#2099)
Source/driver/Castro.cpp
commit d2c86fab9e472e9299f6273a4a294428441a3dc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 25 13:52:12 2022 -0400
remove PRIM_SPEC_HAVE_SOURCES from simplified-SDC (#2093)
we no longer trace under the any of the simplified-SDC sources,
including species, so we don't need to explicitly allocate memory
for them anymore with simplified-SDC
Exec/Make.Castro
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_setup.cpp
Source/hydro/Castro_ctu.cpp
commit feeb82a01399fd9f8b896a93250c4089b935929d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 25 13:18:30 2022 -0400
update the flame_wave time_series.py script for latest yt (#2084)
Exec/science/flame_wave/analysis/time_series.py
commit 1db20a8b457655980edc852a83ecdf7923cf7083
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 25 11:15:51 2022 -0400
Fix sdc compilation (#2098)
Source/sdc/vode_rhs_true_sdc.H
commit 933259a8ddcdf81ce1c69450139729df5a94a970
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 24 12:38:53 2022 -0400
remove NETWORK_HAS_CXX_IMPLEMENTATION (#2097)
all networks are C++ now
Source/driver/Castro_setup.cpp
Source/driver/timestep.cpp
Source/reactions/Castro_react.cpp
Source/sdc/vode_rhs_true_sdc.H
commit 23fc313a74f8db38499ff1cae365d232b06fec11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 22 13:14:16 2022 -0400
subchandra: normalize species after interpolating onto grid + better tols (#2095)
Exec/science/subchandra/inputs_2d.N14
Exec/science/subchandra/problem_initialize_state_data.H
commit a12efaab34eac229743e163e248636373c8231fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 15 15:06:36 2022 -0400
remove some unused metric code (#2071)
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
commit 8d9c88caf598f0d6d83c53c8ee122ee0eb50b4ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 15 15:05:15 2022 -0400
update the massive star inputs (#2086)
this adds the drive convection stuff and syncs up with what Alice
used for her big run
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
commit 6bd0b0997aa19545f0fe266f89018fccb5e1ce44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 15 15:00:56 2022 -0400
this compiles with the latest iso_rewrite PR (#2087)
Source/driver/timestep.cpp
Source/reactions/Castro_react_util.H
Source/sdc/Castro_sdc_util.H
Source/sdc/vode_rhs_true_sdc.H
commit edce6e953f44a541579dc90c672387f852dab7b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 15 14:48:07 2022 -0400
for the helmholtz inputs for Sedov, fix the tagging (#2079)
we were not creating any levels
Exec/hydro_tests/Sedov/inputs.mini-Castro
commit 3a26cf31202831e57e1a59d7019d0a05bbf25612
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 15 14:38:33 2022 -0400
for loading Castro dataset in yt, use hint (#2083)
Docs/source/yt_example.ipynb
commit 4b4cbf7d675097ffee0cda14cf45c99309b4be60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 15 14:36:32 2022 -0400
remove some references to Fortran in the docs (#2078)
Docs/source/FlowChart.rst
Docs/source/Hydrodynamics.rst
Docs/source/build_system.rst
Docs/source/creating_a_problem.rst
Docs/source/development.rst
Docs/source/faq.rst
Docs/source/getting_started.rst
Docs/source/io.rst
Docs/source/regridding.rst
Docs/source/rp_intro.rst
Docs/source/software.rst
commit fc559ae8ad080d704c64f82c31bdc214057ac4df
Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com>
Date: Tue Mar 15 13:57:15 2022 -0400
Changes in input files for flame_wave using subch2 network (#2089)
we now disable the small density timestep reject on densities less than 1 g/cc -- the steep falloff at the edge of the start has a habit of triggering retries.
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
commit 9430aa6d970b36815fdad6a74c00d23811df7583
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 15 09:35:43 2022 -0700
Prefetch radial gravity data before and after MPI reduction (#2091)
When GPU-aware MPI is not being used, it is not generally safe to pass managed memory directly to an MPI call (depending on MPI implementation, this could lead to accessing invalid data). So we need to prefetch the data to the host before calling ParallelDescriptor reduction operations. (This is handled already for multipole gravity, but this was missed when monopole gravity was ported to GPUs.)
This addresses the issue identified in #2080.
CHANGES.md
Source/gravity/Gravity.cpp
external/amrex
commit 5116b7268763c053f463db8d71f722564d0cf48e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 13 19:11:06 2022 -0400
bump up the GCC minimum requirements to GCC 9 with CUDA (#2090)
Docs/source/getting_started.rst
commit 58ae163089790e1dd95f43f34c2d631c58d35db7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 3 14:12:06 2022 -0500
update submodules
external/Microphysics
external/amrex
commit 0d942c92d5773e51b0b80c7a019499ca4369be6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 8 11:26:36 2022 -0500
add CUDA_VERSION to job_info (#2082)
Exec/Make.auto_source
Source/driver/Castro_io.cpp
commit 186ee03f5889b76366865fadc3dfbf21c0d18860
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 7 13:29:53 2022 -0500
use sphinx-prompt to make the bash commands clearer (#2075)
Docs/source/conf.py
Docs/source/getting_started.rst
requirements.txt
commit c32d516dfc7738f9b0adf283f4f54856b18f0d73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 7 10:23:22 2022 -0500
add an inputs file for Sedov strong scaling with helmholtz EOS (#2085)
Exec/hydro_tests/Sedov/inputs.helm_scaling
commit 342411b812f2f4c6672104f3770084a41c437422
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 1 12:47:07 2022 -0500
fix some sphinx issues in the documentation (#2076)
Docs/rp.py
Docs/source/inputs.rst
commit 5bf85dc1fe41909206d80ff71463f2baad22dab5
Merge: 55ee8faab 756d00e43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 1 12:26:02 2022 -0500
Merge branch 'development'
commit 55ee8faab78ccd86801e295fa6988fc5e777e74a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 1 12:25:38 2022 -0500
update modules to 22.02
external/Microphysics
external/amrex
commit 756d00e439effd1d9f9adede0c868d38611da1a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 28 13:21:34 2022 -0500
update to reflect new Microphysics location (#2077)
Microphysics is now part of AMReX-Astro
.gitmodules
CHANGES.md
Docs/source/EOSNetwork.rst
Docs/source/getting_started.rst
commit 958e0cc7aac9999ca6052f47c1670bdee5854b20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 15 14:35:16 2022 -0500
fix some more shadowing warnings (#2074)
Source/driver/Castro.cpp
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/driver/timestep.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_util.H
Source/rotation/rotation_sources.cpp
Source/scf/scf_relax.cpp
Source/sources/Castro_geom.cpp
commit bf16de4d719a244989fded7982e7c0c87a635601
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 14 21:28:28 2022 -0500
add preliminary notes about AMD + HIP (#2073)
Docs/source/Introduction.rst
Docs/source/build_system.rst
Docs/source/mpi_plus_x.rst
commit 169653a90947cae5caa03a40b9c8e919b47351dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 13 19:38:33 2022 -0500
quiet some compiler warnings (#2072)
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/timestep.cpp
commit 1771b2de9f6abd8d9183fc8341035ea19bda5c62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 13 13:01:20 2022 -0500
remove lapack -- rad no longer uses it (#2070)
Exec/Make.Castro
Util/LAPACK/Make.package
Util/LAPACK/lapack.F90
commit 727e39bb61c68c9d9563c9d1dbcef3786c879db9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 6 14:00:36 2022 -0500
sync up with Microphysics build script cleaning (#2069)
Source/driver/parse_castro_params.py
Util/scripts/write_probdata.py
commit c735d2ef96ad49823e51ae0c7c1cfbc6c6b327cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 5 11:10:17 2022 -0500
remove unused function sigs (#2068)
Source/driver/Castro_F.H
Source/radiation/RAD_F.H
commit bdc716b0bf01c1672fb67902e6688f98ea897c28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 5 11:06:25 2022 -0500
remove missing header (#2067)
Source/driver/Castro_setup.cpp
commit 951718cb8ea9c5896f9d79e2a375bf49574b35cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 4 10:19:30 2022 -0500
fix spelling + update years (#2066)
Docs/source/conf.py
commit 74a277d1235b21aab1bc7370b97ddc9738f4a530
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 4 09:36:50 2022 -0500
remove the MICROPHYSICS_FORT code (#2065)
this is no longer implemented
Source/driver/Castro.cpp
Util/exact_riemann/main.cpp
commit f41722cc24da0843210337258b8e6e8d7c2ceaf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 1 17:10:27 2022 -0500
update to 22.01
external/Microphysics
external/amrex
commit 669e452287f5e3f503c8c5abbf52d1efc5725a56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 31 12:33:13 2021 -0500
add a new initial model for subchandra (#2062)
this uses N14 in the model and is the inputs used for the SDC runs
on Cori
Exec/science/subchandra/inputs_2d.N14
commit 98a34a4b3146ad4fe2ed14888150b3dbd3ee88f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 31 12:32:55 2021 -0500
fix wrapping of initial model data (#2061)
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.5.000km
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.N14.5.000km
commit d7ad0a814e9e4dff5d64cc38ce345547caf6d472
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 31 11:21:17 2021 -0500
fix compilation with USE_NONAKA_PLOT and simplified-SDC (#2064)
Source/reactions/Castro_react.cpp
commit c02f0779a3881dd4be42f89b7cdfc7f565e38730
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 10:19:59 2021 -0500
store the strang_half in the nonaka_plot info (#2063)
Source/reactions/Castro_react.cpp
commit 572ee40edec54235c01aa585b9053de723f8b2a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:54:36 2021 -0500
remove the Sedov analytic solution code (#2056)
this came from Frank Timmes' website originally and is there
and in the git repo if ever needed again, but it is not something
we need to run often
Exec/hydro_tests/Sedov/Verification/analytic/sedov3.f
commit 4261d1c3d0fdf29f030df5b74e26f5a1169ecdb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:52:46 2021 -0500
convert radiation ceupd to C++ (#2049)
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Radiation.cpp
commit ecccc98a4ada720a94fd5966d694992c8391aecc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:42:42 2021 -0500
add an image plot of some key mass fractions (#2059)
Exec/science/subchandra/analysis/subch_mass_fraction_slice.py
commit 1d5008707c48a0d30cfd7de7f05f590bf5f37054
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:42:02 2021 -0500
switch RadBreakout to general_null breakout.net (#2058)
Exec/radiation_tests/RadBreakout/GNUmakefile
commit 2eaa7b5209fe2e53c8cb8be73534dcdfd24878b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 21 13:07:27 2021 -0500
update true SDC VODE interface (#2060)
this syncs up with Microphysics changes
Exec/radiation_tests/RadBreakout/GNUmakefile
Source/sdc/vode_rhs_true_sdc.H
commit d7a27ccd5d7ca3edb686718aa97bce69a665dd2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 16 09:50:53 2021 -0500
add info needed for nonaka_plot functionality (#2055)
Source/reactions/Castro_react.cpp
commit ddb60e6820d890b4e1a578e1b249ace216946662
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 12:52:32 2021 -0500
we no longer need Fortran Microphysics (#2052)
radiation still needs AMReX Fortran, but everything else is Fortran-free!
Exec/Make.Castro
Exec/Make.auto_source
commit fad68be09a8ebfdd89d9afe4277a82392d23c29c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 12:51:44 2021 -0500
add volume render scripts for 3-d XRB (#2054)
Exec/science/flame_wave/analysis/vol-xrb-enuc.py
commit 75855e79208b8bf5786039ab69bc7aeed4cd41fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 12:47:32 2021 -0500
remove dpconvert.py script -- this was for Fortran (#2053)
Util/scripts/dpconvert.py
commit a9ee9a3bcb997470c26d75c771e19204650e7bf1
Author: Chris DeGrendele <35853499+ChrisDeGrendele@users.noreply.github.com>
Date: Mon Dec 13 09:38:07 2021 -0800
Remove helmtable rule for clean as it's now in Microphysics_extern (#1174)
Exec/Make.Castro
commit 219080d819b0f5212df72ad1601033bc8b22f2c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 10 07:26:39 2021 -0500
remove rad dependence on Fortran fundamental constants (#2048)
* inelastic scattering is not used since we removed neutrinos
* remove Fortran fundamental constants
* fix compilation
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
Source/radiation/rad_params.F90
commit b0510ce2dfb696a0f1be50af0be5874f8ddf7cd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 9 14:23:06 2021 -0500
inelastic scattering is not used since we removed neutrinos (#2047)
Source/radiation/Castro_radiation.cpp
Source/radiation/MGFLD.cpp
Source/radiation/Make.package
Source/radiation/RadHydro_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit 4babe7c103b6989c8492319fbac2bbe1f85c512a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 7 10:28:04 2021 -0500
colorize the output (#2050)
Source/driver/Castro_advance_ctu.cpp
Source/hydro/Castro_hydro.cpp
Util/model_parser_cxx/model_parser.H
commit bfa4ca3e470e31129f1df333f1c82e47bd98ed30
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 3 11:02:02 2021 -0500
std::cout -> amrex::Print() (#2051)
Source/radiation/Radiation.cpp
commit 4a351ebf382c893d1cfa08709aec115c1dd3ad6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 13:27:42 2021 -0500
fix formatting
CHANGES.md
commit ab4b77c836b057737be22a1f6998f2087deebb91
Merge: 9af5984c5 dede37134
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 13:26:57 2021 -0500
Merge branch 'development'
commit 9af5984c57a38346b8372b054f15afa2f7e210ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 13:26:40 2021 -0500
update to 21.12
external/Microphysics
external/amrex
commit dede371342809a06a23c81980e99c59f75147cb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 13:17:37 2021 -0500
we no longer need state_indices_nd.F90 and only rad needs Fort Microphysics (#2043)
Exec/Make.Castro
Exec/Make.auto_source
Source/driver/Make.package
commit 89adde246bbb66df866c3333d2a842bea1a024e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 11:00:46 2021 -0500
convert radiation nceup to C++ (#2044)
this eliminates one of the places we rely on Fortran
state_indicies_module
Exec/Make.auto_source
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Radiation.cpp
Source/radiation/rad_params.F90
commit d242b6f47cbb988b5a3b7366a990ed4e36249920
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 30 19:18:38 2021 -0500
move some of the inelastic scatter stuff up to C++ (#2045)
this eliminates the need for state_indices in Fortran
Source/driver/Castro_F.H
Source/radiation/MGFLD.cpp
Source/radiation/RadHydro_nd.F90
Source/radiation/Rad_nd.F90
commit d3f9bd616377b191eb3e2e2e3251c497a0d36570
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Tue Nov 30 09:50:48 2021 -0500
Add hse_fixed_temp parameter (#2042)
Adds castro.hse_fixed_temp, which sets the temperature at an HSE boundary if hse_interp_temp = 0.
Addresses #2035.
CHANGES.md
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/problem_initialize.H
Source/driver/_cpp_parameters
Source/problems/hse_fill.cpp
commit c7037c51a453f357548e8d28bc7f7a9862b30025
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 29 09:46:19 2021 -0500
don't trace any SDC sources (#1965)
previously, the pressure and energy source terms were included in the PPM
tracing. Now we no longer do this and instead explicitly add them at the
end of all of the transverse updates. This has the advantage of letting
us check whether the interface states are negative and also removes
their influence from the reference states and eigensystem
Note: this also restores the pure hydro (non-SDC) species sources to the tracing
routines (they were taken out in #1646)
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
commit bf45d36739c02f4407e1e3cf72401289eb31732e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 16 08:48:57 2021 -0500
fix some potential make race conditions on directory access (#2041)
Exec/Make.auto_source
commit 71770027b0c4a8828556dc429a812efca11e7f8d
Author: Joe Hellmers <jlhellmers@sdsu.edu>
Date: Sat Nov 13 07:07:03 2021 -0800
Add tiling to MHD looping (#2039)
CHANGES.md
Source/mhd/Castro_mhd.cpp
commit 3159a2a256ba510cb783d47e6fa8f258697f4892
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 12 09:07:08 2021 -0500
enable PPM and flattening for MHD Sedov (#2037)
this gets negative densities from the start
Exec/hydro_tests/Sedov/inputs.3d.mhd
commit a4619b6947af66dc32716576ca9aacb720a98cf9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 9 11:11:11 2021 -0500
convert exact_riemann to C++ (#2031)
Util/exact_riemann/GNUmakefile
Util/exact_riemann/Make.package
Util/exact_riemann/_parameters
Util/exact_riemann/_prob_params
Util/exact_riemann/exact_riemann.H
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/inputs.bug
Util/exact_riemann/inputs.bug2
Util/exact_riemann/inputs.bug3
Util/exact_riemann/inputs.bug4
Util/exact_riemann/inputs.bug5
Util/exact_riemann/inputs.bug6
Util/exact_riemann/inputs.bug7
Util/exact_riemann/inputs.bug8
Util/exact_riemann/inputs.moving
Util/exact_riemann/inputs.sod-minus.gamma
Util/exact_riemann/inputs.sod.gamma
Util/exact_riemann/inputs.stellarcollapse
Util/exact_riemann/inputs.test1.helm
Util/exact_riemann/inputs.test2.helm
Util/exact_riemann/inputs.test3.helm
Util/exact_riemann/inputs.test4.helm
Util/exact_riemann/main.cpp
Util/exact_riemann/riemann_F.H
Util/exact_riemann/riemann_sample.H
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.H
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.H
Util/exact_riemann/riemann_support.f90
commit a3bd0c7991b2326df2214641910da7a955728466
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Mon Nov 8 13:02:55 2021 -0500
updating nova with corrected initial model (#2033)
Exec/science/nova/GNUmakefile
Exec/science/nova/glasner_T5.hse
Exec/science/nova/glasner_T5.hse.dx_1.000km
Exec/science/nova/glasner_T5_dx_1.000km.hse
Exec/science/nova/inputs.nova
commit 6e8ff6f749802b3977792b76fa611d8800c3b51f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 1 13:16:13 2021 -0400
update to 21.11
external/Microphysics
external/amrex
commit cbb76a23b5afef0a06b746f0d0a79c1d43d1495b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 1 13:07:57 2021 -0400
update the initial models to a cleaner 5 km resolution (#2020)
also add a version with N14 seeded (for using the subch2 net)
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/sub_chandra.M_WD-1.00.M_He-0.040.hse.C.10240
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.2560
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.5.000km
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.N14.5.000km
commit c1c7e318df4bdd1d02607888ca78bd797e138a41
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 21 13:54:18 2021 -0700
Improve quality of printing when convergence fails in establish_hse (#2028)
Util/model_parser_cxx/model_parser.H
commit 23498f2e781a6ee5051132fc35d493f5e275b457
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 20 17:37:14 2021 -0700
Use scientific notation for small and large times (#2027)
Source/driver/sum_integrated_quantities.cpp
commit e3ee7d508712ee02ebdc3d1c1ec2252a0bdd7bcb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 20 17:16:36 2021 -0700
Use proper fixed and scientific formatting on grid_diag.out (#2026)
Source/driver/sum_integrated_quantities.cpp
commit cbf406a75176e3f8e52b88e02bc297957762c2bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 20 13:12:32 2021 -0700
Fix sign of gravitational energy in diags (#2025)
phiGrav is negative now so the total energy is constructed by adding rho*phi instead of subtracting it.
Source/driver/sum_integrated_quantities.cpp
commit f2c4f8df9db1cdebd05157fcabd4b859b43ba02b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 20 10:58:43 2021 -0700
Align header layout on grid_diag.out with other diags (#2024)
Source/driver/sum_integrated_quantities.cpp
commit 6926e4c89b76865dfaec308d7f04169fec8b824c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 20 09:59:24 2021 -0700
Move wdmerger diags so they don't step on main Castro diags (#2023)
The wdmerger diagnostics should now be provided in addition to what is provided by the main sum_integrated_quantities() instead of being a replacement.
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/inputs
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit bcfaa6c6295b502e86cacf7ddac0c85260fc4954
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 16 15:42:28 2021 -0400
add a 3-d inputs for testing (#2019)
Exec/science/massive_star/inputs_3d.nse
commit cd3c36c398c50e47906aecff5c892fc52769ab85
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Thu Oct 14 10:49:56 2021 -0400
update nova initial model (#2013)
this now works with the nova2 network
Exec/science/nova/glasner_T5_dx_1.000km.hse
Exec/science/nova/inputs_2d
commit 37aafd6ed91937a1ee0204f0cf1130d8b9da210d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 13 19:29:26 2021 -0400
don't setVal burn_weights if they are not defined (#2018)
Source/driver/Castro_advance.cpp
commit 181f80a79eae765befcb5268bca1437f2082d256
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 13 14:00:36 2021 -0400
update hypre version (#2016)
AMReX now requires a newer hypre version
Docs/source/radiation.rst
commit 5bb9d45729a7aaefce5ee6c2ec0cc169610b7d08
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Wed Oct 13 13:41:50 2021 -0400
Setting the raction network in nova2 and setting the running input parameters (#2015)
Exec/science/nova/GNUmakefile
Exec/science/nova/glasner_T5.hse.dx_1.000km
Exec/science/nova/inputs.nova
commit 934644ce2a7073288258a1895e4890caa449c0cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 12 17:37:57 2021 -0400
normalize the mass fractions after interpolation (#2014)
Exec/science/nova/problem_initialize_state_data.H
commit 37960cc07839f7928aa0e79486c483697abdba89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 2 14:24:09 2021 -0400
update external to 21.10
external/Microphysics
external/amrex
commit 10aa02a6b2c6143a1b1af78464146992f555f48c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 1 12:14:57 2021 -0400
fix box size for no limiter in estimates_gamPr (#2011)
* fix box size for radiation dt computation
* fix box
Source/radiation/MGFLD.cpp
commit ceb3e492368431179f99d04403d339124a599c8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 30 12:42:35 2021 -0400
blocking_factor: 4 -> 8 (#2009)
blocking_factor = 4 is not a good idea
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite
Exec/gravity_tests/hydrostatic_adjust/inputs
Exec/gravity_tests/hydrostatic_adjust/inputs-subchandra
Exec/hydro_tests/Sedov/inputs.3d.mhd
Exec/mhd_tests/Alfven/inputs-1_0_1d
Exec/mhd_tests/Alfven/inputs-1_0_2d
Exec/mhd_tests/Alfven/inputs-1_1
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-x-inv
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.sod.test
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/LoopAdvection/inputs
Exec/mhd_tests/MagnetosonicWaves/inputs-1_0_2d_fast
Exec/mhd_tests/MagnetosonicWaves/inputs-1_1_slow
Exec/mhd_tests/OrszagTang/inputs
Exec/mhd_tests/OrszagTang/inputs.test
Exec/mhd_tests/RT/inputs_3d
Exec/mhd_tests/RT/inputs_3d_mhd
Exec/mhd_tests/species/inputs
Exec/mhd_tests/species/inputs.test
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/RadBlastWave/inputs.1d
Exec/radiation_tests/RadBlastWave/inputs.2d
Exec/radiation_tests/RadBlastWave/inputs.3d
Exec/radiation_tests/RadBlastWave/inputs.3d.test
Exec/radiation_tests/RadBlastWave/inputs.kp
Exec/radiation_tests/RadBlastWave/inputs.kp.2d
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadSourceTest/inputs-cooling
Exec/radiation_tests/RadSourceTest/inputs-heating
Exec/radiation_tests/RadSourceTest/inputs-heating-mg
Exec/radiation_tests/RadSphere/inputs
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadThermalWave/inputs.1d
Exec/radiation_tests/RadThermalWave/inputs.1d.test
Exec/radiation_tests/RadThermalWave/inputs.2d
Exec/radiation_tests/RadThermalWave/inputs.2d.test
Exec/radiation_tests/RadThermalWave/inputs.3d
Exec/radiation_tests/RadThermalWave/inputs.3d.test
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.32
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/nse_test/inputs.128
Exec/reacting_tests/nse_test/inputs.256
Exec/reacting_tests/nse_test/inputs.512
Exec/reacting_tests/nse_test/inputs.64
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d.sdc_test
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/reacting_tests/reacting_convergence/inputs.1024
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.128.testsuite
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
Exec/reacting_tests/reacting_convergence/inputs.64.testsuite.simplified_sdc
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.128
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.256
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.512
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.64
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.nse
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/Detonation/inputs-det-x.sdc2
Exec/science/Detonation/inputs-det-x.simplified_sdc
Exec/science/Detonation/inputs-det-x.test
Exec/science/Detonation/nse_runs/inputs.template.simple_sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/nse_runs/inputs.template.true_sdc
Exec/science/celldet/inputs.celldet
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/xrb_mixed/inputs_2d
Exec/unit_tests/particles_test/inputs.2d
commit 404d5545a77ed9f2b434b15eec367e2308f20f14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 30 11:51:14 2021 -0400
start of the implementation of drive_initial_convection (#1998)
castro.drive_initial_convection now allows one to setup a convective velocity field by periodically reinitializing the thermodynamics on the grid from the initial conditions + using only the initial model's temperature for the burning.
CHANGES.md
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/reactions/Castro_react.cpp
commit d4efd20c6d6c12c4cffde7e9795310eb1c45e7fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 30 08:50:38 2021 -0400
nova: increase blocking_factor and max_grid_size (#2008)
Exec/science/nova/inputs_2d
commit a26cd39dd61f5dfe309e4d93e9b70a555087921f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 29 09:48:22 2021 -0400
massive_star: split the slices into two separate plots (#2007)
now one is composition and the other is velocity info
Exec/science/massive_star/analysis/massive_star_slice.py
commit c71587611f6c12af6c4e2b19a956e5bf3819148f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 24 18:55:44 2021 -0400
disable Fortran automatically unless needed (#2006)
We only need Fortran for 2 things right now: radiation and a pynucastro net
this now turns off Fortran in Microphysics and AMReX in all other cases
Exec/Make.Castro
commit c51bba988bcdcbaf9100644e9a5301301691fcc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 22 14:47:45 2021 -0700
Port remainder of make_radial_gravity to GPU (#2005)
Source/gravity/Gravity.cpp
commit 46c733f45c63c342929dcbd62caa587cca4ac18f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 22 10:09:59 2021 -0700
Compute radial gravity using a prefix sum (#2004)
This allows the radial gravity calculation to be parallelized on GPU builds.
Source/gravity/Gravity.cpp
commit 3fa8e1a927cba6972bfd724f2da2b329a14b4d58
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 22 10:05:51 2021 -0700
Remove loop-carried dependence of vol in make_radial_grav (#2003)
The code had a loop-carried dependence of both vol and mass enclosed, but the former can be computed based on just on radial zone index. This change is made to enable a future change that implements this loop as a prefix sum over mass enclosed.
Source/gravity/Gravity.cpp
commit 98c4030683808f727c7a488c820c07c631e36cc5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 21 10:55:50 2021 -0700
Simplify monopole grav integral to avoid i == 0 special case (#2002)
The general case works for i == 0 (halfdr == rc for that zone).
Source/gravity/Gravity.cpp
commit 23f32b9a0ed219e6b3b065fe133bf67b13388830
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 21 12:21:01 2021 -0400
update massive star inputs files (#1999)
they now are a narrower domain (better aspect for 2-d axisymmetry)
also turn on burn weights, diagnostics, and the perturbation
Exec/science/massive_star/analysis/massive_star_slice.py
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
Exec/science/massive_star/inputs_2d.nse.sdc.zoom
commit 88c937c1af7d228965a8e13c1a7adad451c59c4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 21 10:48:03 2021 -0400
AMReX no longer has CRSEGRNDOMP option (#2001)
it is now the default
Exec/Make.Castro
external/amrex
commit 12851a6a1487f48e80eea65d6c89761524686cb9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 21 07:23:20 2021 -0700
Remove max_radius_all_in_domain (#2000)
This code path appears to be trying to deal with the case where there might be mass outside the domain, but we don't currently have that in the code, so by removing it we can simplify the calculation of the monopole gravity.
Source/gravity/Gravity.cpp
commit d3907cab09eab697f65fbda34d4e33b73f881628
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 21 09:02:23 2021 -0400
fix compilation of true-SDC (#1996)
Source/driver/Castro.H
Source/driver/Castro_advance_ctu.cpp
Source/reactions/Castro_react.cpp
commit 99e42b0a77762b179a344d978999170432a5d6f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 15 18:10:39 2021 -0400
increase p0 for DustCollapse pointmass test so it runs without crashing (#1993)
we don't remember the reason why p0 was so much lower in this inputs compared to the others.
This fixes #1979
Exec/gravity_tests/DustCollapse/inputs_pointmass
commit 3331897eb90f1ab58bd2b011e3402c438499932b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 15 17:25:31 2021 -0400
eliminate PhiRot_Type from StateData (#1974)
this also increments the checkpoint number
Docs/source/io.rst
Docs/source/software.rst
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/Problem_Derives.H
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
Source/scf/scf_relax.cpp
commit c8f27ec95b29e0b15baa49900acda6d8aeedea61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 15 11:37:54 2021 -0400
fix massive_star CUDA compilation (#1992)
network_species_index() is not available on device
Exec/science/massive_star/_prob_params
Exec/science/massive_star/problem_initialize.H
Exec/science/massive_star/problem_initialize_state_data.H
commit ae46ca75ef7d57739860e872907d31596382b2c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 15 11:04:19 2021 -0400
Det suite updates (#1954)
some changes to SDC, in particular, use jacobian=3
Exec/science/Detonation/nse_runs/detonation.py
Exec/science/Detonation/nse_runs/inputs.template.simple_sdc
Exec/science/Detonation/nse_runs/setup_runs.py
commit 2c249253ee0904bf4af8cde06bd5735158636ac7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 15 11:03:46 2021 -0400
add a 10 km initial model for massive star (#1986)
this also increases the maximum number of points for the model in the GNUmakefile
Exec/science/massive_star/15m_500_sec.aprox19.hse.10.0km
Exec/science/massive_star/GNUmakefile
commit 75136f7ff85ddcdc8bcff4ba39025be124ac1d3e
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Sep 15 14:12:23 2021 +0100
add css files to conf.py (#1991)
Docs/source/conf.py
commit 1bc7b34da9956f367f07a4991dc35c15082d895c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 14 19:34:31 2021 -0400
document the integral quantities (#1990)
This closes #44
Docs/source/io.rst
commit c18f3b924f0159414fb25cd62a20f1b9526e6d12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 11 11:24:41 2021 -0400
move the recent change to the right release (#1984)
CHANGES.md
commit e62ed6adeff02b0331a31a9b4df4ac3f03d90b5b
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Sat Sep 11 10:30:38 2021 -0400
Added parallel plane gravity (#1978)
I introduced a parallel plane gravity inside the function Gravity::add_pointmass_to_gravity and two option parameters in __cpp_parameters.
CHANGES.md
Source/driver/_cpp_parameters
Source/gravity/Gravity.cpp
commit 2b33677a3d985977f360e3191af568a2cd3b2e17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 10 15:32:29 2021 -0400
fix some bounds errors in pointmass for 1 or 2-d (#1983)
Source/gravity/Castro_pointmass.cpp
commit 0061981fcd749bc97d59fb0e8dd3de64c9a4c383
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 10 15:08:58 2021 -0400
disable the point mass acceleration in non-evolved dimensions (#1982)
Source/gravity/Gravity.cpp
commit e64c8d6658a73355b59b1081c75e1ab03ea9825a
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Fri Sep 10 10:14:04 2021 -0400
Fix _prob_params parsing if a final newline is missing (#1981)
If a line doesn't have a comment, then `line.find("#")` returns -1.
Normally, `line[:-1]` will just remove a trailing newline, but if the
file doesn't have a newline at the end, this will instead remove the
last character on the line, which could be a "y" in the 4th column for
letting a parameter be set at runtime (see #1980).
Util/scripts/write_probdata.py
commit 525708d46a8118a8a8a466879a95dc11af7e7d1c
Author: Eric T. Johnson <eric.t.johnson@stonybrook.edu>
Date: Thu Sep 9 17:34:20 2021 -0400
Require castro.change_max to be greater than 1.0 (#1976)
Addresses #1863.
All but one of the changed inputs use fixed_dt, so change_max is unnecessary.
CHANGES.md
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.32
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
commit a5ac027ee6367827fab1cc8d1d523e6945f241a6
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Sep 9 22:18:33 2021 +0100
Add perturbations to the silicon layer of the massive star (#1975)
Exec/science/massive_star/_prob_params
Exec/science/massive_star/problem_initialize_state_data.H
commit deeb8c98b07f2486e7a9d1e824f857941443e58b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 9 12:04:50 2021 -0700
Convert save_flux_in_plotvar to C++ (#1700)
The versions to save the lab or comoving flux were the same up to a minus sign, so I merged them into a single routine.
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/RadPlotvar.cpp
Source/radiation/RadPlotvar_1d.f90
Source/radiation/RadPlotvar_2d.f90
Source/radiation/RadPlotvar_3d.f90
Source/radiation/Radiation.H
Source/radiation/SGRadSolver.cpp
commit f6cea1723a1fa1cf251017dd7d3d834887cf03ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 7 14:56:26 2021 -0700
Zero out flux corrections that would cause small density (#1879)
As observed in #341, it's possible for the reflux operation to result in a small or negative density. Currently this is dealt with via a density reset. Density resets are fairly ugly and should be avoided since they can cause a large change in density (down to small_dens) that has downstream consequences. So instead what we can do is just zero out the flux corrections if they would cause a small or negative density. This PR applies that change. Another option would have been to use the existing limit_hydro_fluxes_on_small_dens() function, however this function's interface currently relies on having the primitive variables, which are not already available in the reflux operation. A future change could do this if desired.
This PR also modifies the update on the fluxes so that they are done on a direction-by-direction basis. While this is not strictly necessary to support this change, it should save on memory since we don't actually need to have all three directional fluxes constructed simultaneously.
Source/driver/Castro.cpp
commit 399a16d0040eb451057b65acb5a08025d2f2c192
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 7 16:00:51 2021 -0400
make burn_weights storage optional (off by default) (#1949)
this also expands the amount of information: we now separately store
the first and second halfs for Strang, and all iterations separately
for SDC (with 1 extra interation in case of a retry bump). Also note
that this information is no longer stored as StateData.
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/reactions/Castro_react.H
Source/reactions/Castro_react.cpp
Source/sdc/sdc_util.cpp
commit bbd7841bc0ac6e8797960705b0eea9439b061cf3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 7 07:39:51 2021 -0700
Implement conservative rotations on edges like gravity (#1130)
Rather than referring to the rotational potential we can consider only the rotational acceleration (-grad(phi), the equivalent of the gravitational acceleration) on edges to implement the conservative rotation source type.
Source/rotation/rotation_sources.cpp
commit 3b9d35266f43ae1162aa3f6a55291de5f94c1d62
Merge: f106c1f1f e6140f69e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 1 19:00:44 2021 -0400
Merge branch 'main' of github.com:amrex-astro/Castro
commit e6140f69e00b47d16b9d7095e52799d626adf766
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 1 13:26:40 2021 -0400
update changes
CHANGES.md
commit 84b3062b0edc6b8d97dcee9a3e785e4f414ec680
Merge: 8443c84ee 4a043fa13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 1 13:23:32 2021 -0400
Merge branch 'development'
commit 8443c84eeb7a6ab6e0bb7243496c4d0b213377b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 1 13:22:37 2021 -0400
update amrex and Microphysics to 21.09
external/Microphysics
external/amrex
commit 4a043fa13dc8ea8098a53f439975d3f27cb1c883
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 1 10:12:16 2021 -0700
Use AMReX BC fill routines for B field (#1713)
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/filfc.f90
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Castro_bc_fill_nd_F.H
Source/problems/Make.package
Source/problems/bc_fill_nd.F90
commit 5b556e16f1dfd645c7b35339cdcc8dae36a7761e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 1 11:56:26 2021 -0400
remove a typo in an inputs (#1972)
Exec/science/massive_star/inputs_1d
commit fa002d22f869dd8264a1b08271a7c4a9fde44be0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 21:05:31 2021 -0400
when using simplified-SDC pay attention to source_term_predictor (#1968)
currently, for the first simplified-SDC iteration we use the old step's
new source as a corrector in create the source term for the interface
states (the hydro sources, e.g., gravity, not reactive). This seems to not
do well, so now we respect castro.source_term_predictor to allow us
to turn this corrector off.
In the future we can revisit this, perhaps restoring the original
approach for iter > 1
Source/driver/Castro.cpp
Source/hydro/Castro_ctu.cpp
commit 7346589ccf85dbc1a5f090cb18a5d3599afd29f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 20:48:58 2021 -0400
add a reacting_bubble inputs that works for simplified-SDC (#1966)
note: I needed to set react_rho_min for this to work
Exec/reacting_tests/reacting_bubble/inputs_2d.sdc_test
commit c01838bccf0543acb66c10cc3251344f1fe0052e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 20:48:23 2021 -0400
add a 1-d test inputs file for SDC (#1956)
Exec/science/massive_star/inputs_1d.nse.sdc
commit 1e5fc79a7949a2bc8a8cd0a6c025aa0a33027a96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 27 11:37:39 2021 -0400
option to disable react source to advection in simplified-SDC (#1969)
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit 194c6540e02448b256cfaf0c3d6a5b7d60151462
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 24 12:28:12 2021 -0400
change how we define the location of the perturbation (#1957)
now we detect the location of the base of the He layer and R_pert
is the distance above the He layer
Exec/science/subchandra/_prob_params
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/problem_initialize.H
Exec/science/subchandra/problem_initialize_state_data.H
commit 185950a446e57dfb9a68f5ddf388682eaa3da888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 18 15:43:31 2021 -0400
fix the species clipping (#1961)
it should only apply to mass fractions, not all passives
Source/hydro/Castro_ctu.cpp
commit 7bb8289c1f0da12e1ade2ab4472e19f4f09e8363
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 16 10:51:30 2021 -0400
set and enforce small_x for massive_star (#1960)
also pick a more reasonable small_dens
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
Exec/science/massive_star/inputs_2d.nse.sdc.zoom
Exec/science/massive_star/problem_initialize_state_data.H
commit 4f2ca42762a64133d957af5bdfe77499905877fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 11 16:27:08 2021 -0400
add some more notes on debugging (#1958)
Docs/source/debugging.rst
Docs/source/faq.rst
commit 30d75d688145f954fad9377e719791303b5e7217
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 11 14:28:10 2021 -0400
some fixes to the dump_and_continue docs typesetting. (#1959)
This makes it clearer that message_int needs to be set.
Docs/source/faq.rst
commit 114ee3427bb354fcb19cc82c5962359f71ec7ae9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 6 09:32:35 2021 -0400
for multilevel simplified-SDC, explicitly fill the react source ghosts (#1953)
we do this before hydro because any average down may have made the ghost
cells inconsistent which can be especially problematic at symmetry boundaries
Source/driver/Castro_advance_ctu.cpp
commit a39ce65f3ecbe1d8f46b5dafcfec95099f5695af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 1 22:01:33 2021 -0400
update to 21.08
external/Microphysics
external/amrex
commit c5879585a5031c4635b487f0a760b09762a28586
Merge: 1fcdccc05 f2498ceb2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 1 22:00:01 2021 -0400
Merge branch 'development'
commit f2498ceb2a6c621ac01fcc097c21c7a633913ad6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 31 11:30:08 2021 -0400
use nse_relax_factor for massive star (#1922)
this also uses a new 20 km model and appropriate resolution in the inputs files (the initial model here was created with initial_models/massive_star using inputs.hires
Exec/science/massive_star/15m_500_sec.aprox19.hse.20.0km
Exec/science/massive_star/15m_500_sec.aprox19.hse.6400
Exec/science/massive_star/analysis/initial_model.py
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.nse.sdc
Exec/science/massive_star/inputs_2d.nse.sdc.zoom
commit 98cf4beb6137d268df03f7fea252e446b503f694
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 28 17:03:36 2021 -0400
fix the burn_weights again with the numerical Jacobian (#1951)
the convention that VODE uses is that it already includes the NEQS RHS
calls in n_rhs so we don't need to readd them for each n_jac
Source/reactions/Castro_react.cpp
commit 5fe14ab5ef159b4760a3786dc6b88e9d2e921253
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 23 11:50:33 2021 -0400
new SDC formulation (#1945)
fix the build for the new SDC formulation
Source/reactions/Castro_react.cpp
commit 0eefe6ef0cc8f699ba0641f8c5c04ddd2c24d6a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 22 09:45:17 2021 -0400
update the docs on the buildsystem + remove some unused defines (#1947)
Docs/source/build_system.rst
Exec/Make.Castro
commit 32b47b0e1049bbf03035256918325761d86b7018
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 22 09:45:00 2021 -0400
Flame wave scaling (#1941)
add 2021 scaling results
Exec/science/flame_wave/scaling/3d_science/flame_wave_scaling.py
Exec/science/flame_wave/scaling/3d_science/scaling_20210606.txt
commit cfb30a11acb8bf3af9100206d61622a29c372299
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 22 09:44:25 2021 -0400
use a more accurate measure of burn_weight (#1946)
this weights things correctly if we are using the numerical Jacobian
Source/reactions/Castro_react.cpp
commit 979d677fe27e79956d240d55575dcdbf2c8495f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 19 19:56:07 2021 -0400
this syncs up with the change to the numerical Jacobian in Microphysics (#1651)
Source/reactions/Castro_react_util.H
Source/sdc/Castro_sdc_util.H
Source/sdc/vode_rhs_true_sdc.H
commit 0c60dcc42e2876d285c11e36e13e2c5af86d045e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 18 12:52:46 2021 -0400
new inputs / initial model for zoomed-in massive star (#1940)
This focuses just on the inner shells, for SDC / Strang comparison.
Exec/science/massive_star/15m_500_sec.aprox19.hse.20km
Exec/science/massive_star/GNUmakefile
Exec/science/massive_star/analysis/initial_model.py
Exec/science/massive_star/inputs_2d.nse.sdc.zoom
commit 8d25c56a1558d0af51692859ca9faa09dd6e90c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 18 12:52:17 2021 -0400
Subch plot (#1944)
Exec/science/subchandra/analysis/subch_slice.py
commit d3d8a3c58ed6d6ae5d14ecfb36c6682aa1d18b20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 16 10:24:17 2021 -0400
fix the Machnumber colormap -- now yellow = highest (#1943)
Exec/science/massive_star/analysis/massive_star_slice.py
commit 6d98b1d5fab9412cf6cba1f33877b0bb54f0b47e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 13 12:20:07 2021 -0400
enforce X interface states are in [0, 1] with SDC reaction source term (#1931)
In an ideal world, the sources from the SDC reaction integration would be well behaved when we apply them to the interface, but sometimes with the lagging or the tracing of species to the interface, we go outside of [0, 1], so this just clips the states. This only applies for simplified-SDC.
Source/hydro/Castro_ctu.cpp
commit 29e8d70579ddf8f16e2b912903a61a49761258de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 13 09:19:12 2021 -0400
add a plot of the composition in RGB channels (#1939)
Exec/science/massive_star/analysis/massive_star_composition.py
commit 6cbda36256b40e46073dfb14ec45b7c463142457
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 13 09:16:29 2021 -0400
add a threshold for linear transition to symlog enuc + NSE contour (#1937)
Exec/science/massive_star/analysis/massive_star_slice.py
commit 409bcd2735d50c5e7f5bcb76c4104ab2179d63ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 12 15:05:47 2021 -0400
add an inputs for the test suite with SDC (#1938)
Exec/science/massive_star/inputs_2d.nse.sdc
commit 59f1dc356817345d93ef56dec5c828cf05c7e130
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 12 09:43:24 2021 -0400
fix bounds issue in e added SDC diagnostic (#1936)
Source/reactions/Castro_react.cpp
commit 81dad677738860b287b26962f69e038212f46910
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 12 09:43:03 2021 -0400
turn off Fortran for the massive star (#1932)
Exec/science/massive_star/GNUmakefile
commit 514f6a00ae5ea023d07955ab868821219b15faf2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 10 14:04:02 2021 -0400
add an optional perturbation to StarGrav (#1935)
this is intended to help test the effect of the source in the reference state
Exec/gravity_tests/StarGrav/_prob_params
Exec/gravity_tests/StarGrav/problem_initialize_state_data.H
commit 2c85f353b4fcbd931506e7410d573ee9de382ae1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 10 14:03:43 2021 -0400
fix the x-axis labels (#1934)
Exec/science/massive_star/analysis/massive_star_slice.py
commit f2c13018ccdac46654c0a4baa328e73bc8795e6b
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Jul 7 18:29:03 2021 +0100
Set up reacting_convergence with silicon burning (#1901)
Sets up initial conditions for the reacting_convergence problem to mimic those in the silicon burning layer in the massive star problem.
Exec/reacting_tests/reacting_convergence/_prob_params
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.128
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.256
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.512
Exec/reacting_tests/reacting_convergence/massive_star_inputs/inputs.64
Exec/reacting_tests/reacting_convergence/problem_initialize.H
commit cdd3950c9f92335c1467d959fa285d2624d91032
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 7 11:01:37 2021 -0400
add job script for massive_star on summit (#1930)
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/job_scripts/summit_gpu.submit
commit 26fb8c23c6c3e904c1cd65f804ab226d34567788
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 6 19:16:31 2021 -0400
sync main -> development to get the submodules updated (#1929)
external/Microphysics
external/amrex
commit 6144722ec1e5f1406bf65778463e75abc359fc41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 6 14:53:45 2021 -0400
add amr_diag.out and grid_diag.out to .gitignore (#1928)
.gitignore
commit 1fcdccc051edcf9d1cbe40164144cceee1ada539
Author: Alexander Smith Clark <alexander.smithclark@stonybrook.edu>
Date: Tue Jul 6 12:31:22 2021 -0400
Initialize riemann_2d (#1924)
I have implemented the Liska & Wedroff (2003) Riemman 2d problem. I am satisfied with the result, but I would like to improve the resolution of each case described here.
Exec/hydro_tests/riemann_2d/GNUmakefile
Exec/hydro_tests/riemann_2d/Make.package
Exec/hydro_tests/riemann_2d/inputs_c12
Exec/hydro_tests/riemann_2d/inputs_c15
Exec/hydro_tests/riemann_2d/inputs_c17
Exec/hydro_tests/riemann_2d/inputs_c3
Exec/hydro_tests/riemann_2d/inputs_c4
Exec/hydro_tests/riemann_2d/inputs_c6
Exec/hydro_tests/riemann_2d/problem_initialize.H
Exec/hydro_tests/riemann_2d/problem_initialize_state_data.H
Exec/hydro_tests/riemann_2d/visualization.ipynb
commit e74b3af8e1a886cc8fb303da8d6e2c371238a1f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 6 12:00:49 2021 -0400
add an initial model plot to help visualize the problem (#1927)
Exec/science/massive_star/analysis/initial_model.py
commit 011e1b205b2ff0026ac36a41f06026c4b503eb25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 5 20:11:29 2021 -0400
add a yt script (#1926)
This plots a few variables. But no matter what I do, I can't get the axis text to be in scientific notation.
Exec/science/massive_star/analysis/massive_star_slice.py
commit 3ad0e0167953c501f3ed2dbed0b5104b6a9e2de2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 2 11:39:43 2021 -0400
use the new initial model from initial_models/rotating_star (#1923)
This uses the new initial model from initial_models/massive_star. The main difference is that we reduce the MESA model down to 19 isotopes before putting into HSE and also preserve Ye from the MESA model and use that in the EOS in NSE regions.
The problem setup is also modified now to use Ye in regions where we are in NSE and use the X's otherwise, and it consistently initializes the other composition variables.
Exec/science/massive_star/15m_500_sec.aprox19.hse.6400
Exec/science/massive_star/15m_aprox19.6400
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/problem_initialize_state_data.H
commit c6aecc279526dc888b6146a3ed9642f5d713c956
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 1 11:24:45 2021 -0400
update to 21.07
external/Microphysics
external/amrex
commit a13dea9a3b8258135d5208af27bf7bca7934f042
Merge: 95a36eddd 7bcddcc23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 1 11:24:17 2021 -0400
Merge branch 'development'
commit 7bcddcc23b7c579f737c5c7feb713ec90bb77469
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 1 11:16:04 2021 -0400
set the tolerances so the subch can successfully burn (#1918)
Exec/science/subchandra/inputs_2d
commit 3ea72bd862da8810b07e8b48919a68868aa585d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 24 16:31:59 2021 -0700
Only apply sponge at the new time without using predictor-corrector (#1876)
See discussion in #1846 for motivation. This change makes the sponge consistent with its original form in Castro.
CHANGES.md
Source/sources/Castro_sources.H
Source/sources/Castro_sponge.cpp
commit 80f42e2ab7eebb0c2af3ea81fb2ee5873f21471b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 24 16:27:55 2021 -0400
fix compilation of exact Riemann (#1910)
Source/hydro is needed for MHD and not needed if USE_ALL_CASTRO = FALSE
Exec/Make.Castro
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/main.cpp
Util/exact_riemann/riemann_F.H
commit 4b21c88fed9ca308e7cd5a9a145e4a1d516cbe57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 23 08:27:53 2021 -0400
update submodules to the latest (#1919)
external/Microphysics
external/amrex
commit 848c15d1a959529b6808779a48b142ed01e45177
Author: melilly <44589025+melilly@users.noreply.github.com>
Date: Mon Jun 21 12:38:18 2021 -0500
Update subchandra input file to do reactions (#1917)
Turn on reactions by default in subchandra inputs
Exec/science/subchandra/inputs_2d
commit fd04b89dd5dd9684f34622d94fdec16ca3f925f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 20 13:08:29 2021 -0700
Convert ca_integrate_grav to C++ (#1915)
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/gravity/Make.package
commit c8c0a63740f6afa7eebf31de51631e9895843e8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 13:53:25 2021 -0400
compile Sedov without any Fortran (#1914)
Exec/Make.auto_source
Exec/hydro_tests/Sedov/GNUmakefile
commit 251b0a2b0e72b75b85629c5e5401244631fe6132
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 13:39:12 2021 -0400
remove ca_set_abort_on_failure (#1913)
this actually didn't do anything, since it was only being used
for true SDC, but true SDC calls VODE on its own and catches that
vode state and aborts automatically already
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
commit a73ca11181119dd5b8c76a96f2a536fa9a4af24a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 11:07:08 2021 -0400
call runtime_init directly if needed (#1911)
this only applies for problems that use Fortran microphysics
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
commit c205089a46b5e8301ce11521c1ec443943c2507c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 11:05:45 2021 -0400
directly call the Fortran microphysics init if needed (#1912)
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
commit 8865fec35319244fc9f689f5d86e5f8610899b51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 11 22:40:45 2021 -0400
use the new AUTO_BUILD_SOURCES amrex GNU Make feature (#1908)
* use the new AUTO_BUILD_SOURCES amrex GNU Make feature
* update submodules to support this build
Exec/Make.auto_source
external/Microphysics
external/amrex
commit f589dd44f4824c88a80e243a991fcaec47fb0fc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 11 13:54:15 2021 -0400
build Sedov and Detonation without an autogen-d Fortran (#1906)
We no longer create extern.F90, actual_network.F90, network_properties.F90, or state_indices_nd.F90
Exec/Make.auto_source
Exec/hydro_tests/Sedov/GNUmakefile
Exec/science/Detonation/GNUmakefile
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
commit 5b5f88960eec8677676e7e4c03b5f177e260b085
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 11 09:06:45 2021 -0400
fix compilation due to recent changes (#1907)
Exec/Make.auto_source
commit 54e9cee355772d6ba68a10de2264df9bbc853d10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 10 21:09:19 2021 -0400
optionally don't build Fortran Microphysics (#1905)
Source/driver/Castro.cpp
Source/driver/Castro_nd.F90
commit 5a973a91858cc0479b16f0212ae1e9b23d8b0472
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 10 20:02:34 2021 -0400
don't create the Fortran state_indices_nd.F90 unless we really need it (#1903)
that is only in radiation now
Exec/Make.auto_source
Source/driver/Make.package
Source/driver/set_variables.py
commit d87f29cea0a377c886e9214dc7cab3a93b7b8ee7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 10 09:06:39 2021 -0700
Floor QREINT in PPM tracing (#1896)
Source/hydro/trace_ppm.cpp
commit 3cdba021b5ce2db5804b1a4f37cc4ce73975b95a
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Jun 10 15:49:31 2021 +0100
remove fortran hacks from docs build (#1902)
Docs/add_doxy_headers.py
Docs/make_api.py
Docs/preprocess_files.py
commit 14c67eee6cd7c07c74cd01dd4cc2c6f6476b842b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 10 07:11:31 2021 -0700
Make small_pres and small_ener consistent with small_dens and small_temp (#1895)
Source/driver/Castro_setup.cpp
commit b35249254a6eb861d10f13e2e9280a9fa4eab08b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 13:29:29 2021 -0400
rename sdc_use_analytic_jac -> sdc_newton_use_analytic_jac (#1899)
this better reinforces the idea that this is only for Newton iteration,
and not for VODE
Docs/source/sdc.rst
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/Detonation/inputs-det-x.sdc2
Exec/science/Detonation/nse_runs/inputs.template.true_sdc
Exec/science/flame/inputs.1d.sdc
Source/driver/_cpp_parameters
Source/reactions/Castro_react_util.H
commit 53890ee2a671b43c94c48876d3025f24428e087f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 12:52:02 2021 -0400
allow for problem.center to be read via inputs (#1888)
Note: we currently define center as having a size "3" regardless of dimensionality,
so we will always need to supply 3 values if we try to set it via inputs.
Source/problems/_prob_params
Util/scripts/write_probdata.py
commit 18453f3e8a149aa8999b272442037def4396786b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 12:22:42 2021 -0400
update submodules so Castro compiles again (#1898)
external/Microphysics
external/amrex
commit 212f60808873d9ff9cb4f4e1df4a5e384b0cfddc
Author: Ishita-S <46733395+Ishita-S@users.noreply.github.com>
Date: Wed Jun 9 12:08:47 2021 -0400
update inputs to the correct values and rename (#1892)
Exec/science/celldet/inputs-det-x
Exec/science/celldet/inputs.celldet
commit 3b293133287d573c6cc1a1f5fe236ac4cdfcfb05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 10:20:37 2021 -0400
use the job_info tests for extern from the C++ header (#1894)
Source/driver/Castro_io.cpp
commit 607a0b5b6c9a5f3506a1f811001df13e99f8dd93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 09:22:57 2021 -0400
nse_test: inputs.64 was accidently deleted (#1893)
Exec/reacting_tests/nse_test/inputs.64
commit 25ddb35df32ca7ffaca9ae710fcca44191c1e821
Author: Ishita-S <46733395+Ishita-S@users.noreply.github.com>
Date: Tue Jun 8 12:45:30 2021 -0400
Cellular Detonation Problem (#1891)
this is the start of an (MHD) cell-detonation problem
Exec/science/celldet/GNUmakefile
Exec/science/celldet/Make.package
Exec/science/celldet/_prob_params
Exec/science/celldet/inputs-det-x
Exec/science/celldet/inputs-det-x.nse
Exec/science/celldet/problem_initialize.H
Exec/science/celldet/problem_initialize_mhd_data.H
Exec/science/celldet/problem_initialize_state_data.H
commit a9d79962371ea47210dd5623ee3722664210c2a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 8 11:18:47 2021 -0400
ignore output temporary files (#1890)
.gitignore
commit 3df5378bf9d98f5663a49120127b96c2130dfcf9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 8 09:34:33 2021 -0400
set AMREX_NO_PROBINIT = TRUE (#1889)
Exec/Make.Castro
Source/problems/Make.package
Source/problems/Prob_nd.F90
commit f938d64ebbb5e591c3d9606c4305ff743fb2e56f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 7 22:09:38 2021 -0400
some fixes for recent versions of yt (#1878)
we need to apply units and work around a bug in the BoxLib frontend detection
Exec/science/flame_wave/analysis/slice_multi_crop.py
Exec/science/flame_wave/analysis/slice_multi_crop_H_He.py
commit 14faaf285775fdb03f989f8ee5c09cb9c8553dbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 7 12:19:00 2021 -0400
move the validate check to after the different classes are setup (#1886)
This catches some quantities that are only read in the different class constructors.
Also add the Microphysics namespaces to the validation check.
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/driver/runtime_parameters.H
commit 05cfca36a28c3ffd3ac8aab58239127a83f9a162
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 7 12:16:14 2021 -0400
mailing list -> github discussions (#1887)
README.md
commit 3e8b18a1ac31c343e8025ae93db43fb624914fc0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 7 12:03:20 2021 -0400
move castro.do_radiation to the automatically managed runtime params (#1880)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
commit 1c54fa91668e737146e76d9c91d81303676c5727
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 7 11:58:32 2021 -0400
allow for optionally static refinement (#1872)
we can now tag based on height instead of density.
This also generalizes the 25 cm runs to work in 2- and 3-d.
Exec/science/flame_wave/_prob_params
Exec/science/flame_wave/inputs_He/inputs.He.25cm.dynamic.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.static.1000Hz
Exec/science/flame_wave/problem_tagging.H
commit c0742cc3d0980884b272337e1177d547fd27d799
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 6 19:41:02 2021 -0400
remove references to print_energy_diagnostics (#1885)
this is an old parameter
Exec/gravity_tests/evrard_collapse/inputs
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/hydro_tests/Noh/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
commit 7e09034eb1f16a7a2899a38a6087049beefd3954
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 6 19:37:54 2021 -0400
remove mhd_plm_slope (#1884)
this is not a valid parameter
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_mhd_test
Exec/gravity_tests/StarGrav/inputs_3d_mhd
Exec/hydro_tests/Sedov/inputs.3d.mhd
Exec/hydro_tests/Sod_stellar/inputs-test1-helm_mhd
Exec/mhd_tests/Alfven/inputs-1_0_1d
Exec/mhd_tests/Alfven/inputs-1_0_2d
Exec/mhd_tests/Alfven/inputs-1_1
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.briowu.test
Exec/mhd_tests/BrioWu/inputs.sod.test
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/LoopAdvection/inputs
Exec/mhd_tests/MagnetosonicWaves/inputs-1_0_2d_fast
Exec/mhd_tests/MagnetosonicWaves/inputs-1_1_slow
Exec/mhd_tests/OrszagTang/inputs
Exec/mhd_tests/OrszagTang/inputs.test
Exec/mhd_tests/RT/inputs_3d
Exec/mhd_tests/RT/inputs_3d_mhd
Exec/mhd_tests/species/inputs
Exec/mhd_tests/species/inputs.test
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
commit 38ec5c6f96af9644164b45a10bd085c13e746ff8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 6 15:25:48 2021 -0400
remove plot_X (#1881)
it is unused and redundant -- we already derive X in Castro_setup.cpp
Source/driver/Castro_io.cpp
commit 7c266a89b48c36f145bb272440ad8ea2005701ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 6 14:36:32 2021 -0400
add a check on the runtime parameters in inputs (#1882)
add a check on the runtime parameters in inputs
this ensures that the parameters specified are valid / known to Castro
enable by setting castro.abort_on_invalid_params=1
Note: this does not cover microphysics presently
CHANGES.md
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/runtime_parameters.H
commit 9305f9db557c0901425406b99ef65760cbe63121
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 5 17:10:10 2021 -0400
use the numerical Jacobian (#1877)
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_2d.nse
commit e558dfb5c823af762bf339d14efc97ec4ba70e3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 5 09:28:40 2021 -0700
Initialize SDC reactions data to zero when do_react = 0 (#1874)
If we have compiled with reactions and USE_SIMPLIFIED_SDC, but have set castro.do_react = 0, there is a bug in the current code where the new-time Reactions_Type data doesn't actually get initialized to zero during the CTU advance. This means that if anything attempts to access the data, such as a derived variable, there may be nonsense results. This change sets the new-time reactions type to zero explicitly so that there will always be valid data to access. For safety, we also set the old-time Reactions_Type data, as well as the Simplified_SDC_React_Type data, to zero.
Source/driver/Castro_advance_ctu.cpp
commit 79b97381bbe6d23f60a9c4fd7be8ceed717a9462
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 5 08:50:08 2021 -0700
Remove CFL violation check for CTU advance (#1873)
The code in question checks the old state (plus, as of #1842, the old-time sources) to see whether it violates the CFL criterion. But this has been superfluous ever since we added the logic at the end of the timestep to see if the timestep constraint is violated at that point. If there is a violation at that point, we will retry the timestep. So this prior additional check is now removed.
Source/driver/Castro_advance_ctu.cpp
commit 7c430d600dd6f6bad757f1c9d3c774958d1d3edb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 5 08:49:12 2021 -0700
Increase timestep for wdmerger_retry test (#1875)
#1873 removes the CFL violation check prior to the CTU hydro update, which is what is being relied on in the wdmerger_retry test to trigger a retry. This change increases the fixed_dt uses by that test to make it more likely to need a retry. Testing with this new dt reveals that even if the CFL violation check is removed, the hydro update will still generate a negative density, so there will be a retry.
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit e8845e8167e468638dde18fffb34711ddd8dbe56
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 3 18:03:16 2021 -0700
Don't limit future timesteps based on previous retries (#1852)
#344, which added dynamic retries, also made a decision to limit the next timestep based on retries in the previous timestep. However with retrospect this appears to have been a bad choice. Because we now always cut by a factor of 2 when we take a retry, this is effectively halving the next timestep. But if the condition that caused the retry (for example, a temporarily large velocity) has gone away by the time we get to the next timestep, there is no need to take a shorter timestep. If the condition is still there, it will appear in the CFL criterion and we will take a shorter timestep anyway. So in the optimistic case, removing this will allow us to take asymptotically larger timesteps.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit f86830c3ad84c7ab1b540c945e12e898eb045856
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 3 17:48:48 2021 -0700
Include the effect of the sources in the reference state (#1725)
As discussed in #1645 it appears to be incorrect that we include the source term in the characteristic tracing but do not include the source term in the reference state. (This is done for PPM only.)
Source/hydro/trace_ppm.cpp
commit d2acfca754a9b65851139d9657203fbddba8a06c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 3 10:21:37 2021 -0700
Merge 2D and 3D inputs to wdmerger (#1829)
This uses the new functionality from AMReX-Codes/amrex#2049.
Exec/science/wdmerger/inputs
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/wdmerger_relaxation/inputs
commit 85ea49ba93f8aea2b6b1c96c2f17309343a4be3e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 3 10:00:59 2021 -0700
Clean Sborder after FillPatch (#1849)
The FillPatch that creates Sborder from S_old can cause thermodynamically inconsistent states and/or small densities in the ghost zones, so we do need to clean Sborder (although as a later enhancement, we could change this clean to only operate on the ghost zones).
Source/driver/Castro_advance.cpp
commit d95281486dca28626e339121b30f018e2f2444e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 3 06:00:54 2021 -0700
Calculate position on grid for SCF relative to center (#1871)
This is a minor bug fix for the SCF calculation -- the positions on the grid should be calculated with respect to center because that's where the stellar edges are placed with respect to. This had no effect on the SCF single star test because the center for that problem happens to be at the origin.
Source/scf/scf_relax.cpp
commit 5d8e35b0e6d701068075c6036dca841d62bce1df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 19:33:31 2021 -0400
fix reacting_convergence compilation (#1866)
for NSE, bion now comes from network::
for pynucastro nets, there is no actual_network.H
Exec/reacting_tests/reacting_convergence/problem_initialize.H
Exec/reacting_tests/reacting_convergence/problem_initialize_state_data.H
commit 9d304dcf84c1b01a62f6e287b17673639eef9293
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 15:49:52 2021 -0400
eliminate meth_params_module (#1862)
Exec/Make.auto_source
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/meth_params.template
Source/driver/parse_castro_params.py
Source/problems/bc_fill_nd.F90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RadPlotvar_1d.f90
Source/radiation/RadPlotvar_2d.f90
Source/radiation/RadPlotvar_3d.f90
Source/radiation/Rad_nd.F90
commit 28d23a683442b79325870e280606bab0716bea4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 14:45:09 2021 -0400
fix a sign error in the Strang docs (#1870)
Docs/source/FlowChart.rst
commit 95a36eddda1b49777ab51c6929810c24f27276db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 13:57:25 2021 -0400
get the equation macros working with Sphinx 4 (#1868)
Docs/source/conf.py
commit f106c1f1f899d36916ed0e4b6db0cbbaea959621
Merge: 8a67d2067 7a09a506c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 14:15:04 2021 -0400
Merge branch 'main' of github.com:amrex-astro/Castro
commit 8a67d2067c0340b38f667735e49eba5c2c7d224f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 13:57:25 2021 -0400
get the equation macros working with Sphinx 4 (#1868)
Docs/source/conf.py
commit e4623eda500557d272a9ef3558a43b77b8ce19c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 2 13:57:25 2021 -0400
get the equation macros working with Sphinx 4 (#1868)
Docs/source/conf.py
commit c92688135cb2d35bd349a92582c375079e75e5a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 2 06:05:53 2021 -0700
Don't let rotation period change by too much in one SCF iteration (#1864)
I observe that due to the numerical sensitivity of the method the rotation period can sometimes change by a large amount in one timestep, resulting in subsequent divergence of the model. Limiting the amount the guess for the rotation period can change in one iteration seems to help.
Source/scf/scf_relax.cpp
commit 48d84874637453530e11c3639ea9c58cba308419
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 20:44:01 2021 -0400
clean up meth_params_module and remove hardcoded stuff (#1861)
Source/driver/meth_params.template
Source/radiation/RAD_F.H
Source/radiation/Radiation.cpp
commit 7cd551e2054dc4615ae3c877abffcc4700f73bdc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 1 13:53:35 2021 -0700
Remove castro_error wrapper (#1860)
Exec/reacting_tests/reacting_bubble/initdata_others.f90
Source/driver/Castro_error_nd.F90
Source/driver/Make.package
Source/driver/meth_params.template
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_support.f90
commit 7a09a506c1388fa85f67af22d38a0409c415bded
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 16:39:25 2021 -0400
update to 21.06
external/Microphysics
external/amrex
commit 7bdf043cbf31240217b905b4bd868303126fb1b6
Merge: 8442a5656 0709be851
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 16:38:46 2021 -0400
Merge branch 'development'
commit 3e7bd45da600091ef76f6c776589775833626005
Merge: 8442a5656 0709be851
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 16:36:48 2021 -0400
Merge branch 'development'
commit 0709be851175c7c9c8341cad91ec9844a74a20fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 1 10:46:11 2021 -0700
Simplify SCF setup by using maximum density and radius as initial guess (#1859)
Exec/scf_tests/single_star/GNUmakefile
Exec/scf_tests/single_star/_prob_params
Exec/scf_tests/single_star/inputs_helm_nonrotating
Exec/scf_tests/single_star/inputs_helm_nonrotating.test
Exec/scf_tests/single_star/inputs_helm_rotating
Exec/scf_tests/single_star/problem_initialize_state_data.H
commit be43cf9267c88f0c4419110ddc4d647031e98fcf
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 1 10:38:26 2021 -0700
Only regrid in SCF if using AMR (#1858)
Also, fix some variable shadowing warnings.
Source/scf/scf_relax.cpp
commit dea9eea49d82869af53b8980847a72898b1d6d17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 13:37:01 2021 -0400
eliminate prob_params_module (#1857)
Nothing uses this Fortran module anymore
Docs/source/gravity.rst
Docs/source/rotation.rst
Docs/source/software.rst
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/prob_params_nd.F90
commit dd8deceaaf38ff514ae1b3e3b5f1027cce1c0ac5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 12:00:46 2021 -0400
don't build the F90 probdata_module (#1845)
we no longer need the Fortran runtime parameters
Exec/Make.auto_source
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/science/wdmerger/wdmerger_data.H
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/driver/prob_params_nd.F90
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit 0dfa05b68ff5a4eee58d53f661963d878dfc4794
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 1 06:51:27 2021 -0700
Merge GR gravity into integrate_grav (#1855)
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit 22da55d60c9fb6e4511d28010e2593b467a8497e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 1 05:46:13 2021 -0700
Remove Fortran ca_ext_src (#1856)
CHANGES.md
Docs/source/FlowChart.rst
Source/driver/Castro_F.H
Source/problems/Castro_problem_source.cpp
Source/problems/Make.package
Source/problems/ext_src_nd.F90
Source/sources/Castro_sources_F.H
Source/sources/Make.package
commit b514877d2316016f0787e7f1bd4ef58e27a94668
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 31 19:29:48 2021 -0700
Remove PrescribedGrav (#1854)
This functionality is untested and probably not used. If needed, the user can replace it with the problem_source functionality.
CHANGES.md
Docs/source/gravity.rst
Source/driver/meth_params.template
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Make.package
Source/gravity/prescribe_grav_nd.F90
Source/gravity/prescribe_phi_nd.F90
commit 8472db2374cd17ec12be37e8f13ee00de4a387f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 31 19:12:15 2021 -0700
Only warn on density reset if below retry_small_density_cutoff (#1848)
If the user sets castro.retry_small_density_cutoff > 0, they are telling the code not to care about density resets below this threshold. So the user probably does not want to be warned about these resets either; this change turns the warning off for that case. It can still be opted into with castro.v = 2.
Source/hydro/advection_util.cpp
commit 371bfb26b08cdb930e41b1fea9bd72583a25d45a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 31 18:56:08 2021 -0700
Protect against negative (rho e) in trans (#1850)
When using transverse_reset_rhoe, the code detects if the (rho E)-based transverse update makes (rho e) negative, and if so resets to an update that is based on the equation for (rho e). But it's possible for the (rho e) update to also result in a negative (rho e), particularly for ambient material. So we check against this case now and turn off the transverse correction if it would result in a negative (rho e). Also, if there was a density reset then we make (rho e) the unmodified edge state, similar to what we do with pressure.
Source/hydro/trans.cpp
commit 9ad7e869d1f27920f22cc4447ba52f094676fe9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 31 20:24:44 2021 -0400
more docs cleaning (#1838)
also remove the list of removed parameters -- we were not keeping this up to date
Docs/source/inputs.rst
Docs/source/rp_intro.rst
commit d803461954c7aaf6d31e5e30137941ad9cb1c7b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 31 20:21:10 2021 -0400
check the problem.* parameters in the inputs file (#1808)
this will catch misspellings, etc.
Source/driver/Castro_setup.cpp
commit 63e2488fade2b420fa704c2e8686c80b80b9fbef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 31 10:16:33 2021 -0400
handle writing prob_params job_info in C++ (#1839)
Source/driver/Castro_io.cpp
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit 7c0bbf75f5be05aa3cd036795628cb1904fd5f25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 30 21:22:35 2021 -0400
remove problem_derive_nd.F90 (#1844)
Source/problems/Make.package
Source/problems/problem_derive_nd.F90
commit e3986122160b3f0fcf23a6f3d4a5d05bd90f8298
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 30 17:48:24 2021 -0700
Use S_new instead of S_old in CFL violation check (#1842)
The CFL violation check just prior to the hydro is intended to guess whether the hydro update will violate the CFL stability criterion. For that we can either use the old state or the state updated with the old-time sources. This change switches from the former to the latter. The motivation is the observation that when we fill new fine grids with data from coarse grids, the momentum may be inaccurate at a sharp density gradient like at the edge of a star. This change allows us to apply the sponge to the state (if a sponge is used) before checking whether it violates the CFL criterion, which will avoid spurious CFL violation warnings.
Source/driver/Castro_advance_ctu.cpp
commit d8b4930ee7d82252a91602889b26823322a961d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 30 18:15:53 2021 -0400
BL_SPACEDIM -> AMREX_SPACEDIM (#1843)
done with:
for i in git grep -l BL_SPACEDIM; do sed -i "s/BL_SPACEDIM/AMREX_SPACEDIM/g" $i; done
Docs/source/gravity.rst
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/sum_utils.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/mhd/Castro_mhd.cpp
Source/particles/CastroParticles.cpp
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGRadBndry.cpp
Source/radiation/NGBndry.H
Source/radiation/RadBndry.cpp
Source/radiation/RadPlotvar.cpp
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
Source/radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/_interpbndry/RadBndryData.cpp
Source/radiation/_interpbndry/RadInterpBndryData.cpp
Source/radiation/energy_diagnostics.cpp
Source/sources/Castro_thermo.cpp
Util/ConvertCheckpoint/Embiggen.cpp
commit 638319feddcdf2efdc824fa0c87151b934855af5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 30 14:36:45 2021 -0700
Remove GPU_COMPATIBLE_PROBLEM from makefiles (#1840)
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hse_convergence/GNUmakefile
Exec/gravity_tests/hse_convergence_general/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/Detonation/GNUmakefile.nse
Exec/science/flame_wave/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
commit aa59e63f4e0b72a8ee8193bb3e8473660e1cd9ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 30 12:00:18 2021 -0700
Convert SCF initial model construction to C++ (#1774)
The restriction preventing its use with the GPU build is removed.
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/scf/Make.package
Source/scf/scf_relax.cpp
Source/scf/scf_relax_F.H
Source/scf/scf_relaxation.F90
commit 37430d057bb3d8c6af96d624c34ace9307172d2c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 30 11:14:14 2021 -0700
Remove GPU compatible problem define (#1833)
Exec/Make.Castro
Source/driver/Castro.cpp
commit fea41e234a555c270a0710396891d6cc11e17847
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 30 14:01:00 2021 -0400
more docs updating to reflect C++ way (#1837)
Docs/source/creating_a_problem.rst
Docs/source/software.rst
commit c864a37180f503d54001388d34c643b16eb4ca93
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 30 09:54:47 2021 -0700
Remove legacy tagging functionality (#1834)
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_error_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/Tagging_nd.F90
commit fe57a73b88dfb30eb990bd46b27f9622f1a953ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 30 11:14:38 2021 -0400
update and clean some docs issues (#1836)
Docs/source/Introduction.rst
Docs/source/Preface.rst
Docs/source/getting_started.rst
Docs/source/index.rst
Docs/source/refs.bib
commit 3dee631b2cfbab46c304e74c4618bccbdcb636bf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 30 07:46:46 2021 -0700
Merge compute_avgpres into compute_radial_mass (#1835)
This is a simple way to convert this functionality to C++. This also indirectly fixes errors in the subgrid calculation of the volume fraction per zone that were present in the Fortran code for various geometries and/or for drdxfac > 1.
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit 0f46329fa9d0048cf9c1e5d60cc983fa1b28985d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 17:58:18 2021 -0700
Remove Fortran set_problem_tags hook (#1828)
CHANGES.md
Docs/source/creating_a_problem.rst
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_error_F.H
Source/problems/Make.package
Source/problems/problem_tagging_nd.F90
commit b60a74f1839d801ff990c9fa250066a4aa2c9100
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 17:56:20 2021 -0700
Updates to the EOS documentation (#1832)
Docs/source/EOSNetwork.rst
commit a24063e2e2ac6831c483ba9b2a891a07653c3b55
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 17:36:45 2021 -0700
Remove obsolete docs on GPU porting (#1831)
Docs/source/gpu_porting.rst
Docs/source/index.rst
commit 95a3d2baeb461b1dd38dea966131f23831aa1ac3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 20:35:33 2021 -0400
update the docs for life after probin (#1830)
Docs/source/AMR.rst
Docs/source/EOSNetwork.rst
Docs/source/MAESTRO_restart.rst
Docs/source/Verification.rst
Docs/source/build_system.rst
Docs/source/creating_a_problem.rst
Docs/source/diffusion.rst
Docs/source/inputs.rst
Docs/source/radiation.rst
Docs/source/rp_intro.rst
Docs/source/software.rst
commit 83c0e0b2da346585043f9593f6959afd57cf0499
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 15:08:46 2021 -0700
Convert diffusion_test from probin to inputs (#1817)
Exec/unit_tests/diffusion_test/inputs.1d
Exec/unit_tests/diffusion_test/inputs.1d.sph
Exec/unit_tests/diffusion_test/inputs.2d
Exec/unit_tests/diffusion_test/inputs.2d.sph
Exec/unit_tests/diffusion_test/inputs.3d
Exec/unit_tests/diffusion_test/probin.1d
Exec/unit_tests/diffusion_test/probin.2d
Exec/unit_tests/diffusion_test/probin.3d
Exec/unit_tests/diffusion_test/problem_initialize.H
commit 74c97833f079658f7d208f5096698bdde3800c34
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:21:22 2021 -0700
Convert model_burner from probin to inputs (#1818)
Exec/unit_tests/model_burner/inputs
Exec/unit_tests/model_burner/probin
commit c02627bf24c884675f2367769f19bc2ce6610a97
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:20:58 2021 -0700
Convert particles_test from probin to inputs (#1819)
Exec/unit_tests/particles_test/inputs.2d
Exec/unit_tests/particles_test/probin.2d
commit dcb63a0699d500e566fa4ac58d816ad5d9f45c48
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:20:15 2021 -0700
Convert OrszagTang from probin to inputs (#1821)
Exec/mhd_tests/OrszagTang/inputs
Exec/mhd_tests/OrszagTang/inputs.test
Exec/mhd_tests/OrszagTang/probin
Exec/mhd_tests/OrszagTang/probin.test
commit 3dd12ee9111f6a30007d95e79431e0640753e665
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:19:04 2021 -0700
Convert MHD RT from probin to inputs (#1820)
Exec/mhd_tests/RT/inputs_3d
Exec/mhd_tests/RT/inputs_3d_mhd
Exec/mhd_tests/RT/probin
Exec/mhd_tests/RT/probin_3d_mhd
commit b707c9351a3ae652c9eb43cd55ceab32553bfb97
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:16:47 2021 -0700
Convert BrioWu from probin to inputs (#1822)
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-x-inv
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.briowu.test
Exec/mhd_tests/BrioWu/inputs.sod.test
Exec/mhd_tests/BrioWu/probin-briowu-x
Exec/mhd_tests/BrioWu/probin-briowu-y
Exec/mhd_tests/BrioWu/probin-briowu-z
Exec/mhd_tests/BrioWu/probin-sod-x
Exec/mhd_tests/BrioWu/probin-sod-x-inv
Exec/mhd_tests/BrioWu/probin-sod-y
Exec/mhd_tests/BrioWu/probin-sod-z
Exec/mhd_tests/BrioWu/probin.briowu.test
Exec/mhd_tests/BrioWu/probin.sod.test
commit 5ecfe14010ec08ce290a5c7a2831c9248b55419a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:02:09 2021 -0700
Convert FastRarefaction from probin to inputs (#1823)
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/FastRarefaction/probin
commit 20ab10dd9b4071c0cb5a969ec2569600391cdc76
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:01:25 2021 -0700
Convert LoopAdvection from probin to inputs (#1824)
Exec/mhd_tests/LoopAdvection/inputs
Exec/mhd_tests/LoopAdvection/probin
commit 4478f432cbc0cfe291ea174464fba2f8bfa3a3f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 12:00:50 2021 -0700
Convert MagnetosonicWaves from probin to inputs (#1825)
Exec/mhd_tests/MagnetosonicWaves/inputs-1_0_2d_fast
Exec/mhd_tests/MagnetosonicWaves/inputs-1_1_slow
Exec/mhd_tests/MagnetosonicWaves/probin-1_0_fast
Exec/mhd_tests/MagnetosonicWaves/probin-1_1_slow
commit 4853cb136b554046dc4f481003705de38ce2a2e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 11:59:34 2021 -0700
Convert MHD species from probin to inputs (#1826)
Exec/mhd_tests/species/inputs
Exec/mhd_tests/species/inputs.test
Exec/mhd_tests/species/probin
Exec/mhd_tests/species/probin.test
commit cc803fef6fcc1c11ea77505fc6c5e430b8690a4f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 14:58:30 2021 -0400
eliminate probin for massive star (#1756)
this also removes some old inputs file and syncs the 1-d options to
the 2-d version.
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_2d
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.sdc_test
Exec/science/massive_star/inputs_2d.strang_test
Exec/science/massive_star/probin
Exec/science/massive_star/probin.nse
Exec/science/massive_star/probin.sdc_test
commit 3cda3e756076c9ab10b9a0bf1d68b94c0a7ec0d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 11:56:30 2021 -0700
Remove make flags to use system BLAS (#1827)
These are no longer relevant -- we removed all the BLAS calls because we can't rely on system calls for the GPU build.
Docs/source/build_system.rst
Docs/source/faq.rst
Exec/Make.Castro
commit d938d2d3219ca11abcdc778c76e96d3430587ebc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 09:34:59 2021 -0700
Convert Sedov from probin to inputs (#1814)
Exec/hydro_tests/Sedov/README
Exec/hydro_tests/Sedov/inputs.1d.cyl
Exec/hydro_tests/Sedov/inputs.1d.sph
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/inputs.3d.mhd
Exec/hydro_tests/Sedov/inputs.mini-Castro
Exec/hydro_tests/Sedov/inputs.mini-Castro.gpu_test
Exec/hydro_tests/Sedov/probin.1d.cyl
Exec/hydro_tests/Sedov/probin.1d.sph
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords.gammae
Exec/hydro_tests/Sedov/probin.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/probin.3d.mhd
Exec/hydro_tests/Sedov/probin.mini-Castro
commit 6f4692aa27ec79c5ccb1b37d6511656dcd45a4f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 09:27:29 2021 -0700
Convert RadSourceTest from probin to inputs (#1815)
Exec/radiation_tests/RadSourceTest/inputs-cooling
Exec/radiation_tests/RadSourceTest/inputs-heating
Exec/radiation_tests/RadSourceTest/inputs-heating-mg
Exec/radiation_tests/RadSourceTest/probin-cooling
Exec/radiation_tests/RadSourceTest/probin-heating
commit 0170459a9c1b12b9e00986abb305bc800b4f1a53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 12:21:02 2021 -0400
remove unused probin (#1816)
Exec/hydro_tests/acoustic_pulse_general/probin
commit f986e068c7b79d2237e8c5a8c2639178a96740c5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 09:10:10 2021 -0700
Convert hydrostatic_adjust from probin to inputs (#1812)
Exec/gravity_tests/hydrostatic_adjust/inputs
Exec/gravity_tests/hydrostatic_adjust/inputs-subchandra
Exec/gravity_tests/hydrostatic_adjust/probin
Exec/gravity_tests/hydrostatic_adjust/probin.subchandra
commit 88376a17e9369120f97b1d6c0b084b0b566d29a4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 09:04:14 2021 -0700
Convert Vortices_LWAcoustics from probin to inputs (#1813)
Exec/hydro_tests/Vortices_LWAcoustics/inputs.2d
Exec/hydro_tests/Vortices_LWAcoustics/probin
commit 2e415b2fec4ab83fc0835bcbab8a6c4245afb1aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 11:40:32 2021 -0400
eliminate problem for flame (#1810)
Exec/science/flame/inputs.1d
Exec/science/flame/inputs.1d.aprox13
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame/inputs.H_He
Exec/science/flame/probin
Exec/science/flame/probin.H_He
Exec/science/flame/probin.sdc
Exec/science/flame/probin.sdc.3alpha
commit 05d0c4812b38b31866de57a1055f3a7f6219cede
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 11:35:29 2021 -0400
remove the probins (#1809)
these were left behind in #1799
Exec/science/bwp-rad/probin
Exec/science/bwp-rad/probin.dens_sponge
commit d198e7e7f3f5f137976f4a0c4123bdad1fe99e13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 11:35:15 2021 -0400
remove empty probin (#1811)
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/probin
commit ebea8e42a16538182de44096f83016b5554cc93a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 08:25:38 2021 -0700
Convert wdmerger from probin to inputs (#1798)
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_mhd/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_relaxation/inputs
Exec/science/wdmerger/tests/wdmerger_relaxation/probin
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit 6c31c4525710abda00dac9c86746329d286e72de
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 05:28:14 2021 -0700
Convert RadFront from probin to inputs (#1794)
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadFront/probin1d
Exec/radiation_tests/RadFront/probin2d
commit 0fbf40861ccbd0c55ceaf1e3eb4326982da3cb74
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 05:27:02 2021 -0700
Convert RadThermalWave from probin to inputs (#1795)
Exec/radiation_tests/RadThermalWave/inputs.1d
Exec/radiation_tests/RadThermalWave/inputs.1d.test
Exec/radiation_tests/RadThermalWave/inputs.2d
Exec/radiation_tests/RadThermalWave/inputs.2d.test
Exec/radiation_tests/RadThermalWave/inputs.3d
Exec/radiation_tests/RadThermalWave/inputs.3d.test
Exec/radiation_tests/RadThermalWave/probin.1d
Exec/radiation_tests/RadThermalWave/probin.2d
Exec/radiation_tests/RadThermalWave/probin.3d
commit 7dc105d9987237e0b691ed78c0b2f3cf089ccfd8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 05:15:57 2021 -0700
Convert Sod_stellar from probin to inputs (#1797)
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm_mhd
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/probin-test1-helm
Exec/hydro_tests/Sod_stellar/probin-test1-helm-y
Exec/hydro_tests/Sod_stellar/probin-test1-helm-z
Exec/hydro_tests/Sod_stellar/probin-test2-helm
Exec/hydro_tests/Sod_stellar/probin-test3-helm
Exec/hydro_tests/Sod_stellar/probin-test4-helm
commit 23792b95fa6a90bb78824da0decc7a510fffaef2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 05:11:11 2021 -0700
Convert bwp-rad from probin to inputs (#1799)
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
commit e209cb4bd384def729ee2aaee93627c410dfc527
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:46:54 2021 -0700
Remove empty probin files from Sod (#1796)
Exec/hydro_tests/Sod/README.md
Exec/hydro_tests/Sod/inputs-double-rarefaction
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test1-helm
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-test2-helm
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-helm
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod/probin-double-rarefaction
Exec/hydro_tests/Sod/probin-slowshock-x
Exec/hydro_tests/Sod/probin-sod-x
Exec/hydro_tests/Sod/probin-sod-y
Exec/hydro_tests/Sod/probin-sod-z
Exec/hydro_tests/Sod/probin-test1-helm
Exec/hydro_tests/Sod/probin-test2-1d
Exec/hydro_tests/Sod/probin-test2-helm
Exec/hydro_tests/Sod/probin-test2-x
Exec/hydro_tests/Sod/probin-test2-y
Exec/hydro_tests/Sod/probin-test2-z
Exec/hydro_tests/Sod/probin-test3-helm
Exec/hydro_tests/Sod/probin-test3-x
Exec/hydro_tests/Sod/probin-test3-y
Exec/hydro_tests/Sod/probin-test3-z
commit d7977d9390b91c635c7a3f330032e1fbb7b6dd1d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:45:16 2021 -0700
Convert acoustic_pulse to inputs (#1801)
Exec/hydro_tests/acoustic_pulse/README.md
Exec/hydro_tests/acoustic_pulse/convergence_plm_as_1d.sh
Exec/hydro_tests/acoustic_pulse/convergence_ppm_as_1d.sh
Exec/hydro_tests/acoustic_pulse/inputs.128
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc2.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.64.sdc_ml
Exec/hydro_tests/acoustic_pulse/inputs.512
Exec/hydro_tests/acoustic_pulse/inputs.64
Exec/hydro_tests/acoustic_pulse/probin
Exec/hydro_tests/acoustic_pulse/probin-x
Exec/hydro_tests/acoustic_pulse/probin-y
Exec/hydro_tests/acoustic_pulse/probin-z
commit 6845ddc0eecf069429c3241d89a0e2a8586f7bf6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:43:26 2021 -0700
Convert planet from probin to inputs (#1800)
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/planet/probin
commit 2cfa1d7198087b272dd8f99cb20966e72c879e33
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:42:02 2021 -0700
Convert test_convect from probin to inputs (#1803)
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/test_convect/probin
commit 0d62779f307e6cd4fd99863b484cead81d9e5786
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:41:42 2021 -0700
Convert toy_convect from probin to inputs (#1802)
Exec/hydro_tests/toy_convect/inputs_2d
Exec/hydro_tests/toy_convect/probin
commit a5ca574f0f73d6c0ebb04824f34e8402096861ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:40:33 2021 -0700
Convert acoustic_pulse_general from probin to inputs (#1804)
Exec/hydro_tests/acoustic_pulse_general/README.md
Exec/hydro_tests/acoustic_pulse_general/inputs.128
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.256
Exec/hydro_tests/acoustic_pulse_general/inputs.512
Exec/hydro_tests/acoustic_pulse_general/inputs.64
commit d4d417178835fb9ce78e11ba25f3011157a12987
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:36:49 2021 -0700
Convert hse_convergence from probin to inputs (#1805)
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite
Exec/gravity_tests/hse_convergence/probin.128
Exec/gravity_tests/hse_convergence/probin.256
Exec/gravity_tests/hse_convergence/probin.512
Exec/gravity_tests/hse_convergence/probin.64
commit ec7adf2af1723444befbfb5e1f50585879a9d48c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:34:04 2021 -0700
Convert hse_convergence_general from probin to inputs (#1807)
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
Exec/gravity_tests/hse_convergence_general/probin.hse_test
commit ce43907c15ee41ddfaeb013f9c0c32543c8e3df1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 29 04:32:07 2021 -0700
Convert StarGrav from probin to inputs (#1806)
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/StarGrav/inputs_3d
Exec/gravity_tests/StarGrav/inputs_3d_mhd
Exec/gravity_tests/StarGrav/probin
commit e7e5141fe650d7e6b835d4ca2b2f4a3c74576e35
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 28 11:31:16 2021 -0400
eliminate probin for Detonation (#1780)
note: this fixes the dxnuc refinement -- previously it was not refining because we had the max level = 0
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.nse
Exec/science/Detonation/inputs-det-x.regrid
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/Detonation/inputs-det-x.sdc2
Exec/science/Detonation/inputs-det-x.simplified_sdc
Exec/science/Detonation/inputs-det-x.subch
Exec/science/Detonation/inputs-det-x.test
Exec/science/Detonation/nse_runs/inputs.template.simple_sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/nse_runs/inputs.template.true_sdc
Exec/science/Detonation/nse_runs/probin-det-x.nse_disabled
Exec/science/Detonation/nse_runs/setup_runs.py
Exec/science/Detonation/probin-collision
Exec/science/Detonation/probin-det-x
Exec/science/Detonation/probin-det-x.nse_disabled
Exec/science/Detonation/probin-det-x.regrid
Exec/science/Detonation/probin-det-x.simplified_sdc
Exec/science/Detonation/probin-det-x.subch
commit f11abac0a4755f2d9c48b7485c0e6f9030392432
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 08:00:02 2021 -0700
Protect against divide-by-zero in rotation (#1792)
Source/rotation/Rotation.cpp
commit 9ec19e14538bfef9cf157a5f7f034afa46619fba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 28 10:13:32 2021 -0400
don't do Fortran microphysics cleanup if we didn't init (#1791)
Source/driver/Castro.cpp
commit e4946085232aa0f3383c820831ea56221758f345
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 06:30:52 2021 -0700
Convert double_mach_inputs from probin to inputs (#1781)
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/inputs.2d.test
Exec/hydro_tests/double_mach_reflection/probin.2d
commit b12c70146b1c0d1f60fe2a8013c6c246810e4438
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 06:28:00 2021 -0700
Convert RT from probin to inputs (#1783)
Exec/hydro_tests/RT/inputs_2d
Exec/hydro_tests/RT/inputs_3d
Exec/hydro_tests/RT/probin
commit 9bf81928efdaee2c0aa9352e5c115985f24fc1ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 06:27:22 2021 -0700
Convert gresho_vortex from probin to inputs (#1782)
Exec/hydro_tests/gresho_vortex/inputs.2d
Exec/hydro_tests/gresho_vortex/probin
commit 470a26f386ba2148ab87269402811a43af69425e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 06:24:59 2021 -0700
Convert RadBreakout from probin to inputs (#1784)
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/inputs.1d.test
Exec/radiation_tests/RadBreakout/probin.1d.87a.23
commit 6715c9670c0c51e1ffe3cd5901cbdd9e48c3bddf
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 06:20:09 2021 -0700
Convert RadSphere from probin to inputs (#1785)
Exec/radiation_tests/RadSphere/inputs
Exec/radiation_tests/RadSphere/probin
commit e543b65b6a6f05e959943c2d2884a3b34fdfb2a4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 05:56:09 2021 -0700
Convert RadSuOlson from probin to inputs (#1786)
Exec/radiation_tests/RadSuOlson/inputs
Exec/radiation_tests/RadSuOlson/probin
commit f42a360a70e1cbe3019bf73c5b4649bc31f8b962
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 05:53:38 2021 -0700
Convert RadSuOlsonMG from probin to inputs (#1787)
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadSuOlsonMG/probin.common
commit bd121d15385e442f2cb2a17a356c8023ba8eef7d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 05:50:58 2021 -0700
Convert RadShestakovBolstad from probin to inputs (#1788)
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadShestakovBolstad/probin.common
commit 265f322f5f9617c1047f7cec1c69bf6c951bb93c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 05:46:58 2021 -0700
Convert Rad2Tshock from probin to inputs (#1789)
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/Rad2Tshock/probin.M2
Exec/radiation_tests/Rad2Tshock/probin.M5
commit c7f6e66fe128ec38a33a2fa9546fd683865a2665
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 28 05:27:10 2021 -0700
Convert RadBlastWave from probin to inputs (#1790)
Exec/radiation_tests/RadBlastWave/inputs.1d
Exec/radiation_tests/RadBlastWave/inputs.2d
Exec/radiation_tests/RadBlastWave/inputs.3d
Exec/radiation_tests/RadBlastWave/inputs.3d.test
Exec/radiation_tests/RadBlastWave/inputs.kp
Exec/radiation_tests/RadBlastWave/inputs.kp.2d
Exec/radiation_tests/RadBlastWave/probin.1d
Exec/radiation_tests/RadBlastWave/probin.2d
Exec/radiation_tests/RadBlastWave/probin.3d
Exec/radiation_tests/RadBlastWave/probin.3d.test
Exec/radiation_tests/RadBlastWave/probin.kp
Exec/radiation_tests/RadBlastWave/probin.kp.2d
commit b25b24605b4bb5f649807e8e08fc76a477094f56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 27 20:47:18 2021 -0400
add error buf to scf_test and create a test suite version that runs (#1776)
also eliminate probin
Exec/scf_tests/single_star/inputs_helm_nonrotating
Exec/scf_tests/single_star/inputs_helm_nonrotating.test
Exec/scf_tests/single_star/inputs_helm_rotating
Exec/scf_tests/single_star/probin_helm_nonrotating
Exec/scf_tests/single_star/probin_helm_rotating
commit e8003fa26c7d5fa0d49733eeaa45f84b3052db7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 27 18:54:09 2021 -0400
reduce the size of Reactions_Type (#1770)
this StateData is only for the plotfile in its current usage
we now only store the omegadot's in the plotfile if store_omegadot=1 is
explicitly set. We also no longer need ghost cells here.
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/timestep.cpp
Source/reactions/Castro_react.cpp
Source/sdc/sdc_util.cpp
commit 354f9450d6343c6496d3980983f03cb451cb88b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 27 18:47:38 2021 -0400
eliminate probin for convective_flame (#1778)
also remove the old exploration stuff
Exec/science/convective_flame/exploration/README
Exec/science/convective_flame/exploration/flamefront.py
Exec/science/convective_flame/exploration/index_temp.html
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/exploration/probin_temp
Exec/science/convective_flame/exploration/process.py
Exec/science/convective_flame/exploration/runtests.py
Exec/science/convective_flame/exploration/setup_explore.py
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/inputs.3d.test
Exec/science/convective_flame/probin
Exec/science/convective_flame/probin_good
commit 9d83bf8ff47f2233e0b765767f787fdf5e4de86c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 27 06:16:19 2021 -0700
Convert double_bubble from probin to inputs (#1771)
Exec/hydro_tests/double_bubble/inputs_2d
Exec/hydro_tests/double_bubble/inputs_2d.single
Exec/hydro_tests/double_bubble/inputs_2d.single.equal
Exec/hydro_tests/double_bubble/inputs_2d.test
Exec/hydro_tests/double_bubble/probin
Exec/hydro_tests/double_bubble/probin.single
Exec/hydro_tests/double_bubble/probin.single.equal
commit 12930041cab525fe13f224a0a6b068ff097d8b2c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 27 06:13:11 2021 -0700
Convert evrard_collapse from probin to inputs (#1773)
Exec/gravity_tests/evrard_collapse/inputs
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/gravity_tests/evrard_collapse/probin
Exec/gravity_tests/evrard_collapse/probin.test
commit 632efa52dffc07bd5b6e6dfbc337a51dc9a79019
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 27 06:09:45 2021 -0700
Convert xrb_mixed from probin to inputs (#1775)
Exec/science/xrb_mixed/inputs_2d
Exec/science/xrb_mixed/probin
commit d87a42271d1c6a457e61f70462fa72341fd152f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 27 06:09:01 2021 -0700
Convert uniform_cube_sphere from probin to inputs (#1772)
Exec/gravity_tests/uniform_cube_sphere/inputs
Exec/gravity_tests/uniform_cube_sphere/probin
commit 4bce2ce8e99778d6a830015e5267d34372a86b43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 20:37:50 2021 -0400
apply the burn state directly to the conserved state (#1723)
this will allow for the eventual removal or shrinking of the
Reactions_Type statedata.
Source/reactions/Castro_react.cpp
commit 78bdb7d68516174ce1e8442aa0615c52c892c9f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 20:28:51 2021 -0400
eliminate probin for oddeven (#1769)
Exec/hydro_tests/oddeven/inputs.2d
Exec/hydro_tests/oddeven/inputs.3d
Exec/hydro_tests/oddeven/probin
commit a9fa5d3e4dfdf3a4f9e1917332961cc0faf003cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 20:21:36 2021 -0400
eliminate the probin for rotating_torus
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
Exec/hydro_tests/rotating_torus/probin
commit 7d7bfea3ef829d7a9f6f3f783931091a9e685111
Merge: 993d5e501 f4f9c2611
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 20:00:59 2021 -0400
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit f4f9c261103280a1902560b255aff2993d6fe476
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 20:00:04 2021 -0400
eliminate probin for gamma_law_bubble (#1768)
also remove the old MAESTRO restart inputs
Exec/hydro_tests/gamma_law_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/inputs_2d_MAESTRO.big
Exec/hydro_tests/gamma_law_bubble/probin
Exec/hydro_tests/gamma_law_bubble/probin.big
commit 993d5e5011603528854c547c5634ace0e7c9aa90
Merge: 045c5fbe4 ed1013de8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:59:24 2021 -0400
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit ed1013de8c53dd92fb33ca633331161cbdd470cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:52:00 2021 -0400
convert reacting_bubble to no probin (#1762)
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/reacting_tests/reacting_bubble/probin
Exec/reacting_tests/reacting_bubble/probin.zoom
commit d9e401d3e1f07786f79403f60cd918c0ceed64c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:29:13 2021 -0400
convert reacting_convergence to be probin-free (#1763)
Exec/reacting_tests/reacting_convergence/inputs.1024
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.128.testsuite
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
Exec/reacting_tests/reacting_convergence/inputs.64.testsuite.simplified_sdc
Exec/reacting_tests/reacting_convergence/probin
commit 045c5fbe4018ee8859440de481adb3267294e8c3
Merge: 16db8f967 6a6f136fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:22:59 2021 -0400
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit 6a6f136fc3c161a933b6cee0304e3396efe025a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:22:18 2021 -0400
eliminate probin for nse_test (#1764)
Exec/reacting_tests/nse_test/inputs.128
Exec/reacting_tests/nse_test/inputs.256
Exec/reacting_tests/nse_test/inputs.512
Exec/reacting_tests/nse_test/inputs.64
Exec/reacting_tests/nse_test/probin
commit 31094dfa1aae43d39fa241fc3df46faeab1d48f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:18:49 2021 -0400
move away from probin for bubble_convergence (#1761)
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.32
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/probin.128
Exec/reacting_tests/bubble_convergence/probin.128.nopert
Exec/reacting_tests/bubble_convergence/probin.256
Exec/reacting_tests/bubble_convergence/probin.256.nopert
Exec/reacting_tests/bubble_convergence/probin.32
Exec/reacting_tests/bubble_convergence/probin.512
Exec/reacting_tests/bubble_convergence/probin.64
Exec/reacting_tests/bubble_convergence/probin.64.nopert
commit ce0d7e8ffed7fd82e7cbd019483570e9736886d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:07:01 2021 -0400
eliminate probin for toy_flame (#1765)
Exec/reacting_tests/toy_flame/exploration/flamefront.py
Exec/reacting_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/reacting_tests/toy_flame/exploration/probin_temp
Exec/reacting_tests/toy_flame/exploration/process.py
Exec/reacting_tests/toy_flame/exploration/setup_explore.py
Exec/reacting_tests/toy_flame/inputs.1d
Exec/reacting_tests/toy_flame/inputs.1d.testsuite
Exec/reacting_tests/toy_flame/probin
commit ea4baf242626183cbe11630600aa9d487eea1cfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 19:03:26 2021 -0400
eliminate probin for Alfven (#1766)
Exec/mhd_tests/Alfven/inputs-1_0_1d
Exec/mhd_tests/Alfven/inputs-1_0_2d
Exec/mhd_tests/Alfven/inputs-1_1
Exec/mhd_tests/Alfven/probin-1_0
Exec/mhd_tests/Alfven/probin-1_1
commit b742a5c5be33ca3609eb969cbdd4d076f92702c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 18:56:58 2021 -0400
eliminate probin for DaiWoodward (#1767)
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/DaiWoodward/probin
commit 16db8f967d63540470370b96ef325c45673d305a
Merge: 67cb1f0d9 36bffc149
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 12:43:49 2021 -0400
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit 67cb1f0d9abb5973c0251329238b116f88df270b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 26 12:43:31 2021 -0400
move away from probin for bubble_convergence
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.32
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/probin.128
Exec/reacting_tests/bubble_convergence/probin.128.nopert
Exec/reacting_tests/bubble_convergence/probin.256
Exec/reacting_tests/bubble_convergence/probin.256.nopert
Exec/reacting_tests/bubble_convergence/probin.32
Exec/reacting_tests/bubble_convergence/probin.512
Exec/reacting_tests/bubble_convergence/probin.64
Exec/reacting_tests/bubble_convergence/probin.64.nopert
commit 36bffc149ef5704c3c4b7d96ba1839a0cb842d9e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 26 09:19:03 2021 -0700
Convert DustCollapse from probin to inputs (#1758)
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/DustCollapse/probin.fullstar
Exec/gravity_tests/DustCollapse/probin.fullstar.1d
Exec/gravity_tests/DustCollapse/probin.halfstar
Exec/gravity_tests/DustCollapse/probin.octant
Exec/gravity_tests/DustCollapse/probin.pointmass
Exec/gravity_tests/DustCollapse/probin_3d_poisson_regtest
commit e70907bb9e1cd3521461d98ba2fd3438821ed3e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 26 08:01:17 2021 -0700
Convert Noh from probin to inputs (#1759)
Exec/hydro_tests/Noh/inputs_3d
Exec/hydro_tests/Noh/probin
commit d605d2f2a7f0b67aa9d9fd7ef3450b0aee3439f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 26 07:58:27 2021 -0700
Convert KH from probin to inputs (#1760)
Exec/hydro_tests/KH/inputs.2d
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/inputs.3d
Exec/hydro_tests/KH/probin
Exec/hydro_tests/KH/probin.p3
commit 6a53ed69d9a27d5948b50a667cdfb3166f0c0ab6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 25 21:30:31 2021 -0400
fix some sphinx errors (#1757)
Docs/source/AMR.rst
Docs/source/FlowChart.rst
Docs/source/development.rst
Docs/source/faq.rst
Docs/source/io.rst
Docs/source/problem_setups.rst
Docs/source/software.rst
commit b2180f0262b5a4ed219668262ec04745db99bc78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 25 09:41:57 2021 -0400
switch nova to inputs params for refinement, problem, and microphysics (#1750)
Exec/science/nova/inputs_2d
Exec/science/nova/probin
commit 39d27075376891d8c94ac62e0e63fd6cd2361722
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 25 08:54:28 2021 -0400
flame_wave: fix "T" -> 1 in inputs (#1755)
Exec/science/flame_wave/inputs_He/inputs.He.25cm.1000Hz.3d
commit 3b118bfdf46f425766137bb6abcf4d4755c0aa16
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 25 05:52:52 2021 -0700
Convert Sod from probin to inputs (#1751)
Exec/hydro_tests/Sod/inputs-double-rarefaction
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test1-helm
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-test2-helm
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-helm
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod/probin-double-rarefaction
Exec/hydro_tests/Sod/probin-slowshock-x
Exec/hydro_tests/Sod/probin-sod-x
Exec/hydro_tests/Sod/probin-sod-y
Exec/hydro_tests/Sod/probin-sod-z
Exec/hydro_tests/Sod/probin-test1-helm
Exec/hydro_tests/Sod/probin-test2-1d
Exec/hydro_tests/Sod/probin-test2-helm
Exec/hydro_tests/Sod/probin-test2-x
Exec/hydro_tests/Sod/probin-test2-y
Exec/hydro_tests/Sod/probin-test2-z
Exec/hydro_tests/Sod/probin-test3-helm
Exec/hydro_tests/Sod/probin-test3-x
Exec/hydro_tests/Sod/probin-test3-y
Exec/hydro_tests/Sod/probin-test3-z
commit b6c78ca7719ba6dc256accdc7ee0ce3331e71d94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 24 22:16:47 2021 -0400
get rid of probin for flame_wave (#1753)
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.1000Hz.3d
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
Exec/science/flame_wave/inputs_He/probin.He
Exec/science/flame_wave/inputs_He/probin.He.25cm
Exec/science/flame_wave/probin.hse_test
Exec/science/flame_wave/probin.testsuite
Exec/science/flame_wave/scaling/3d_science/inputs.noboost.25cm.1000Hz.3d
Exec/science/flame_wave/scaling/3d_science/probin.noboost.25cm.1000Hz
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/flame_wave/scaling/probin.boost_10_10
commit fb034ca8a63317d8d20b5f255603180fd95a4a4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 24 22:02:13 2021 -0400
don't try to read in probin if it doesn't exist (#1754)
together with Microphysics PR 674, we no longer need a probin
Sedov 3d was updated in this fashion
Exec/hydro_tests/Sedov/inputs.3d.sph
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sedov/probin.3d.sph
Source/driver/Castro_nd.F90
Util/scripts/prob_params.template
commit 9fc7e83fd4c6cc9d22ec79448353762454c76fef
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 24 17:53:49 2021 -0700
Remove old Sod figures (#1752)
Exec/hydro_tests/Sod/Figure1/128/den_0034.pla
Exec/hydro_tests/Sod/Figure1/128/eint_0034.pla
Exec/hydro_tests/Sod/Figure1/128/grdlog
Exec/hydro_tests/Sod/Figure1/128/pres_0034.pla
Exec/hydro_tests/Sod/Figure1/128/vel_0034.pla
Exec/hydro_tests/Sod/Figure1/inputs-sod-1d
Exec/hydro_tests/Sod/Figure1/paper_sod.gp
Exec/hydro_tests/Sod/Figure1/probin-sod-x
Exec/hydro_tests/Sod/Figure1/sod-exact.out
Exec/hydro_tests/Sod/Figure1/todo_paper
Exec/hydro_tests/Sod/Figure2/128/den_0015.pla
Exec/hydro_tests/Sod/Figure2/128/eint_0015.pla
Exec/hydro_tests/Sod/Figure2/128/grdlog
Exec/hydro_tests/Sod/Figure2/128/pres_0015.pla
Exec/hydro_tests/Sod/Figure2/128/vel_0015.pla
Exec/hydro_tests/Sod/Figure2/2048/den_0015.pla
Exec/hydro_tests/Sod/Figure2/2048/eint_0015.pla
Exec/hydro_tests/Sod/Figure2/2048/grdlog
Exec/hydro_tests/Sod/Figure2/2048/pres_0015.pla
Exec/hydro_tests/Sod/Figure2/2048/vel_0015.pla
Exec/hydro_tests/Sod/Figure2/512/den_0015.pla
Exec/hydro_tests/Sod/Figure2/512/eint_0015.pla
Exec/hydro_tests/Sod/Figure2/512/grdlog
Exec/hydro_tests/Sod/Figure2/512/pres_0015.pla
Exec/hydro_tests/Sod/Figure2/512/vel_0015.pla
Exec/hydro_tests/Sod/Figure2/inputs-test2-1d
Exec/hydro_tests/Sod/Figure2/paper_double_rarefaction.gp
Exec/hydro_tests/Sod/Figure2/test2-exact.out
Exec/hydro_tests/Sod/Figure2/todo_paper
Exec/hydro_tests/Sod/Figure3/128/den_0046.pla
Exec/hydro_tests/Sod/Figure3/128/eint_0046.pla
Exec/hydro_tests/Sod/Figure3/128/grdlog
Exec/hydro_tests/Sod/Figure3/128/pres_0046.pla
Exec/hydro_tests/Sod/Figure3/128/vel_0046.pla
Exec/hydro_tests/Sod/Figure3/inputs-test3-1d
Exec/hydro_tests/Sod/Figure3/paper_strong.gp
Exec/hydro_tests/Sod/Figure3/probin-test3-x
Exec/hydro_tests/Sod/Figure3/test3-exact.out
Exec/hydro_tests/Sod/Figure3/todo_paper
commit ee1b3f78a85d0c4064904c5a001ef492c6059e74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 24 16:05:44 2021 -0400
some clean ups of the sub-ch inputs (#1749)
move to new refinement system
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/probin
commit f55b4931e9143107091df931414dbf7379071a08
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 24 12:13:09 2021 -0700
Convert MHD tests to inputs-based tagging (#1748)
Exec/mhd_tests/Alfven/inputs-1_0_1d
Exec/mhd_tests/Alfven/inputs-1_0_2d
Exec/mhd_tests/Alfven/inputs-1_1
Exec/mhd_tests/Alfven/probin-1_0
Exec/mhd_tests/Alfven/probin-1_1
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-x-inv
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.briowu.test
Exec/mhd_tests/BrioWu/inputs.sod.test
Exec/mhd_tests/BrioWu/probin-briowu-x
Exec/mhd_tests/BrioWu/probin-briowu-y
Exec/mhd_tests/BrioWu/probin-briowu-z
Exec/mhd_tests/BrioWu/probin-sod-x
Exec/mhd_tests/BrioWu/probin-sod-x-inv
Exec/mhd_tests/BrioWu/probin-sod-y
Exec/mhd_tests/BrioWu/probin-sod-z
Exec/mhd_tests/BrioWu/probin.briowu.test
Exec/mhd_tests/BrioWu/probin.sod.test
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/DaiWoodward/probin
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/FastRarefaction/probin
Exec/mhd_tests/LoopAdvection/inputs
Exec/mhd_tests/LoopAdvection/probin
Exec/mhd_tests/MagnetosonicWaves/inputs-1_0_2d_fast
Exec/mhd_tests/MagnetosonicWaves/inputs-1_1_slow
Exec/mhd_tests/MagnetosonicWaves/probin-1_0_fast
Exec/mhd_tests/MagnetosonicWaves/probin-1_1_slow
Exec/mhd_tests/OrszagTang/inputs
Exec/mhd_tests/OrszagTang/inputs.test
Exec/mhd_tests/OrszagTang/probin
Exec/mhd_tests/OrszagTang/probin.test
Exec/mhd_tests/RT/inputs_3d
Exec/mhd_tests/RT/inputs_3d_mhd
Exec/mhd_tests/RT/probin
Exec/mhd_tests/RT/probin_3d_mhd
Exec/mhd_tests/species/inputs
Exec/mhd_tests/species/inputs.test
Exec/mhd_tests/species/probin
Exec/mhd_tests/species/probin.test
commit b2d7935602cd0db37a1ea22e7b766a20fec2a091
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 24 12:05:24 2021 -0700
Convert gravity tests to inputs-based tagging (#1747)
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/DustCollapse/probin.fullstar
Exec/gravity_tests/DustCollapse/probin.fullstar.1d
Exec/gravity_tests/DustCollapse/probin.halfstar
Exec/gravity_tests/DustCollapse/probin.octant
Exec/gravity_tests/DustCollapse/probin_3d_poisson_regtest
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/StarGrav/inputs_3d
Exec/gravity_tests/StarGrav/inputs_3d_mhd
Exec/gravity_tests/StarGrav/probin
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/gravity_tests/evrard_collapse/probin
Exec/gravity_tests/evrard_collapse/probin.test
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite
Exec/gravity_tests/hse_convergence/probin.128
Exec/gravity_tests/hse_convergence/probin.256
Exec/gravity_tests/hse_convergence/probin.512
Exec/gravity_tests/hse_convergence/probin.64
Exec/gravity_tests/uniform_cube_sphere/inputs
Exec/gravity_tests/uniform_cube_sphere/probin
commit 425233d4960aac69090d2ae9455a23bd37744f7d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 24 11:28:31 2021 -0700
Add support for relative gradient tagging in inputs (#1730)
We now use the new functionality from AMReX-Codes/amrex#2044 and switch over all probin-based tagging on relative gradients to use the inputs.
Docs/source/AMR.rst
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/DustCollapse/probin.pointmass
Exec/hydro_tests/Sedov/inputs.mini-Castro
Exec/hydro_tests/Sedov/inputs.mini-Castro.gpu_test
Exec/hydro_tests/Sedov/probin.mini-Castro
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/Rad2Tshock/probin.M2
Exec/radiation_tests/Rad2Tshock/probin.M5
Exec/radiation_tests/RadThermalWave/inputs.1d
Exec/radiation_tests/RadThermalWave/inputs.1d.test
Exec/radiation_tests/RadThermalWave/inputs.2d
Exec/radiation_tests/RadThermalWave/inputs.2d.test
Exec/radiation_tests/RadThermalWave/inputs.3d
Exec/radiation_tests/RadThermalWave/inputs.3d.test
Exec/radiation_tests/RadThermalWave/probin.1d
Exec/radiation_tests/RadThermalWave/probin.2d
Exec/radiation_tests/RadThermalWave/probin.3d
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probin-collision
Source/driver/Castro.cpp
commit 819526d041919c560963bb7223fc8235af1d4a83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 23 20:49:18 2021 -0400
allow the problem parameters to be read in from inputs (#1532)
A problem-specific runtime parameter can now be set in the inputs file as
problem.param = XX
This will allow us to get rid of the Fortran namelists in the future.
Sedov 3d was updated to this new format.
Exec/hydro_tests/Sedov/inputs.3d.sph
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sedov/probin.3d.sph
Source/driver/Castro_F.H
Source/driver/Castro_setup.cpp
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit 255dc82ed85a04b148a5b1da4fa3bfd54dbabbe0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 17:14:21 2021 -0700
Remove Sod_stellar runs paper (#1745)
These inputs/probin files don't keep up with changes in the code; a user can always check out the old code if they want to reproduce what was in the paper.
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/PROCESS
Exec/hydro_tests/Sod_stellar/runs/dataRead.py
Exec/hydro_tests/Sod_stellar/runs/exact/test1.exact.128.out
Exec/hydro_tests/Sod_stellar/runs/exact/test1.exact.out
Exec/hydro_tests/Sod_stellar/runs/exact/test1A.exact.out
Exec/hydro_tests/Sod_stellar/runs/exact/test2.exact.128.out
Exec/hydro_tests/Sod_stellar/runs/exact/test2.exact.out
Exec/hydro_tests/Sod_stellar/runs/exact/test3.exact.128.out
Exec/hydro_tests/Sod_stellar/runs/exact/test3.exact.out
Exec/hydro_tests/Sod_stellar/runs/exact/test4.exact.128.out
Exec/hydro_tests/Sod_stellar/runs/exact/test4.exact.out
Exec/hydro_tests/Sod_stellar/runs/flash/test1/flash.par.test1.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/flash.par.test1.nocharlimit.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash.par.test1
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash.par.test1.nocharlimiting
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm.dat
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm.out
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_dens.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_dens_nocharlimiting.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_initial.out
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_nocharlimiting.dat
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_pres.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_pres_nocharlimiting.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_temp.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_temp_nocharlimiting.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_velx.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1/old/flash_test1_helm_velx_nocharlimiting.data
Exec/hydro_tests/Sod_stellar/runs/flash/test1A/flash_test1A_helm.out
Exec/hydro_tests/Sod_stellar/runs/flash/test2/flash.par.test2.data
Exec/hydro_tests/Sod_stellar/runs/flash/test2/flash.par.test2.nocharlimit.data
Exec/hydro_tests/Sod_stellar/runs/flash/test3/flash.par.test3.data
Exec/hydro_tests/Sod_stellar/runs/flash/test3/flash.par.test3.nocharlimit.data
Exec/hydro_tests/Sod_stellar/runs/flash/test4/flash.par.test4.data
Exec/hydro_tests/Sod_stellar/runs/flash/test4/flash.par.test4.nocharlimit.data
Exec/hydro_tests/Sod_stellar/runs/makePlot-MC-CGF.py
Exec/hydro_tests/Sod_stellar/runs/makePlot-MC-CW.py
Exec/hydro_tests/Sod_stellar/runs/makePlot-MC-final.py
Exec/hydro_tests/Sod_stellar/runs/norms.py
Exec/hydro_tests/Sod_stellar/runs/old/makePlot-MC-dt.py
Exec/hydro_tests/Sod_stellar/runs/old/makePlot-MC-eigen.py
Exec/hydro_tests/Sod_stellar/runs/old/makePlot-Tfixes.py
Exec/hydro_tests/Sod_stellar/runs/old/makePlot.py
Exec/hydro_tests/Sod_stellar/runs/old/makePlotZoom.py
Exec/hydro_tests/Sod_stellar/runs/relnorms.py
commit cb9950efb33914ca6e08c5a90d8cbfe5c40be185
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 17:12:07 2021 -0700
Convert remaining hydro tests to inputs-based tagging (#1744)
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/probin-test1-helm
Exec/hydro_tests/Sod_stellar/probin-test1-helm-y
Exec/hydro_tests/Sod_stellar/probin-test1-helm-z
Exec/hydro_tests/Sod_stellar/probin-test2-helm
Exec/hydro_tests/Sod_stellar/probin-test3-helm
Exec/hydro_tests/Sod_stellar/probin-test4-helm
Exec/hydro_tests/Vortices_LWAcoustics/inputs.2d
Exec/hydro_tests/Vortices_LWAcoustics/probin
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/probin.2d
Exec/hydro_tests/gresho_vortex/inputs.2d
Exec/hydro_tests/gresho_vortex/probin
Exec/hydro_tests/oddeven/inputs.2d
Exec/hydro_tests/oddeven/inputs.3d
Exec/hydro_tests/oddeven/probin
commit ff250d0755dd24112ecaf3d9444cfd88cf074f03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 23 20:00:00 2021 -0400
don't turn on the sponge if we aren't really using it (#1746)
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.32
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
commit 83de5acfeee9ab1f7fd8b59920372dac24e159d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 12:19:52 2021 -0700
Remove custom radiation boundary hook (#1743)
CHANGES.md
Source/radiation/MGRadBndry.cpp
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/RadBndry.cpp
Source/radiation/RadBndry_1d.f90
Source/radiation/RadBndry_2d.f90
Source/radiation/RadBndry_3d.f90
commit 9cbf5d102e4112751c52aa15bf59f9c24eb4fcb7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 11:41:52 2021 -0700
Convert acoustic_pulse, gamma_law_bubble, and double_bubble tagging to inputs (#1739)
Exec/hydro_tests/acoustic_pulse/inputs.128
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc2.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.64.sdc_ml
Exec/hydro_tests/acoustic_pulse/inputs.512
Exec/hydro_tests/acoustic_pulse/inputs.64
Exec/hydro_tests/acoustic_pulse/probin
Exec/hydro_tests/acoustic_pulse/probin-x
Exec/hydro_tests/acoustic_pulse/probin-y
Exec/hydro_tests/acoustic_pulse/probin-z
Exec/hydro_tests/acoustic_pulse_general/inputs.128
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.256
Exec/hydro_tests/acoustic_pulse_general/inputs.512
Exec/hydro_tests/acoustic_pulse_general/inputs.64
Exec/hydro_tests/acoustic_pulse_general/probin
Exec/hydro_tests/double_bubble/inputs_2d
Exec/hydro_tests/double_bubble/inputs_2d.single
Exec/hydro_tests/double_bubble/inputs_2d.single.equal
Exec/hydro_tests/double_bubble/inputs_2d.test
Exec/hydro_tests/double_bubble/probin
Exec/hydro_tests/double_bubble/probin.single
Exec/hydro_tests/double_bubble/probin.single.equal
Exec/hydro_tests/gamma_law_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/inputs_2d_MAESTRO.big
Exec/hydro_tests/gamma_law_bubble/probin
Exec/hydro_tests/gamma_law_bubble/probin.big
commit e66c9b7d2279bae52a697a513fba6cd0f0f90332
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 11:27:11 2021 -0700
Convert set_dterm_face to C++ (#1740)
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
commit 61921681344614fa2335e47d2b00a55091e77382
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 11:18:20 2021 -0700
Remove Fortran copy of the ambient state (#1742)
The namelist parameters are also moved to the inputs file.
CHANGES.md
Docs/source/creating_a_problem.rst
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_mhd/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_relaxation/probin
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/problems/Make.package
Source/problems/ambient_nd.F90
commit 50861ca5a0537091864b601bc0023e1019a11450
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 23 08:26:46 2021 -0700
Set CUDA-specific make option under USE_CUDA (#1741)
Exec/Make.Castro
commit 5bd377b48cc67ea0392e2f46ff359e5bc77f9de5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 23 11:24:56 2021 -0400
move the call to init_prob_parameters() to after the Fortran read (#1531)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
commit 1adbd12e88d016fe487a02b9ce9682142a38a07f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 22 19:17:25 2021 -0700
Convert KH, RT, and Sod tagging to inputs (#1738)
Exec/hydro_tests/KH/inputs.2d
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/inputs.3d
Exec/hydro_tests/KH/probin
Exec/hydro_tests/KH/probin.p3
Exec/hydro_tests/Noh/probin
Exec/hydro_tests/RT/inputs.dungeon
Exec/hydro_tests/RT/inputs_2d
Exec/hydro_tests/RT/inputs_2d.particles
Exec/hydro_tests/RT/inputs_3d
Exec/hydro_tests/RT/probin
Exec/hydro_tests/Sod/inputs-double-rarefaction
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test1-helm
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-test2-helm
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-helm
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod/probin-double-rarefaction
Exec/hydro_tests/Sod/probin-slowshock-x
Exec/hydro_tests/Sod/probin-sod-x
Exec/hydro_tests/Sod/probin-sod-y
Exec/hydro_tests/Sod/probin-sod-z
Exec/hydro_tests/Sod/probin-test1-helm
Exec/hydro_tests/Sod/probin-test2-1d
Exec/hydro_tests/Sod/probin-test2-helm
Exec/hydro_tests/Sod/probin-test2-x
Exec/hydro_tests/Sod/probin-test2-y
Exec/hydro_tests/Sod/probin-test2-z
Exec/hydro_tests/Sod/probin-test3-helm
Exec/hydro_tests/Sod/probin-test3-x
Exec/hydro_tests/Sod/probin-test3-y
Exec/hydro_tests/Sod/probin-test3-z
commit 268ab075014a6407cfb3dada5c420692e704307b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 22 20:24:01 2021 -0400
rename rotating_star to massive_star (#1737)
this is a more appropriate name for this problem
Exec/science/massive_star/15m_aprox19.6400
Exec/science/massive_star/GNUmakefile
Exec/science/massive_star/Make.package
Exec/science/massive_star/_prob_params
Exec/science/massive_star/inputs_1d
Exec/science/massive_star/inputs_2d
Exec/science/massive_star/inputs_2d.nse
Exec/science/massive_star/inputs_2d.sdc_test
Exec/science/massive_star/inputs_2d.strang_test
Exec/science/massive_star/probin
Exec/science/massive_star/probin.nse
Exec/science/massive_star/probin.sdc_test
Exec/science/massive_star/problem_initialize.H
Exec/science/massive_star/problem_initialize_state_data.H
commit 5f7ec384f170175aa4a98028256a48a06652ce7c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 22 17:06:15 2021 -0700
Add some asserts on the sponge parameters (#1736)
Closes #1733
Source/driver/Castro.cpp
commit e1a082f70a22a553fb7aaceee4461ec9cb456f73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 22 19:39:30 2021 -0400
we only need bc_fill_nd.F90 and filfc.f90 for MHD (#1735)
Source/driver/Make.package
Source/problems/Make.package
commit 2f74f09e13d9750f6e07815da9d6084397fb3eb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 22 19:21:07 2021 -0400
we no longer need dg() in Fortran (#1734)
Docs/source/software.rst
Source/driver/Castro_nd.F90
Source/driver/prob_params_nd.F90
commit 2eef3793ca2c7470d55fabfbaa714c65a0edfd1f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 22 15:52:16 2021 -0700
Sponge parameters are now set in the inputs file (#1731)
CHANGES.md
Docs/source/inputs.rst
Docs/source/sponge.rst
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/DustCollapse/probin.fullstar
Exec/gravity_tests/DustCollapse/probin.fullstar.1d
Exec/gravity_tests/DustCollapse/probin.halfstar
Exec/gravity_tests/DustCollapse/probin.octant
Exec/gravity_tests/DustCollapse/probin.pointmass
Exec/gravity_tests/DustCollapse/probin_3d_poisson_regtest
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/StarGrav/inputs_3d
Exec/gravity_tests/StarGrav/inputs_3d_mhd
Exec/gravity_tests/StarGrav/probin
Exec/gravity_tests/hse_convergence_general/probin.hse_test
Exec/gravity_tests/hydrostatic_adjust/inputs
Exec/gravity_tests/hydrostatic_adjust/inputs-subchandra
Exec/gravity_tests/hydrostatic_adjust/probin
Exec/gravity_tests/hydrostatic_adjust/probin.subchandra
Exec/hydro_tests/toy_convect/inputs_2d
Exec/hydro_tests/toy_convect/probin
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/reacting_tests/reacting_bubble/probin
Exec/reacting_tests/reacting_bubble/probin.zoom
Exec/reacting_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/reacting_tests/toy_flame/exploration/probin_temp
Exec/reacting_tests/toy_flame/inputs.1d
Exec/reacting_tests/toy_flame/inputs.1d.testsuite
Exec/reacting_tests/toy_flame/probin
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
Exec/science/bwp-rad/probin
Exec/science/bwp-rad/probin.dens_sponge
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/exploration/probin_temp
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/inputs.3d.test
Exec/science/convective_flame/probin
Exec/science/convective_flame/probin_good
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.1000Hz.3d
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
Exec/science/flame_wave/inputs_He/probin.He
Exec/science/flame_wave/inputs_He/probin.He.25cm
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13/probin.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/probin.boost.aprox13
Exec/science/flame_wave/probin.hse_test
Exec/science/flame_wave/probin.testsuite
Exec/science/flame_wave/scaling/3d_science/inputs.noboost.25cm.1000Hz.3d
Exec/science/flame_wave/scaling/3d_science/probin.noboost.25cm.1000Hz
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/flame_wave/scaling/probin.boost_10_10
Exec/science/nova/probin
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/planet/probin
Exec/science/rotating_star/inputs_1d
Exec/science/rotating_star/inputs_2d
Exec/science/rotating_star/inputs_2d.nse
Exec/science/rotating_star/inputs_2d.sdc_test
Exec/science/rotating_star/inputs_2d.strang_test
Exec/science/rotating_star/probin
Exec/science/rotating_star/probin.nse
Exec/science/rotating_star/probin.sdc_test
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/probin
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_mhd/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_relaxation/probin
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Exec/science/xrb_mixed/inputs_2d
Exec/science/xrb_mixed/probin
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/sources/Castro_sources.H
Source/sources/Castro_sponge.cpp
Source/sources/Make.package
Source/sources/sponge_defaults.H
Source/sources/sponge_nd.F90
Source/sources/sponge_params.H
commit 184248c505ee0114c2c1f192c8314692b1236c23
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 22 15:51:59 2021 -0700
Remove Fortran initdata interfaces (#1732)
CHANGES.md
Docs/source/creating_a_problem.rst
Docs/source/mhd.rst
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/problems/Make.package
Source/problems/Prob_mhd_nd.F90
Source/problems/Prob_nd.F90
commit b6a51ea10d949df999379183ec217f63367adece
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 22 10:28:43 2021 -0400
don't initialize F90 Microphysics unless it is needed (#1729)
This will be a first step to turning off the compilation of the F90 Microphysics
Source/driver/Castro_setup.cpp
commit 00890f3fc150aa153dd773066bb673d7de9c63e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 21 17:04:42 2021 -0700
Declare Fortran problem setups unsupported (#1728)
CHANGES.md
commit edbe203cf99449a45b927216cf0ed278aa8b6fa4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 08:12:02 2021 -0400
Convert RadSourceTest to C++ (#1534)
This also fixes the EOS, so the problem runs
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/_prob_params
Exec/radiation_tests/RadSourceTest/analytic.f90
Exec/radiation_tests/RadSourceTest/inputs-cooling
Exec/radiation_tests/RadSourceTest/inputs-heating
Exec/radiation_tests/RadSourceTest/probin-cooling
Exec/radiation_tests/RadSourceTest/probin-heating
Exec/radiation_tests/RadSourceTest/problem_initialize.H
Exec/radiation_tests/RadSourceTest/problem_initialize_rad_data.H
Exec/radiation_tests/RadSourceTest/problem_initialize_state_data.H
commit a155c5cd97577381082d69b706ba899b4ba739df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 20 21:04:38 2021 -0400
convert scf single_star to C++ (#1726)
Exec/scf_tests/single_star/Prob_nd.F90
Exec/scf_tests/single_star/problem_initialize.H
Exec/scf_tests/single_star/problem_initialize_state_data.H
commit 41304bfd26977baf1c2e22c11e3e206764cc46c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 17 10:17:36 2021 -0700
Set up separate probin for 1D dustcollapse (#1724)
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/probin.fullstar.1d
commit 02b26e3e82ca2fcd83fbe13c2390ba5311b1ba4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 17 05:17:28 2021 -0700
USE_CUDA -> USE_GPU (#1722)
Exec/Make.Castro
Source/driver/Castro.cpp
Source/driver/Castro_nd.F90
Source/driver/Make.package
Source/mhd/mhd_util.cpp
Source/problems/hse_fill.cpp
Source/radiation/trace_ppm_rad.cpp
Source/scf/Make.package
Source/sdc/Castro_sdc.H
Source/sdc/Make.package
commit 5db4d35c4d80ed7adfb73d036f5826b27d056b9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 16 14:29:50 2021 -0700
Convert flux_face2center to C++ (#1721)
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/Make.package
Source/radiation/RadSolve.cpp
commit f0f7d32fd4416e654bf8583f7d92db2ae1d8b2b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 16 13:31:44 2021 -0700
Convert DustCollapse setup to C++ (#1717)
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/_prob_params
Exec/gravity_tests/DustCollapse/problem_initialize.H
Exec/gravity_tests/DustCollapse/problem_initialize_state_data.H
Source/driver/Castro.H
Source/driver/Castro_util.H
commit b31c7b7cdf87dc394135fe6cc0310825fa49d712
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 16 12:14:36 2021 -0700
Use AMReX vendor-agnostic interface for cudaProfilerStart (#1720)
Source/driver/Castro.cpp
commit ad58a28259f6d4414043369a3566af5f7a7ae7dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 16 10:49:27 2021 -0700
Convert filt_prim to C++ (#1719)
Exec/radiation_tests/RadBreakout/filt_prim.H
Exec/radiation_tests/RadBreakout/filt_prim_1d.f90
Source/radiation/Make.package
Source/radiation/Radiation.cpp
Source/radiation/filt_prim.H
Source/radiation/filt_prim_1d.f90
Source/radiation/filt_prim_2d.f90
Source/radiation/filt_prim_3d.f90
Source/radiation/filter.H
commit 3495b320d27f5fd89d5a5186f8cf797c2b62778e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 16 10:17:57 2021 -0700
Remove old problem files (#1718)
These were supposed to be deleted in #1311 but it looks like they were missed.
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
Source/problems/Make.package
Source/problems/Problem.f90
commit b0f876f9cd6a68712ae840fb5e0a531f1a9b6e56
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 15 17:06:20 2021 -0700
Remove unused update_sponge_params hook (#1716)
CHANGES.md
Source/sources/Castro_sources_F.H
Source/sources/Castro_sponge.cpp
Source/sources/Make.package
Source/sources/update_sponge_params.f90
commit 5fa9b8b7cee1ee91fe3853b1113aa383d3ac70c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 15 10:24:34 2021 -0700
Remove remaining OpenACC directives (#1715)
Source/driver/Castro_nd.F90
Source/driver/prob_params_nd.F90
commit 4a081d028648092bbdd15f3dd08b38b35d2da6eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 14 05:38:55 2021 -0700
Use density-based sponge in DustCollapse (#1714)
DustCollapse uses a radius-based sponge, but since the radius of the spherical shell moves inward over time, the problem needs to recalculate the sponge radius at every timestep. This is what necessitated the update_sponge_params functionality.
After DustCollapse was implemented we added a density-based sponge. This more neatly solves the problem without requiring any problem-specific functionality. Switching to the density sponge for this problem will allow us to remove that custom sponge hook, which was only ever used for this problem.
Exec/gravity_tests/DustCollapse/probin.fullstar
Exec/gravity_tests/DustCollapse/probin.halfstar
Exec/gravity_tests/DustCollapse/probin.octant
Exec/gravity_tests/DustCollapse/probin.pointmass
Exec/gravity_tests/DustCollapse/probin_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
commit ae1952d9faa7b639d0c050f392e39e8105c7b19b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 13 20:39:28 2021 -0400
remove sources_for_hydro (#1711)
we don't need the sources_for_hydro MF. We can add the predictor to the old sources
directly in src_to_prim
Docs/source/FlowChart.rst
Docs/source/software.rst
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/mhd/Castro_mhd.cpp
commit 4c6089dbffd01bef01b2e331e550561a4b408934
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 13 18:56:47 2021 -0400
don't use sources_for_hydro with SDC / MOL (#1709)
Source/driver/Castro_advance_sdc.cpp
Source/hydro/Castro_mol_hydro.cpp
commit b984d2295cbd871d76aa6e9b7c8b61a3247616b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 13 18:27:15 2021 -0400
remove castro.reactions_max_solve_level (#1710)
this option was not widely used and is generally not thought to be a good idea
Exec/science/Detonation/inputs-collision
Source/driver/_cpp_parameters
Source/reactions/Castro_react.cpp
commit 2ba95124e7e7f6b1d8dc0062b2d4b16405aeedd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 13 16:18:50 2021 -0400
don't store Reactions_Type in checkpoint files (#1712)
we don't need it on restart
CHANGES.md
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
commit c275e053a9f5f5f0e7e4c018800dcb81d7357c07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 13 11:52:54 2021 -0400
remove the old plm_well_balanced stuff (#1708)
this parameter no longer exists, and instead well-balancing for PLM
is enabled via use_pslope, which is on by default.
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs_1d.well_balance
Exec/reacting_tests/bubble_convergence/inputs_1d.well_balance
Exec/reacting_tests/bubble_convergence/inputs_2d.well_balance
commit 72cc2999be1301865ceab43a8bcdc80e7aa6be03
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 12 07:02:52 2021 -0700
Convert state_energy_update to C++ (#1702)
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
commit b558498d3969bab3a3ee02c25edf58dfae1e75f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 12 06:26:28 2021 -0700
Fix CUDA compilation of RadBreakout (#1687)
Exec/radiation_tests/RadBreakout/_prob_params
Exec/radiation_tests/RadBreakout/problem_initialize.H
Exec/radiation_tests/RadBreakout/problem_initialize_state_data.H
commit 237400836da3eced1d6c82c938fb44147f1bd665
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 12 06:24:42 2021 -0700
Convert estdt_rad to C++ (#1704)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/timestep.cpp
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
commit 5f908e5005e7035cd4e431eb13e43333cd7872a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 12 08:54:13 2021 -0400
remove some runtime parameters from Fortran (#1701)
Source/driver/_cpp_parameters
commit 6a0b4d91fed39bdcec29e46ad2ceb160036a93fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 12 05:33:42 2021 -0700
Add more BL_PROFILE to HypreMultiABec (#1703)
Source/radiation/HypreMultiABec.cpp
commit 3451865de97efc59aea52e7c7adb6bb4c654d694
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 10 16:37:11 2021 -0700
FabArray::copy is deprecated, switch to MultiFab::Copy (#1698)
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.cpp
Source/radiation/Castro_radiation.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
commit f5cac3e7c41691d52ac08d70c7173ebde82c51d3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 10 05:39:30 2021 -0700
Convert face2center to C++ (#1699)
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/RAD_F.H
Source/radiation/RadPlotvar.cpp
Source/radiation/RadSolve.cpp
commit a0fcad33c10f7f1a7c9c1f87fec1f9cf6557cc6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 9 17:30:43 2021 -0400
fix the size of qaux (#1697)
we were wasting a lot of memory here
Source/hydro/Castro_ctu_hydro.cpp
commit f06f01e1ae670b154f5bb1367188b1011cd55c7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 9 11:40:13 2021 -0700
gamma_law_general -> gamma_law (#1696)
Docs/source/EOSNetwork.rst
Docs/source/radiation.rst
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/mhd_tests/Alfven/GNUmakefile
Exec/mhd_tests/BrioWu/GNUmakefile
Exec/mhd_tests/DaiWoodward/GNUmakefile
Exec/mhd_tests/FastRarefaction/GNUmakefile
Exec/mhd_tests/LoopAdvection/GNUmakefile
Exec/mhd_tests/MagnetosonicWaves/GNUmakefile
Exec/mhd_tests/OrszagTang/GNUmakefile
Exec/mhd_tests/RT/GNUmakefile
Exec/mhd_tests/species/GNUmakefile
Exec/radiation_tests/RadBlastWave/GNUmakefile
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Util/exact_riemann/GNUmakefile
commit aef121f0727a6c1be319a99ae9306081ce30e48e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 9 14:21:08 2021 -0400
adjust the number of ghost cells for source terms (#1694)
sources that undergo reconstruction for tracing only need 3, not 4
ghost cells. PPM requires 4 only for p, in the computation of the
flatting coefficient.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_setup.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/sources/Castro_sources.cpp
commit 402c0d1f397b2457e456ecd5e9103d70acfdaa62
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 19:33:57 2021 -0700
Fix variable shadowing (#1686)
Source/radiation/rad_util.H
commit 2122a4d303719816105dfe73515b2d8f2a96200d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 14:48:58 2021 -0700
Add inline functions for computing geometry factors (#1689)
Begins to address #1688. The new functions are used in consup as a demonstration.
Source/driver/Castro_util.H
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
commit 1802cfde78ef9a252c0f7601e1c9d83923e7c181
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 12:06:44 2021 -0700
Avoid accesses to static radiation data in device code (#1684)
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/radiation/RadDerive.cpp
Source/radiation/RadPlotvar.cpp
commit bf0605394d71b01d207b0c7781966917840fed07
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 10:24:25 2021 -0700
Convert spalpha to C++ (#1683)
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/fluxlimiter.F90
Source/radiation/fluxlimiter.H
commit e609c63080e75fcd5548d818f5994f26da07e839
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 10:20:15 2021 -0700
Address unused variable warnings (#1685)
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
commit c61467f6af2a3db180ecc62ab5bc367bb88e9dce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 09:01:05 2021 -0700
Convert er_com2lab to C++ (#1681)
This plot routine is active if radiation.plot_lab_Er = 1 and radiation.comoving=1. This isn't active by default, but I did check that it works on the 3D planet case by setting comoving to 1.
Source/radiation/RAD_F.H
Source/radiation/RadPlotvar.cpp
Source/radiation/RadPlotvar_1d.f90
Source/radiation/RadPlotvar_2d.f90
Source/radiation/RadPlotvar_3d.f90
commit f877ac7c0e6c2511e4d313a1d32f17c0796f2aeb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 8 11:48:30 2021 -0400
we no longer need to know about the pointmass in Fortran (#1682)
this removes the hooks and some unused headers
Docs/source/gravity.rst
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/gravity/Castro_gravity_F.H
Source/gravity/Castro_pointmass.cpp
Source/gravity/Make.package
commit dd5433275ae8571242b05475d652f0c454780131
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 7 22:03:24 2021 -0400
we only need GDRHO if we are doing hybrid momentum (#1677)
Source/driver/_variables
Source/hydro/riemann_solvers.H
Source/hydro/riemann_util.cpp
commit bb54bb7fc34545b0b7ff3b90e27b168f54cc9384
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 7 21:59:27 2021 -0400
convert some radiation derives to C++ (#1679)
Source/driver/Castro_setup.cpp
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/RadDerive.H
Source/radiation/RadDerive.cpp
Source/radiation/RadDerive_nd.F90
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 41ce3ca9314008b96f9b5d9e2da26e1075a4c2f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 7 21:58:21 2021 -0400
remove some legacy headers (#1680)
Source/driver/Castro_F.H
commit b3ea73f1ae058d0fdd21c395989892f51144a3cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 7 20:58:22 2021 -0400
we no longer need to override rot_axis in Fortran (#1678)
we never access it in Fortran
Source/driver/Castro_nd.F90
commit 8db603c24067e78e9ec4c63bff977c1a4c793677
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 7 18:59:42 2021 -0400
reduce max_grid_size to 64 (#1676)
this is how we are running on Summit
this gives better performance on groot too
Exec/science/flame_wave/inputs_3d.testsuite.gpu
commit 3c4571fea44c1a8ef0a06ab47be170dbb94ecdd5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 7 17:15:32 2021 -0400
update backtrace docs (#1675)
Docs/source/faq.rst
commit eebe5211ffbea55546791ab76410f61f2f63d097
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 7 06:23:56 2021 -0700
Fix loop bounds in estimate_gamrPr (#1674)
PR #1554 introduced a bug for CPU builds (with tiling) by making the bounds of the loop based on the valid box, while the extent of the gPr array that is being filled is only the tile box.
Source/radiation/MGFLD.cpp
commit 9c51b523f1a0e5ec61eb6d985edbbfd7ec28b99d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 7 05:49:19 2021 -0700
Fix CUDA compilation of planet problem (#1672)
Exec/science/planet/problem_source.H
commit afbf31541acd45a3b4cfdbd0534f44d07ae8dccf
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 7 05:48:01 2021 -0700
Fix box used in moving center from #1665 (#1671)
Source/driver/Castro.cpp
commit 5e8a228fc4e3b05fec53acca2d2a7dd2de0ab290
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 21:25:41 2021 -0400
we don't seem to use the outflow data in Fortran anymore (#1669)
this looks like it was originally used for the case where we wanted to average the data on the grid into the boundaries to account for the case where we might not have an entire star in the domain. But we don't actually use this. This was the "spherical_star" functionality.
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/driver/meth_params.template
commit 57e68c6f3881bb6fe7925666e5489ff075ce275e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 21:06:33 2021 -0400
rot_vec is no longer used in Fortran (#1670)
Source/driver/Castro_nd.F90
Source/driver/meth_params.template
commit 0fa9201a91fd07aa5656456aed6a27cd52a9a8a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:50:31 2021 -0400
convert particle_test to C++ (#1664)
Exec/unit_tests/particles_test/GNUmakefile
Exec/unit_tests/particles_test/Prob_nd.F90
Exec/unit_tests/particles_test/problem_initialize.H
Exec/unit_tests/particles_test/problem_initialize_state_data.H
commit 5a39e881313223070ce16d90f2da093f421b062e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:48:24 2021 -0400
fix some sphinx errors (#1656)
Docs/source/AMR.rst
commit f71ab405cdb4f06bcdc2e72670daa5c6c62faa84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:47:31 2021 -0400
get rid of the Fortran get_omega (#1666)
we don't seem to have any code that uses this
Source/rotation/Make.package
Source/rotation/Rotation_frequency.F90
commit 1bab503500ce37f4d26beeecc7659330d7d1443f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:38:51 2021 -0400
remove the Fortran kavg -- this is not used (#1668)
there was a residual call there that basically set the value of opt
that was Fortran "saved" in kavg, but we can remove that because
nothing is using the kavg routine in Fortran anymore
Docs/source/radiation.rst
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/inputs.1d.test
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/kavg.F90
commit 1c4ad3398ae340f7baaf684026be29adaf8550e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:29:08 2021 -0400
remove rad_util_module -- nothing uses it (#1667)
Source/radiation/Make.package
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/rad_util_nd.F90
commit 8ed6d3cee0b96624fbd07ea75396131876f5d245
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:11:47 2021 -0400
convert FastRarefaction to C++ (#1658)
Exec/mhd_tests/FastRarefaction/Prob_mhd_nd.F90
Exec/mhd_tests/FastRarefaction/Prob_nd.F90
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/FastRarefaction/problem_initialize.H
Exec/mhd_tests/FastRarefaction/problem_initialize_mhd_data.H
Exec/mhd_tests/FastRarefaction/problem_initialize_state_data.H
commit a48ef0a9a757a8b749485c674795b64d3a572b1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 19:07:04 2021 -0400
convert DaiWoodward to C++ (#1657)
Exec/mhd_tests/DaiWoodward/Prob_mhd_nd.F90
Exec/mhd_tests/DaiWoodward/Prob_nd.F90
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/DaiWoodward/problem_initialize.H
Exec/mhd_tests/DaiWoodward/problem_initialize_mhd_data.H
Exec/mhd_tests/DaiWoodward/problem_initialize_state_data.H
commit 546a1cdad506c7f95866581351040e8e36932f18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 18:23:00 2021 -0400
convert ca_find_center to C++ (#1665)
note: we don't really use this, but it runs w/o crashing when
I set castro.moving_center = 1
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util_nd.F90
Source/driver/Make.package
commit e02c412a202d194c4d9e3ba01acd1a6a40725731
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 09:04:18 2021 -0400
update CI docs (#1662)
Docs/source/development.rst
commit 45204227083473e67b2c7b889fbfc35abacadea2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 08:36:49 2021 -0400
convert the magnetosonic wave problem to C++ (#1659)
Exec/mhd_tests/MagnetosonicWaves/Prob_mhd_nd.F90
Exec/mhd_tests/MagnetosonicWaves/Prob_nd.F90
Exec/mhd_tests/MagnetosonicWaves/problem_initialize.H
Exec/mhd_tests/MagnetosonicWaves/problem_initialize_mhd_data.H
Exec/mhd_tests/MagnetosonicWaves/problem_initialize_state_data.H
commit 36db6495d5c7736b9dc83bc00b81ead1575bbaa9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 08:36:33 2021 -0400
convert MHD RT to C++ (#1660)
Exec/mhd_tests/RT/Prob_mhd_nd.F90
Exec/mhd_tests/RT/Prob_nd.F90
Exec/mhd_tests/RT/problem_initialize.H
Exec/mhd_tests/RT/problem_initialize_mhd_data.H
Exec/mhd_tests/RT/problem_initialize_state_data.H
commit 9ff3bdd448fbff9c11a61f1e8b743cd51dc23aad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 6 08:36:15 2021 -0400
port species MHD problem to C++ (#1661)
Exec/mhd_tests/species/Prob_mhd_nd.F90
Exec/mhd_tests/species/Prob_nd.F90
Exec/mhd_tests/species/problem_initialize.H
Exec/mhd_tests/species/problem_initialize_mhd_data.H
Exec/mhd_tests/species/problem_initialize_state_data.H
commit 61422c951c3b2b4d1b57095875cf826eada93c79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 4 19:42:56 2021 -0400
update the amr tagging docs (#1655)
Docs/source/AMR.rst
commit 160a7aba17094c6e0e3613a9dd64e86299189ee7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 3 20:33:18 2021 -0400
this physbc_* info is no longer needed in Fortran (#1654)
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/prob_params_nd.F90
commit 35a63d2ef08ffba9a6c6ed2dd96cc4ae960eb059
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 3 20:29:12 2021 -0400
remove the fortran flush_output() (#1653)
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Make.package
Source/driver/io_nd.F90
Source/hydro/Castro_mol_hydro.cpp
commit 4997dc288688fc4f43a065d097673beb58621b18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 3 12:32:31 2021 -0400
remove references to [ra]tol_temp (#1652)
this is no longer used
Syncs up with Microphysics PR 665
Exec/science/Detonation/nse_runs/probin-det-x.nse_disabled
Exec/science/Detonation/probin-collision
Exec/science/Detonation/probin-det-x.nse_disabled
Exec/science/Detonation/probin-det-x.simplified_sdc
Exec/science/nova/probin
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/xrb_mixed/probin
commit 8442a5656c1c9e4fcedc7e837fe59a2192d8a52c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 2 14:22:30 2021 -0400
update to 21.05
external/Microphysics
external/amrex
commit bc0a767a367599434af517b323f4ab9cf3485b9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 29 10:42:02 2021 -0400
some better parameters for the rotating star (#1649)
in particular, the numerical Jacobian is key with this network
this also refines a larger region
this runs well with Strang
Exec/science/rotating_star/inputs_2d.nse
Exec/science/rotating_star/probin.nse
commit eefb5ab871a0e7f6e299c5d410f94a7c4ca72ee0
Author: Nicole F <73133869+nmford20@users.noreply.github.com>
Date: Tue Apr 27 18:35:19 2021 -0400
Tracer particle analysis scripts (#1648)
make_particles.py: creates a list of locations to distribute particles in the simulation domain
trajectories_info.py: Reads particles Timestamps files and outputs txt files for each particle, storing the particle's trajectory information
trajectories_plot.py: Creates a plot for each txt file created with trajectories_info.py
trajectories_stackedplot.py: Creates a plot for a selection of trajectories
Exec/science/flame_wave/analysis/make_particles_file.py
Exec/science/flame_wave/analysis/trajectories_info.py
Exec/science/flame_wave/analysis/trajectories_plot.py
Exec/science/flame_wave/analysis/trajectories_stackedplot.py
commit 6c866fca462f6cd8894fefe00d2444d28f42b00c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 27 18:34:12 2021 -0400
remove hydro_source (#1641)
we go back to the original idea of updating S_new directly with the
hydro term. This frees up a lot of memory.
Docs/source/software.rst
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_rad.cpp
Source/hydro/Castro_hydro.H
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/mhd_util.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
commit e22ab9d365cf40d113a2c4727eef0325aa2ba759
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Tue Apr 27 23:50:36 2021 +0200
changes in initialize_mhd_data to be compatible without initial_model.H (#1647)
compilation of wdmerger with mhd works now
this PR changes initialize_mhd_data to be compatible without initial_model.H
Exec/science/wdmerger/problem_initialize_mhd_data.H
commit 9b5e64e69ac32105c38f4a5154b922bace335cce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 27 10:31:48 2021 -0400
change how we handle species sources in simplified-SDC (#1646)
instead of adding the Iq source to the normal interface state before the
transverse corrections, we now wait until the end. This is still 2nd order
accurate, but because we don't trace the state or put it through the
different transverse operations, there is no danger of it violating
sum{Iq} = 0
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
commit 8ab52269f0b55ab1d475640417a3c9343d7acbc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 26 20:22:54 2021 -0400
remove the only lagged Iq terms from NSE + SDC (#1644)
Source/reactions/Castro_react.cpp
commit 31dfeaf89074bac570761e165b57a9df280d5826
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 21 09:39:36 2021 -0400
fix GPU compilation with MHD (#1643)
Source/mhd/mhd_eigen.H
commit 68ef35b7fc75b99614331aa4b8ca1304ffca0133
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 20 14:24:16 2021 -0400
simplify the logic for when we add the hydro gradp for radiation (#1642)
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_rad.cpp
commit 5bede1ca7db57085bf19b364925da4162faadaa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 19 19:29:34 2021 -0400
make Riemann state memory independent of NumSpec (#1638)
This changes the output of the riemann_state() function to produce a
RiemannState object that does not contain the species info. We will deal
with the species separately when we do the fluxes.
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
commit fc698bf243d107670b133cd33481ed4d587741d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 18 21:50:43 2021 -0400
riemann_solvers.cpp is no longer needed (#1640)
it was already removed from the build system
Source/hydro/riemann_solvers.cpp
commit 4a7ad901ec9f6618afd9a6019cf42098a43bf368
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 18 17:35:55 2021 -0400
remove apply_sources_consecutively (#1636)
we no longer use this option
CHANGES.md
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_mhd_test
Exec/mhd_tests/RT/inputs_3d
Exec/mhd_tests/RT/inputs_3d_mhd
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Source/driver/_cpp_parameters
Source/sources/Castro_sources.cpp
commit ba3d96ec0fe9b703fe3410db1e590f638e2ead91
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 18 14:28:05 2021 -0700
Compile with MPI_THREAD_MULTIPLE support by default (#1637)
This allows us to use amrex.async_out=1 at runtime.
Exec/Make.Castro
commit f50a2855ee92de49b79d286c74cfc5115dc656fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 18 14:06:32 2021 -0400
make riemann_state a single-zone inline function (#1629)
Source/driver/Castro.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/hydro/riemann_util.cpp
commit b79e07a7b9550da38aefebae1c3464f160a24de3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 17 18:15:17 2021 -0400
move the Riemann loop over interfaces out of the solvers (#1624)
Source/hydro/Castro_hydro.H
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/hydro/riemann_solvers.cpp
commit e6e5d6a94138a9cdd975a8a7d8d9d9b7dbd4f08e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 17 12:18:33 2021 -0400
remove the unused compute_gammas option in Riemann (#1633)
also use some simpler eos types
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/riemann.H
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
commit 75b3ec798bfa1bc030ff407c810188ddab0fc5e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 16 17:55:27 2021 -0400
convert some loops from old macros to parallel fors (#1634)
Source/hydro/Castro_ctu_hydro.cpp
commit a3d83dbdf3224621a29df5abc58777045fce7ec9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 15 16:11:36 2021 -0400
rename load_ppm_stencil -> load_stencil + use in plm (#1628)
Source/hydro/ppm.H
Source/hydro/reconstruction.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
commit 4bcc191d5917af575c692a7336ed2eaa4ac9c235
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 15 10:48:14 2021 -0400
move the passive upwinding out of the core Riemann solvers (#1622)
All the approximate state solvers do the same thing, so we move this out to the caller. Soon this will be merged with a call to the solver over just a single interface.
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
commit 69d606ea427ed4820a66bb4ec070c9a564d8fbc7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 15 09:02:30 2021 -0400
fix compilation of the RT problem (#1627)
Exec/hydro_tests/RT/problem_initialize_state_data.H
commit b5695d42f53fe468730dddb3c193765a3039f310
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 21:33:18 2021 -0400
for ppm, only reconstruct and trace the quantities we need (#1615)
This saves on memory by not allocating NQ*2*3 interface states on each thread, but instead
just constructing the states we absolutely need.
Source/hydro/ppm.H
Source/hydro/trace_ppm.cpp
commit 2b55acea874cabff241643444e306fc7b882ddfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 20:49:43 2021 -0400
start working on a new interface for the approx state Riemann solvers (#1618)
note that some problems like rotating_torus will have small diffs since immediately when we start, they have interface p or rhoe < 0, and we now reset this differently in the unified initialization approach.
In particular, we now use smallt and rho to get the interface state while previously we just did a max(p, small_pres).
Source/hydro/riemann.H
Source/hydro/riemann_solvers.cpp
commit c6ceab5615c0614c4404ec6ab8de81e4b4e3ca6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 19:13:56 2021 -0400
use simpler EOS types where we can (#1626)
Source/driver/Derive.cpp
Source/driver/timestep.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/edge_util.cpp
Source/problems/hse_fill.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit 61d33d30590c9d5409088855e59c6213637a31df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 12:52:08 2021 -0400
remove the use_eos_in_riemann parameter (#1623)
I could find no instance where this was used
CHANGES.md
Source/driver/_cpp_parameters
Source/hydro/riemann_solvers.cpp
commit 2ff2d2e3266afb508df1e2328c5e06c9d9ad1f9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 09:00:50 2021 -0400
remove the enforce_eos option from compute_flux_q (#1619)
we were not using it anywhere
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_util.cpp
commit 0f1c5e89f7556ec03908a116631efb03d173684c
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri Apr 9 11:35:23 2021 -0400
Fix rho_nse for rotating_star problem (#1617)
Exec/science/rotating_star/probin.nse
commit af4d2980dcc5865f20c8e145a424772baf371aab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 6 14:30:12 2021 -0400
add job script for 3-d (#1611)
Exec/science/flame_wave/job_scripts/summit/summit_3d_512.submit
commit fdeebc501853f578d8c3b4a852d716918bb32004
Merge: f767999bf 797f304b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 1 11:51:39 2021 -0400
Merge branch 'development' into main
commit f767999bf8a9bc23774455c26bd196e1b601aaa0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 1 11:50:43 2021 -0400
update to 21.04
external/Microphysics
external/amrex
commit 797f304b57c11df37a7a9b82cf2a95820004ae76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 1 10:01:10 2021 -0400
sync the 3-d run up to the 3.e8 K run from paper II (#1608)
This sets up the 1000 Hz 3d run using the same parameters as the 3.e8 K run in paper II
Exec/science/flame_wave/inputs_He/inputs.He.25cm.1000Hz.3d
Exec/science/flame_wave/inputs_He/probin.He.25cm
commit 57717cfd4e96e350083c4c9b9a65ca4fb2452c5d
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Tue Mar 30 16:30:00 2021 -0700
Fix issue where Castro was using tracer particle parameters in an uninitialized unnamed namespace instead of the 'particles' namespace defined with _cpp_parameters. (#1610)
CastroParticles.cpp was previously using an unitialized, unnamed namespace in that file to hold tracer particle parameters that were also defined in the particles namespace defined with _cpp_parameters and included through:
#include <particles_params.H>
#include <particles_declares.H>
As a result, the code inside this source file was using the uninitialized parameters in the unnamed namespace instead of the parameters by the same names in the particles namespace.
This removes the duplicate parameters from the unnamed namespace and adds the particles:: namespace specifier where necessary.
Source/particles/CastroParticles.cpp
commit e0e85872b627aee58208af0c46401919c3790589
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 25 16:05:56 2021 -0400
add "works with | yt" badge (#1606)
README.md
commit 5f9e7c1020c2269355c13c7dd811ba7025330e9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 25 13:54:00 2021 -0400
initialize found_aux in model_parser.H (#1605)
Util/model_parser_cxx/model_parser.H
commit 50593610f444583dd33473a1b94eb5c5891adf56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 21 21:18:02 2021 -0400
for simplified-SDC store only reactive part in plotfile (#1602)
we were storing the entire update, including the advection in the enuc update
CHANGES.md
Source/reactions/Castro_react.cpp
commit 994b57a8a875973079a721f51b0a863396a6f525
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 20 16:56:55 2021 -0400
simplify computation of simplified-SDC reactive source (#1601)
Source/sources/Castro_sources.cpp
commit c554b6eb0e9f7fe0108fd3dfde999e53a688fb87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 20 16:08:37 2021 -0400
output info on offending X in a normalization abort (#1600)
Source/driver/Castro.cpp
commit 29c5a8cd1a93d6f54b6e71a618fb0a5e49a1331a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 19 16:28:34 2021 -0400
fix reported (rho e) after burn (#1593)
we were printing out the number of RHS calls instead of the total (rho e) from the burn.
Source/reactions/Castro_react.cpp
commit b513fad2ad2e8fac19ea196620dce4241e5845af
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 19 13:28:11 2021 -0700
Perform a more efficient reduction in multipole BCs (#1564)
The multipole reduction works by summing a quantity from every zone to a set of arrays in a weighted linear combination. This is presently implemented with fully atomic reductions on GPUs. The overhead from atomic serialization becomes very large with hundreds of thousands of threads updating the same quantity simultaneously. We can improve on this with reductions that do some of the work within a threadblock using amrex::Gpu::deviceReduceSum(). The main changes that are required are:
Every thread must be doing the same reduction at the same time, so we have to move the reduction outside of the conditional that checks whether we're contributing to the upper or lower multiple arrays
We must use the four-argument variant of the device lambda which provides a amrex::Gpu::Handler to help implement the reduction
The ParallelFor must be launched with setReduction(true) which indicates to AMReX the relevant information needed to perform this reduction safely (we will launch more threads than there are valid grid zones and we need to take special care in the boxes where not every active thread is in a zone, to avoid possible deadlocks)
For a 128^3 grid, this improves the performance of this kernel by a factor of 5.
Source/gravity/Gravity.cpp
Source/gravity/Gravity_util.H
commit 420b77cee7152dd3f2909c9a92235a6dd85f6cfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 19 11:46:03 2021 -0400
the BACKTRACE stuff no longer seems to be the ifdef (#1591)
Docs/source/faq.rst
commit 26f906e4c42c40df6ec6aea44bc126be25a910d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 19 10:28:55 2021 -0400
loosen the tolerances for flame setups -- atol of 1.e-10 is tough (#1595)
also remove the irrelevant sponge stuff
Exec/science/flame/probin
Exec/science/flame/probin.H_He
Exec/science/flame/probin.sdc
Exec/science/flame/probin.sdc.3alpha
commit 00333ca619eab825f3e80da9737fcde49ae68212
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 18 09:41:33 2021 -0700
Update for new Amr constructor that takes a LevelBld (#1592)
See AMReX-Codes/amrex#1852.
Source/driver/main.cpp
external/amrex
commit 310e158dac00e7938797ff61b47332d30ccc2284
Merge: 25c53a944 5e0a1b9cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 18 08:57:40 2021 -0400
Merge branch 'main' into development
commit 25c53a944e571408079c652dfa50f1c093027f97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 16 11:58:50 2021 -0400
fix bounds error in the true SDC Jacobian (#1594)
Source/sdc/vode_rhs_true_sdc.H
commit e6de96f78374474b095384da8501b9f41628da13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 12 20:26:38 2021 -0500
explicitly ensure we have the nuclei needed to understand our initial model (#1590)
plus get rid of the network_spec_index on the device
Exec/gravity_tests/hydrostatic_adjust/_prob_params
Exec/gravity_tests/hydrostatic_adjust/problem_initialize.H
Exec/gravity_tests/hydrostatic_adjust/problem_source.H
commit f09342acce4eecd83ed5f412efbd42b30c3181e4
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Mar 10 14:06:36 2021 -0500
Add in_nse plot variable (#1589)
This addresses #1588 and creates an in_nse plot variable
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
commit 33fb30eec2ddc35106f42e78f376e7e114af9445
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 8 10:45:40 2021 -0800
Convert compute_avgstate to C++ (#1586)
This also merges most of the old-time and new-time code paths in make_radial_data since they were nearly identical.
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util_nd.F90
commit 092f1a57b2765d145383d4c569fedd182c3e24d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 8 06:26:52 2021 -0800
Revert "Use the async arena in CTU hydro (#1578)" (#1587)
This reverts commit 2c9b8a0da9a572900076e7c9f5c5bcd968550c65.
Source/hydro/Castro_ctu_hydro.cpp
commit b1067e18d55171c7c66361933cd84b34f1b1934b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 7 15:20:35 2021 -0500
some updates for reacting_convergence (#1577)
the original create_pretty_tables.py is now called
create_pretty_tables_suite.py -- this verion works on all of the output
from the different integrators and was used for the SDC paper
a single test create_pretty_tables.py was added -- this takes 2 outputs
from the RichardsonConvergenceTest program and makes either a latex or
plain text table
better refinement was added to probin
a 1024 test was added
a script merge_3_converge.sh was added -- this combines the output from
2 tables into a single table representing 5 different resolutions,
4 errors and 3 convergence rates.
Exec/reacting_tests/reacting_convergence/analysis/create_pretty_tables.py
Exec/reacting_tests/reacting_convergence/analysis/create_pretty_tables_suite.py
Exec/reacting_tests/reacting_convergence/analysis/merge_3_converge.sh
Exec/reacting_tests/reacting_convergence/convergence_strang.sh
Exec/reacting_tests/reacting_convergence/inputs.1024
Exec/reacting_tests/reacting_convergence/probin
commit 0d66dcaef400c1d4c96a1bfcd0063c26b30e70f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 7 08:17:33 2021 -0800
Abort if mass fraction is unphysical (#1379)
Source/driver/Castro.cpp
commit 34acb66d6609205ead81d5b10eec09ed0d21c443
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 7 10:05:36 2021 -0500
fix clean_state in true SDC advance (#1585)
the clean_state at the end of the update from node m to m+1 was operating on the wrong state. This fixes this to make it consistent.
Source/driver/Castro_advance_sdc.cpp
commit 6e6d148de41ab71daccced99ecd27025763b7052
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 3 21:57:54 2021 -0500
make U_cc threadprivate for OpenMP with SDC-4 (#1582)
Source/hydro/Castro_hydro.cpp
commit a0b8e77738be637e51c93824ab4ed9342590312c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 3 18:38:20 2021 -0800
Turn off reactions max solve level in test suite setup (#1581)
Exec/science/Detonation/inputs-collision.testsuite
commit 5e0a1b9cbc259f4dd17f5453ba59808b4da5c3ab
Merge: 24990728d 6e075fa7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 1 14:29:09 2021 -0500
Merge branch 'development' into main
commit 24990728dc5fef400148e4e45f33a9716e30c7df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 1 14:28:44 2021 -0500
update amrex and microphysics to 21.03
external/Microphysics
external/amrex
commit 6e075fa7bf50c12364ca032b3b5819edf77fd900
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 25 11:38:43 2021 -0500
use the burn_t in the eos call for nuclear dt estimation (#1579)
Source/driver/timestep.cpp
commit 2c9b8a0da9a572900076e7c9f5c5bcd968550c65
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 22 15:30:06 2021 -0800
Use the async arena in CTU hydro (#1578)
This functionality is added in AMReX-Codes/amrex#1804. By allocating the Fab data in the async arena, it is implicitly given the same lifetime that explicitly adding an elixir gave us.
Source/hydro/Castro_ctu_hydro.cpp
commit 9e6baa0b5d2dd2c3a9f3e4bfabff03000d8f1fc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 15 19:23:21 2021 -0500
port true SDC to the new e integration scheme for Microphysics (#1557)
this syncs with starkiller-astro/Microphysics#496 and starkiller-astro/Microphysics#550
Source/reactions/Castro_react_util.H
Source/sdc/Castro_sdc_util.H
Source/sdc/vode_rhs_true_sdc.H
commit 3cb0be81a77abb1180723ffc920b110c28b309f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 11 15:18:05 2021 -0500
update the initial model (#1574)
Exec/science/rotating_star/probin
commit 49bdb0b3f8e3d601de44a32c4bdf76579ce8446f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 10 20:22:01 2021 -0500
remove the mask for simplified SDC (#1570)
it is not clear it was actually doing anything useful
this also syncs us up with Strang
Source/reactions/Castro_react.cpp
commit 70c20339845d0d4a1b522e363324636ed79bab2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 10 15:46:23 2021 -0500
fix the check on whether we are in NSE for SDC in dtnuc_e (#1573)
the complication is that in_nse operating on a burn_t expects the data to come from
burn_t.y[] for simplified-SDC. So we need to use the eos_t interface instead.
Source/driver/timestep.cpp
commit c684c2ad1b2ff60021c51b002152b5385705285d
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Feb 9 18:31:38 2021 -0500
Ignore dtnuc_e if the region is in NSE (#1218)
This modifies the timestep calculation so that dtnuc_e is ignored if the region is in NSE.
Source/driver/timestep.cpp
commit 981c7bd93e3b1c8eaafde8e8a7d8698ce4f53494
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Feb 9 16:21:17 2021 -0500
switch massive star problem to use aprox19 and NSE (#1572)
Switches the rotating_star problem to use aprox19 and NSE
Exec/science/rotating_star/15m_500_sec.hse.6400
Exec/science/rotating_star/GNUmakefile
Exec/science/rotating_star/probin
commit e264704dd4648d9e9a7475ae61a444a434452743
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 19:31:51 2021 -0500
remove the old megafortran concatenation (#1569)
Exec/Make.Castro
commit 178e56fe3dd42dbddfacc83c6e14343d6db3ff82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 13:08:56 2021 -0500
pass reactive source for NSE+SDC (#1514)
Exec/reacting_tests/nse_test/convergence_simplified_sdc.sh
Exec/reacting_tests/nse_test/create_pretty_tables.py
Source/reactions/Castro_react.cpp
commit 521a12c3459ee4a60bbac84a7fc424292755f576
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 3 05:30:01 2021 -0800
Convert wdmerger to set extern parameters in the inputs (#1563)
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_mhd/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_relaxation/probin
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit feac3f27a0a1d10d97d90b15dda2755399012c8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 21:31:07 2021 -0500
fix an implicit capture of this with USE_SIMPLIFIED_SDC (#1565)
Source/reactions/Castro_react.cpp
commit 4c42e995d49e83df159b398a5078d159934ec7f6
Author: jmsexton03 <jmsexton@lbl.gov>
Date: Tue Feb 2 14:42:14 2021 -0800
Replace AMREX_USE_CUDA => AMREX_USE_GPU (#1566)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_generic_fill.H
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
commit 9a544ededf9c5bdc98263a44b7ec068a2b28ca0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 10:27:01 2021 -0500
Fortran cleaning (#1561)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/prob_params_nd.F90
commit 79d33b3d8ed7477b1b0479003c75e3cd0d9f3420
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 1 13:26:05 2021 -0500
remove amrinfo module (#1562)
this is no longer needed
Exec/hydro_tests/rotating_torus/Prob.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/amrinfo_nd.F90
commit b154d09e18699e0d73eaab2fa4e696cf5b427cf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 1 13:23:37 2021 -0500
Extra thermo hack (#1560)
Exec/Make.Castro
commit d498bc1b65cb77f887c5a250e0a9fb6c91650994
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 1 11:42:42 2021 -0500
update AMReX and Microphysics to 21.02
external/Microphysics
external/amrex
commit 62a6112d9cd65946cf219c6ff72fc74ed97102af
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 30 07:41:22 2021 -0800
Use eos_re_t in places where it is sufficient (#1559)
Source/driver/Castro.cpp
Source/radiation/MGFLD.cpp
Source/radiation/Radiation.cpp
commit e5caa15ee6fd44579dc748006e7f8a1d9f5fdfd5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 20:03:36 2021 -0500
remove the old regression test stuff (#1558)
we have a separate repo for this now
Util/regression_testing/boxlib/Castro-SBU-tests.ini
Util/regression_testing/boxlib/Castro-tests.ini
Util/regression_testing/hash_pairings.txt
Util/regression_testing/test_pairings.py
commit 058adcc4229d0bc687f5de527567ac8bad3d9c45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 11:40:55 2021 -0500
fix the error checking on the axisymmetric geom term (#1556)
this also adds an abort if we try to use the new geometry term with state_in_rotating_frame=0
CHANGES.md
Exec/science/rotating_star/probin.sdc_test
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/sources/Castro_geom.cpp
commit e3129816ffd0194f3b1ab1eca54cb74037298dcc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 24 10:42:20 2021 -0800
Add RadBlastWave test from Castro paper II (#1555)
This is from section 6.9 and 6.10 of the gray radiation paper. Closes #1525.
Exec/radiation_tests/RadBlastWave/GNUmakefile
Exec/radiation_tests/RadBlastWave/Make.package
Exec/radiation_tests/RadBlastWave/README.md
Exec/radiation_tests/RadBlastWave/_prob_params
Exec/radiation_tests/RadBlastWave/inputs.1d
Exec/radiation_tests/RadBlastWave/inputs.2d
Exec/radiation_tests/RadBlastWave/inputs.3d
Exec/radiation_tests/RadBlastWave/inputs.3d.test
Exec/radiation_tests/RadBlastWave/inputs.kp
Exec/radiation_tests/RadBlastWave/inputs.kp.2d
Exec/radiation_tests/RadBlastWave/probin.1d
Exec/radiation_tests/RadBlastWave/probin.2d
Exec/radiation_tests/RadBlastWave/probin.3d
Exec/radiation_tests/RadBlastWave/probin.3d.test
Exec/radiation_tests/RadBlastWave/probin.kp
Exec/radiation_tests/RadBlastWave/probin.kp.2d
Exec/radiation_tests/RadBlastWave/problem_initialize.H
Exec/radiation_tests/RadBlastWave/problem_initialize_rad_data.H
Exec/radiation_tests/RadBlastWave/problem_initialize_state_data.H
commit b029b0a6d585ff16150e8fdc57c29f68403dc488
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 24 10:39:58 2021 -0800
Convert estimate_gamrPr to C++ (#1554)
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
commit ae79f3cd80188ed901c4e277e09fa1c0a09e48bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 12:58:02 2021 -0500
add axisymmetric geometric sources (#923)
In axisymmetric geometry, there are additional forces that arise due to the changing direction of the unit vectors in the div{rho U U} term. The paper by Bernand-Champmartin discusses this. See issue #913. Note that the way we handle the Coriolis force for 2-d axisymmetry is already consistent with a righthanded coordinate system even though we order the state as (r, z, theta).
Note: at the moment, this is not compatible with the idea from Byerly et al. to do rotation with the state data in the inertial frame, but that is off by default.
CHANGES.md
Source/driver/Castro.H
Source/driver/_cpp_parameters
Source/sources/Castro_geom.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Make.package
commit 4bcb5ab223f8940adfb38ee612e630edc3e8cbab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 12:56:09 2021 -0500
update the names of the small plot variables (#1553)
enuc is now a derived variable
the species are now in caps
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.1000Hz.3d
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
Exec/science/flame_wave/inputs_He/inputs.noboost.3d
commit af3a8490752da060ae800739b38967f726adb9ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 18:24:12 2021 -0500
enable Jacobian caching for the flame_wave always (#1551)
experiments on Summit show that we get about a 20% speed up when we
turn on Jacobian caching in the integrator. It is off by default on
GPUs to save memory.
Exec/science/flame_wave/GNUmakefile
commit 799457e632ffbfc9800aac82c0ecc18be934429e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 22 15:09:29 2021 -0800
Hardcode oversubscription threshold at 10 MB (#1552)
Source/hydro/Castro_ctu_hydro.cpp
commit c732b48cd46721eb05c2d58f8b7aa857eae6ef9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 22 09:50:52 2021 -0800
Move C++ probinit and prob params to buildMetrics (#1549)
Currently in C++, problem_initialize() and the read of the C++ parameters is not happening on a restart (as well as the setting of the C++ ambient data, the proximal cause for the issue in #1548). Moving to buildMetrics() fixes this, as it is also done on a restart.
Source/driver/Castro.cpp
commit 45418ecfd67e448690fe238a60e0725e60e6185e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 11:34:40 2021 -0500
fix compilation for cases where we have a Fortran RHS in the network (#1550)
Source/driver/timestep.cpp
commit a35f139ff634f8103f15fef83ab8ed12b27eec28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 20:47:20 2021 -0500
remove the RadSlope problem (#1540)
it doesn't seem to do anything and we don't have any notes about
its original purpose
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSlope/Make.package
Exec/radiation_tests/RadSlope/Prob_nd.F90
Exec/radiation_tests/RadSlope/_prob_params
Exec/radiation_tests/RadSlope/inputs
Exec/radiation_tests/RadSlope/probin
commit 29105d71ad152ffb07707d085b388cb2b29266bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 19:24:04 2021 -0500
clean up the various flame_wave inputs and probin files (#1547)
We now have separate directories for the He and H/He flames and get rid of redundant probin files. This also removes all of the boosted inputs, since we no longer run boosted.
Exec/science/flame_wave/README.md
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He
Exec/science/flame_wave/inputs_H_He/probin.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.2000Hz
Exec/science/flame_wave/inputs_He/inputs.He.1000Hz
Exec/science/flame_wave/inputs_He/inputs.He.250Hz
Exec/science/flame_wave/inputs_He/inputs.He.25cm.1000Hz.3d
Exec/science/flame_wave/inputs_He/inputs.He.500Hz
Exec/science/flame_wave/inputs_He/inputs.noboost.3d
Exec/science/flame_wave/inputs_He/probin.He
Exec/science/flame_wave/inputs_He/probin.He.25cm
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_boost/probin.boost_10_10
Exec/science/flame_wave/inputs_boost/probin.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/probin.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/probin.boost_5_5
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.250Hz
Exec/science/flame_wave/probin.H_He
Exec/science/flame_wave/probin.noboost
Exec/science/flame_wave/probin.noboost.1000Hz
commit 0bb7eb6b57eb5dd88b18502bc5457ec5fd3137c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 12:56:56 2021 -0500
remove vestigial Fortran (#1546)
Source/driver/Castro_F.H
Source/sdc/Castro_sdc_F.H
Source/sdc/Make.package
commit f91aa80fb2276bf68b7e6613fb5cdbc720864fcf
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Jan 20 11:36:11 2021 -0500
Convert SDC to C++ (#1208)
Converts all of the "true" SDC code paths to C++. This integrates with the C++ VODE solver in Microphysics (if you are using VODE for the SDC solver). For most of the test problems the agreement is O(1.e-8) or better. bubble_convergence and reacting_convergence converge as 4th order, as expected. You now need to specify that you want to use the numerical Jacobian for the VODE solver via integrator.jacobian=2 (it no longer uses castro.sdc_use_analytic_jac -- that only applies to the Newton solver). The 4th order detonation problem is very sensitivity (and it is probably not a good idea to do a detonation 4th order because it is so discontinuous), and it works best with the numerical Jacobian + VODE.
Co-authored-by: Michael Zingale <michael.zingale@stonybrook.edu>
Co-authored-by: Max Katz <maxpkatz@gmail.com>
Exec/science/flame/probin.sdc
Exec/science/rotating_star/inputs_2d.nse
Source/driver/_cpp_parameters
Source/driver/timestep.cpp
Source/reactions/Castro_react_util.H
Source/reactions/Make.package
Source/reactions/react_util.F90
Source/sdc/Castro_sdc.cpp
Source/sdc/Castro_sdc_util.H
Source/sdc/Make.package
Source/sdc/sdc_util_nd.F90
Source/sdc/sdc_vode_nd.F90
Source/sdc/vode_rhs_true_sdc.H
commit 0cc2d208d911ef5cbbd921de7d4f948dfa75efce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 10:14:02 2021 -0500
convert LoopAdvection to C++ (#1545)
Exec/mhd_tests/LoopAdvection/Prob_mhd_nd.F90
Exec/mhd_tests/LoopAdvection/Prob_nd.F90
Exec/mhd_tests/LoopAdvection/problem_initialize.H
Exec/mhd_tests/LoopAdvection/problem_initialize_mhd_data.H
Exec/mhd_tests/LoopAdvection/problem_initialize_state_data.H
commit 50208e72f2a260436132e3c8537f1caca82b1f73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 10:11:04 2021 -0500
convert Alfven to C++ (#1543)
Exec/mhd_tests/Alfven/Prob_mhd_nd.F90
Exec/mhd_tests/Alfven/Prob_nd.F90
Exec/mhd_tests/Alfven/problem_initialize.H
Exec/mhd_tests/Alfven/problem_initialize_mhd_data.H
Exec/mhd_tests/Alfven/problem_initialize_state_data.H
commit b273ad5837c50f07c30600f55de7599388f04c18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 10:07:31 2021 -0500
convert RadSuOlsonMG to C++ (#1536)
Exec/radiation_tests/RadSuOlsonMG/Prob_nd.F90
Exec/radiation_tests/RadSuOlsonMG/problem_initialize.H
Exec/radiation_tests/RadSuOlsonMG/problem_initialize_rad_data.H
Exec/radiation_tests/RadSuOlsonMG/problem_initialize_state_data.H
commit e2400afe64c2446033a3fe33f55b01756ef66ba4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 10:06:44 2021 -0500
convert RadThermalWave to C++ (#1537)
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/problem_initialize.H
Exec/radiation_tests/RadThermalWave/problem_initialize_rad_data.H
Exec/radiation_tests/RadThermalWave/problem_initialize_state_data.H
commit f440e72153c4fbade049ae7d32392ed9e653363d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 09:57:42 2021 -0500
RadShestakovBolstad to C++ (#1535)
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
Exec/radiation_tests/RadShestakovBolstad/problem_initialize.H
Exec/radiation_tests/RadShestakovBolstad/problem_initialize_rad_data.H
Exec/radiation_tests/RadShestakovBolstad/problem_initialize_state_data.H
commit fae03fc93170c8d8d84a0811d716fbc1233f01a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 11:57:05 2021 -0500
fix the data type of parameter in probin (#1544)
Exec/reacting_tests/bubble_convergence/probin.32
commit 2adda1e857d26bf21941f329a7bda0876ff02bb6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 16 15:30:47 2021 -0800
AMReX now calls HYPRE_init() so we don't have to (#1541)
We also update to use the AMReX GNU make package for Hypre instead of doing it on our own.
Exec/Make.Castro
Source/driver/main.cpp
commit 8b08d83b885b1c2f41d7b6937be4d6e618f50cd4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 15 17:52:57 2021 -0800
Document that CUDA build of Hypre now requires recent code (#1542)
Docs/source/radiation.rst
commit 5fd0ec0cd97fa20ed9cccb89642cea69cdba5255
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 13 09:02:49 2021 -0500
convert RadSphere to C++ (#1533)
Exec/radiation_tests/Rad2Tshock/problem_initialize_rad_data.H
Exec/radiation_tests/RadBreakout/problem_initialize_rad_data.H
Exec/radiation_tests/RadFront/problem_initialize_rad_data.H
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/radiation_tests/RadSphere/problem_initialize.H
Exec/radiation_tests/RadSphere/problem_initialize_rad_data.H
Exec/radiation_tests/RadSphere/problem_initialize_state_data.H
Exec/radiation_tests/RadSuOlson/problem_initialize_rad_data.H
Exec/reacting_tests/reacting_convergence/convergence_simplified_sdc.sh
Exec/science/bwp-rad/problem_initialize_rad_data.H
Source/driver/Castro.cpp
Source/problems/problem_initialize_rad_data.H
commit 9799defd04f1d68bfe1da8d4f2734cef111901a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 12 22:25:28 2021 -0500
fix a comment warning during compilation (continuation) (#1530)
Exec/science/flame_wave/initial_model.H
commit 85592708a033e8853c0a783288c578a87c0c1c45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 11 22:14:18 2021 -0500
some work on centraliing the prob params script (#1529)
This uses a lot of the Microphysics runtime_parameters.py stuff
Exec/Make.auto_source
Exec/gravity_tests/DustCollapse/_prob_params
Exec/gravity_tests/hydrostatic_adjust/_prob_params
Exec/hydro_tests/acoustic_pulse/_prob_params
Exec/hydro_tests/acoustic_pulse_general/_prob_params
Exec/reacting_tests/reacting_convergence/_prob_params
Exec/science/Detonation/_prob_params
Exec/science/flame/_prob_params
Exec/science/wdmerger/_prob_params
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit 1ece4d9629b724a5ffd45ec9ab077d5eb1eaa0b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 14:55:42 2021 -0500
remove testsuite-specific probin for sedov that just changed gamma (#1528)
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/probin.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/probin.3d.sph.testsuite
commit 2aa520cbe9c1cfa7fa3173eee6b6b7e3f008182e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 10:31:20 2021 -0500
add the ability to set Microphysics parameters in inputs/C++
CHANGES.md
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
commit e3318bd9bbfae2f3d68f43b68240af6495f56b33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 04:30:37 2021 -0500
remove the extern_probin.template (#1526)
we can use the default Microphysics one
Exec/Make.auto_source
Source/driver/extern_probin.template
commit ef03b057b2ffb961fb25285123c0b0a53d550d87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 9 14:02:31 2021 -0500
reasses which runtime parameters are needed in Fortran (#1524)
Source/driver/_cpp_parameters
commit dd784d01f560bd663e8c9d3af64455ed75805ddb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 9 13:19:19 2021 -0500
update the way we handle Fortran strings in meth_params (#1523)
this syncs up with Microphysics PR 525
Source/driver/extern_probin.template
Source/driver/meth_params.template
Source/driver/parse_castro_params.py
commit 659fe175cafcdc758705ba2a0203aee858f4a5f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 8 13:00:33 2021 -0500
update docs to reflect no more findparams.py (#1522)
Docs/source/rp_intro.rst
commit f5e98ab0010d99dde258237c6c2223032ed29b88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 8 12:43:58 2021 -0500
some cleaning of the nse_convergence scripts (#1513)
Exec/reacting_tests/nse_test/convergence_strang.sh
Exec/reacting_tests/nse_test/create_pretty_tables.py
Exec/science/Detonation/nse_runs/inputs.template.simple_sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/nse_runs/inputs.template.true_sdc
Exec/science/Detonation/nse_runs/setup_runs.py
Exec/science/Detonation/nse_runs/show_status.py
commit 2c735f53c72a24956e3e944c60e057acf76526f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 8 12:38:09 2021 -0500
remove the old convergence stuff -- this never was used (#1519)
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
Exec/science/flame/convergence_strang.sh
Exec/science/flame/extract.sh
Exec/science/flame/inputs.1d.aprox13.boost
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.512
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc2.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc4.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.strang.slurm
Exec/science/flame/probin.boost
Exec/science/flame/test_conv.sh
Exec/science/flame/test_sdc2.sh
Exec/science/flame/test_sdc4.sh
commit 67500bf2de5ce04858bee770d14dd646b6d37d4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 8 12:37:31 2021 -0500
hook into the Microphysics runtime_parameters.py (#1521)
Exec/Make.auto_source
Source/driver/parse_castro_params.py
commit 80465fd56d2beac5e72ed37b6c4196463bd8fa4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 11:56:13 2021 -0500
update format to match Microphysics changes (#1520)
This syncs us up with starkiller-astro/Microphysics#510
In particular, we no longer make things private, since we were marking everything public anyway.
Source/driver/extern_probin.template
commit 3f416dcc0235c9122ba60fc7d6b098e0bdb0988c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 5 17:38:57 2021 -0500
fix CUDA 11 + Hypre linking (#1518)
Exec/Make.Castro
commit 82757e16b6cb7ba330484021de70ce9beff6eb17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 3 14:58:11 2021 -0500
remove the SDC defines (#1515)
these are now handled for us by Make.Microphysics_extern
Exec/Make.Castro
commit 8b1edb570dc5862b20ffe7637d12f110a7303dad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 3 14:56:56 2021 -0500
port radfront to C++ (#1516)
Exec/radiation_tests/RadFront/Prob_nd.F90
Exec/radiation_tests/RadFront/README.md
Exec/radiation_tests/RadFront/problem_initialize.H
Exec/radiation_tests/RadFront/problem_initialize_rad_data.H
Exec/radiation_tests/RadFront/problem_initialize_state_data.H
commit 94180bde14a492dee119fc51748ea9a38cc454ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 3 14:51:14 2021 -0500
we don't need the class name in the _cpp_parameters (#1517)
they are no longer class members
Source/driver/_cpp_parameters
Source/driver/parse_castro_params.py
commit 3edb69ff9100ce72398b7650769e69556c23856c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 2 14:36:28 2021 -0500
update amrex and Microphysics to 21.01
external/Microphysics
external/amrex
commit fe3e9c8de85ef8ff0d4040caf237d6a93f653daf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 27 18:41:47 2020 -0500
simplify how we set the aux data in reacting_convergence (#1512)
Exec/reacting_tests/reacting_convergence/problem_initialize_state_data.H
commit d9afbedb2367993e12a2040f4e0d853170edca88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 27 14:45:56 2020 -0500
reacting_convergence script cleaning (#1511)
make the number of SDC iterations a script variable
Exec/reacting_tests/reacting_convergence/convergence_simplified_sdc.sh
commit 0e6ad81e813a01c25061684b61a8ce4b343f3181
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 25 13:15:40 2020 -0500
update the docs and scripts for bubble_convergence (#1478)
The bubble_convergence problem tests the 4th order SDC convergence with hydro, reactions, gravity, and reflecting BCs. It was shown in the Castro SDC paper. This PR updates the documentation to explain how to run it locally. It also fixes the main convergence script -- it was measuring the convergence at the midpoint in time and not at the end of the simulation, so it didn't agree with what was in the paper. With these updates, we get the same convergence that was printed in the paper. Finally, we add a 32^2 problem to explore the convergence at even lower resolution.
Exec/reacting_tests/bubble_convergence/README.md
Exec/reacting_tests/bubble_convergence/converge_test.sh
Exec/reacting_tests/bubble_convergence/create_pretty_tables.py
Exec/reacting_tests/bubble_convergence/inputs_2d.32
Exec/reacting_tests/bubble_convergence/probin.32
commit 303af2b0efc23f8b133a6bc0c615b73881798662
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 25 06:29:21 2020 -0800
Remove noexcept from ParallelFor lambda (#1507)
This works around an nvcc issue with -std=c++17.
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive.cpp
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.cpp
Exec/radiation_tests/RadSphere/Problem_Derive.cpp
Exec/radiation_tests/RadThermalWave/Problem_Derive.cpp
Exec/reacting_tests/reacting_bubble/Problem_Derive.cpp
Exec/reacting_tests/toy_flame/Prob.cpp
Exec/science/Detonation/Prob.cpp
Exec/science/flame/Prob.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/unit_tests/diffusion_test/Problem_Derive.cpp
Source/diffusion/diffusion_util.cpp
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Derive.cpp
Source/driver/MGutils.cpp
Source/driver/sum_utils.cpp
Source/driver/timestep.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_rad.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/edge_util.cpp
Source/hydro/flatten.cpp
Source/hydro/fourth_center_average.cpp
Source/hydro/fourth_order.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/hydro/trans.cpp
Source/mhd/Castro_mhd.cpp
Source/mhd/ct_upwind.cpp
Source/mhd/electric.cpp
Source/mhd/hlld.cpp
Source/mhd/mhd_plm.cpp
Source/mhd/mhd_ppm.cpp
Source/mhd/mhd_util.cpp
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Castro_problem_source.cpp
Source/problems/ambient_fill.cpp
Source/problems/hse_fill.cpp
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit 85afa84ee25d7ae0a4535c175947bedb4e8ed1dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 24 07:19:41 2020 -0800
Fix particles test (#1510)
Closes #1505
Exec/unit_tests/particles_test/Make.package
Exec/unit_tests/particles_test/Prob.cpp
Exec/unit_tests/particles_test/Prob_nd.F90
Exec/unit_tests/particles_test/_prob_params
Exec/unit_tests/particles_test/probdata.F90
commit abdaf4afcaae4cb181eeacb0200d3b83e9c22a11
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 24 07:18:08 2020 -0800
Add diagnostics for AMR driver (#1508)
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/driver/Castro.cpp
Source/driver/sum_integrated_quantities.cpp
commit e125a396d127cd6d02dd75ebb2ba9de3587f89c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 24 07:17:08 2020 -0800
Fix particles parameters (#1509)
Closes #1258
Source/particles/CastroParticles.cpp
commit 533748950889f6ee83ca6954d124f06435f7bcb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 15:14:13 2020 -0800
Update to C++17 as minimum standard (#1506)
C++17 is now the minimum supported standard for Castro. 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
Docs/source/getting_started.rst
Exec/Make.Castro
commit 5fdb3cf55388f3992d1e749a4d2c9e4b4e11c17c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 22 20:47:35 2020 -0500
update the detonation suite for testing integrators (#1502)
This removes the old sdc_tests directory and updates nse_runs so that it can test Strang, simplified-SDC, and true SDC
all on the same problem.
Exec/science/Detonation/nse_runs/detonation.py
Exec/science/Detonation/nse_runs/inputs.template.simple_sdc
Exec/science/Detonation/nse_runs/inputs.template.true_sdc
Exec/science/Detonation/nse_runs/make_plots.py
Exec/science/Detonation/nse_runs/probin-det-x.nse_disabled
Exec/science/Detonation/nse_runs/setup_runs.py
Exec/science/Detonation/nse_runs/show_status.py
Exec/science/Detonation/sdc_tests/make_plots.py
Exec/science/Detonation/sdc_tests/setup_runs.sh
commit c210671b8ab935952862a7c3bfe5d52bbf70a4df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 22 20:43:53 2020 -0500
remove the old model parser and document the C++ one (#1477)
closes #852
Docs/source/creating_a_problem.rst
Docs/source/software.rst
Exec/Make.Castro
Util/model_parser/Make.package
Util/model_parser/model_parser.F90
commit 40553aff5353c2d0b642a5061d1134f4b7b4fd67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 22 20:30:30 2020 -0500
convert bubble_convergence to C++ (#1476)
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/bubble_convergence/Make.package
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/_prob_params
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/initial_model.H
Exec/reacting_tests/bubble_convergence/probin.128
Exec/reacting_tests/bubble_convergence/probin.128.nopert
Exec/reacting_tests/bubble_convergence/probin.256
Exec/reacting_tests/bubble_convergence/probin.256.nopert
Exec/reacting_tests/bubble_convergence/probin.512
Exec/reacting_tests/bubble_convergence/probin.64
Exec/reacting_tests/bubble_convergence/probin.64.nopert
Exec/reacting_tests/bubble_convergence/problem_initialize.H
Exec/reacting_tests/bubble_convergence/problem_initialize_state_data.H
commit a334e46b633558286909ff05ea56ed03b71bb619
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 22 20:21:40 2020 -0500
convert LWAcoustics to C++ (#1498)
Exec/hydro_tests/Vortices_LWAcoustics/Prob_nd.F90
Exec/hydro_tests/Vortices_LWAcoustics/problem_initialize.H
Exec/hydro_tests/Vortices_LWAcoustics/problem_initialize_state_data.H
commit 970e2d581863c77742a6ee50b86658b486ed421e
Merge: d7bf4a186 56db4fdc7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 21 08:23:57 2020 -0500
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit d7bf4a186ea8265179bce71114867869bbdd268a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 21 08:23:02 2020 -0500
update to include the true SDC runs
Exec/science/Detonation/nse_runs/show_status.py
commit 56db4fdc7138316453b0badc195c2b39862f2105
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 20 23:19:17 2020 -0500
Extern findparams (#1503)
get rid of the findparams.py for finding the _parameters files and instead do it in make
Exec/Make.auto_source
commit 11ecaddf114f8a417276bcccd0d64c5021cdd9db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 20 23:18:25 2020 -0500
remove the riemann_test_zone problem (#1504)
we never really used this anymore
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/riemann_test_zone/Make.package
Exec/hydro_tests/riemann_test_zone/Prob_nd.F90
Exec/hydro_tests/riemann_test_zone/README
Exec/hydro_tests/riemann_test_zone/_prob_params
Exec/hydro_tests/riemann_test_zone/inputs.2d
Exec/hydro_tests/riemann_test_zone/probin
commit caef5d5269c95ff74e41061c699ae1a72a0de592
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 20 18:32:33 2020 -0500
allow for multiple _prob_param files (#1500)
we now search all of the Castro source directories
the problem's own parameters are always parsed last.
We also get rid of _default_prob_params in Source/problems and just treat it like
any other _prob_params file.
CHANGES.md
Exec/Make.auto_source
Source/problems/_prob_params
Util/scripts/write_probdata.py
commit 341bdc26dca07f992e0202adce1997bef452da1a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 20 10:00:19 2020 -0800
Remove the dtnuc_T timestep limiter (#1501)
This was added as an experiment but was never used in production and is mostly redundant with the dtnuc_e limiter.
CHANGES.md
Source/driver/_cpp_parameters
Source/driver/timestep.cpp
commit 7fdbe8ba01642ebdc7b34d4f87ad7acee8de9835
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 19 20:00:38 2020 -0500
clarify some of the SDC parameter docs (#1499)
Source/driver/_cpp_parameters
commit de0a5fc1169314a2b716a93756772d308aa7f739
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 13:12:11 2020 -0800
Add species diagnostics to sum_integrated_quantities (#1496)
This is copied from wdmerger.
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/driver/Castro.cpp
Source/driver/sum_integrated_quantities.cpp
commit 0410c073662fcaf9125bf98a20004489b6c5619e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 17 20:28:51 2020 -0500
convert uniform_cube_sphere to C++ (#1495)
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/problem_initialize.H
Exec/gravity_tests/uniform_cube_sphere/problem_initialize_state_data.H
commit 6ddb631565b7df151a5dc7cda5bc53ba705aa5e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 17 16:45:29 2020 -0800
Fix uniform cube problem namespace issues (#1489)
Closes #1487
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
commit 4368a82a4a152a89d21bde61724ad735bdb85ef2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 17 14:57:35 2020 -0500
fix true SDC-2 with reactions (#1494)
we were passing the wrong array into the nonlinear solve
closes #1492
CHANGES.md
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Source/sdc/sdc_util_nd.F90
commit e57fbd9ded90b120ac220ac9a0fa636a2cb6614e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 17 12:04:22 2020 -0500
fix the node weights for Radau SDC (#1493)
we were resetting them to Simpsons rule
Source/driver/Castro_setup.cpp
commit 26e30a1997c98842382ead0f2d3b46023bb6223a
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Dec 16 14:19:17 2020 -0500
Add an action to test GPU compilation (#1491)
This adds another action which will compile the code using the USE_CUDA=TRUE flag
.github/workflows/c-linter.yml
.github/workflows/gpu_action.yml
commit 98955364a3ae4f69377e836b1fa112ec47d2f5f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 16 11:18:45 2020 -0800
Remove remaining references to GPU pragma/PGI compiler requirements (#1490)
CHANGES.md
Docs/source/build_system.rst
Docs/source/mpi_plus_x.rst
Docs/source/radiation.rst
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Source/driver/amrinfo_nd.F90
Source/driver/meth_params.template
Source/driver/parse_castro_params.py
Source/driver/prob_params_nd.F90
Source/problems/Prob_nd.F90
Source/problems/ambient_nd.F90
Source/problems/ext_src_nd.F90
Source/problems/problem_tagging_nd.F90
Source/radiation/fluxlimiter.F90
Source/radiation/rad_params.F90
Source/radiation/rad_util_nd.F90
Source/reactions/react_util.F90
Source/rotation/Rotation_frequency.F90
Source/sdc/sdc_util_nd.F90
Source/sources/sponge_nd.F90
Util/model_parser/model_parser.F90
Util/scripts/write_probdata.py
commit d8e2087acd753a671c90f76ff8949f753bbad35d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 16 04:58:50 2020 -0800
Only calculate GW strain if user requests (#1488)
The user must ask for an observation distance (in kpc) greater than zero if they want the strain calculated.
Closes #1480
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/tde/inputs.test
Source/driver/_cpp_parameters
Source/driver/sum_utils.cpp
commit 88230042d5f75f0b1ea29605d1383626febe3a79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 15 13:44:32 2020 -0500
update README.md docs location (#1486)
README.md
commit 52f32998fddd1afacf9b2ddda0cfc2fb1aa01dd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 15 08:19:09 2020 -0500
convert flame to C++ (#1485)
Exec/science/flame/Prob_nd.F90
Exec/science/flame/problem_initialize.H
Exec/science/flame/problem_initialize_state_data.H
commit 02e42cf1b51e2de5dc471d09aa182565d69a0882
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 15 08:12:48 2020 -0500
remove some more unused radiation functions (#1484)
Source/radiation/Make.package
Source/radiation/Rad_nd.F90
Source/radiation/blackbody.F90
commit b84d2c2d45ad084b6cff53efd72f946f3d00ce6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 14 20:21:42 2020 -0500
convert Rad2Tshock to C++ (#1483)
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/problem_initialize.H
Exec/radiation_tests/Rad2Tshock/problem_initialize_rad_data.H
Exec/radiation_tests/Rad2Tshock/problem_initialize_state_data.H
commit 3e60fe275f382a9605c87cab01c88764314e72f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 14 14:24:27 2020 -0500
turn off sum_interval diagnostics (#1482)
we never looked at these, and they just waste flops
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.250Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/scaling/3d_science/inputs.noboost.25cm.1000Hz.3d
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
commit adebaff5a1b7036719c4a067dc7a0478e78d39a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 14 14:23:32 2020 -0500
disable the sum_interval diagnostics for this problem (#1481)
this gets around issue #1479
Exec/reacting_tests/bubble_convergence/inputs_1d.well_balance
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/inputs_2d.well_balance
commit c355f2e65a7674adaab104951568465c13ed16c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 13 15:15:17 2020 -0500
remove unused code (#1475)
Source/driver/Castro_util_nd.F90
Source/radiation/HABEC_nd.F90
Source/radiation/Make.package
commit 01048f112435ffdbd34ce95e119761184d908a04
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 11:00:15 2020 -0800
Convert rad_source to C++ (#1474)
The new C++ name is problem_rad_source. For now we leave the Fortran interface, however we should remove it when we remove the other Fortran problem interfaces.
Exec/radiation_tests/RadSuOlsonMG/problem_rad_source.H
Exec/radiation_tests/RadSuOlsonMG/rad_source.F90
Source/problems/Make.package
Source/problems/problem_rad_source.H
Source/radiation/RadSolve.cpp
Source/radiation/rad_source.F90
commit dba73f7ec9b92d4f435935aa6c2e9f282c7d7960
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 13 13:16:40 2020 -0500
convert evrard_collapse to C++ (#1470)
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
Exec/gravity_tests/evrard_collapse/problem_initialize.H
Exec/gravity_tests/evrard_collapse/problem_initialize_state_data.H
commit 4ed9e53857e040f766712ee40c4986966a3f82a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 10:15:45 2020 -0800
Convert set_abec_flux to C++ (#1472)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/RadSolve.cpp
commit 3518c4c98dc9b16c1364f562121bc43296ca26b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 09:31:21 2020 -0800
Convert laceofmgfld to C++ (#1473)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 557521f57f90709331c0ff39eba28eab65d35b6e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 05:28:01 2020 -0800
Fix misplaced ifdef from #1460 (#1471)
Source/driver/sum_integrated_quantities.cpp
commit 002d49072a723ba96fd97f4a56a35da121756c89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 13 08:21:41 2020 -0500
convert planet to C++ (#1469)
Note: we currently don't build on development, because of the variable size of xloc_vortices on GPU -- this is fixed
in the port.
Exec/science/planet/GNUmakefile
Exec/science/planet/Prob_nd.F90
Exec/science/planet/_prob_params
Exec/science/planet/probin
Exec/science/planet/problem_initialize.H
Exec/science/planet/problem_initialize_rad_state.H
Exec/science/planet/problem_initialize_state_data.H
commit a58ca368443d06fc52b202f551ed9598c31b2e7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 12 11:46:42 2020 -0500
remove reactions_driver_test since we never used it (#1468)
Docs/source/problem_setups.rst
Exec/unit_tests/reactions_driver_test/GNUmakefile
Exec/unit_tests/reactions_driver_test/Make.package
Exec/unit_tests/reactions_driver_test/Prob_nd.F90
Exec/unit_tests/reactions_driver_test/README.md
Exec/unit_tests/reactions_driver_test/inputs.ignition.16
Exec/unit_tests/reactions_driver_test/make_react_model.py
Exec/unit_tests/reactions_driver_test/model.ignition_simple.16
Exec/unit_tests/reactions_driver_test/probdata.F90
Exec/unit_tests/reactions_driver_test/probin.ignition.16
Exec/unit_tests/reactions_driver_test/xin.ignition.16
commit d6f0d55fd5c24a5e81b212cba423bb208f9186b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 12 11:36:34 2020 -0500
update to the new sphinxcontrib-bibtex requirements (#1467)
Docs/source/conf.py
Docs/source/creating_a_problem.rst
commit 1076ace0028eda31075915a7c4acb5f1fa1a4f2f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 08:20:01 2020 -0800
Convert xrb_mixed to new problem diagnostics scheme (#1459)
Exec/science/xrb_mixed/inputs_2d
Exec/science/xrb_mixed/problem_diagnostics.H
Exec/science/xrb_mixed/problem_initialize.H
Exec/science/xrb_mixed/sum_integrated_quantities.cpp
commit 38908e4e0cbda7e404e9404527841a9d1ff387fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 08:16:40 2020 -0800
Move gravitational wave strain calculation to main diagnostic sums (#1460)
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/probin
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
commit 619643904ee9f8866d60061911711283867c0019
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 07:54:24 2020 -0800
Convert lrhs to C++ (#1466)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 5c95384cf010e951a045f593f7a6b0d9337a6772
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 17:24:59 2020 -0800
Convert dcoefs to C++ (#1465)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 87f81695523a10b7a29f70021f059535e69fc3f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 15:00:17 2020 -0800
Convert hmmat3 to C++ (#1464)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
commit 1c7de36719c67ea967f137e34ad2279ed95ff6b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 15:54:00 2020 -0500
convert model_burner to C++ (#1457)
Exec/unit_tests/model_burner/GNUmakefile
Exec/unit_tests/model_burner/Prob_nd.F90
Exec/unit_tests/model_burner/problem_initialize.H
commit b71ed8e1012a62927bdb55788131e8822c908b2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 12:53:42 2020 -0800
Convert toy_flame to new problem diagnostics scheme (#1458)
Exec/reacting_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/reacting_tests/toy_flame/inputs.1d
Exec/reacting_tests/toy_flame/inputs.1d.testsuite
Exec/reacting_tests/toy_flame/problem_diagnostics.H
Exec/reacting_tests/toy_flame/problem_initialize.H
Exec/reacting_tests/toy_flame/sum_integrated_quantities.cpp
commit 0c7e57e8642456c39e4013f5734aa2e442936c5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 10:52:15 2020 -0800
Convert hmmat to C++ (#1462)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
commit d4438314a9711bc3bfeaa16f114adf8d212a261a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 04:38:18 2020 -0800
Fix access to radiation member xnu (#1463)
xnu is not a static class member.
Source/driver/Castro.cpp
commit 9111587c10ee1f0ad9cc5a58edc892214b1cfc33
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 04:37:38 2020 -0800
Only IO processor should open diag files (#1461)
Exec/hydro_tests/test_convect/problem_initialize.H
Exec/hydro_tests/toy_convect/problem_initialize.H
commit dca42c1dfd38144ff2475aba96577eecc4a625cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 10 08:13:39 2020 -0500
convert bwp to C++ (#1456)
Exec/gravity_tests/hse_convergence/initial_model.H
Exec/science/bwp-rad/GNUmakefile
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/bwp-rad/problem_initialize.H
Exec/science/bwp-rad/problem_initialize_rad_data.H
Exec/science/bwp-rad/problem_initialize_state_data.H
commit fcd7abe17e2f7f3bd0ebc734fb62930ab8877694
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 10 00:21:51 2020 -0500
remove unused variables (#1455)
Source/driver/Castro.cpp
commit 60ba1748720600728fc89054cf5fa62ed8dea7a9
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 08:22:38 2020 -0800
Move wdmerger initial model constructor to model_parser (#1454)
The isothermal initial model generator is moved from wdmerger into the C++ model parser. This will allow it to be reused multiple times in the coming split of wdmerger into separate problem setups for mergers, collisions, and TDEs. At some point we can also merge this with the initial model generator for the setups like flame_wave.
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/probin
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_util.H
Exec/science/wdmerger/wdmerger_util.cpp
Util/model_parser_cxx/model_parser.H
Util/model_parser_cxx/model_parser_data.H
Util/model_parser_cxx/model_parser_data.cpp
commit 1872f1e2b28d7a89bc37ab76e620df4a7346b842
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 12:16:00 2020 -0500
for Sedov we should be refining on the gradients (#1453)
Exec/hydro_tests/Sedov/inputs.3d.sph
commit 38bccfbf451944ab4b2daf9d6f8f37d50a9b3710
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 8 07:56:33 2020 -0800
Rework diagnostic sums to be more customizable (#1452)
The current diagnostic sums functionality (castro.sum_interval = 1) has two limitations. First, customizing it for a problem setup currently means that the whole sum_integrated_quantities.cpp file has to be copied, which means that if the functionality from the main sum_integrated_quantities routine is desired, the problem has to duplicate that code. Second, even if you did customize it, the Amr class ownership of the data logs means that customizing the number and name of the logs is brittle. One unfortunate way that brittleness plays out is that you must specify amr.data_log in the inputs file with the exact ordering of the diagnostic names.
The intent of this change is that problems should have not have to override sum_integrated_quantities.cpp to get custom diagnostics. A new hook is provided, problem_diagnostics.H, which is called at the end of sum_integrated_quantities() for problem-specific diagnostics. To support this change, we stop depending on the Amr ownership of the data logs. Two new Castro class members are added, data_logs and problem_data_logs. The former is managed by Castro and can be changed over time if we want to add more diagnostic routines, with initialization done in Castro::read_params(). The latter is managed by the problem itself, with initialization done in problem_initialize(). The log names are coded directly into the source, which means that you don't need to remember to put those names in your inputs file.
test_convect and toy_convect are converted to the new scheme.
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/test_convect/problem_diagnostics.H
Exec/hydro_tests/test_convect/problem_initialize.H
Exec/hydro_tests/toy_convect/inputs_2d
Exec/hydro_tests/toy_convect/problem_diagnostics.H
Exec/hydro_tests/toy_convect/problem_initialize.H
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/sum_integrated_quantities.cpp
Source/problems/Make.package
Source/problems/problem_diagnostics.H
commit afc76154ec3137dfeb17fd70451552fde773048e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 09:22:01 2020 -0500
convert radbreakout to C++ (#1443)
this also extends the C++ model parser to handle aux and vel data
this was the last problem to directly use the interpolate module, so that is removed now
also, we remove some old initial models in this problem setup
Exec/Make.Castro
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadBreakout/Prob_nd.F90
Exec/radiation_tests/RadBreakout/_prob_params
Exec/radiation_tests/RadBreakout/model.input.87a.23
Exec/radiation_tests/RadBreakout/model.input.bo
Exec/radiation_tests/RadBreakout/model.input.envel
Exec/radiation_tests/RadBreakout/probin.1d
Exec/radiation_tests/RadBreakout/problem_initialize.H
Exec/radiation_tests/RadBreakout/problem_initialize_rad_data.H
Exec/radiation_tests/RadBreakout/problem_initialize_state_data.H
Exec/radiation_tests/RadSuOlson/problem_initialize_rad_data.H
Source/driver/Castro.cpp
Source/problems/problem_initialize_rad_data.H
Source/radiation/Radiation.H
Util/interpolate/Make.package
Util/interpolate/interpolate.H
Util/interpolate/interpolate_nd.F90
Util/model_parser_cxx/model_parser.H
Util/model_parser_cxx/model_parser_data.H
commit 19a1171121fcc13b639d53e079c9658f0db7cf7d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 7 15:41:16 2020 -0800
Move wdmerger subsampled interpolation scheme into model_parser header (#1436)
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Util/model_parser_cxx/model_parser.H
commit 8ad86d81d7e113e44a9f8f995344e5e32f3aeaa4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 7 15:37:44 2020 -0800
Convert hmac and hbac to C++ (#1442)
This uses the same approach as #1419.
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
commit 4654e7e71132ff06b56f99796bc6abf966d69e20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 13:59:57 2020 -0500
fix case of "Density" (#1451)
Exec/hydro_tests/Sedov/inputs.3d.sph
commit e5a2c7d2d1193019de85e1d705bde51ef98eb1e6
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Dec 7 11:15:57 2020 -0500
remove non-reacting species update (#1450)
Source/sdc/sdc_util_nd.F90
commit d82ec0e76d14de47080bbaae3c19e36589d8c299
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 09:22:22 2020 -0500
fix inlining of rad function (#1449)
Source/radiation/blackbody.H
commit a08ba0e848201f2885f72c363ddd01d5982a6d60
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 7 05:06:19 2020 -0800
Sync wdmerger on inertial_to_rotational_velocity (#1445)
wdmerger was redundantly implementing conversion functions to convert between rotational and inertial quantities, so now it uses the main code interfaces. To support this, a function to convert from the rotational to the inertial frame is added, and we remove the redundant inertial_to_rotational_velocity_c.
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/problem_source.H
Exec/science/wdmerger/wdmerger_util.H
Source/driver/Derive.cpp
Source/driver/timestep.cpp
Source/hydro/advection_util.cpp
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
commit b51c8636e4d9559cbfccb0d09c2315dea2e74167
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 07:51:23 2020 -0500
port hse_convergence_general to C++ (#1444)
Exec/gravity_tests/hse_convergence_general/GNUmakefile
Exec/gravity_tests/hse_convergence_general/Make.package
Exec/gravity_tests/hse_convergence_general/Prob_nd.F90
Exec/gravity_tests/hse_convergence_general/README.md
Exec/gravity_tests/hse_convergence_general/_prob_params
Exec/gravity_tests/hse_convergence_general/initial_model.F90
Exec/gravity_tests/hse_convergence_general/initial_model.H
Exec/gravity_tests/hse_convergence_general/probin.hse_test
Exec/gravity_tests/hse_convergence_general/problem_initialize.H
Exec/gravity_tests/hse_convergence_general/problem_initialize_state_data.H
commit 077130c47e019844d556f0ea9c24fad8fce06ffd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 6 15:18:18 2020 -0800
Pass small_temp and small_dens into eos_init (#1447)
See starkiller-astro/Microphysics#459 for details.
Source/driver/Castro_setup.cpp
external/Microphysics
commit ea9b07d9358ad7fbc4e26516ffd2f4e272717822
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 6 17:00:15 2020 -0500
temporary fix the upper boundary condition (#1448)
this will let us establish a benchmark for the C++ conversion
Exec/gravity_tests/hse_convergence_general/Prob_nd.F90
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
commit 664e6ed6a55e649f536626b6ffe396ad54134602
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 6 06:52:20 2020 -0800
Reorder header includes to fix EOS compilation (#1446)
Source/driver/Castro_setup.cpp
commit 658c7bd0e4cea9580ce5a0eac7de30fc52ecb454
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 05:25:35 2020 -0800
Convert hbmat3 to C++ (#1425)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
commit a79736e2ffdd6c82df406faad56aff1f0d90eb6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 08:04:30 2020 -0500
allow radiation initialization in C++ (#1439)
this also converts RadSuOlson to C++
Exec/radiation_tests/RadSuOlson/Prob_nd.F90
Exec/radiation_tests/RadSuOlson/problem_initialize.H
Exec/radiation_tests/RadSuOlson/problem_initialize_rad_data.H
Exec/radiation_tests/RadSuOlson/problem_initialize_state_data.H
Source/driver/Castro.cpp
Source/problems/Prob_nd.F90
Source/problems/problem_initialize_rad_data.H
commit f53732f573a72b23c464cb9506213e6b53536a6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 08:04:08 2020 -0500
check_for_nan.F90 is no longer needed (#1441)
We no longer work with FABs in Fortran, so we don't need this util
Docs/source/debugging.rst
Source/driver/check_for_nan_nd.F90
commit d5aaf883a92b4138c00299962c4c1b533923b3a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 21:36:10 2020 -0500
math_nd.F90 is no longer needed (#1440)
Docs/source/software.rst
Source/driver/Make.package
Source/driver/math_nd.F90
commit 59a56d87eb65ee171dd7ef9d6d14b14c9c07acc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 20:41:44 2020 -0500
the problems don't need USE_INTERPOLATE=TRUE (#1438)
Exec/science/convective_flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
commit bfb4f92e4532cfc6570b704e0120492621336f12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 20:20:15 2020 -0500
remove the conservative mapping option for flame (#1437)
this was done as an experiment to see how the flame converges, but we never
wound up using it.
Exec/Make.Castro
Exec/science/flame/GNUmakefile
Exec/science/flame/Prob_nd.F90
Exec/science/flame/_prob_params
Exec/science/flame/inputs.1d.sdc.map
Exec/science/flame/inputs.1d.sdc.map.avg
Exec/science/flame/mapping_tests/setup_runs.sh
Exec/science/flame/probin.sdc.map
Exec/science/flame/probin.sdc.map.avg
Util/conservative_interpolate/Make.package
Util/conservative_interpolate/conservative_map.F90
commit 7a0cbff8c4c3f3a8a8b2c481c193be0a324ec4f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 3 10:47:47 2020 -0800
Switch wdmerger to model parser interpolater (#1435)
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/problem_initialize_state_data.H
Util/model_parser_cxx/model_parser.H
commit 9b2bd166b4741f63649db312815f76a0ff64d68b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 3 07:33:49 2020 -0800
Move wdmerger initial model data into the main Castro struct (#1430)
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/wdmerger_util.H
Exec/science/wdmerger/wdmerger_util.cpp
commit a2db177ee84aa6a9f04a91fbaffe5a1c748f0175
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 10:28:57 2020 -0500
reduce the derives for the test suite problem (#1434)
Exec/science/wdmerger/tests/tde/inputs.test
commit 31243487464ab75df17d5b95af7cd3c46f6c4eb2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 3 06:59:25 2020 -0800
Remove old scaling results directory (#1433)
this now lives in workflow
Util/scaling/bwp/edison_20160609/scaling.txt
Util/scaling/sedov/summit_201905/CPU_runs/inputs.3d.sph
Util/scaling/sedov/summit_201905/CPU_runs/inputs.3d.sph_1level
Util/scaling/sedov/summit_201905/CPU_runs/probin.3d.sph
Util/scaling/sedov/summit_201905/CPU_runs/summit_16node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_32node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_4node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_64node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_8node_nogpu.sh
Util/scaling/sedov/summit_201905/GPU_runs/inputs.3d.sph
Util/scaling/sedov/summit_201905/GPU_runs/inputs.3d.sph_1level
Util/scaling/sedov/summit_201905/GPU_runs/probin.3d.sph
Util/scaling/sedov/summit_201905/GPU_runs/summit_16nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_32nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_4nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_64nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_8nodes.sh
Util/scaling/sedov/summit_201905/plot_scaling.py
Util/scaling/sedov/summit_201905/summit_scaling_may19.txt
Util/scaling/sedov/titan_20171011/1level/avg_time.sh
Util/scaling/sedov/titan_20171011/1level/inputs.starlord
Util/scaling/sedov/titan_20171011/1level/probin.starlord
Util/scaling/sedov/titan_20171011/1level/titan-MPI1024-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP16-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/avg_time.sh
Util/scaling/sedov/titan_20171011/1level_4x/inputs.starlord
Util/scaling/sedov/titan_20171011/1level_4x/probin.starlord
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/inputs.starlord
Util/scaling/sedov/titan_20171011/64_1024/probin.starlord
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI2-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/inputs.starlord
Util/scaling/sedov/titan_20171011/64_1536/probin.starlord
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI2-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/64_512/avg_time.sh
Util/scaling/sedov/titan_20171011/64_512/inputs.starlord
Util/scaling/sedov/titan_20171011/64_512/probin.starlord
Util/scaling/sedov/titan_20171011/64_512/titan-512-MPI-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-MPI2-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/castro-sedov-scaling.txt
Util/scaling/wdmerger/cori_201710/cori-nodes_128.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_16.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_32.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_64.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_96.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/inputs_test_wdmerger_3D
Util/scaling/wdmerger/cori_201710/probin_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/inputs_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/probin_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/scaling.txt
Util/scaling/wdmerger/summitdev_201806/summitd-160MPI.run
Util/scaling/wdmerger/summitdev_201806/summitd-320MPI.run
Util/scaling/wdmerger/summitdev_201806/summitd-80MPI.run
Util/scaling/wdmerger/titan_041516/README
Util/scaling/wdmerger/titan_041516/one_level_omp4.txt
Util/scaling/wdmerger/titan_041516/three_level_omp4.txt
Util/scaling/wdmerger/titan_041516/three_level_omp8.txt
Util/scaling/wdmerger/titan_041516/two_level_omp4.txt
Util/scaling/wdmerger/titan_20171011/256_0amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/256_0amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_0amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI128-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI2-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI64-PE16.run
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Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx4-OMP4-PE16.run
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Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx8-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/256_1amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_1amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI2-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPIx2-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPIx4-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPIx8-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-MPI128-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-MPI512-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/256_2amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_2amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPI-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPI2-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPIx2-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPIx4-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPIx4-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/512_0amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_0amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI1024-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI2048-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI512-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/512_1amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_1amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI1024-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI512-PE16.run
Util/scaling/wdmerger/titan_20171011/avg_time.sh
Util/scaling/wdmerger/titan_20171011/castro-wdmerger-scaling.txt
commit 012b3ea2557e07028fede9a3e18a8f0c7bbefbef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 1 21:40:03 2020 -0500
hide more stuff from github-linguist (#1429)
.gitattributes
commit f6aea3b6901b2cb5336804e19a98b2b949923a7e
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Dec 1 14:07:25 2020 -0500
fix release action (#1428)
.github/workflows/create_release.yml
.github/workflows/get_release_txt.py
commit 39874b15ece3c4e676d68ed4895510f9ffcd1a40
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 1 10:43:08 2020 -0800
Update Microphysics and AMReX to 20.12 (#1427)
external/Microphysics
external/amrex
commit 52885763613986620f0de1cfb8cb7c6c96843e86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 1 12:45:12 2020 -0500
port KH to C++ (#1423)
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/KH/problem_initialize.H
Exec/hydro_tests/KH/problem_initialize_state_data.H
commit 62c60ec401523662834ebbbc29138736c3bfadd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 1 11:39:37 2020 -0500
remove the code_comp problem (#1421)
this is probably not the final set of ICs and we are not working
on the comparison anymore
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Make.package
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/Problem_Derive.H
Exec/gravity_tests/code_comp/Problem_Derive.cpp
Exec/gravity_tests/code_comp/Problem_Derives.H
Exec/gravity_tests/code_comp/README.md
Exec/gravity_tests/code_comp/_prob_params
Exec/gravity_tests/code_comp/inputs_2d.sdc4
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/inputs_3d.sdc4
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.F90
Exec/gravity_tests/code_comp/probin
Exec/gravity_tests/code_comp/problem_source.H
Exec/gravity_tests/code_comp/simple.net
commit 424170828c010a5b26030439b813a5e0e7022178
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Dec 1 10:26:56 2020 -0500
fix release python script (#1426)
.github/workflows/get_release_txt.py
commit a2f2a8c1b7b655b23e2724794291983e23ced0fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 1 07:18:36 2020 -0500
fix a small T issue (#1424)
Exec/hydro_tests/KH/inputs.2d
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/inputs.3d
commit bb8a23cc618d2ba5931942261065fa7b303aca02
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 30 09:33:49 2020 -0800
Convert hbmat to C++ (#1420)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
commit 2fd5ca76308a5a88c59244478916aac850e5369b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 29 16:26:15 2020 -0800
Convert hacoef and hbcoef to C++ (#1419)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
commit f0a88453e983fa59c8468134421a99dd7d41e45d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 29 18:35:28 2020 -0500
remove unused Castro_react_F.H (#1417)
Source/driver/Castro_F.H
Source/reactions/Castro_react_F.H
Source/reactions/Make.package
commit ddc24c3f9c552f17db3f08c0f3f0fb32ec92bddf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 29 18:33:20 2020 -0500
Make github detect *.H as C++ (#1418)
.gitattributes
commit bd53392adf449f482c717098c2dca9a6aa47832d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 29 18:18:55 2020 -0500
exclude Jupyter notebooks and .tex from github language stats (#1416)
.gitattributes
commit a9fdb61f7720a801c7e4f44fadfe0ae360f878d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 29 17:49:53 2020 -0500
convert convective_flame to C++ (#1412)
Exec/science/convective_flame/GNUmakefile
Exec/science/convective_flame/Make.package
Exec/science/convective_flame/Prob_nd.F90
Exec/science/convective_flame/_prob_params
Exec/science/convective_flame/exploration/probin_temp
Exec/science/convective_flame/initial_model.H
Exec/science/convective_flame/initial_model.f90
Exec/science/convective_flame/probin
Exec/science/convective_flame/probin_good
Exec/science/convective_flame/problem_initialize.H
Exec/science/convective_flame/problem_initialize_state_data.H
commit 0e5f5fa35253486ca9ceee5f065119911204735d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 29 14:58:52 2020 -0500
convert the nova to C++ (#1411)
Exec/science/nova/GNUmakefile
Exec/science/nova/Prob_nd.F90
Exec/science/nova/problem_initialize.H
Exec/science/nova/problem_initialize_state_data.H
commit bfdd9d7f3653ac595e6db31401b75a1dda87d354
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 29 05:55:28 2020 -0800
Limit amount of info in the wdmerger initial_model (#1415)
All data other than the radius, density, temperature, pressure, and composition is moved out of the initial_model struct (mostly into _prob_params data).
PR motivation
This sets up, as a following change, storing the remaining model data in the main Castro initial model functionality.
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/wdmerger_util.cpp
commit 427e3c3f14be73f04a01f48437a2e1211242b772
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 18:50:37 2020 -0500
convert xrb_mixed to C++ (#1410)
Exec/science/xrb_mixed/GNUmakefile
Exec/science/xrb_mixed/Prob_nd.F90
Exec/science/xrb_mixed/_prob_params
Exec/science/xrb_mixed/probin
Exec/science/xrb_mixed/problem_initialize.H
Exec/science/xrb_mixed/problem_initialize_state_data.H
commit 6662dfa7cdf827ec935e64fe2125024c59f71462
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 18:43:03 2020 -0500
convert double_mach_reflection to C++ (#1413)
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/_prob_params
Exec/hydro_tests/double_mach_reflection/problem_initialize.H
Exec/hydro_tests/double_mach_reflection/problem_initialize_state_data.H
commit 69c6bc271117c95709ae273a7ed2a5d516acbc1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 18:38:41 2020 -0500
convert test_convect to C++ (#1414)
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/test_convect/Prob_nd.F90
Exec/hydro_tests/test_convect/_prob_params
Exec/hydro_tests/test_convect/probin
Exec/hydro_tests/test_convect/problem_initialize.H
Exec/hydro_tests/test_convect/problem_initialize_state_data.H
commit c9f9ad0888df79c0da5c4bed0ac82cc06d2e9ded
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 28 07:41:09 2020 -0800
Convert hbvec3 to C++ (#1409)
Source/driver/Castro_util.H
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.cpp
Source/radiation/rad_util.H
commit f8037df7e54f7158288335b420622a82a3a3cc49
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 27 12:31:13 2020 -0800
Move wdmerger initial profile data into struct (#1408)
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/wdmerger_util.cpp
commit df252697218264e90587c912f4ecda3be28abc44
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 27 11:26:54 2020 -0800
Convert compute_rhs to C++ (#1404)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 68944b91ff542bfa719a0d69dc69cfd0d8ce9010
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 27 07:22:15 2020 -0800
Convert wdmerger to C++ (#1407)
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_mhd_nd.F90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/binary.F90
Exec/science/wdmerger/binary.H
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/initial_model_nd.F90
Exec/science/wdmerger/problem_initialize.H
Exec/science/wdmerger/problem_initialize_mhd_data.H
Exec/science/wdmerger/problem_initialize_state_data.H
Exec/science/wdmerger/problem_io.f90
Exec/science/wdmerger/problem_restart.H
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_F.H
Exec/science/wdmerger/wdmerger_util.H
Exec/science/wdmerger/wdmerger_util.cpp
Exec/science/wdmerger/wdmerger_util_nd.F90
Source/driver/Castro.H
Util/interpolate/Make.package
Util/interpolate/interpolate.H
commit f352956b31d3f872c7cb863c4906986b2e58f027
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 17:35:14 2020 -0800
Separate out initialization routines into separate, consistent headers (#1403)
We've been moving in the direction where each problem-related header has exactly one routine and the name of that routine is the same as the header file. This PR makes that consistent for the problem setup routines as well.
Docs/source/creating_a_problem.rst
Exec/gravity_tests/StarGrav/problem_initialize.H
Exec/gravity_tests/StarGrav/problem_initialize_mhd_data.H
Exec/gravity_tests/StarGrav/problem_initialize_state_data.H
Exec/gravity_tests/hse_convergence/problem_initialize.H
Exec/gravity_tests/hse_convergence/problem_initialize_state_data.H
Exec/gravity_tests/hydrostatic_adjust/problem_initialize.H
Exec/gravity_tests/hydrostatic_adjust/problem_initialize_state_data.H
Exec/hydro_tests/Noh/problem_initialize.H
Exec/hydro_tests/Noh/problem_initialize_state_data.H
Exec/hydro_tests/RT/problem_initialize.H
Exec/hydro_tests/RT/problem_initialize_state_data.H
Exec/hydro_tests/Sedov/problem_initialize.H
Exec/hydro_tests/Sedov/problem_initialize_state_data.H
Exec/hydro_tests/Sod/problem_initialize.H
Exec/hydro_tests/Sod/problem_initialize_state_data.H
Exec/hydro_tests/Sod_stellar/problem_initialize.H
Exec/hydro_tests/Sod_stellar/problem_initialize_state_data.H
Exec/hydro_tests/acoustic_pulse/problem_initialize.H
Exec/hydro_tests/acoustic_pulse/problem_initialize_state_data.H
Exec/hydro_tests/acoustic_pulse_general/problem_initialize.H
Exec/hydro_tests/acoustic_pulse_general/problem_initialize_state_data.H
Exec/hydro_tests/double_bubble/problem_initialize.H
Exec/hydro_tests/double_bubble/problem_initialize_state_data.H
Exec/hydro_tests/gamma_law_bubble/problem_initialize.H
Exec/hydro_tests/gamma_law_bubble/problem_initialize_state_data.H
Exec/hydro_tests/gresho_vortex/problem_initialize.H
Exec/hydro_tests/gresho_vortex/problem_initialize_state_data.H
Exec/hydro_tests/oddeven/problem_initialize.H
Exec/hydro_tests/oddeven/problem_initialize_state_data.H
Exec/hydro_tests/rotating_torus/problem_initialize.H
Exec/hydro_tests/rotating_torus/problem_initialize_state_data.H
Exec/hydro_tests/toy_convect/problem_initialize.H
Exec/hydro_tests/toy_convect/problem_initialize_state_data.H
Exec/mhd_tests/BrioWu/problem_initialize.H
Exec/mhd_tests/BrioWu/problem_initialize_mhd_data.H
Exec/mhd_tests/BrioWu/problem_initialize_state_data.H
Exec/mhd_tests/OrszagTang/problem_initialize.H
Exec/mhd_tests/OrszagTang/problem_initialize_mhd_data.H
Exec/mhd_tests/OrszagTang/problem_initialize_state_data.H
Exec/reacting_tests/nse_test/problem_initialize.H
Exec/reacting_tests/nse_test/problem_initialize_state_data.H
Exec/reacting_tests/reacting_bubble/problem_initialize.H
Exec/reacting_tests/reacting_bubble/problem_initialize_state_data.H
Exec/reacting_tests/reacting_convergence/problem_initialize.H
Exec/reacting_tests/reacting_convergence/problem_initialize_state_data.H
Exec/reacting_tests/toy_flame/problem_initialize.H
Exec/reacting_tests/toy_flame/problem_initialize_state_data.H
Exec/science/Detonation/problem_initialize.H
Exec/science/Detonation/problem_initialize_state_data.H
Exec/science/flame_wave/problem_initialize.H
Exec/science/flame_wave/problem_initialize_state_data.H
Exec/science/rotating_star/problem_initialize.H
Exec/science/rotating_star/problem_initialize_state_data.H
Exec/science/subchandra/problem_initialize.H
Exec/science/subchandra/problem_initialize_state_data.H
Exec/unit_tests/diffusion_test/problem_initialize.H
Exec/unit_tests/diffusion_test/problem_initialize_state_data.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/problems/Make.package
Source/problems/problem_initialize.H
Source/problems/problem_initialize_mhd_data.H
Source/problems/problem_initialize_state_data.H
commit 3dd28d8edb3f48f4de06b503c7cf0d81170dd2c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 12:00:52 2020 -0800
Convert hbvec to C++ (#1405)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.cpp
commit 2c40d51a9af087ae37a8eed03aef564a144aa288
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 11:06:33 2020 -0800
Convert wdmerger initialize_model to C (#1402)
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/initial_model_nd.F90
Exec/science/wdmerger/wdmerger_util_nd.F90
commit 346236d2759bf7ae0614dd5838fc45c4ed93fd9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 11:04:39 2020 -0800
Replace master/slave terminology with primary/secondary (#1406)
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
commit 7145210b768211668c3a80d48222a54fc55f0047
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 25 12:01:23 2020 -0500
convert flame_wave to C++ (#1401)
Exec/science/flame_wave/GNUmakefile
Exec/science/flame_wave/Make.package
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/initial_model.F90
Exec/science/flame_wave/initial_model.H
Exec/science/flame_wave/problem_setup.H
commit f4110c6109cdde252517430bde181aad6a669733
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 24 19:11:56 2020 -0500
add support for multiple initial models (#1400)
The C++ model parser is extended to allow for multiple initial models. Set the make variable NUM_MODELS
to the number of models you need.
Exec/Make.Castro
Exec/gravity_tests/hse_convergence/initial_model.H
Exec/gravity_tests/hydrostatic_adjust/problem_setup.H
Exec/hydro_tests/double_bubble/initial_model.H
Exec/hydro_tests/gamma_law_bubble/initial_model.H
Exec/hydro_tests/toy_convect/problem_setup.H
Exec/reacting_tests/reacting_bubble/problem_setup.H
Util/model_parser_cxx/model_parser.H
Util/model_parser_cxx/model_parser_data.H
Util/model_parser_cxx/model_parser_data.cpp
commit 6942ead26de18bb9479e5b3e239b978c16371311
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 23 13:23:31 2020 -0800
Convert HypreExtMultiABec::loadMatrix() to C++ (#1399)
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreExtMultiABec.cpp
commit 5f6c82df03b09e9529a707d6c3af3d74b11a4861
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 23 06:03:01 2020 -0800
Convert bclim to C++ (#1398)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
Source/radiation/rad_util.H
commit 77069a18cf5124bbc9852fbdd9de91b8e37ca1bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 23 08:22:12 2020 -0500
convert diffusion_test setup to C++ (#1397)
Exec/unit_tests/diffusion_test/Make.package
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/diffusion_test/Problem_Derive.cpp
Exec/unit_tests/diffusion_test/prob_util.F90
Exec/unit_tests/diffusion_test/prob_util.H
Exec/unit_tests/diffusion_test/problem_setup.H
commit 0d5636f3ba4fbd041b00b76780bdb5b5575033b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 23 08:20:46 2020 -0500
convert OrszagTang to C++ (#1396)
Exec/mhd_tests/OrszagTang/Prob_mhd_nd.F90
Exec/mhd_tests/OrszagTang/Prob_nd.F90
Exec/mhd_tests/OrszagTang/problem_mhd_setup.H
Exec/mhd_tests/OrszagTang/problem_setup.H
commit c3a1684ca40b275af48ece659148f30ce0f86b93
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 22 12:43:03 2020 -0800
Convert accel_acoe and accel_ccoe to C++ (#1395)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit c362a89139d8a721de99c9d8f8d4dc0fb775aaed
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 22 09:31:24 2020 -0800
Convert wdmerger establish_hse to C++ (#1394)
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/initial_model.H
Exec/science/wdmerger/initial_model.cpp
Exec/science/wdmerger/initial_model_nd.F90
Exec/science/wdmerger/wdmerger_util_nd.F90
commit 24141b14da14cd3f35f1b88c8bc4003557677472
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 22 07:02:52 2020 -0800
Convert multrs to C++ (#1393)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 22c3ec49cbe2df6d29f881873a66572217bfcfab
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 22 05:57:45 2020 -0800
Convert compute_emissivity to C++ (#1392)
To support this change, emissity_override.F90 was converted to problem_emissivity.H, and the blackbody routines were converted to C++.
Exec/radiation_tests/RadShestakovBolstad/emissivity_override.F90
Exec/radiation_tests/RadShestakovBolstad/problem_emissivity.H
Exec/radiation_tests/RadSuOlsonMG/emissivity_override.F90
Exec/radiation_tests/RadSuOlsonMG/problem_emissivity.H
Source/problems/Make.package
Source/problems/emissivity_override.F90
Source/problems/problem_emissivity.H
Source/radiation/MGFLD.cpp
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/blackbody.H
commit 08098b11dee1ec4b7d381f388d046fbbbc775e9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 20:37:26 2020 -0500
convert Detonation to C++ (#1391)
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/_prob_params
Exec/science/Detonation/problem_setup.H
commit b90b1d1edc54175148cfeba1bc145683e535bd80
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 19:08:16 2020 -0500
convert the NSE test to C++ (#1378)
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/nse_test/problem_setup.H
commit 6658c8be74f8d24aff142dcfc582e1a2769bb2a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 16:07:35 2020 -0800
Remove eos_t from wdmerger initial model (#1390)
Exec/science/wdmerger/initial_model.F90
commit 8867701ab959a6b2efbe574f9ccabfbabd4b7482
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 15:45:43 2020 -0800
Convert get_rhoe to C++ (#1389)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 2a1efc1fdbbc4a7e98d7b071c5e384912e2d2c24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 17:53:13 2020 -0500
port the rotating_star setup to C++ (#1387)
Note: this fixes a bug in the rotating_star setup with NSE. We were calling the NSE table with state(i,j,k,UFS-1+iye), but it should use UFX, not UFS.
Exec/science/rotating_star/GNUmakefile
Exec/science/rotating_star/Prob_nd.F90
Exec/science/rotating_star/problem_setup.H
commit e8f125cee655fb14a703b7e4d6d6c2d0f4cb4eb2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 14:27:00 2020 -0800
Hardcode the maximum number of points in the wdmerger initial models (#1388)
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/wdmerger_util_nd.F90
commit c7d4fe26b099ee0d96c1deb67d1423179035ade3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 10:58:39 2020 -0800
Convert lacoef to C++ (#1385)
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 45ebb22a4525debd664f37d7858d2d5b0fbab84a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 10:56:14 2020 -0800
Convert compute_scattering to C++ (#1384)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 12c6be41d242d4dda4949bc8c460115a68e63a33
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 09:59:43 2020 -0800
Convert scaledGradient to C++ (#1383)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
Source/radiation/rad_util.H
commit 57f4b54397c1173e5d4b774f81bf9119a674a2d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 09:19:46 2020 -0800
Convert rhstoer to C++ (#1376)
This includes a port of cell_center_metric to rad_util.H.
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/rad_util.H
commit e994ff67e63b67a104e9d03f43850ca0abe5dc6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 08:16:33 2020 -0800
Error if density is exactly zero (#1382)
Closes #1345.
Source/hydro/advection_util.cpp
commit da4d0fa2081c186e9f1a31801a9e61b3b291e688
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 21 06:17:47 2020 -0800
Apply the same interpolation scheme to all StateData (#1380)
Source/driver/Castro_setup.cpp
commit e0fdaf7f1660132334d9c89d7e9b4fbfbc263fa8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 02:35:52 2020 -0500
convert toy_flame to C++ (#1377)
Exec/reacting_tests/toy_flame/Prob_nd.F90
Exec/reacting_tests/toy_flame/_prob_params
Exec/reacting_tests/toy_flame/problem_setup.H
commit 01ebecf159c688c332c44e51143031d63510184a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 02:23:39 2020 -0500
convert rotating_torus to C++ (#1381)
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/problem_setup.H
commit 2b5a7f21020ef18aa00e5b5d2ce35e17e3eea70f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 07:58:56 2020 -0800
Convert compute_c_v to C++ (#1375)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 1985bfcd6c9086bc4baa49be58f845350399f787
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 07:29:35 2020 -0800
Convert Rosseland opacity to C++ (#1374)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit e846b1724dbd742d7aeb19891b817ed940e0b2eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 09:53:19 2020 -0500
convert StarGrav to C++ (#1299)
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/StarGrav/Prob_mhd_nd.F90
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/gravity_tests/StarGrav/problem_mhd_setup.H
Exec/gravity_tests/StarGrav/problem_setup.H
commit 4cc458bcbed28e0fdd086d304c68a57b57b5d31f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 06:39:55 2020 -0800
Avoid roundoff issues in normalize_species_fluxes (#1373)
The CMA procedure in normalize_species_fluxes scales the species fluxes by the ratio of the density flux to the sum of the species of the fluxes. The idea is that this scaling ensures that the sum of the (rho X) fluxes is equal to the (rho) flux.
This can go wrong if the sum of the species fluxes is very small but non-zero. In particular, there can be numerical problems if the density flux is approximately zero at the interface but not exactly, resulting in division by a small number and/or resulting in one of the species fluxes being negative because of roundoff error. There are also other terms like artificial viscosity which can cause these problems. So checking that sum is sufficiently large helps avoid this.
#1299 exposed this issue for the StarGrav problem. The star starts at rest, and during the first few timesteps the velocity is either exactly zero or close enough to zero that the Riemann solver zeros them out for safety. The artificial viscosity, which comes before normalize_species_fluxes as currently written, then sets the density flux and species fluxes to very small but non-zero numbers due to roundoff error. The roundoff error results in a species flux that may be negative for one species and positive for another, so they cancel out resulting in sum < epsilon. Then the division by zero goes poorly, resulting in unphysically large species fluxes.
Source/hydro/advection_util.cpp
commit 3801d819621917fd1e1d5c1c8debe7de264ee1b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 09:03:50 2020 -0800
Convert conservative matter update to C++ (#1372)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 0a3e06b8541947c8522a5752a4043e5cbccadb48
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 08:08:02 2020 -0800
Convert compute_planck to C++ (#1371)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit aeef834fcb6862039215e073e78aca32c3721cd3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 12:58:35 2020 -0800
Convert ca_opacs to C++ (#1368)
Source/driver/Castro_setup.cpp
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit f769d7385ecd392987ed9265d8d6e1664afcecd5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 10:03:01 2020 -0800
Convert compute_temp_from_rhoe to C++ (#1367)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit c9aa7136acac3dad46d444766b49ef1d7c214c74
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 08:49:24 2020 -0800
Convert nonconservative matter update to C++ (#1366)
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
commit 976b1c7612b1e743455c7bdffc10bca2ccdbe43b
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Nov 18 09:37:42 2020 -0500
fix create_release action (#1370)
This fixes the create_release action to remove the set_env command
.github/workflows/create_release.yml
commit cc4ce1bbc4a21c3c3796db197477cfa17dbab248
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 06:33:38 2020 -0800
Convert lbcoefna to C++ (#1365)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 011f433aea42a5bf42d51e62e7327abbf85f1d51
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 06:30:09 2020 -0800
Convert kepler_third_law and freefall_velocity to C (#1364)
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/wdmerger_util.H
Exec/science/wdmerger/wdmerger_util.cpp
Exec/science/wdmerger/wdmerger_util_nd.F90
Source/driver/math.H
Source/rotation/Rotation.H
commit f6650cda848d706e36b3d3fbc6f7ad86bb21a4a6
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Nov 18 09:29:03 2020 -0500
Fix c-linter action as set-env is no longer supported (#1369)
.github/workflows/c-linter.yml
commit b7fe43e5a9cb8813b2ff696ecf8c536e337da96c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 05:23:05 2020 -0800
Turn off GPU pragma for everything but radiation (#1363)
Radiation is the only code that substantively uses it at this point. The exception is a few problem-related routines -- problems that want to benefit from GPUs on these should migrate to the new C++ interfaces.
Exec/Make.Castro
Exec/hydro_tests/Sedov/GNUmakefile
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/problems/Castro_problem_source.cpp
Source/sdc/Castro_sdc.cpp
commit 2858f32cdb5996c05356c33a7a4fe7af9658c405
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 17 19:43:05 2020 -0500
port the subchandra problem to C++ (#1362)
this also fixes a few issues:
the small density cutoff has too high
the temperature perturbation was not convolving the X(He) correctly
the runtime parameters were not in the namelist
Exec/science/subchandra/GNUmakefile
Exec/science/subchandra/Prob_nd.F90
Exec/science/subchandra/_prob_params
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/probin
Exec/science/subchandra/problem_setup.H
commit 46363d7c4271987983e25f8d5172dc6ce4667aa8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 16:21:53 2020 -0800
Convert nfloor to C++ (#1361)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit bdf999176ff8351e92a7f2774c9241456ba12cd2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 12:44:15 2020 -0800
Rename Castro_ext_src.H to problem_source.H (#1360)
This is more consistent with the naming convention we've been using for other files. Also, I moved the files in Source/ to problems/ instead of sources/.
Exec/gravity_tests/code_comp/problem_source.H
Exec/gravity_tests/hydrostatic_adjust/problem_source.H
Exec/hydro_tests/test_convect/problem_source.H
Exec/hydro_tests/toy_convect/problem_source.H
Exec/science/Detonation/problem_source.H
Exec/science/planet/problem_source.H
Exec/science/wdmerger/problem_source.H
Source/problems/Castro_problem_source.cpp
Source/problems/Make.package
Source/problems/ext_src_nd.F90
Source/problems/problem_source.H
Source/sources/Castro_ext_src.H
Source/sources/Make.package
commit 1ac32b89ab7c8d70dfd515a68a09f44be2d2c5c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 10:31:30 2020 -0800
Remove ext_denfill (#1356)
As discussed in #154 and several other issues, we have been using ext_denfill incorrectly for a long time. When we come into the BC routine with a single component, it is usually not the density, usually it is a derive and it may be any quantity, so filling with the density is simply wrong. So the easy solution here is just to remove the application of ext_denfill. This should not have very large effects, as we were only getting it wrong during derives, whose only effect on the simulation is through tagging (and this error would only have occurred at physical domain boundaries). We already fill the data with FOEXTRAP and this should be good enough for most cases. (This does not preclude future efforts to actually do the BCs on those drives correctly, taking into account HSE and problem-specific BCs.)
I've also used this opportunity to do a small bit of cleanup to GpuBndryFuncFab, and to remove the redundant call to CpuBndryFuncFab (the former should do the right thing even if not in a launch region, and in any case we do not ever turn off the launch region).
CHANGES.md
Source/driver/Castro_generic_fill.H
Source/driver/Castro_generic_fill.cpp
Source/problems/Castro_bc_ext_fill_nd_F.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
Source/problems/bc_ext_fill.H
Source/problems/bc_ext_fill_nd.F90
commit 993bbbee3bbbc9afdf4f2a3f088a935e40785fb1
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 07:31:42 2020 -0800
Remove redundant copy of Castro_external.cpp (#1359)
wdmerger originally had its own copy due to a custom interface, but now it is even with the main copy.
Exec/science/wdmerger/Castro_external.cpp
commit 0a806e0595a228fa951857785ce5bad7f28d146f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 07:11:42 2020 -0800
Convert cetot to C++ (#1357)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit ee40923c2d637b0ace38e8c6a4c972fb6dcaf295
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 06:38:10 2020 -0800
Convert flxlim and FLDlambda to C++ (#1358)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
Source/radiation/rad_util.H
commit 5831d24bd507f4f07ccbaf64715334edd33b43b9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 16 18:40:23 2020 -0800
Convert ambient BC fill to C++ (#1354)
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
Source/problems/ambient_fill.cpp
Source/problems/bc_fill_nd.F90
commit 82d98fa98033513c3f36d2526dc9799bb48f1f07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 16 21:37:11 2020 -0500
port hydrostatic_adjust to C++ (#1355)
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/Make.package
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive.H
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive.cpp
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive_F.H
Exec/gravity_tests/hydrostatic_adjust/_prob_params
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
Exec/gravity_tests/hydrostatic_adjust/problem_setup.H
commit 7f4007d7f66a0d8e13459f368a631dc6b27b3c39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 16 13:21:25 2020 -0500
remove the old pass_map arrays (#1351)
we use the inline function now, as that is GPU safe
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/hydro/trace_ppm.cpp
Source/radiation/trace_ppm_rad.cpp
commit cc7317b7c95389d7a328bfc7d256bcc5e4a77022
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 16 08:58:48 2020 -0800
Convert get_omega to C++ (#1352)
get_omega is ported to C++ as an inline function. All current uses of get_omega in C++ (which were calling into Fortran) are now replaced with the new implementation.
Since no part of the rotation simulation capability remains in Fortran, the interface to Fortran is removed. The Fortran version of get_omega is left for now because two problem setups in Fortran still depend on it.
(This change does cause a slight issue for wdmerger, which modifies rotational_period in probinit. However the impact is minor and should have no outcome on the simulation result, and at any rate will be fixed when its initialization is converted to C++.)
Exec/science/wdmerger/Castro_ext_src.H
Exec/science/wdmerger/Castro_external.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_F.H
Exec/science/wdmerger/wdmerger_util.F90
Exec/science/wdmerger/wdmerger_util.H
Source/driver/Castro_F.H
Source/driver/timestep.cpp
Source/hydro/advection_util.cpp
Source/rotation/Castro_rotation_F.H
Source/rotation/Make.package
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
Source/rotation/Rotation_frequency.F90
Source/rotation/rotation_sources.cpp
Source/scf/scf_relax.cpp
commit 02449b7388802c6fd99dabfbd639d68761fa6711
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 16 11:40:44 2020 -0500
convert the HSE boundary conditions to C++ (#1324)
As part of this change the *_ext_bc_type inputs parameters were changed from string to int.
This makes it easier to parse them.
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs_1d.well_balance
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
Exec/hydro_tests/double_bubble/inputs_2d
Exec/hydro_tests/double_bubble/inputs_2d.single
Exec/hydro_tests/double_bubble/inputs_2d.single.equal
Exec/hydro_tests/double_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/inputs_2d_MAESTRO.big
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/toy_convect/inputs_2d
Exec/reacting_tests/bubble_convergence/inputs_1d.well_balance
Exec/reacting_tests/bubble_convergence/inputs_2d.well_balance
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.250Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/scaling/3d_science/inputs.noboost.25cm.1000Hz.3d
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/nova/inputs_2d
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/xrb_mixed/inputs_2d
Source/driver/_cpp_parameters
Source/driver/meth_params.template
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
Source/problems/bc_ext_fill_nd.F90
Source/problems/ext_bc_types.H
Source/problems/hse_fill.cpp
commit 185945ed1773bc2d8c33ef91c5f48da2847b713b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 16 11:29:28 2020 -0500
fix a bug in the 3-d flame_wave compilation (#1353)
Exec/science/flame_wave/problem_tagging.H
commit 19af4b03a4f97b34e277be5cf701d150bee2e828
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 16 05:29:28 2020 -0800
Convert ceta2 to C++ (#1350)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 8f1cdef936b603800f352f1abe39b2d70c28f537
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 16 04:54:06 2020 -0800
Convert local_accel to C++ (#1349)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit b8a2e7419c7a28854b5baaf7e01c9c90c5e6fe29
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 11:03:36 2020 -0800
Convert double_mach_reflection BCs to C++ (#1346)
In order to avoid conflicting with the HSE BCs, the inputs files are set to outflow, but the outflow BCs are overridden by the problem-specific BC.
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/inputs.2d.test
Exec/hydro_tests/double_mach_reflection/problem_bc_fill.H
commit 2e015a57fadd9459bbb744a5b4dcf9aadc706469
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 10:47:57 2020 -0800
Convert ljupna to C++ (#1347)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 5e26a3906359dbb96da200986f6b7056e0209094
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 13:17:15 2020 -0500
convert double_bubble to C++ (#1343)
This changes the boundary conditions to use the centralized BCs and also puts the initial
model into the model_parser data structures.
The old BC integrated the initial model analytic profile into the ghost cells. For an isentropic atmosphere, this used the proper isentropic profile. Now we interpolate T into the ghost cells and integrate p via HSE. So it is not exactly the same as the analytic profile. I think it is good enough for a general HSE BC.
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/double_bubble/Make.package
Exec/hydro_tests/double_bubble/Prob_nd.F90
Exec/hydro_tests/double_bubble/_prob_params
Exec/hydro_tests/double_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/double_bubble/initial_model.H
Exec/hydro_tests/double_bubble/inputs_2d
Exec/hydro_tests/double_bubble/inputs_2d.single
Exec/hydro_tests/double_bubble/inputs_2d.single.equal
Exec/hydro_tests/double_bubble/inputs_2d.test
Exec/hydro_tests/double_bubble/model_stuff.f90
Exec/hydro_tests/double_bubble/probin
Exec/hydro_tests/double_bubble/probin.single
Exec/hydro_tests/double_bubble/probin.single.equal
Exec/hydro_tests/double_bubble/problem_setup.H
Exec/hydro_tests/gamma_law_bubble/initial_model.H
commit e147e0189e4e5e15fdae08597f28e33d9b1d4f3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 10:06:05 2020 -0800
Convert cfrhoe to C++ (#1348)
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
commit 27853dac54f903391ffba807f0be4a9412bbabdb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 09:13:57 2020 -0800
Convert Rad2Tshock BCs to C++ (#1342)
Rad2Tshock's BCs are converted to C++. Since it was previously using EXT_DIR and then overriding with ext_fill, simply moving the BCs to problem_bc_fill.H is not sufficient, because that will still have the main Castro EXT_DIR routines be called, which is not what we want. So the inputs files are updated to use outflow BCs along the problem direction -- the outflow fill will get overwritten anyway.
This does cause a breaking change in the regression suite. Previously this problem was also using ext_denfill and filling the density on either end. We do not attempt to replace it, since ext_denfill is usually incorrect to use in the way it is used here. In this case, because this was being used for derives, it caused spurious tagging at either end of the domain, where the temperature saw a "gradient" due to a density-scaled value being located adjacent to the temperature-scaled value in the interior. In this new configuration, the spurious tagging at the domain edges is avoided.
Exec/radiation_tests/Rad2Tshock/bc_ext_fill_nd.F90
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/Rad2Tshock/problem_bc_fill.H
commit f5f3785ce6d37a3cbc4e6018399cea86bea03ffa
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 09:08:53 2020 -0800
Include ghost zones when filling data on new level (#1344)
This addresses the issue that was unintentionally exposed by #1342. When we're creating a new fine level and filling data from the coarse level below it, we need to include the ghost zones in the fillpatch operation, or else they will be uninitialized and cause problems during the subsequent advance.
This can affect radiation and simplified-SDC problems.
Source/driver/Castro.cpp
commit 0452d39471b04926f2609514b4a967d6c3613797
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 05:35:08 2020 -0800
Convert accel_rhs to C++ (#1341)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit a1c1525d7e206a97d2a6bb699ec7bd0e4aa7b109
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 14:24:28 2020 -0800
Convert accel_spec to C++ (#1339)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit b188d46b37fff67fcd3a4cce54124ff0f7077308
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 17:13:00 2020 -0500
remove heating_verification (#1340)
this problem was never used. It was an idea to have an analytic verification problem but it didn't work.
Exec/hydro_tests/heating_verification/Castro_ext_src.H
Exec/hydro_tests/heating_verification/GNUmakefile
Exec/hydro_tests/heating_verification/Make.package
Exec/hydro_tests/heating_verification/Prob_nd.F90
Exec/hydro_tests/heating_verification/_prob_params
Exec/hydro_tests/heating_verification/bc_ext_fill_nd.F90
Exec/hydro_tests/heating_verification/inputs
Exec/hydro_tests/heating_verification/probin
commit 2009c87ce127343b1eca2410b7c2132a970a0d73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 16:49:06 2020 -0500
convert gamma_law_bubble to C++ (#1338)
The switches the initial model generation to be stored in the model_parser data structures.
It also removes the custom boundary conditions that were done previously to instead use
our general HSE BCs. This change will cause some differences in the output, but it should
be fine. The old BCs were essentially integrating the initial model into the BCs, so it was fixed
in time.
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/Make.package
Exec/hydro_tests/gamma_law_bubble/Prob_nd.F90
Exec/hydro_tests/gamma_law_bubble/_prob_params
Exec/hydro_tests/gamma_law_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/gamma_law_bubble/initial_model.H
Exec/hydro_tests/gamma_law_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/probin
Exec/hydro_tests/gamma_law_bubble/probin.big
Exec/hydro_tests/gamma_law_bubble/problem_setup.H
Source/driver/Castro.cpp
commit 802972551a859c76e170e25d5567cbcf37a14664
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 10:45:47 2020 -0800
ifdef out prints for GPU build (#1330)
Exec/gravity_tests/hydrostatic_adjust/Castro_ext_src.H
commit 4be89d4afea397f3b880a018d003e9a822ee39b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 10:45:08 2020 -0800
Catch up to latest Hypre (#1333)
HYPRE_Init() no longer accepts arguments as of 2.19. We should update the test suite to 2.20.
CHANGES.md
Docs/source/radiation.rst
Source/driver/main.cpp
commit ad9907545315395fcee133c7ac1e304d0768939b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 13:44:17 2020 -0500
clean up the cpp parameters python script (#1337)
we now ignore case in the _cpp_parameters file for the data type.
we also remove the option for the Fortran version of a parameter to
use a different name or data type. One Fortran runtime parameter
was changed as a result (rot_periond -> rotational_period).
Docs/source/rp_intro.rst
Exec/science/wdmerger/wdmerger_util.F90
Source/driver/_cpp_parameters
Source/driver/parse_castro_params.py
Source/rotation/Rotation_frequency.F90
commit 6125cbf88e5d9328a2383bfd2548a12e1d03888b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 08:17:53 2020 -0800
Convert radiation reductions to C++ (#1332)
Two reductions that were using the old Fortran style reductions have been converted to C++. Since these were the last bits in the code using the Fortran reduction code, it is now removed.
Source/driver/Make.package
Source/driver/reduction_nd.F90
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 592234490356a4ec46c733386c298666fbd6f8a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 07:32:28 2020 -0800
Convert compute_etat to C++ (#1334)
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit dac654efa7a81951b2c1bc932cfefca40d1dc485
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 06:53:27 2020 -0800
Convert get_v_dcf to C++ (#1335)
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Radiation.cpp
commit e2dc03598512d12fc433ccd00d822573160f3db4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 06:08:51 2020 -0800
Convert update_dcf to C++ (#1336)
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Radiation.cpp
commit 11039070b1c26cc6ad38a8ec3f5d6b6accfa373b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 05:26:59 2020 -0800
Convert hydrostatic_adjust BC fill to C++ (#1329)
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
Exec/gravity_tests/hydrostatic_adjust/problem_bc_fill.H
commit 2e18533ed0457aeafcae2bf59f426a0ff055ae77
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 17:49:48 2020 -0800
If using arrays sized nspec, allow them in C++ (#1328)
This allows arrays sized with (nspec, network) in _prob_params to be used in C++ by manually rewriting them as size NumSpec in C++.
Exec/science/Detonation/problem_bc_fill.H
Util/scripts/write_probdata.py
commit ea229de34c3502028138e259584ab5f42d932b9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 07:33:25 2020 -0800
Convert Noh setup to C++ (#1327)
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/Noh/problem_bc_fill.H
Exec/hydro_tests/Noh/problem_setup.H
commit 38b00cdad0a4de2377c25f4eaf17ddcb329bc39b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 12 12:53:08 2020 -0500
the "interp" external BC option was removed long ago (#1326)
most of these instances were not actually used, but a few were changed to
outflow
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/xrb_mixed/inputs_2d
commit 82cc04f88b045c5000f9f02a111b43f541d45894
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 12 12:33:44 2020 -0500
remove old flame_wave inputs / models (#1325)
these files were never used for a publication
Exec/science/flame_wave/old/inputs.boost_25_4
Exec/science/flame_wave/old/inputs/inputs_2d
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/science/flame_wave/old/inputs/probin.boost.base
Exec/science/flame_wave/old/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.aprox13
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.cool
Exec/science/flame_wave/old/probin
Exec/science/flame_wave/old/probin.boost
Exec/science/flame_wave/old/probin.boost.hires
Exec/science/flame_wave/old/probin.boost_25_4
commit 56f0a1d3169866c1cfcae51febe8f089a6ed6e13
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 11 07:47:32 2020 -0800
Convert toy_convect problem tagging to C++ (#1319)
Exec/hydro_tests/toy_convect/problem_tagging.H
Exec/hydro_tests/toy_convect/problem_tagging_nd.F90
commit 60f631711af528a881a96b31248ec7746021fa5c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 11 07:44:16 2020 -0800
Convert convective_flame problem tagging to C++ (#1320)
Exec/science/convective_flame/problem_tagging.H
Exec/science/convective_flame/problem_tagging_nd.F90
commit f2c4caf88eff641fef2c02d3d915fbecc4772c23
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 11 07:22:05 2020 -0800
Convert xrb_mixed problem tagging to C++ (#1321)
Exec/science/xrb_mixed/problem_tagging.H
Exec/science/xrb_mixed/problem_tagging_nd.F90
commit 3177d172046c923b0fb2179865393afee00ab473
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 11 07:19:36 2020 -0800
Add C++ interface for problems to override BCs (#1323)
A problem-facing hook, problem_bc_fill, is added in C++ for problems to set custom boundary conditions. The idea is that this should replace previous uses of overriding bc_fill_nd.F90. DustCollapse and Detonation are updated to the new scheme.
Note: we are not going to provide an equivalent of denfill, which would most likely be misused.
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
Exec/gravity_tests/DustCollapse/problem_bc_fill.H
Exec/science/Detonation/bc_fill_nd.F90
Exec/science/Detonation/problem_bc_fill.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
Source/problems/problem_bc_fill.H
commit c88fd5e14762075a03f88b78b8b4721c95734c17
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 11 05:27:09 2020 -0800
Add static assertion on NETWORK_HAS_CXX_IMPLEMENTATION with CUDA (#1322)
Source/reactions/Castro_react.cpp
commit 06b0f63568b2422cd0e3041182cfb65d03d3e781
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 14:20:35 2020 -0800
Remove some old uses of dt_cutoff (#1318)
Docs/source/timestepping.rst
Exec/science/rotating_star/inputs_2d.sdc_test
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Util/scaling/sedov/summit_201905/CPU_runs/inputs.3d.sph
Util/scaling/sedov/summit_201905/CPU_runs/inputs.3d.sph_1level
Util/scaling/sedov/summit_201905/GPU_runs/inputs.3d.sph
Util/scaling/sedov/summit_201905/GPU_runs/inputs.3d.sph_1level
Util/scaling/sedov/titan_20171011/1level/inputs.starlord
Util/scaling/sedov/titan_20171011/1level_4x/inputs.starlord
Util/scaling/sedov/titan_20171011/64_1024/inputs.starlord
Util/scaling/sedov/titan_20171011/64_1536/inputs.starlord
Util/scaling/sedov/titan_20171011/64_512/inputs.starlord
Util/scaling/wdmerger/cori_201710/inputs_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_0amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_1amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_2amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_0amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_1amr/inputs_test_wdmerger_3D
commit 011e129a7ba74cf7d7876efb3198fe47979e3ce7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 14:55:40 2020 -0500
remove the unused setup (#1165)
Exec/hydro_tests/Sedov/scaling/sc20/GNUmakefile
Exec/hydro_tests/Sedov/scaling/sc20/README.md
Exec/hydro_tests/Sedov/scaling/sc20/inputs
Exec/hydro_tests/Sedov/scaling/sc20/plot.py
Exec/hydro_tests/Sedov/scaling/sc20/probin
Exec/hydro_tests/Sedov/scaling/sc20/run_scaling.sh
Exec/hydro_tests/Sedov/scaling/sc20/run_script.sh
Exec/science/Detonation/science/sc20/GNUmakefile
Exec/science/Detonation/science/sc20/inputs
Exec/science/Detonation/science/sc20/probin
Exec/science/flame_wave/science/sc20/GNUmakefile
Exec/science/flame_wave/science/sc20/inputs
Exec/science/flame_wave/science/sc20/probin
Exec/science/flame_wave/science/sc20/run_script.sh
Exec/science/wdmerger/science/sc20/GNUmakefile
Exec/science/wdmerger/science/sc20/README.md
Exec/science/wdmerger/science/sc20/collision_ml0/inputs
Exec/science/wdmerger/science/sc20/collision_ml0/probin
Exec/science/wdmerger/science/sc20/collision_ml0/run_script.sh
Exec/science/wdmerger/science/sc20/collision_ml1/inputs
Exec/science/wdmerger/science/sc20/collision_ml1/probin
Exec/science/wdmerger/science/sc20/collision_ml1/run_script.sh
Exec/science/wdmerger/science/sc20/collision_ml2/inputs
Exec/science/wdmerger/science/sc20/collision_ml2/probin
Exec/science/wdmerger/science/sc20/collision_ml2/run_script.sh
commit 18ca68790b64f20ba571567793ac75069149ec7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 14:49:04 2020 -0500
if we are doing NSE, then abar was getting added to the derives twice (#1139)
Source/driver/Castro_setup.cpp
commit 2693489379c0d8f1e3da470aadb67b730d40b108
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 14:40:54 2020 -0500
update Microphysics submodule
external/Microphysics
external/amrex
commit 23db1cf250e93f8067137a69e00d0cda11195416
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 11:39:15 2020 -0800
Switch from Fortran to C++ reactions (#1313)
The Fortran reactions interfaces (except for true SDC) are removed.
CHANGES.md
Exec/Make.Castro
Exec/science/Detonation/science/sc20/GNUmakefile
Exec/science/flame_wave/science/sc20/GNUmakefile
Exec/science/rotating_star/GNUmakefile
Exec/science/wdmerger/science/sc20/GNUmakefile
Source/driver/Castro.H
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/timestep.cpp
Source/driver/timestep_nd.F90
Source/reactions/Castro_react.cpp
Source/reactions/Make.package
Source/reactions/React_nd.F90
Source/reactions/react_util.F90
commit 293f5382923be7bd9718f40a9db1f214a4360464
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 12:31:45 2020 -0500
convert flame_wave tagging to C++ (#1312)
Exec/science/flame_wave/problem_tagging.H
Exec/science/flame_wave/problem_tagging_nd.F90
commit a2dd455b8de1fe11dd08e9f8ac1979c391bb3784
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 12:29:57 2020 -0500
update indentation and namest (#1317)
Docs/source/software.rst
commit d987c92a8e6a25dae8283c0e236d94a2c5c8f24f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 15:11:45 2020 -0800
Update for Amr change to make data member class static (#1315)
Source/driver/Castro.cpp
external/amrex
commit 1b4e6ee3057920061ff83dd6129334fa2289e3b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 9 15:01:34 2020 -0500
update the test problem to actually have burning (#1316)
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/probin.testsuite
commit 47255bc73a982615b0cb61dfea2f076ba2424753
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 06:10:46 2020 -0800
Fix GPU build by removing references to deleted data (#1314)
These were removed in #1300.
Source/driver/meth_params.template
commit f7c17f431c6442b0f4953f33dbaef2f321069458
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 17:04:12 2020 -0800
Implement estdt_burning in C++ (#1286)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/reduction_nd.F90
Source/driver/timestep.cpp
commit b4c9573724dcad9c3cff405d9fe3a8b5cf14d2c4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 14:07:00 2020 -0800
Convert problem_checkpoint and problem_restart to C++ (#1311)
problem_checkpoint and problem_restart are moved to C++ from Fortran. At this point, only wdmerger still implemented them, so that is switched over, and stubs are placed in Source/problems. Since those were the only two routines in Problem_F.H and Problem.f90, those files are deleted.
CHANGES.md
Docs/source/creating_a_problem.rst
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/problem_checkpoint.H
Exec/science/wdmerger/problem_restart.H
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_F.H
Exec/science/wdmerger/wdmerger_util.F90
Exec/unit_tests/diffusion_test/Prob.cpp
Exec/unit_tests/particles_test/Prob.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/problems/Make.package
Source/problems/Prob.cpp
Source/problems/Problem_F.H
Source/problems/problem_checkpoint.H
Source/problems/problem_restart.H
commit c797c71113a77a11e35926afbd12701e4d9d74d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 8 12:31:21 2020 -0500
rotating_star defaults to USE_CXX_REACTIONS = TRUE (#1310)
Exec/science/rotating_star/GNUmakefile
commit 8b4c4e9156e33f225d8a52c497dd000d4413ff77
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 08:20:02 2020 -0800
Convert toy_flame properties to C++ (#1308)
Exec/reacting_tests/toy_flame/Prob.cpp
Exec/reacting_tests/toy_flame/Problem.f90
Exec/reacting_tests/toy_flame/Problem_F.H
commit 9edf88f7065c3d70ca8c0c92d98d4252a2df0481
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 08:17:27 2020 -0800
Convert flame properties to C++ (#1306)
Exec/science/flame/Prob.cpp
Exec/science/flame/Problem.f90
Exec/science/flame/Problem_F.H
commit a919736836106c3d734e8ce7740cfd2c0913f1c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 07:49:17 2020 -0800
Convert Detonation early stopping to C++ (#1305)
Exec/science/Detonation/Prob.cpp
Exec/science/Detonation/Problem.H
Exec/science/Detonation/Problem.f90
Exec/science/Detonation/Problem_F.H
Exec/science/Detonation/_prob_params
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probin-collision
commit 67d14c3442385e0e12c8132f217d27390a1c063a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 06:24:57 2020 -0800
Calculate wdmerger GW strain in C++ (#1309)
A number of interfaces that are no longer used are removed.
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/wdmerger_util.F90
commit 258610fbe8db75fae4b224d66457fa565a2beabc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 06:01:47 2020 -0800
Convert wdmerger problem tagging to C++ (#1304)
Since wdmerger needs to know what level we're on, the level is added to the interface.
Exec/hydro_tests/rotating_torus/problem_tagging.H
Exec/science/wdmerger/problem_tagging.H
Exec/science/wdmerger/problem_tagging_nd.F90
Source/driver/Castro.cpp
Source/problems/problem_tagging.H
commit 976ec326a0ab9f09d5e35f2d0c2fcaca2082b617
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 05:58:34 2020 -0800
Add another attributes(managed) guard (#1307)
Util/conservative_interpolate/conservative_map.F90
commit 06e2b16cbac926032bd6fd882d60ab7caead86ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 7 16:10:33 2020 -0800
Remove wdmerger tagging capability based on distance from center (#1303)
This capability is not currently used in any science setup so it is no longer needed.
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/probin
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/science/sc20/collision_ml0/probin
Exec/science/wdmerger/science/sc20/collision_ml1/probin
Exec/science/wdmerger/science/sc20/collision_ml2/probin
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit 91e7e2a024cae791804e0ca5ae12433015dd0a02
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 7 11:44:52 2020 -0800
Apply Poisson gravity tagging restriction to all setups (#1302)
Poisson gravity doesn't have support for fine levels that touch the physical domain boundary (that is, the boundary is not either periodic or symmetric). This is enforced as an abort in the Poisson solver, but we can also do better by just preventing this from happening directly. This was already the case in wdmerger; this PR applies this across all problems that use Poisson gravity.
CHANGES.md
Docs/source/AMR.rst
Exec/science/wdmerger/problem_tagging_nd.F90
Source/driver/Castro.H
Source/driver/Castro.cpp
commit b3fe13f35673e47cf22d89950432d9d8d2fbf2c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 7 10:59:09 2020 -0800
Sync F90 parameters with C++ after C++ problem_initialize (#1301)
Source/driver/Castro.cpp
Util/scripts/write_probdata.py
commit ec65c1d2d0131dfd99b9c3d056288ddf6f0ccea6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 7 13:40:14 2020 -0500
allow for MHD problems to use C++ initialization (#1298)
This converts BrioWu as a demonstration
CHANGES.md
Exec/mhd_tests/BrioWu/Prob_mhd_nd.F90
Exec/mhd_tests/BrioWu/Prob_nd.F90
Exec/mhd_tests/BrioWu/problem_mhd_setup.H
Exec/mhd_tests/BrioWu/problem_setup.H
Source/driver/Castro.cpp
Source/problems/Make.package
Source/problems/Prob_mhd_nd.F90
Source/problems/problem_mhd_setup.H
commit ffa2f4e95853a1641a3aa4f669c283ae3583aad7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 7 12:11:30 2020 -0500
remove the old passmap's -- they are not used in Fortran (#1300)
Source/driver/Castro_nd.F90
Source/driver/meth_params.template
commit e51e875f3ce2f1fb601fee8260305e3f2fbb29df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 6 19:49:45 2020 -0500
convert reacting_bubble to C++ (#1296)
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/Problem_Derive.H
Exec/reacting_tests/reacting_bubble/Problem_Derive.cpp
Exec/reacting_tests/reacting_bubble/Problem_Derive_F.H
Exec/reacting_tests/reacting_bubble/problem_derive_nd.F90
Exec/reacting_tests/reacting_bubble/problem_setup.H
commit 1add0eaeff86fdb035c76aaac793f24dc67e4495
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 5 21:43:02 2020 -0500
convert hse_convergence setup to C++ (#1254)
Exec/gravity_tests/hse_convergence/GNUmakefile
Exec/gravity_tests/hse_convergence/Make.package
Exec/gravity_tests/hse_convergence/Prob_nd.F90
Exec/gravity_tests/hse_convergence/initial_model.F90
Exec/gravity_tests/hse_convergence/initial_model.H
Exec/gravity_tests/hse_convergence/problem_setup.H
commit 399481418244ac5f14ba339c528d454322c74f24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 5 17:28:08 2020 -0500
fix compilation (#1297)
Source/problems/bc_ext_fill.H
commit 979f09fdcd82b9fb12724e56b28d55d88864392f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 5 10:38:22 2020 -0800
Guard attributes(managed) with AMREX_USE_GPU_PRAGMA (#1292)
Exec/science/wdmerger/initial_model.F90
Source/driver/amrinfo_nd.F90
Source/driver/meth_params.template
Source/driver/parse_castro_params.py
Source/driver/prob_params_nd.F90
Source/driver/reduction_nd.F90
Source/problems/ambient_nd.F90
Source/sources/sponge_nd.F90
Util/model_parser/model_parser.F90
Util/scripts/write_probdata.py
commit 0fdf24cf9492d1a099ad0f5a80af33ae6bec1340
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 5 12:00:00 2020 -0500
start porting the model parser to C++ (#1247)
You can now parse the initial model in a C++ problem setup by using USE_CXX_MODEL_PARSER=TRUE
Exec/Make.Castro
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/_prob_params
Exec/hydro_tests/toy_convect/probin
Exec/hydro_tests/toy_convect/problem_setup.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
Source/problems/bc_ext_fill.H
Source/problems/bc_ext_fill_nd.F90
Util/model_parser_cxx/Make.package
Util/model_parser_cxx/model_parser.H
Util/model_parser_cxx/model_parser_data.H
Util/model_parser_cxx/model_parser_data.cpp
commit 9823c754f04d885643395f1efbf255bb5f6301c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 5 06:45:41 2020 -0800
Clone the ambient state to C++ (#1295)
A copy of the ambient_state is now retained in C++, and we use it for the call that implements clamp_temp.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_util_nd.F90
Source/problems/Make.package
Source/problems/ambient.H
Source/problems/ambient.cpp
Source/problems/ambient_nd.F90
commit a87a09382456aac568843ab9c7e6233d078d3f3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 4 17:10:58 2020 -0500
only support USE_SIMPLIFIED_SDC with USE_CXX_REACTIONS=TRUE (#1294)
Now that we have wrappers that provide C++ interfaces for any pure-Fortran network, we can enforce that
simplified-SDC only works with a C++ integrator. This will make it easier for use to develop new features by not requiring us to port those features to both the C++ and Fortran code paths.
CHANGES.md
Exec/Make.Castro
Source/reactions/Castro_react.cpp
Source/reactions/Castro_react_F.H
Source/reactions/React_nd.F90
commit 4cb8f565a5601d53e1ff54441aeb9ccf217f9ab4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 11:06:16 2020 -0800
Avoid some Castro class accesses in device code (#1291)
Given the AMReX implementation for CUDA code, we cannot access Castro class member data and methods in device code. For data it should be declared as local data prior to the ParallelFor. For functions they should just be moved outside the class, for example as header implementations.
Source/driver/timestep.cpp
Source/hydro/advection_util.cpp
Source/rotation/Castro_rotation.H
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
commit 26d44eb7199978423ec49a4332129cdec6216ae1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 09:09:53 2020 -0800
Convert tagging routines to C++ (#1293)
For now the parameters continue to reside in Fortran so that user code does not break, so we use helper routines to bring the values of the module parameters over to C++.
Source/driver/Castro.cpp
Source/driver/Castro_error_F.H
Source/driver/Tagging_nd.F90
commit 2d479dc5cf31ae2c6af2b03310f95ef6780df07f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 3 20:17:49 2020 -0500
finish porting the radiation consup + advect_fspace to C++ (#1189)
Source/driver/Castro_F.H
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_rad.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/advection_util.cpp
Source/hydro/flatten.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/slope.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/mhd/ct_upwind.cpp
Source/mhd/mhd_util.cpp
Source/radiation/Make.package
Source/radiation/RadHydro.H
Source/radiation/RadHydro_nd.F90
Source/radiation/rad_params.F90
Source/radiation/trace_ppm_rad.cpp
Source/sdc/Castro_sdc.cpp
commit b7f8e3f2fb1e7ab41ed98d78bc1429e6e838d56c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 07:55:00 2020 -0800
Convert problem tagging to C++ (#1289)
As in #1227, the interface is added as an inline header which, if not overridden by a problem setup, does nothing. rotating_torus is converted as a demonstration.
CHANGES.md
Docs/source/AMR.rst
Docs/source/creating_a_problem.rst
Exec/hydro_tests/rotating_torus/problem_tagging.H
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Source/driver/Castro.cpp
Source/problems/Make.package
Source/problems/problem_tagging.H
commit dc1edf2fdeaa3bd32379783a33e4140d4eab2708
Merge: f8760a19d 354e3189b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 2 16:35:59 2020 -0500
Merge branch 'development' into main
commit f8760a19d9aa37b792bc0407082d34fc7324f9b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 2 16:35:51 2020 -0500
update AMReX and Microphysics to 20.11
external/Microphysics
external/amrex
commit 354e3189b4bf525f2783a816a294f39be52f5ac9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 1 09:40:23 2020 -0800
Fix rotating_star compilation for non-NSE (#1288)
Exec/science/rotating_star/Prob_nd.F90
commit 1e55be4f05f28d621a91034693284be83623c6a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 1 09:21:33 2020 -0800
Fix some xrb_mixed issues (#1287)
Exec/science/xrb_mixed/Prob_nd.F90
Exec/science/xrb_mixed/_prob_params
Exec/science/xrb_mixed/probin
commit 79127152ed0c5f1516cd0f9b22e951ef2fa1d892
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 18:45:53 2020 -0700
Convert some Rad_nd routines to C++ (#1285)
Source/driver/Castro.H
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 41624c26dd9cb420fcd00ed70e804d89d1510212
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 13:15:56 2020 -0700
Bump up minimum C++ standard to C++14 (#1284)
C++14 is now required as the minimum C++ standard. This should cause no changes except for RHEL 7/CentOS 7 systems where users will be required to use a more recent gcc than the system default.
This will support some C++14 constructs we want to add to Microphysics.
CHANGES.md
Docs/source/getting_started.rst
Exec/Make.Castro
commit c2f698c01ec546c3b9efd21c33e3c15121bc8f41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 31 07:53:02 2020 -0400
implement SDC C++ reactions (#1280)
When we compile with USE_SIMPLIFIED_SDC=TRUE and USE_CXX_REACTIONS=TRUE, the SDC is now handled by C++
Exec/reacting_tests/nse_test/probin
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
commit 25bbd452ab9da82668bd136a178aea6f9c110970
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 12:41:45 2020 -0700
Allow problems to turn off use of GPU pragma (#1282)
If a problem is known to not require the GPU pragma script anymore, this can now be disabled by setting USE_GPU_PRAGMA = FALSE in its GNUmakefile. We implement this for Sedov and thus this closes #1203. Technically we have not eliminated all of the places in the Sedov build where pragma gpu is still in a compile path -- as mentioned there, the relevant places are set_problem_tags and then hypfill/denfill and ext_fill and ext_denfill. However, set_problem_tags does no work for Sedov, so there's no need for a GPU compile (it will just be a no-op on the CPU). A similar comment is true for the BC fill routines -- they only still do work at this point if we're using ambient BCs (hypfill/denfill) or HSE BCs (ext_fill/ext_denfill). So we should be able to eliminate the GPU build for those routines and trust that there is no performance impact because the loops that do any work never get evaluated.
Exec/Make.Castro
Exec/hydro_tests/Sedov/GNUmakefile
commit ca6b746807e7fd09887ebc0587a6a63633d0d6d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 30 14:01:26 2020 -0400
fix compilation when not using NSE (#1283)
Exec/reacting_tests/reacting_convergence/problem_setup.H
commit ac58a35b363f637fc49b2b30cbeac75aa61c9925
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 30 13:50:57 2020 -0400
remove an extra interface for the ext fill stuff (#1259)
This is no longer needed since we removed the register capping in 1281.
Source/problems/Castro_bc_ext_fill_nd.H
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
commit 7b0ffcf1a080f139064c21aefe0a88790a127c03
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 06:39:09 2020 -0700
Remove old CUDA make rules (#1281)
We had rules in the build system that capped the number of registers per thread used in the CUDA build for the boundary condition routines. This allowed us to be consistent with similar logic I had inserted in AMReX in the Fortran filcc. However, we no longer use that boundary condition interface, so the special handling we have in the build system is no longer necessary (#819, #1048, #1049). These CUDA build rules are a holdover from that time and have been obsolete for a while.
Exec/Make.Castro
Exec/Make.cuda_rules
commit d0c4c451ecbbe7149105b47f00f2599d22e47b71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 30 08:22:05 2020 -0400
allow the reacting_convergence test to run with NSE (#1275)
Exec/reacting_tests/reacting_convergence/problem_setup.H
commit 3e1de4c693a00ea45369d8455e6317e8c82338f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 29 22:24:22 2020 -0400
some updates to the flowchart to reflect past changes (#1278)
Docs/source/FlowChart.rst
Docs/source/timestepping.rst
commit 941fd60f6cf249bc8c4c49a5b168dc7d721e96d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 29 14:00:18 2020 -0400
rename just_the_mhd to construct_ctu_mhd_source (#1279)
Source/driver/Castro_advance_ctu.cpp
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
commit 8e48be7554a6dfae35e156a743771a101cd3d9a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 28 13:41:21 2020 -0400
ifdef out some SDC-only MFs (#1277)
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit b56044b69377be938df8608f8cc5f74a3a1fa438
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 27 09:30:42 2020 -0700
Allow retry to be skipped if starting density is too small (#1273)
A new option, castro.retry_small_density_cutoff, has been added. In some cases a small or negative density retry may be triggered on an update that moves a zone already close to small_dens just below it. This is not uncommon for "ambient"/"fluff" material outside a star. Since these zones are not dynamically important anyway, triggering a retry is unnecessary (and possibly counterproductive, since it may require a very small timestep to avoid). By setting this cutoff value appropriately, the retry will be skipped if the density of the zone prior to the update was below the cutoff. The zone will be reset using the standard approach in enforce_min_dens.
This is done in conjunction with #1272, which provides us the necessary data for making this determination. I have observed that the WD collision problem can get into situations where densities just above small_dens get pushed just below it. It's very hard to fix this problem with a smaller dt, since the difference between the starting and ending densities may be very small already in absolute terms. So the problem setup can crash after hitting too many retry subcycles. Since we don't care about zones near small_dens anyway, it is more efficient to just skip the retry in that case and let clean_state handle it.
CHANGES.md
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit 558f2c92215f51255df3160dec17e67e5c1cdd28
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 27 07:48:41 2020 -0700
Add GPU memory consumption diagnostics to wdmerger (#1274)
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit 58e59cf527cc07acd196d73b02a748d3a3c177d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 27 06:40:04 2020 -0700
Add diagnostic information if we retry for small/neg density (#1272)
On a retry we print the new density, the old density, and the zone index, to help the user understand the context for where the update went wrong. Although this adds some parallel reductions, they only occur on a retry, which should be uncommon.
Source/driver/Castro_advance_ctu.cpp
commit 58962895ab6bef259d6e088faccbc1ae6ddba0ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 27 07:54:54 2020 -0400
Nse test updates (#1270)
a better version of the convergence test combining script
Exec/reacting_tests/nse_test/create_pretty_tables.py
commit 8e0b14f98e0ddac82fae145a061090f9dc03fb0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 27 04:48:52 2020 -0700
Fix namelist for ambient parameters (#1271)
This setup must have been missed when we converted to the ambient namelist.
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
commit 70b27985824114ffe9a09a60fbcf78fdcf2017d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 09:19:19 2020 -0400
convert RT to C++ (#1251)
Exec/hydro_tests/RT/Prob_nd.F90
Exec/hydro_tests/RT/problem_setup.H
commit 95aef339e6e64c651c093f4e2f6b885eb92d7388
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 08:39:00 2020 -0400
add the JOSS badge and cite information (#1269)
CITATION.md
README.md
commit e4791f8d536868308ac64aeb2865ebb688dfedb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 23 11:34:23 2020 -0400
address EIC JOSS paper comments (#1267)
paper/paper.bib
paper/paper.md
commit 8a0c2de0b34895cdd29aa53b4cb99b47b7e31807
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 23 11:31:48 2020 -0400
add another resolution + a script to make a nice table (#1268)
Exec/reacting_tests/nse_test/README.md
Exec/reacting_tests/nse_test/convergence_strang.sh
Exec/reacting_tests/nse_test/create_pretty_tables.py
Exec/reacting_tests/nse_test/inputs.64
commit 8c9acdaa21ca5b77259a6a1303cf28c5ec4dacd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 21 14:25:30 2020 -0400
update the detonation nse inputs/probin (#1266)
this set of parameters actually works for aprox19
Exec/science/Detonation/inputs-det-x.nse
Exec/science/Detonation/probin-det-x.nse_disabled
commit 6a76d03b49bda20d45e7e0ba827eef45aacc9c33
Author: Eloisa Bentivegna <eloisabentivegna@users.noreply.github.com>
Date: Wed Oct 21 00:22:37 2020 +0100
Add one more missing DOI. (#1264)
Co-authored-by: Eloisa Bentivegna <eloisa.bentivegna@stfc.ac.uk>
paper/paper.bib
commit 2969bd9d99e754221dd0f34ca6b8ca1b4de4adfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 16 13:20:11 2020 -0400
get the nova problem compiling again (#1263)
Exec/science/nova/Prob_nd.F90
Exec/science/nova/_prob_params
Exec/science/nova/probin
commit 8af9f98ac044089aa6c5731e07ead9d313a205af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 16 11:13:32 2020 -0400
update the NSE test problem (#1231)
This revives the NSE test problem to use the new NSE network. We will use this for convergence testing with NSE + SDC
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/nse_test/README
Exec/reacting_tests/nse_test/README.md
Exec/reacting_tests/nse_test/_prob_params
Exec/reacting_tests/nse_test/convergence_strang.sh
Exec/reacting_tests/nse_test/inputs.128
Exec/reacting_tests/nse_test/inputs.256
Exec/reacting_tests/nse_test/inputs.512
Exec/reacting_tests/nse_test/probin
commit 0f955d8a49ce9a78070d9017f78f26e871ec5b2e
Author: Eloisa Bentivegna <eloisabentivegna@users.noreply.github.com>
Date: Fri Oct 16 14:13:11 2020 +0100
Fix missing/invalid DOIs in paper.bib. (#1262)
paper/paper.bib
commit 93ade34a5ea320c619a327f060a28fd5b272672b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 13 13:58:31 2020 -0400
Permit level dependent thresholds in new tagging scheme (#1260)
We take advantage of AMReX-Codes/amrex#1441 to allow the user to specify a tagging threshold that can vary by level. If a value for every level is not provided, we assume the last value holds for all remaining levels, similar to how we treat quantities like amr.n_error_buf.
Source/driver/Castro.cpp
commit 2275df32387aa2843738cb1e5abfaeb05de99754
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 8 12:12:50 2020 -0400
move all of the runtime parameter initialization to a central place (#1257)
this moves all of the parmparse stuff for the _cpp_parameter initialization into a single initialization routine (except for the radsolve parameters for now). This change allows the C++ initialization to use the values of other runtime parameters, like gravity.
Source/diffusion/Diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_util.H
Source/driver/Make.package
Source/driver/runtime_parameters.H
Source/gravity/Gravity.cpp
Source/particles/CastroParticles.cpp
Source/radiation/Radiation.cpp
commit f6d891c789c65e329301475de0e8634bbf97e3ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 7 08:12:05 2020 -0400
for some reason we were disabling the ext denfill BCs for the x-direction on GPUs (#1248)
Source/problems/bc_ext_fill_nd.F90
commit 0568ab1aec88f83f6c82900249f3b5ffe2f3eb84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 6 11:00:41 2020 -0400
convert oddeven to C++ (#1250)
Exec/hydro_tests/oddeven/Prob_nd.F90
Exec/hydro_tests/oddeven/problem_setup.H
commit cf9019c1bc8bb43eca58f03b022f8e0cf5c9cd2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 6 10:57:34 2020 -0400
remove the symmetry problem setup (#1252)
this problem does not seem to have ever been used for anything and
the acoustic_pulse problem is largely the same idea and better
developed
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/symmetry/Make.package
Exec/hydro_tests/symmetry/Prob_nd.F90
Exec/hydro_tests/symmetry/README
Exec/hydro_tests/symmetry/_prob_params
Exec/hydro_tests/symmetry/inputs.1d
Exec/hydro_tests/symmetry/inputs.2d
Exec/hydro_tests/symmetry/inputs.3d
Exec/hydro_tests/symmetry/probin
commit 1938efc299cfc1cef11cfc8dd4983ea70fdae036
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 6 10:52:34 2020 -0400
convert gresho vortex to C++ (#1253)
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/gresho_vortex/Prob_nd.F90
Exec/hydro_tests/gresho_vortex/problem_setup.H
commit c5733063b798ee1503f828d5d4b8e0bf8cd26c79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 12:09:15 2020 -0400
update AMReX and Microphysics to 20.10
external/Microphysics
external/amrex
commit 7c37a5f2f7f2918b82c62600c0beab67fcefbfe1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 07:44:00 2020 -0400
we were not updating the kinetic energy to account for the perturbation (#1249)
Exec/hydro_tests/toy_convect/Prob_nd.F90
commit 45db979ae24cc30a9764572a9ef4b74dc7176ce1
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 29 14:45:52 2020 -0700
Add gradient to inputs-based error tagging (#1246)
Sedov is converted to the new scheme as a demonstration.
CHANGES.md
Docs/source/AMR.rst
Exec/hydro_tests/Sedov/inputs.1d.cyl
Exec/hydro_tests/Sedov/inputs.1d.sph
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/inputs.3d.mhd
Exec/hydro_tests/Sedov/inputs.3d.sph
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sedov/probin.1d.cyl
Exec/hydro_tests/Sedov/probin.1d.sph
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords.gammae
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/probin.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/probin.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/probin.3d.mhd
Exec/hydro_tests/Sedov/probin.3d.sph
Exec/hydro_tests/Sedov/probin.3d.sph.testsuite
Source/driver/Castro.cpp
commit 10184e3fdb82666d77f6536d26c41fffbdfea004
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 11:04:57 2020 -0400
switch the code_comp derives over to C++ (#1236)
Exec/gravity_tests/code_comp/Problem_Derive.H
Exec/gravity_tests/code_comp/Problem_Derive.cpp
Exec/gravity_tests/code_comp/Problem_Derive_F.H
Exec/gravity_tests/code_comp/problem_derive_nd.F90
commit 6291e8202cf1bdfe7daf2ee3b1a7b7a7a51ba371
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 11:00:54 2020 -0400
switch Sod_stellar to C++ (#1242)
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/_prob_params
Exec/hydro_tests/Sod_stellar/probin-test1-helm
Exec/hydro_tests/Sod_stellar/probin-test1-helm-y
Exec/hydro_tests/Sod_stellar/probin-test1-helm-z
Exec/hydro_tests/Sod_stellar/probin-test2-helm
Exec/hydro_tests/Sod_stellar/probin-test3-helm
Exec/hydro_tests/Sod_stellar/probin-test4-helm
Exec/hydro_tests/Sod_stellar/problem_setup.H
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/probin-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/probin-test4-helm
commit 55fdb1fee59b8a95ba6b557b16846a72748bf150
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 10:57:30 2020 -0400
convert Radsphere derives to C++ (#1239)
Exec/radiation_tests/RadSphere/Make.package
Exec/radiation_tests/RadSphere/Problem_Derive.H
Exec/radiation_tests/RadSphere/Problem_Derive.cpp
Exec/radiation_tests/RadSphere/Problem_Derive_F.H
Exec/radiation_tests/RadSphere/Problem_Derives.H
Exec/radiation_tests/RadSphere/problem_derive_nd.F90
Exec/radiation_tests/RadSphere/problem_util.H
commit 7dbc8e9ad1e50cf1b12f18f3b188561edda084d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 10:57:07 2020 -0400
fix compilation of RadThermalWave (#1244)
it got caught between 2 PRs
Exec/radiation_tests/RadThermalWave/Problem_Derive.cpp
commit 2e5afbdaa17ff7c969ce23e1df856fed16b36ad4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 29 06:36:54 2020 -0700
Implement new AMReX tagging format (#1243)
The refinement scheme from AMReX-Codes/amrex#1166 is implemented. Rather than using the Fortran tagging namelist, applications may use the inputs file. The scheme looks like:
```
amr.refinement_indicators = dens temp
amr.refine.dens.max_level = 1
amr.refine.dens.value_greater = 2.0
amr.refine.dens.field_name = Density
amr.refine.temp.max_level = 2
amr.refine.temp.value_less = 1.0
amr.refine.temp.field_name = Temp
```
amr.refinement_indicators is a list of user-defined names for refinement schemes. For each defined name, amr.refine.<name> accepts predefined fields describing when to tag. In the current implementation, these are max_level (maximum level to refine to), start_time (when to start tagging), end_time (when to stop tagging), value_greater (value above which we refine), and value_less (value below which to refine), and field_name (name of the string defining the field in the code). If a refinement indicator is added, either value_greater or value_less must be provided. (In the future we will support other refinement schemes such as gradients.)
A wdmerger setup is converted to the new scheme as a test.
CHANGES.md
Docs/source/AMR.rst
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Source/driver/Castro.H
Source/driver/Castro.cpp
commit 0f2590aa5c6406da03852bbc062de67ce2b0d8a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 28 13:49:59 2020 -0400
set the composition if we are in NSE appropriately (#1241)
Exec/science/rotating_star/Prob_nd.F90
commit 0c3b6de9607f68564b7c9f7ba85468dd8161f7ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 11:34:41 2020 -0400
switch the gamma_law_bubble derives over to C++ (#1237)
Exec/hydro_tests/gamma_law_bubble/Make.package
Exec/hydro_tests/gamma_law_bubble/Prob_nd.F90
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.H
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.cpp
Exec/hydro_tests/gamma_law_bubble/Problem_Derive_F.H
Exec/hydro_tests/gamma_law_bubble/_prob_params
Exec/hydro_tests/gamma_law_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/gamma_law_bubble/prob_util.H
Exec/hydro_tests/gamma_law_bubble/probin
Exec/hydro_tests/gamma_law_bubble/probin.big
Exec/hydro_tests/gamma_law_bubble/problem_derive_nd.F90
commit bea35717a45f9c5e94a58386c0276520355bfa08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 11:05:43 2020 -0400
convert diffusion_test derives to C++ (#1238)
Exec/unit_tests/diffusion_test/Make.package
Exec/unit_tests/diffusion_test/Problem_Derive.H
Exec/unit_tests/diffusion_test/Problem_Derive.cpp
Exec/unit_tests/diffusion_test/Problem_Derive_F.H
Exec/unit_tests/diffusion_test/Problem_Derives.H
Exec/unit_tests/diffusion_test/extra_derives_nd.F90
commit 3722a8bb8f7c275b6bf43c4e914ab0de98f7841e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 10:56:58 2020 -0400
convert the RadThermalWave derives to C++ (#1240)
Exec/radiation_tests/RadThermalWave/Problem_Derive.H
Exec/radiation_tests/RadThermalWave/Problem_Derive.cpp
Exec/radiation_tests/RadThermalWave/Problem_Derive_F.H
Exec/radiation_tests/RadThermalWave/Problem_Derives.H
Exec/radiation_tests/RadThermalWave/problem_derive_nd.F90
commit 539e18be902589ef7cb11104bd61a5d53e7456c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 10:45:38 2020 -0400
convert Sod to C++ (#1235)
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod/README.md
Exec/hydro_tests/Sod/_prob_params
Exec/hydro_tests/Sod/probin-test1-helm
Exec/hydro_tests/Sod/probin-test2-helm
Exec/hydro_tests/Sod/probin-test3-helm
Exec/hydro_tests/Sod/problem_setup.H
Exec/hydro_tests/Sod/todo
Exec/hydro_tests/Sod/todo_paper
commit 51412de4031e3c4bd86bcd84d397c8ef7554e791
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 22:35:06 2020 -0400
convert this to C++ (#1233)
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/problem_setup.H
commit 1a775cebdbcd697b3e01a431c3b2d55b21a06f03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 22:33:19 2020 -0400
convert reacting_convergence to C++ (#1234)
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/reacting_convergence/problem_setup.H
commit 0d1c84699b55e197719e0c9c5d699694a255a854
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 15:37:39 2020 -0700
Add prob_params variables to a C++ namespace (#1232)
Variables are added to the problem namespace.
CHANGES.md
Docs/source/creating_a_problem.rst
Exec/gravity_tests/code_comp/Castro_ext_src.H
Exec/gravity_tests/hydrostatic_adjust/Castro_ext_src.H
Exec/hydro_tests/Sedov/problem_setup.H
Exec/hydro_tests/acoustic_pulse/problem_setup.H
Exec/hydro_tests/heating_verification/Castro_ext_src.H
Exec/hydro_tests/test_convect/Castro_ext_src.H
Exec/science/Detonation/Castro_ext_src.H
Exec/science/planet/Castro_ext_src.H
Exec/science/wdmerger/Castro_ext_src.H
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Derive.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_util.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/hybrid.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
Source/sources/Castro_sponge.cpp
Util/scripts/write_probdata.py
commit a62d9b6500c973991d2701af925ad1de211270c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 12:08:28 2020 -0400
convert the acoustic_pulse problem setup to C++ (#1228)
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/problem_setup.H
commit cbb25daf44d4b86dda94c55f377ce48ef1b60207
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 25 06:01:34 2020 -0700
Add hook for C++ problem initialization (#1227)
Sedov is converted to the new scheme as a demonstration.
CHANGES.md
Docs/source/creating_a_problem.rst
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sedov/_prob_params
Exec/hydro_tests/Sedov/problem_setup.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/problems/Make.package
Source/problems/Prob_nd.F90
Source/problems/problem_setup.H
commit 9cb37015a622620538b47168c790708dbbfeb207
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 23 17:10:24 2020 -0700
Convert center to auto prob params (#1222)
CHANGES.md
Exec/gravity_tests/code_comp/Castro_ext_src.H
Exec/gravity_tests/hydrostatic_adjust/Castro_ext_src.H
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/heating_verification/Castro_ext_src.H
Exec/hydro_tests/test_convect/Castro_ext_src.H
Exec/hydro_tests/toy_convect/Castro_ext_src.H
Exec/science/Detonation/Castro_ext_src.H
Exec/science/planet/Castro_ext_src.H
Exec/science/wdmerger/Castro_ext_src.H
Exec/science/wdmerger/Castro_external.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Castro_util_nd.F90
Source/driver/Derive.cpp
Source/driver/prob_params_nd.F90
Source/driver/timestep.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_nd.F90
Source/gravity/Gravity_util.H
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.H
Source/hydro/advection_util.cpp
Source/hydro/hybrid.H
Source/hydro/riemann_util.cpp
Source/problems/_default_prob_params
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
Source/scf/scf_relaxation.F90
Source/sources/Castro_ext_src.H
Source/sources/Castro_external.cpp
Source/sources/Castro_sponge.cpp
Util/scripts/write_probdata.py
commit b820e315b9675a9b74de625b80b21782841a550c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 23 12:09:22 2020 -0700
Call probdata_init() for all problem setups (#1226)
Rather than rely on problems to manually call probdata_init() in amrex_probinit(), this is now called by default for all setups.
While this has no specific benefit at present (other than simplifying code), it becomes functionally relevant when we start adding parameters to _default_prob_params (#1222).
CHANGES.md
Docs/source/creating_a_problem.rst
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
Exec/gravity_tests/hse_convergence/Prob_nd.F90
Exec/gravity_tests/hse_convergence_general/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/RT/Prob_nd.F90
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/double_bubble/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/gamma_law_bubble/Prob_nd.F90
Exec/hydro_tests/gresho_vortex/Prob_nd.F90
Exec/hydro_tests/heating_verification/Prob_nd.F90
Exec/hydro_tests/oddeven/Prob_nd.F90
Exec/hydro_tests/riemann_test_zone/Prob_nd.F90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/symmetry/Prob_nd.F90
Exec/hydro_tests/test_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/mhd_tests/Alfven/Prob_nd.F90
Exec/mhd_tests/BrioWu/Prob_nd.F90
Exec/mhd_tests/DaiWoodward/Prob_nd.F90
Exec/mhd_tests/FastRarefaction/Prob_nd.F90
Exec/mhd_tests/LoopAdvection/Prob_nd.F90
Exec/mhd_tests/MagnetosonicWaves/Prob_nd.F90
Exec/mhd_tests/OrszagTang/Prob_nd.F90
Exec/mhd_tests/RT/Prob_nd.F90
Exec/mhd_tests/species/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/RadBreakout/Prob_nd.F90
Exec/radiation_tests/RadFront/Prob_nd.F90
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
Exec/radiation_tests/RadSlope/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/radiation_tests/RadSuOlsonMG/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/toy_flame/Prob_nd.F90
Exec/scf_tests/single_star/Prob_nd.F90
Exec/science/Detonation/Prob_nd.F90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/convective_flame/Prob_nd.F90
Exec/science/flame/Prob_nd.F90
Exec/science/flame_wave/Prob_nd.F90
Exec/science/nova/Prob_nd.F90
Exec/science/planet/Prob_nd.F90
Exec/science/rotating_star/Prob_nd.F90
Exec/science/subchandra/Prob_nd.F90
Exec/science/wdmerger/problem_io.f90
Exec/science/xrb_mixed/Prob_nd.F90
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/model_burner/Prob_nd.F90
Source/driver/Castro_setup.cpp
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit 56e5f63a10744139fc99450a4543c0567271424d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 23 07:58:19 2020 -0400
linear_to_hybrid is no longer used in Fortran (#1225)
Source/hydro/Make.package
Source/hydro/hybrid_advection_nd.F90
commit 1c584e90e82621537c723b8c1a62b131871ae181
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 22 20:06:22 2020 -0400
we don't use the Fortran version of mom_flux_has_p anymore (#1184)
Source/driver/Castro_nd.F90
Source/driver/prob_params_nd.F90
commit c78eeb712a04a2b96202a81470653c953fd13163
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 16:15:40 2020 -0700
Problem parameters not in namelist also have a C++ version (#1224)
Previously you could add parameters to _prob_params that were not in the Fortran namelist. No C++ version was made of these parameters. However, there is a need for even the ones not in the namelist to have a C++ version, since we may set those variables in probinit and want them later in C++. This implements that change, with the exception of parameters whose size depends on a Fortran module parameter (since we have no direct analogue of that in C++). As a demonstration, many of the wdmerger C++ problem parameters (which were manually managed as duplicates of the corresponding Fortran parameters) are converted to this new format.
This will also be helpful for finishing up #1222 since we will need center in C++.
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/_prob_params
Exec/science/wdmerger/Castro_ext_src.H
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_data.H
Exec/science/wdmerger/wdmerger_data.cpp
Exec/science/xrb_mixed/Prob_nd.F90
Exec/science/xrb_mixed/_prob_params
Util/scripts/write_probdata.py
commit 5de6428fe3b35183ce2ff455b7dffaad50c8ab28
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 14:14:34 2020 -0700
Add riemann.h constants to a namespace (#1223)
This helps avoid conflicts with other global parameters.
Source/hydro/riemann.H
Source/hydro/riemann_solvers.cpp
commit 3d8944f5b11efaa2d790aa8cddd06d338c2b61ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 22 13:12:37 2020 -0400
convert part of the CTU rad stuff to C++ (#1213)
This just converts the main consup radiation part to C++, and leaves the fspace advection in Fortran.
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_ctu_rad.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Make.package
Source/radiation/RadHydro_nd.F90
commit 9cb7a4dd0205858107e262bcdb32304b8ee641d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 05:19:38 2020 -0700
Add a _default_prob_params file (#1210)
This opens up the option to have parameters that are defined for every problem (and thus effectively for the code as a whole). We may want some global parameters to live in the problem parameters namespace because they're updated in the F90 amrex_probinit and so it's easiest to have them automatically updated afterward, using already existing functionality. In particular, the goal is to do center this way (which will be added in a later PR).
This will make it easier to convert Fortran problem setups to C++ (the goal is for every variable that is modified/set in probinit to be part of _prob_params so that it's automatically updated for us in C++).
CHANGES.md
Docs/source/build_system.rst
Docs/source/creating_a_problem.rst
Exec/Make.Castro
Exec/Make.auto_source
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hse_convergence/GNUmakefile
Exec/gravity_tests/hse_convergence_general/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sedov/scaling/sc20/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/double_mach_reflection/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/heating_verification/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/mhd_tests/Alfven/GNUmakefile
Exec/mhd_tests/BrioWu/GNUmakefile
Exec/mhd_tests/DaiWoodward/GNUmakefile
Exec/mhd_tests/FastRarefaction/GNUmakefile
Exec/mhd_tests/LoopAdvection/GNUmakefile
Exec/mhd_tests/MagnetosonicWaves/GNUmakefile
Exec/mhd_tests/OrszagTang/GNUmakefile
Exec/mhd_tests/RT/GNUmakefile
Exec/mhd_tests/species/GNUmakefile
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/reacting_convergence/GNUmakefile
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/scf_tests/single_star/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/Detonation/GNUmakefile.nse
Exec/science/Detonation/science/sc20/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/flame_wave/science/sc20/GNUmakefile
Exec/science/nova/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/science/rotating_star/GNUmakefile
Exec/science/subchandra/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/model_burner/GNUmakefile
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/problems/_default_prob_params
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit f9834d9ab4eb92e71e436edca93b48b5565c5bca
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 18:41:38 2020 -0700
Convert RadBreakout to USE_PROB_PARAMS (#1220)
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadBreakout/Make.package
Exec/radiation_tests/RadBreakout/Prob_nd.F90
Exec/radiation_tests/RadBreakout/_prob_params
Exec/radiation_tests/RadBreakout/probdata.F90
commit 53553f45add1439acd6d4816cf9dac9ca17a2b8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 14:13:31 2020 -0700
Convert bwp to USE_PROB_PARAMS (#1221)
Exec/science/bwp-rad/GNUmakefile
Exec/science/bwp-rad/Make.package
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/bwp-rad/_prob_params
Exec/science/bwp-rad/probdata.F90
commit fde8e7926ef5712be9c4abeb2b4139000f4a732f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 18 11:00:02 2020 -0400
the size of the reactions array was incorrectly dimensioned (#1217)
Source/reactions/React_nd.F90
commit 16411354c68d485fd1ebbde86b81d26384398a25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 16 11:46:03 2020 -0400
add a change entry (#1216)
CHANGES.md
commit 2500cefdba5b65c85181086086b180a2b23ecdba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 16 09:06:19 2020 -0400
some docs updates (#1215)
CITATIONS was moved to markdown and the papers updated
the list of core developers was removed from the Preface and linked instead to the webpage.
This way they don't get out of sync.
CITATION
CITATION.md
Docs/source/Preface.rst
commit eb77ea713d03502871ab1920af0a365c7cef7ff9
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Sep 15 19:08:44 2020 -0400
Aprox19 initial data (#1214)
aprox19 initial data for the rotating star problem
Exec/science/rotating_star/15m_aprox19.6400
commit ab0eba6240ed0bd06f6f9cf8327a559da19650aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 15 12:33:57 2020 -0400
remove reference to paraview + add workflow docs (#1212)
Docs/source/getting_started.rst
README.md
commit dcbc63575e58efd869c9f06da05b75b20031f072
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 15 11:46:31 2020 -0400
fix GPU compilation (#1211)
Exec/gravity_tests/code_comp/Castro_ext_src.H
Exec/gravity_tests/hydrostatic_adjust/Castro_ext_src.H
Exec/hydro_tests/heating_verification/Castro_ext_src.H
Exec/hydro_tests/test_convect/Castro_ext_src.H
Exec/hydro_tests/toy_convect/Castro_ext_src.H
Exec/science/Detonation/Castro_ext_src.H
Exec/science/planet/Castro_ext_src.H
Source/sources/Castro_ext_src.H
commit 0fffef59b3b91a501e0d2c005bc81bc393389a9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 05:00:04 2020 -0700
Decrease small_temp for Noh problem (#1209)
The temperature is O(1e-15) since we're using the gamma law EOS.
Exec/hydro_tests/Noh/inputs_3d
commit 26638187817d67926d152379d9896c93585b01f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 11 14:45:26 2020 -0400
this Fortran function is not used (#1207)
Source/rotation/Make.package
Source/rotation/Rotation_nd.F90
commit eff49104e95fb876bf00c42e9abeca5783cfc58d
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri Sep 11 12:27:32 2020 -0400
Convert ext_src to C++ (#1191)
This address #1187. fill_ext_source is moved from Castro_external.cpp into its own source file so that this can be overwritten for individual problems.
.github/workflows/c-linter.yml
Exec/gravity_tests/code_comp/Castro_ext_src.H
Exec/gravity_tests/code_comp/ext_src_nd.F90
Exec/gravity_tests/hydrostatic_adjust/Castro_ext_src.H
Exec/gravity_tests/hydrostatic_adjust/ext_src_nd.F90
Exec/hydro_tests/heating_verification/Castro_ext_src.H
Exec/hydro_tests/heating_verification/ext_src_nd.F90
Exec/hydro_tests/test_convect/Castro_ext_src.H
Exec/hydro_tests/test_convect/ext_src_nd.F90
Exec/hydro_tests/toy_convect/Castro_ext_src.H
Exec/hydro_tests/toy_convect/ext_src_nd.F90
Exec/hydro_tests/toy_convect/probin
Exec/science/Detonation/Castro_ext_src.H
Exec/science/Detonation/ext_src_nd.F90
Exec/science/planet/Castro_ext_src.H
Exec/science/planet/Prob_nd.F90
Exec/science/planet/ext_src_nd.F90
Exec/science/wdmerger/Castro_ext_src.H
Exec/science/wdmerger/Castro_external.cpp
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/ext_src_nd.F90
Source/driver/timestep.cpp
Source/hydro/advection_util.cpp
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
Source/sources/Castro_ext_src.H
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.H
Source/sources/Make.package
commit 751b6c88809c38908968eb50101210548f552547
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Sep 9 20:50:30 2020 -0400
Check include statements for "" (#1206)
This adds a stage to the cpp linter action to check for include statements which use "" instead of <>. If it finds any then the action shall fail.
.github/workflows/c-linter.yml
commit 5dd40e6a5e00b5e0c3d497249ebb234bee348303
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 9 20:49:41 2020 -0400
switch include style to use <> instead of "" (#1205)
This addresses #331, and allows for us to override headers in problem directories.
This conversion was largely done with:
for i in git grep -l "#include \""; do sed -r -i -E "s/#include "(\w+.\w+)"/#include <\1>/g" $i; done
Diagnostics/DustCollapse/main.cpp
Diagnostics/Radiation/Radiation_utils.H
Diagnostics/Radiation/gaussian_pulse.cpp
Diagnostics/Radiation/lgt_frnt1d.cpp
Diagnostics/Radiation/rad_shock.cpp
Diagnostics/Radiation/rad_source.cpp
Diagnostics/Radiation/rad_sphere.cpp
Diagnostics/Radiation/rhd_shocktube.cpp
Diagnostics/Sedov/main.cpp
Diagnostics/timestep_limiter/main.cpp
Exec/gravity_tests/code_comp/Problem_Derive.cpp
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.cpp
Exec/hydro_tests/rotating_torus/Prob.cpp
Exec/radiation_tests/RadSphere/Problem_Derive.cpp
Exec/radiation_tests/RadThermalWave/Problem_Derive.cpp
Exec/reacting_tests/reacting_bubble/Problem_Derive.cpp
Exec/reacting_tests/toy_flame/Prob.cpp
Exec/science/Detonation/Prob.cpp
Exec/science/flame/Prob.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_Derive.cpp
Exec/unit_tests/diffusion_test/Prob.cpp
Exec/unit_tests/particles_test/Prob.cpp
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/diffusion_util.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/CastroBld.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Castro_util.H
Source/driver/Derive.cpp
Source/driver/main.cpp
Source/driver/timestep.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.H
Source/hydro/advection_util.cpp
Source/hydro/flatten.cpp
Source/hydro/fourth_center_average.cpp
Source/hydro/fourth_order.cpp
Source/hydro/hybrid.H
Source/hydro/ppm.H
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/slope.H
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/hydro/trans.cpp
Source/mhd/Castro_mhd.cpp
Source/mhd/ct_upwind.cpp
Source/mhd/electric.cpp
Source/mhd/hlld.cpp
Source/mhd/mhd_eigen.H
Source/mhd/mhd_plm.cpp
Source/mhd/mhd_ppm.cpp
Source/mhd/mhd_util.H
Source/mhd/mhd_util.cpp
Source/particles/CastroParticles.cpp
Source/problems/Prob.cpp
Source/problems/Problem_Derive.cpp
Source/radiation/Castro_radiation.cpp
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGRadBndry.H
Source/radiation/MGRadBndry.cpp
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RadBndry.H
Source/radiation/RadBndry.cpp
Source/radiation/RadMultiGroup.cpp
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
Source/radiation/_interpbndry/RadInterpBndryData_1d.F90
Source/radiation/_interpbndry/RadInterpBndryData_2d.F90
Source/radiation/_interpbndry/RadInterpBndryData_3d.F90
Source/radiation/energy_diagnostics.cpp
Source/radiation/trace_ppm_rad.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
Source/scf/scf_relax.cpp
Source/sdc/Castro_sdc.cpp
Source/sdc/sdc_util.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
Util/ConvertCheckpoint/Embiggen.cpp
Util/exact_riemann/main.cpp
commit 46fb6dc8a14a44083f8b58acc608142c45c7e567
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 19:11:38 2020 -0400
use the Microphysics version of findparams.py (#1202)
Exec/Make.auto_source
commit 5e5d0f6d3f87ff953fd42057006574cfef4d0728
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 7 15:03:49 2020 -0700
GPU_COMPATIBLE_PROBLEM setups must USE_PROB_PARAMS (#1198)
This helps set us up for C++-ifying some of the problem setups.
Exec/Make.Castro
commit c8cf7ea442c1e4af98e4f76d5e03b1bcd5674f70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 17:53:09 2020 -0400
switch more problems to prob_params (#1200)
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/radiation_tests/RadThermalWave/Make.package
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/_prob_params
Exec/radiation_tests/RadThermalWave/probdata.F90
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/diffusion_test/Make.package
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/diffusion_test/_prob_params
Exec/unit_tests/diffusion_test/probdata.F90
commit 8b2a4d7192b576a21bc143230a77686c1031e189
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 7 14:17:48 2020 -0700
ca_initdata does not abort if unused (#1204)
Source/problems/Prob_nd.F90
commit fb6896d5da3ccca738573ecb468bcb8c7ccbb8e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 15:36:15 2020 -0400
move interpolate_nd.F90 to Util/ (#1197)
Only a few problems need this interpolation routine, so now we only compile it in if USE_INTERPOLATE=TRUE.
CHANGES.md
Exec/Make.Castro
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.F90
Exec/gravity_tests/hse_convergence_general/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/reacting_tests/reacting_bubble/problem_derive_nd.F90
Exec/science/convective_flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Source/driver/Make.package
Util/interpolate/Make.package
Util/interpolate/interpolate_nd.F90
commit 39b7b286994dac612f8b3f22d3aa75a9950b48f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 13:56:37 2020 -0400
remove some unused routines (#1196)
this also puts ca_normalize_species in sdc since that's the only place it is used.
Source/driver/Castro_F.H
Source/driver/Castro_util_nd.F90
Source/sdc/Castro_sdc_F.H
Source/sdc/sdc_util_nd.F90
commit 248ebcd0929224f895d71c2697da716d25acb73b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 6 22:07:07 2020 -0400
add some accessors for radiation to C++ (#1201)
these are needed for the radiation derives.
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 8a908a906ea2a2aec31cf8aa4f58c7cc7e334fc0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 6 14:58:43 2020 -0700
Don't prevent problems from having initial dt < epsilon (#1199)
#1160 attempted to catch problems whose initial dt was zero from subcycling indefinitely. However, it unintentionally broke certain radiation problems with dt < 1.e-15. This resolves the issue by just making the check on dt_subcycle a <= rather than a <, so that we'll catch dt == 0 at time == 0 but not catch dt merely being very small.
Source/driver/Castro_advance_ctu.cpp
commit 8e91486d95008f2dbffcf39c70f9e0bb55883f43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 6 14:40:23 2020 -0400
switch to the init provided by Microphysics (#1195)
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
commit 12d35934202a7089e4eb7fc413ebf57afac08c75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 4 20:08:31 2020 -0400
this file is the same as rad_util_nd.F90, and not in the build system (#1193)
Source/radiation/rad_util.F90
commit 6827ea11039ccb203782e1d4447da53ed8046af2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 4 10:18:59 2020 -0400
fix a bounds issue in ca_initgroups3 (#1192)
In RadMultiGroup.cpp we are allocating xnu as size nGroups+1, but in the Fortran, we dimensioned it as 0:ngroups+2.
Source/radiation/Rad_nd.F90
commit 70b2e723f4ecf49d04c9823b1d7517da0650e796
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 4 09:25:40 2020 -0400
remove a bunch on unused functions (#1190)
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_F.H
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadDerive_nd.F90
Source/radiation/RadTypes.H
Source/radiation/Rad_nd.F90
commit 1b8fccb32992e0e809f817deb6e2ac4009ca121e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 4 09:23:25 2020 -0400
remove the unused nnuspec (#1188)
we no longer have neutrino support
Source/radiation/RadHydro_nd.F90
Source/radiation/RadPlotvar_1d.f90
Source/radiation/RadPlotvar_2d.f90
Source/radiation/RadPlotvar_3d.f90
Source/radiation/Rad_nd.F90
Source/radiation/rad_params.F90
commit 8b1da109c99412a6c1af9d7dd2d6b381a1c7939b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 3 14:21:53 2020 -0400
update AMReX and Microphysics to 20.09
external/Microphysics
external/amrex
commit 55cf7ae2aa13bda48b01ebf2705aa1b275c1649a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 3 09:43:50 2020 -0400
remove unused Fortran rotation routine (#1185)
Source/rotation/Rotation_nd.F90
commit 8608d554d0b0ac31f9ad63d543bfb0a28f19b014
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 3 09:43:29 2020 -0400
only compile in the conservative_interpolate routines if we ask for them (#1183)
also make scf wrapped with GRAVITY
Exec/Make.Castro
Exec/science/flame/GNUmakefile
Source/driver/Castro_F.H
Source/problems/bc_ext_fill_nd.F90
commit 0742517d91a4249467fb54bb7914a0a1b442b25c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 2 14:06:16 2020 -0400
remove references to unused rpar parameters (#1182)
We removed the t_sound based burning limiter, this now removes references to those parameters. This is needed
once we merge starkiller-astro/Microphysics#388
Source/driver/timestep_nd.F90
Source/reactions/React_nd.F90
commit 97ead0b202d6d26f2f2b8dadb7569e2fe9a5e049
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 2 09:42:18 2020 -0400
remove burning_mode = 1 parameters (#1181)
we removed burning_mode from Microphysics
Exec/science/Detonation/probin-collision
Exec/science/Detonation/science/sc20/probin
Exec/science/wdmerger/probin
Exec/science/wdmerger/science/sc20/collision_ml0/probin
Exec/science/wdmerger/science/sc20/collision_ml1/probin
Exec/science/wdmerger/science/sc20/collision_ml2/probin
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
Exec/science/wdmerger/tests/wdmerger_relaxation/probin
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Exec/science/xrb_mixed/probin
commit 5e9eb627a736bcdd1e154558751bc016e0ee8aa8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 09:40:57 2020 -0400
some Flowchart documentation fixes (#1173)
Docs/source/FlowChart.rst
Docs/source/software.rst
commit b21d441fc9316a9641539f976a1d77b4cdf25b6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 31 09:41:40 2020 -0400
fix the clean_state calls when we do MHD + reactions (#1179)
also make the reacting_convergence inputs work for 3-d
CHANGES.md
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
Source/driver/Castro_advance_ctu.cpp
commit afa1e7deb6f9ee653a6eb94ab7f2980e7cc4b497
Author: shardi2 <56055254+shardi2@users.noreply.github.com>
Date: Thu Aug 27 21:10:53 2020 -0400
Rprox probin and inputs file (#1152)
better settings for the rprox flame
Exec/science/flame/README.md
Exec/science/flame/inputs.H_He
Exec/science/flame/probin.H_He
Exec/science/flame_wave/inputs_H_He/probin.H_He.2000Hz
commit d4aafd24d361af16808865263641df82be411e59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 25 15:57:53 2020 -0400
fix a bunch more compiler warnings (#1175)
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Derive.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/trace_ppm.cpp
Source/hydro/trans.cpp
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit 0b451d80d7216fdf8178c9fb9a687f71ffc6584f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 24 11:00:21 2020 -0400
Compiler warnings 2 (#1145)
address more compiler warnings
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_generic_fill.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/problems/Castro_bc_fill_nd_F.H
commit c49ac04cc613eac203a203fd3f1edd788d6ec8bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 11:38:01 2020 -0400
fix non-NSE compilation (#1172)
commit 8d78b7f721c63bba070bb738021da90348fc0f90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 10:30:20 2020 -0400
setup a suite of detonations with Strang + SDC and NSE (#1169)
this cleans up the submission scripts, adds some docs, and slightly tweaks the initial conditions
Exec/science/Detonation/GNUmakefile.nse
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/inputs-det-x.nse
Exec/science/Detonation/nse_runs/README.md
Exec/science/Detonation/nse_runs/detonation.py
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.template.sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/nse_runs/make_plots.py
Exec/science/Detonation/nse_runs/probin.nse_test.sdc
Exec/science/Detonation/nse_runs/setup_runs.py
Exec/science/Detonation/nse_runs/show_status.py
Exec/science/Detonation/probin-det-x.nse_disabled
commit 83e3bce42840ebad1eee07676b485c7df4f3fd56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 21 08:51:18 2020 -0400
if we are doing NSE, then set the aux quantities (#1166)
Exec/science/Detonation/Prob_nd.F90
commit a034c11cb7b2c38614f4a8ea5581272ac96625b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 21 08:47:41 2020 -0400
fix the size of the domain (#1171)
we can have the domain width be < number of ghost cells
Exec/mhd_tests/RT/inputs_3d_mhd
commit 9dd95278b58121990fb8dd8b2a8ec0aed7eef6e9
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Aug 20 11:37:57 2020 -0400
React utils bug (#1168)
This fixes a bug in react_utils.F90 where two subroutines were not being included, leading to a linker error.
Source/reactions/react_util.F90
commit b62b23f642a1dbcdfaa3c73865fe0d4c9c98c98e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 19 10:22:50 2020 -0400
Reacting convergence updates (#1164)
add plm option to Strang
add different # of SDC iterations to simplified-SDC
Exec/reacting_tests/reacting_convergence/convergence_simplified_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_strang.sh
commit 1f43aa675f649a018161efc019f9e5f577df1f06
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sat Aug 15 20:13:56 2020 +0200
Magnetic dipole setups (#1124)
add a magnetic dipole initial condition for wdmerger and stargrav
Exec/gravity_tests/StarGrav/Prob_mhd_nd.F90
Exec/gravity_tests/StarGrav/_prob_params
Exec/gravity_tests/StarGrav/inputs_3d_mhd
Exec/science/wdmerger/Prob_mhd_nd.F90
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/tests/wdmerger_mhd/GNUmakefile
commit 9f06d5f4b1966e3b89ee578453878ec8ad3d0525
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 15 12:42:44 2020 -0400
update the MHD docs (#1163)
CHANGES.md
Docs/source/mhd.rst
commit 325856dc815f672a0a6acc781d723d882a638f55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 15 11:43:20 2020 -0400
use the main slope routine with MHD (#1058)
this removes the MHD's own slope routines and instead uses the main hydro ones for when we do PLM reconstruction. By default this does characteristic limiting, but there is now an option to limit on the primitive variables directly.
Source/driver/_cpp_parameters
Source/mhd/mhd_plm.cpp
Source/mhd/mhd_ppm.cpp
Source/mhd/mhd_slope.H
commit 5de168b32e792ac58e15f4f26997b86e342d2cb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 13 13:27:49 2020 -0400
bump up required make version (#1162)
we don't compile with 3.81 (but that version is from 2006)
Docs/source/getting_started.rst
commit 9574d77be112163f8831f372e55041b7c23b1784
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 10 15:45:36 2020 -0700
Remove dependence on AMReX C_CellMG which is now removed (#1159)
This was removed in AMReX-Codes/amrex#1238.
Exec/Make.Castro
commit 93718c3035ab5cfd71445285acd63871f5983357
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Aug 10 13:09:39 2020 -0400
Check timestep is not too short at time = 0 (#1160)
This checks if dt_subcycle < eps if the time is zero
If dt = 0 at the beginning of the simulation, then there is nothing here to stop it running indefinitely with dt = 0.
Source/driver/Castro_advance_ctu.cpp
commit 5ae81786bcc05893ed91dfdc91fa68ec08fda4c9
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Aug 4 11:20:35 2020 -0400
Selective clang format (#1158)
This amends the C++ linter action so that it selects which problem(s) to compile depending on the files that have been changed in the PR. The action will fail on the first problem that fails to compile. An example of this working can be seen here: https://github.com/harpolea/Castro/runs/945245388.
Most of the work done to select the files and do the processing is done by https://github.com/AMReX-Astro/cpp-linter-action/blob/master/find_changed_files.py and https://github.com/AMReX-Astro/cpp-linter-action/blob/master/run_on_changed_files.py.
.github/workflows/c-linter.yml
commit 974af00d8710e008bbef96b71cadae4a104c0fa6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 2 12:34:52 2020 -0400
update submodules to 20.08 (#1157)
external/Microphysics
external/amrex
commit 774ee4e8d2bb42827d75be4c74b5c63b75443bb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 09:47:48 2020 -0400
add Jean to the .zenodo.json (#1153)
sync up the names in the Zenodo list with the core developers from #1150
.zenodo.json
commit fffd565417ee21346293877022fe466d24f6aed8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 09:47:11 2020 -0400
add some documentation about the build requirements (#1156)
This explains the build requirements in more detail, addressing some of #1155
Docs/source/build_system.rst
Docs/source/getting_started.rst
Docs/source/mpi_plus_x.rst
commit 626cbbda34bc21ec87f5429e307c84f7f443d377
Author: shardi2 <56055254+shardi2@users.noreply.github.com>
Date: Wed Jul 29 18:23:09 2020 -0400
New input files for rprox (#1151)
this models an H/He flame
Exec/science/flame/inputs.H_He
Exec/science/flame/probin.H_He
commit 5a8df73669c56046538ee7a863d4b35e09d4d2ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 27 09:21:41 2020 -0400
fix compilation due to aux no longer being available (#1149)
Source/driver/Castro_setup.cpp
commit 5617a7bb2fcb623dfc24efd8033a2cb089d48470
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 27 09:21:18 2020 -0400
initialize aux for the NSE rotating star (#1136)
Exec/science/rotating_star/15m_aprox19.6400
Exec/science/rotating_star/Prob_nd.F90
commit 96fea6b953d848edfaf45b919b2f6b4bab160aef
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 26 15:32:46 2020 -0700
Perform a clean_state after a regrid (#1148)
Even though we do a clean_state prior to each advance, the timestep is calculated based on the state immediately after the regrid, so applying clean_state may be helpful.
Source/driver/Castro.cpp
commit 5d1bfaa1a3636588340334b2703c6956814964fb
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri Jul 24 15:23:43 2020 -0400
Cause clang-tidy action to fail on failed compilation (#1144)
This will cause the action to fail if flame_wave fails to compile.
It also fixes the build so that the development branch of the Microphysics submodule is checked out.
.github/workflows/c-linter.yml
commit 804cd8d6225c5015ef05a0e466a8a017e10b5a2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 15:21:45 2020 -0400
address some compiler warnings (#1141)
Source/driver/Derive.cpp
Source/driver/parse_castro_params.py
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/advection_util.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_util.cpp
Source/hydro/trans.cpp
commit 79828a6de1952b84093b0415f2239c5a5df92ca7
Author: Andrew Myers <atmyers2@gmail.com>
Date: Fri Jul 24 12:21:19 2020 -0700
remove direct access of id and cpu, which will be removed from amrex (#1146)
These data members are currently implemented using an anonymous struct, which is not part of the C++ standard. They will be removed from amrex as part of a larger effort to eliminate common compiler warnings. You can still get and set them with p.id() and p.cpu().
Exec/unit_tests/particles_test/Prob.cpp
commit 7f84b30c1b9ab2b218f885bef1667b9c355d97e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 11:21:17 2020 -0400
update the submodule (#1143)
external/Microphysics
commit e8e6abf28a72935e11da663600cd17c8cba7d064
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 05:31:02 2020 -0400
C++ doesn't like size 0 arrays for eos_t's aux (#1142)
block them out if NAUX_NET = 0
Source/diffusion/diffusion_util.cpp
Source/driver/Castro.cpp
Source/driver/Derive.cpp
Source/driver/timestep.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/edge_util.cpp
Source/hydro/fourth_order.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/mhd/mhd_plm.cpp
Source/mhd/mhd_ppm.cpp
Source/mhd/mhd_util.H
Source/mhd/mhd_util.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit 0640dd83ce309b6a23d6532710d19f8eb0f67afd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 22 17:42:58 2020 -0400
add a note about the units on B (#1140)
Docs/source/mhd.rst
commit 22ebe33af9d8ed95a3ef419f7f3fc41e882796bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 17 19:18:40 2020 -0400
fix the indexing into rho_auxdot for the derived (#1138)
Source/driver/Castro_setup.cpp
commit 1030807031bd0ec31be06e59cf0e3d0c964ff94b
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri Jul 17 16:51:30 2020 -0400
Aprox19 initial data (#1137)
Instead of rerunning the initial model script, I just added Fe56 and Cr56 to Fe54 in the existing initial model file.
Exec/science/rotating_star/15m_aprox19.6400
commit c5a8d0dd3bbe7e0b38633e8baceec96b000766e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 17 15:32:50 2020 -0400
add NSE inputs (#1135)
This inputs file is for running with the aprox19_nse network + Strang integration.
Exec/science/rotating_star/inputs_2d.nse
Exec/science/rotating_star/probin.nse
commit 7f31b4c9ab376a14d7069e2aa685f98a8e7e42e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 08:30:19 2020 -0700
Move hydro device functions to headers (#1134)
Due to AMReX-Codes/amrex#1148, accesses to class members and functions in device code will fail to compile with CUDA 11. So we need to put these in headers.
Source/hydro/Castro_hydro.H
Source/hydro/Make.package
Source/hydro/advection_util.H
Source/hydro/advection_util.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.H
Source/hydro/riemann_solvers.cpp
commit 95f2c938aa43548321178ba2b2584e7507179ab5
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Jul 16 08:55:20 2020 -0400
Massive star aprox19 initial data (#1133)
This adds initial data for the massive star using the aprox19 network
cr56 and fe56 added fe54
Exec/science/rotating_star/15m_aprox19.6400
commit acf51f9391e007328260a9b872f9206144165deb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 13 05:00:31 2020 -0700
Throw an error if building with both OpenMP and CUDA (#1132)
I plan to eventually build support for this case, but I don't expect it to work correctly right now, so we should disable it for safety.
Exec/Make.Castro
commit 7cfc82a345b580d37d04e0150f4fa6ea772b5852
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 12 13:22:10 2020 -0400
allow the acoustic pulse problem to be "1d" in multi-d (#1131)
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/README.md
Exec/hydro_tests/acoustic_pulse/_prob_params
Exec/hydro_tests/acoustic_pulse/convergence_plm_as_1d.sh
Exec/hydro_tests/acoustic_pulse/convergence_ppm_as_1d.sh
Exec/hydro_tests/acoustic_pulse/probin-x
Exec/hydro_tests/acoustic_pulse/probin-y
Exec/hydro_tests/acoustic_pulse/probin-z
commit c27fe90b91bfdd75d33439de41354a916b96fda5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 14:43:15 2020 -0700
Convert wdmerger derives to C++ (#1129)
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/Problem_Derive.H
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/problem_derive_nd.F90
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_data.H
Exec/science/wdmerger/wdmerger_data.cpp
commit 1d7aa67e5eef2b2e24c8f6ddb7ecaedef14fd899
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 07:03:23 2020 -0700
Calculate rotational acceleration inline and remove Rotation_Type (#1128)
Rather than calculate rotational acceleration first and then use it in the rotation sources, we calculate it on demand in the source evaluation. Rotation_Type is removed from StateData.
CHANGES.md
Docs/source/io.rst
Docs/source/software.rst
Exec/science/wdmerger/Problem_Derives.H
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Rotation.cpp
Source/rotation/rotation_sources.cpp
commit 822170496ed928a2309bea5c1f51cd3d3e5ccec4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 10 05:31:06 2020 -0700
JOSS paper updates (#1125)
paper/paper.bib
paper/paper.md
commit 6f03f4767a42956c13392b425c0cde90b2590c2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 10:47:43 2020 -0700
use_post_step_regrid unconditionally triggers a post-step regrid (#898)
use_post_step_regrid previously would check if the set of tagged zones at the old time did not cover all zones tagged at the new time, and conditionally asked for a post-step regrid if so. However this was expensive on GPUs due to the serial nature of the algorithm (#887). Rather than sort this out, we just unconditionally regrid at the end of every step when the user uses this option. While regridding is expensive, the expectation is that this option is only used when the user expects their tagging criteria to be unconditionally satisfied at all times, and this comes with a performance tradeoff.
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
commit f8e8439f97a55aeb99c756d5842a2f7902a3c453
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 10:32:45 2020 -0700
Use the new AMReX face interpolator for grad phi (#1123)
This fixes #469 and fixes #1118 by ensuring that the interpolator for grad phi (used when gravity.max_solve_level is in play) is valid for nodal data.
CHANGES.md
Source/driver/Castro.cpp
Source/gravity/Gravity.cpp
commit 6cf00f754d650e0efebadc7322f67f8fde5ebb14
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 07:20:04 2020 -0700
Copy additional data from old Castro level on regrid (#1122)
On a regrid where we're copying data from an existing level, we need to make sure we copy the class data relevant to post_timestep if a retry has occurred. This change copies some of these scalar parameters, and also fillpatches the old data in addition to the new data (if the old data is available in the state we're copying from).
Source/driver/Castro.cpp
commit 9d189eb61ba404fde0c4370909ae9aec1a7e8a41
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed Jul 8 13:42:14 2020 -0400
mhd protections to division by 0 (#1120)
adressing potential cases where the division by a very small number (~0) could lead to erroneous calculations
modifying values of alf and als as mentioned in Stone08 and some star states as commented in Miyoshi&Kusano
Source/mhd/hlld.cpp
Source/mhd/mhd_eigen.H
commit 276156bd40fccd5f017ebb1e3ae309e1c85c86c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 8 10:07:18 2020 -0400
fix compilation and add some protection to alf als (#1119)
Source/mhd/hlld.cpp
Source/mhd/mhd_eigen.H
commit afd325daa4404233bfc8dd8314b94df43fbf4e56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 7 18:12:38 2020 -0400
add some comments to the HLLD solver + one simplification (#1117)
Source/mhd/hlld.cpp
commit 5a2277a711ea5c10883bf54392914c87c7dfe429
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 7 05:12:18 2020 -0700
Enforce castro.speed_limit on the magnitude of the velocity (#1115)
Previously this parameter only applied if we were using castro.limit_fluxes_on_large_vel.
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/hydro/advection_util.cpp
commit db6220b66ec55833686597060668333cbf0e1028
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 7 05:10:29 2020 -0700
Lower wdmerger speed limit from 0.1c to 0.05c (#1116)
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 519b569d4986b4392e0391ca9dc7f0b9b817f159
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 6 10:38:25 2020 -0700
Ensure mass fluxes are correct in reflux after a retry (#1112)
As described in #1020, if a retry occurred during a timestep then the mass_fluxes data would not have been correct during the reflux operation. This is now fixed so that the mass fluxes just copy the URHO component of the fluxes.
Fixes #1020
CHANGES.md
Source/driver/Castro.cpp
commit c4c2c9ca531ef1ee1856975502d6ff0e8ce0e09f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 6 08:39:30 2020 -0700
Always refine on non-zero dxnuc in Detonation collision (#1114)
It seems to be the case for this problem that if we refine from the very beginning of the burning, even if we just subcycle the hydro on the fine levels with castro.reactions_max_solve_level=0, that helps avoid the spurious prompt ignition with a low base resolution. With the previous dxnuc_min, we were responding far too late to move the setup away from its course to ignition.
Exec/science/Detonation/probin-collision
commit f589e82f4f7e81308ed1106a9e357b620c05fc29
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 6 10:38:55 2020 -0400
remove some C++ prob param interfaces (#1113)
We no longer pass logicals to C++ -- we should switch the problems to use integers if needed. We also eliminate
the "set" routine for strings -- we don't anticipate needing C++ to update a Fortran string.
Util/scripts/write_probdata.py
commit c0a7a2c17c07c8792829d61a60dee7e02dfa0123
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon Jul 6 10:17:27 2020 -0400
add a factor of 1/2 to the coef in eq.46 (#1111)
in an analogous way with eq. 39
Source/mhd/ct_upwind.cpp
commit 4e8d3fb544d9bb229d60f24a2795c74de4e118f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 5 19:21:20 2020 -0400
add missing refs (#1110)
paper/paper.bib
commit 7e56a1d454d2275b8d85e5545dff24bdcbe54003
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 5 12:23:37 2020 -0400
clarify "physics sources" is source terms (#1109)
paper/paper.md
commit 04cbfcb4217b9a192ed54f76f83f9f768ffb6af0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 5 09:20:02 2020 -0700
Convert uniform_cube_sphere problem_post_init to C++ (#1108)
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Problem.H
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
commit 54360624092cb3b94c0d97a750bf5bf7fed529a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 5 07:05:39 2020 -0700
Fix tolerance specification to uniform_cube_sphere (#1106)
This should have been using the relative tolerance but was using the absolute tolerance.
Exec/gravity_tests/uniform_cube_sphere/inputs
commit 0bfb7df677a36568efd70a08a0c6716db334fc0a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 5 07:05:06 2020 -0700
Add cxx sets to auto prob params (#1107)
Now if we need to modify a parameter from C++, we can make sure the updated value gets back to Fortran.
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit 7971e6723e2c098c73c8bc6222280938adca812b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 14:47:29 2020 -0700
Fix compilation of uniform_cube_sphere (#1104)
This was broken in #1078.
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
commit c4f5283ab817998c17a78a73c747f320e2979da4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 11:58:44 2020 -0700
Remove make_radial_phi (#1103)
This no longer has any effect.
Also, some obsolete interfaces to Fortran are removed.
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit d7efd2f300d364d936b28450525771ce676e9d04
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 10:56:19 2020 -0700
Enable multipole BCs in 1D (#1101)
At the moment this has no effect since Poisson gravity is not enabled in 1D.
This is the last step needed to be able to remove make_radial_phi.
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit ca6a66e94e3ca349cb6403f7701153966f07c7ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 4 13:04:23 2020 -0400
remove pragma gpu (#1102)
Source/hydro/Castro_mol_hydro.cpp
commit ffcbef5a9d2cbfc2b88ce8063519f2dad217be4b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 09:52:55 2020 -0700
Convert more wdmerger functions to C++ (#1100)
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/wdmerger_util.F90
commit bd239c315664a41f96fd6ad69e66910c267de377
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 09:20:10 2020 -0700
Convert multipole gravity to C++ (#1097)
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/gravity/Gravity_util.H
commit b9ce0c8d4136a856b6c108d21c65bf47f1bfde39
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 08:07:51 2020 -0700
Fix assignment for abort_on_failure (#1099)
Source/driver/Castro_nd.F90
commit 8f91394b082b0119d9892ec8fdab173dd20e4058
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 3 08:09:14 2020 -0700
Always use previous phi as guess for solve (#1078)
The Poisson solve has an option to not use the previous gravitational potential as a guess for the new solve (instead, a monopole solve is done and used to fill the domain). This is only used after initialization or restart. This option is now turned off, so that we always use the previous phi. At initialization we will pay a (one-time) larger cost to do the solve, but this should have no other effects.
I would like to remove make_radial_phi; for the most part we don't need it and it makes monopole gravity harder to maintain. If this bit is removed then the only remaining use of make_radial_phi is in the BCs for the Poisson solve, and there it can be replaced entirely with the multipole BCs.
Source/driver/Castro.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit 0cd49961caf9d0755a82cc7346caf09c36e5d571
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 3 10:45:19 2020 -0400
make problem parameters available to C++ (#1093)
For problems that are using USE_PROB_PARAMS = TRUE, this now makes all of the problem runtime parameters
available in C++ in addition to Fortran. This applies only to the problem runtime parameters that are controlled by the namelist, and not any other variables that we're put in _prob_params just to be included in the Fortran module.
The way this works is similar to how we do the extern runtime parameters -- the reading is still controlled by Fortran via the namelist, but now the write_probdata.py script also writes a "get" routine for each of the Fortran parameters that is accessible from C++. These are then all called by init_prob_parameters() just before we do the initialization of the state.
This closes #1065. This depends on starkiller-astro/Microphysics#336
CHANGES.md
Exec/Make.auto_source
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/extern_probin.template
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit bd3adf2c1940d1d34f94bc556a830bcc58f7aadb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 2 18:56:56 2020 -0700
Convert compute_direct_sum_bc to C++ (#1087)
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/gravity/Gravity_util.H
Source/gravity/Make.package
commit 5346932ba6cdbb4d974c60b74d26a3e0a20e4f38
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Thu Jul 2 15:02:17 2020 -0700
Fix typo and wording re general EOS & networks. (#1096)
paper/paper.md
commit dd7f0d60108b80eb639a3fb1c153391bd7ff3f99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 2 15:35:25 2020 -0400
add Jean (#1094)
paper/paper.md
commit 7c70c5d11df53a17b3231992049f03dfb4c911ba
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Jul 2 14:47:19 2020 -0400
Magnetic loop advection (#1095)
adding magnetic loop advection test based on description in Gardiner&Stone 2005
This helps studying multi-D, and is initializing the magnetic field using a vector potential
Exec/mhd_tests/LoopAdvection/GNUmakefile
Exec/mhd_tests/LoopAdvection/Make.package
Exec/mhd_tests/LoopAdvection/Prob_mhd_nd.F90
Exec/mhd_tests/LoopAdvection/Prob_nd.F90
Exec/mhd_tests/LoopAdvection/_prob_params
Exec/mhd_tests/LoopAdvection/inputs
Exec/mhd_tests/LoopAdvection/probin
commit c797c075a83bce84bce7119aed6ef57970d0658b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 2 10:06:46 2020 -0400
fix some JOSS typos (#1092)
paper/paper.md
commit 4d30cba1cafda080cb2c3459f1645d5f30a8ed0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 2 05:09:47 2020 -0700
Correctly capture level by value in device lambda (#1091)
We cannot capture the Castro class member level by value, we need to make a local copy.
Source/driver/Castro.cpp
commit 537ad468f16c02bd300b103f2323536d391c6ad4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 1 13:53:55 2020 -0400
update AMReX and Microphysics to 20.07 (#1090)
external/Microphysics
external/amrex
commit 7ebf8f26546a6ee8b4362b026d6c3cd9b5282545
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Jul 1 09:35:14 2020 -0400
Remove travis files (#1089)
The tests in the travis test suite are no longer required (as everything is done using GitHub actions now), so this PR removes them. It also removes the travis badge from the README
.travis.yml
README.md
id_rsa_travis.enc
commit 97d0bfd072f2960c5df0d72dc2539b973cbfe077
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Jul 1 09:12:25 2020 -0400
Joss paper typos (#1088)
This fixes a few minor typos in the JOSS paper
paper/paper.md
commit a49d4f125936d6970ad56c9a5957861b9b9c1ca8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 30 12:11:20 2020 -0700
Convert interpolate_monopole_grav to C++ (#1085)
Source/gravity/Gravity.cpp
Source/gravity/Gravity_nd.F90
commit 6adfdcfd57e5305b243329033f6659718e814688
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 30 07:56:34 2020 -0700
Convert quadrupole_tensor_double_dot to C++ (#1080)
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/wdmerger_util.F90
Exec/science/wdmerger/wdmerger_util.H
commit 9b0bee3bdae39db6a799866a92d9595baa662684
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 30 07:37:19 2020 -0700
Convert put_direct_sum_bc to C++ (#1086)
This also fixes what looks like a bug in the indexing, which wouldn't have been detectable on the uniform_cube_sphere problem due to the symmetry of the cube.
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit 405135af0b71f51d28a95b4d825d076ad78300e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 29 17:32:39 2020 -0700
Update CHANGES for master -> main renaming (#1084)
CHANGES.md
commit b50e04009ff9d900ea33897034e5ae06ea49d763
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 29 07:47:21 2020 -0700
Switch some more references from master to main (#1083)
* Switch some more references from master to main
* Remove deploy_docs.sh
README.md
deploy_docs.sh
commit 06ab8e1ee297b358563a3f8e734c5c5b58b4e625
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Jun 29 10:37:06 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 (#1082)
.github/workflows/gh-pages.yml
Docs/source/Introduction.rst
Docs/source/Preface.rst
Docs/source/_templates/dev_layout.html
Docs/source/_templates/layout.html
Docs/source/conf.py
Docs/source/debugging.rst
Docs/source/development.rst
Docs/source/getting_started.rst
Docs/source/index.rst
deploy_docs_action.sh
commit 593fd55e60717ef681165b89aacdf34cd7ec9f94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 29 09:46:31 2020 -0400
fix compilation (#1081)
adding missing UFX
Source/sdc/sdc_util_nd.F90
Source/sdc/sdc_vode_nd.F90
commit cee41fabdc07f2007de668f2c4fcfe39d1e572ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 28 20:05:53 2020 -0700
Fix typo from #1076 (#1079)
Source/hydro/Castro_ctu_hydro.cpp
commit 6486220ce4ca4af6703153e0a657292a1e6fbadb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 28 16:12:40 2020 -0700
Don't call EOS on zones with rho = 0 (#1077)
ca_compute_avgpres is called for GR gravity. For monopole gravity we add contributions from multiple levels but mask out the contributions from coarse zones underlying fine levels. This means that in some calls to this function the state will be zeroed out. In that case we want to avoid calling the EOS as this generates NaNs (e.g. when evaluating 1 / rho).
Source/gravity/Gravity_nd.F90
commit 65b01d7ad136bd7d4b7b0cd9449b67728f624c97
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 28 15:41:42 2020 -0700
Convert wdmerger check_relaxation Fortran to C++ (#1057)
The Fortran routines in check_relaxation are converted to C++.
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/binary.F90
Exec/science/wdmerger/binary.H
Exec/science/wdmerger/wdmerger_util.F90
commit cf70a3633c01db9f0ca558b4c34129c180231519
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 28 14:01:45 2020 -0400
clarify that aux variables are defined in the network (#1066)
Docs/source/Hydrodynamics.rst
commit ad63bec730c7fc377579324bb03ad7d9462e9586
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 28 10:57:03 2020 -0700
Fix cases of illegal accesses to cellsizearray (#1076)
CellSizeArray() is dimensioned as AMREX_SPACEDIM so we have to avoid accessing off the end of the array in 1D or 2D.
Source/driver/Derive.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/fourth_order.cpp
Source/mhd/Castro_mhd.cpp
Source/mhd/ct_upwind.cpp
Source/mhd/mhd_util.cpp
Source/sources/Castro_sponge.cpp
commit 9b5e531369ce93e18f2e0182ec21df211ce7d3cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 28 10:44:48 2020 -0700
Convert compute_radial_mass to C++ (#1075)
This Fortran routine is moved into the Gravity class as a C++ function.
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit 01a74fa6cf16f290240d5ee0558c671b70796955
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 28 09:06:15 2020 -0700
Specify some more setVal runon spaces (#1064)
Source/gravity/Gravity.cpp
commit 68616107fc1365e41c540a3806f11c05d5fdbcd2
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sun Jun 28 10:28:33 2020 -0400
checking if divergence of B is 0 at initialization (#1070)
Adding a check during the initialization, for the divergence of magnetic field to be 0
Source/driver/Castro.H
Source/driver/Castro.cpp
commit 9f782e815a9a8a7f29a7f9d151ec7eb4d30d7371
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 27 18:21:55 2020 -0700
Use ParallelFor launches for tagging routines (#1069)
Tagging is converted off of the GPU pragma script. The Fortran routines are marked AMREX_CUDA_FORT_DEVICE and operate on a zone-by-zone basis.
Source/driver/Castro.cpp
Source/driver/Castro_error_F.H
Source/driver/Tagging_nd.F90
commit 0a9b5bceb61ba6d704622ae8964af8189a8da26c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 27 17:10:37 2020 -0700
Add missing module use for UFX (#1074)
Source/problems/bc_ext_fill_nd.F90
commit a5f55406c6eff133b1d9c87c95032e2854da3b15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 27 19:51:27 2020 -0400
add some missing aux inits for eos calls (#1073)
Source/hydro/fourth_order.cpp
Source/mhd/mhd_plm.cpp
Source/mhd/mhd_ppm.cpp
Source/mhd/mhd_util.H
Source/mhd/mhd_util.cpp
Source/problems/bc_ext_fill_nd.F90
Source/sdc/sdc_util_nd.F90
Source/sdc/sdc_vode_nd.F90
commit 03fddba1c9f7a343f6763cf225b02425a2e15dbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 27 18:52:47 2020 -0400
change the preprocessor check from naux to NAUX_NET (#1072)
it is not clear that the naux check ever worked
(it didn't in Microphysics), but now the network explicitly sets NAUX_NET
Source/driver/Castro_setup.cpp
Source/driver/timestep_nd.F90
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
Source/reactions/react_util.F90
Source/sdc/sdc_util.cpp
commit c06d0a2156d0aaa479cc24ea55acfec3661babb1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 27 12:39:16 2020 -0700
Convert ca_clamp_temp to pure device function (#1068)
Convert ca_clamp_temp to a CUDA Fortran device function for the CUDA build.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util_nd.F90
commit 3d07cf82f10575342fb49a537383ba16441e457e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 27 12:07:03 2020 -0700
Add wdmerger relaxation test case (#1071)
Add a test case which explicitly exercises both the wdmerger relaxation functionality and the logic that disables it when the WDs have begun overflowing their Roche lobe.
Exec/science/wdmerger/tests/wdmerger_relaxation/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_relaxation/README.md
Exec/science/wdmerger/tests/wdmerger_relaxation/inputs
Exec/science/wdmerger/tests/wdmerger_relaxation/probin
commit 7810a8e7e8735631993688e527e5ddffe296f919
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Fri Jun 26 18:26:19 2020 -0400
Mhd add magnetic contribution to energy density (#1067)
add the magnetic contribution to the energy density after initialization, rather than in the initdata routine
Docs/source/mhd.rst
Exec/mhd_tests/Alfven/Prob_nd.F90
Exec/mhd_tests/BrioWu/Prob_nd.F90
Exec/mhd_tests/DaiWoodward/Prob_nd.F90
Exec/mhd_tests/FastRarefaction/Prob_nd.F90
Exec/mhd_tests/MagnetosonicWaves/Prob_nd.F90
Exec/mhd_tests/OrszagTang/Prob_nd.F90
Exec/mhd_tests/species/Prob_nd.F90
Exec/science/wdmerger/Prob_mag_nd.F90
Source/driver/Castro.H
Source/driver/Castro.cpp
commit 9df53cf38d7778381bb1522bc29dd7aeb6bbe052
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 26 12:36:12 2020 -0700
Convert pointmass to C++ (#1056)
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Make.package
Source/gravity/pointmass_nd.F90
commit bf6cc17b73fed279a1e0639d4ca214c4d0ac3ab6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 25 22:15:11 2020 -0400
port more rotation stuff to C++ (#1061)
This moves fill_rotational_potential and fill_rotational_psi to C++
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Castro_rotation_F.H
Source/rotation/Make.package
Source/rotation/Rotation.H
Source/rotation/Rotation.cpp
Source/rotation/Rotation_nd.F90
Source/scf/scf_relax.cpp
commit 54d9c4ade93f4b2be68f665fa2145eed96fa9cf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 25 17:45:03 2020 -0400
mark rotational_acceleration routine as HOST_DEVICE (#1063)
This fixes #1062
Source/rotation/Castro_rotation.H
Source/rotation/Rotation.cpp
commit 6eac752ec950d8c4f49e7d37965e391d89c8945b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 24 13:29:05 2020 -0400
remove unused routines (#1060)
No Fortran calls these routines anymore.
Source/hydro/hybrid_advection_nd.F90
commit e37845c230699bacc9b9c51877c4344040111f93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 23 14:44:35 2020 -0400
we were not setting the flattening coefficient over the correct box (#1059)
Source/mhd/Castro_mhd.cpp
commit bfe8efecec42caa29eb73dabde336abf2ebc4e23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 23 11:48:20 2020 -0400
port rotation_sources to C++ (#1053)
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Source/driver/Make.package
Source/driver/math.H
Source/hydro/hybrid.H
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Castro_rotation_F.H
Source/rotation/Make.package
Source/rotation/Rotation.cpp
Source/rotation/Rotation_nd.F90
Source/rotation/rotation_sources.cpp
Source/rotation/rotation_sources_nd.F90
commit 596ef58d49218ee0395f121b1e0be4a18a3c710a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 23 08:07:52 2020 -0700
Convert corrgsrc to C++ (#1054)
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_gravity_F.H
Source/gravity/Make.package
Source/gravity/gravity_sources_nd.F90
commit 87be0913edcb3a848a1c558e7554b80b924a73de
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 22 04:44:49 2020 -0700
Update probins for wdmerger tde test (#1055)
These probins weren't running due to recent updates in the wdmerger namelist parameters.
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
commit 71b3eebff4115bc20d91ad5b235beb11e7b676d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 21 15:48:33 2020 -0700
Convert ca_gsrc to C++ (#1052)
Source/gravity/Castro_gravity.cpp
Source/gravity/gravity_sources_nd.F90
commit f88234acec5e8883429338533cbc47c5b5372df4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 21 11:51:46 2020 -0700
Remove restriction on CUDA that amr.blocking_factor be a multiple of 8 (#1049)
Though using a blocking factor >= 8 is recommended for performance reasons, it was previously required due to correctness reasons because of the use of an AMReX Fortran function, amrex_filccn. As noted in #1048, this function is no longer required due to recent changes in Castro (problems overriding bc_fill_nd.F90 or bc_ext_fill_nd.F90 do not need to provide an initial fill of the ghost zone data before implementing their specific boundary conditions; this is now done for them). Calling this function may now result in race conditions and correctness issues in the CUDA build, so it should be removed from any problem setups.
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_generic_fill.H
Source/driver/Castro_setup.cpp
Source/problems/Castro_bc_fill_nd.cpp
commit 89e3ca19f5b6d3ece61e9cf9d53e6611b3039272
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 21 11:14:26 2020 -0700
Dimension agnostic ca_compute_avgpres (#1051)
Source/gravity/GR_Gravity_1d.F90
Source/gravity/GR_Gravity_2d.F90
Source/gravity/GR_Gravity_3d.F90
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/gravity/Make.package
commit f47d366eb89bd7ba424aba4e4f00bccdc2436f76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 21 13:41:50 2020 -0400
new scaling results for INCITE 2020 (#1043)
Exec/science/flame_wave/scaling/3d_science/flame_wave_scaling.py
Exec/science/flame_wave/scaling/3d_science/inputs.noboost.25cm.1000Hz.3d
Exec/science/flame_wave/scaling/3d_science/probin.noboost.25cm.1000Hz
Exec/science/flame_wave/scaling/3d_science/scaling_20200613.txt
commit 3cda073ee81c20f93c32e2b681c70c4750ae6bf7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 21 10:31:49 2020 -0700
Dimension agnostic ca_put_radial_grav (#1050)
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.F90
Source/gravity/Gravity_2d.F90
Source/gravity/Gravity_3d.F90
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/gravity/Make.package
commit 37d18d60efdc377e0e82f9a7ebf7274004b51fd7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 21 09:45:02 2020 -0700
Remove remaining calls to amrex_filccn (#1048)
PR #837 removed the need for any problem setup to call amrex_filccn in its local bc_fill_nd.F90 routines, hypfill and denfill, because now we will always call the AMReX BC routines prior to entering hypfill or denfill. However that PR did not remove the calls to it from the problem setups that used it, noting that these calls are now redundant. These calls are now removed.
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Source/problems/bc_ext_fill_nd.F90
Source/problems/bc_fill_nd.F90
commit aa3521e6b5be37e2ccc7eed2523ec2ac7945dcc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 16 22:36:15 2020 -0400
allow convergence testing in 3d + plm/ppm (#1047)
Exec/hydro_tests/acoustic_pulse/convergence_plm.sh
Exec/hydro_tests/acoustic_pulse/convergence_ppm.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4_outflow.sh
Exec/hydro_tests/acoustic_pulse/inputs.128
Exec/hydro_tests/acoustic_pulse/inputs.256
Exec/hydro_tests/acoustic_pulse/inputs.512
Exec/hydro_tests/acoustic_pulse/inputs.64
commit d5930dd9deaf34b7da6814fadb778a6a2b77b98b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 16 15:43:09 2020 -0700
Remove domegadt (#1045)
The functionality that permitted the rotation rate to change as a function of time, castro.rotation_include_domegadt and castro.rotational_dPdt, has been removed.
CHANGES.md
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_util.F90
Source/driver/_cpp_parameters
Source/driver/timestep.cpp
Source/hydro/advection_util.cpp
Source/rotation/Castro_rotation_F.H
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.F90
Source/rotation/rotation_sources_nd.F90
commit 5a062ba953e49cd0a145f5554f944fd4115587e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 15 09:37:41 2020 -0700
Restore OpenMP parallel region (#1044)
Source/hydro/Castro_ctu_hydro.cpp
commit cf03e86a400a30dbfc8f9375bd9561e669dc9101
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 14 13:15:56 2020 -0400
remove inlined functions from Castro class (#1042)
Source/hydro/Castro_hydro.H
Source/hydro/fourth_center_average.H
Source/hydro/riemann.H
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/slope.H
Source/mhd/Castro_mhd.H
Source/mhd/mhd_eigen.H
Source/mhd/mhd_util.H
commit 1a0dc2e7d9531b8396525880318700730af1d805
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 13 21:07:14 2020 -0400
add some documentation (#1037)
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/ppm.H
Source/hydro/riemann.H
Source/hydro/slope.H
commit 399dc8a7f54b98a05ed659727dbfe7029dc10b98
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 13 15:32:28 2020 -0700
Convert gravity test residual to C++ (#1041)
ca_test_residual is converted from Fortran to a C++ member of the Gravity class, test_residual. It is made dimension agnostic in the process.
Note: this function is only evaluated in DEBUG mode, and has no effect on the time evolution (it just prints a residual to stdout if gravity.v >= 2).
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.F90
Source/gravity/Gravity_2d.F90
Source/gravity/Gravity_3d.F90
Source/gravity/Gravity_F.H
commit c1af3f742a66e7b12e51241f14594491e384b7c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 13 12:15:53 2020 -0700
Fix lambda capture of dx in MGutils (#1039)
Device lambda capture of dx in the MGutils routines (apply_metric, etc.) requires that we use a GpuArray (geom.CellSizeArray()) rather than a raw pointer. The current code resulted in an illegal memory access error in CUDA when run with 2D Poisson gravity (and there were likely issues in diffusion in 2D as well). This issue was introduced in the port of this code from Fortran to C++ (#854).
CHANGES.md
Source/diffusion/Diffusion.cpp
Source/driver/MGutils.H
Source/driver/MGutils.cpp
Source/gravity/Gravity.cpp
commit 206c3910bdcf6a463e4bbea8ae9b04c6fbfc7d59
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 13 11:42:47 2020 -0700
Write a wrapper for print_update_diagnostics (#1038)
Code redundancy is reduced because a few places that were repeating logic for how to sum up and print the contributions to the state are combined into a single wrapper function.
The diagnostics for the CTU hydro source are moved into the CTU advance rather than being called directly in the source constructor.
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
commit d3bde22277e560d1efe074e2f9a28f97903c5f3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 12 15:16:48 2020 -0400
JOSS paper (#776)
start of the JOSS paper
paper/paper.bib
paper/paper.md
commit e4551d4c9ed4a1abf7078620158845d6d0199164
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 12 15:15:53 2020 -0400
lots of updates to problem descriptions (#1034)
Docs/source/getting_started.rst
Docs/source/index.rst
Docs/source/mhd.rst
Docs/source/problem_setups.rst
Docs/source/refs.bib
Docs/source/sdc.rst
commit 839e58557f511d36acb4155d47d906f08a639eca
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 12 08:51:07 2020 -0700
Remove castro.track_grid_losses parameter (#1035)
This parameter summed up mass/momentum/energy that exited the domain. It was used for a research project several years ago but is no longer actively used.
CHANGES.md
Docs/source/FlowChart.rst
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/_cpp_parameters
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
commit 34a4f993c74577eb1c18c298a5024118cff7953c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 12 05:15:23 2020 -0700
Remove obsolete castro.print_fortran_warnings (#1036)
This parameter no longer had any effect, since the Fortran routines that used it have all been converted to C++.
CHANGES.md
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/inputs.3d.test
Source/driver/_cpp_parameters
commit bd8a5417585c9ba4b2dbe19549ba999ee4820060
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 11 10:25:31 2020 -0700
Do ctoprim on a fab-by-fab basis (#1033)
Closes #908.
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Make.package
commit 66c6b7461c2c2d46907c24bbf993d3859188ffec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 11 09:05:36 2020 -0400
convert the slope routine to a header implementation (#1028)
Now uslope and pslope are header implementations that work zone by zone. This makes it easier to share them (e.g., with MHD) and saves a lot of memory, since we don't need to create a FAB for the slopes.
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol.cpp
Source/hydro/Make.package
Source/hydro/ppm.H
Source/hydro/reconstruction.H
Source/hydro/slope.H
Source/hydro/slope.cpp
Source/hydro/trace_plm.cpp
commit fd6dd4d1a60153b5c377ee11335bf715ae84f366
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 10 21:16:52 2020 -0400
add PPM to MHD (#1002)
This implements PPM reconstruction in the CTU portion of the MHD solver.
CHANGES.md
Exec/mhd_tests/BrioWu/GNUmakefile
Exec/mhd_tests/BrioWu/inputs.sod.test
Source/hydro/ppm.H
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Make.package
Source/mhd/mhd_eigen.H
Source/mhd/mhd_ppm.cpp
commit 816398bd2d17782fc2a944c9a708ffe373db3384
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 10 18:06:18 2020 -0400
fix MHD use_flattening=0 (#1032)
If we are not flattening, then flatn should be 1, not 0
Source/mhd/Castro_mhd.cpp
commit 570f9a85b1cd4fb9aad8f464f3af46e653bde88c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 9 19:50:14 2020 -0400
remove HCBubble (#1031)
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/HCBubble/Make.package
Exec/hydro_tests/HCBubble/Prob_nd.F90
Exec/hydro_tests/HCBubble/_prob_params
Exec/hydro_tests/HCBubble/inputs-sod-x
Exec/hydro_tests/HCBubble/inputs.L0
Exec/hydro_tests/HCBubble/probin-sod-x
commit 89009161f21faea18a6cd5f8d5e0fd4c0cab3c84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 9 19:03:50 2020 -0400
some test inputs for hse_convergence (#1029)
This updates the README.md and adds some test suite inputs files
Exec/gravity_tests/hse_convergence/README.md
Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite
Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite
Exec/gravity_tests/hse_convergence/network_properties.F90
commit b724a8dda16580622f942756cbd5ee59ff133b30
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 9 07:58:10 2020 -0700
Use conservative state in check_for_cfl_violation (#1027)
Previously this routine used the primitive state; now it uses the conserved state.
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
commit 9a43c878e8b515c23dae3dabf0e0dc693acbc0c5
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Jun 9 09:13:35 2020 -0400
Release action (#1025)
This creates an action which will automatically create a release whenever a version is tagged that matches the format xx.xx. The release text is scraped from CHANGES.md using a python script. If no text is found matching the tag, then it is left blank.
.github/workflows/200px-Octicons-git-pull-request.png
.github/workflows/create_release.yml
.github/workflows/get_release_txt.py
.github/workflows/slack-notify.yml
Docs/source/visualization.rst
requirements.txt
commit 52154e6dcf27a952a95894e4c64bbe765834c7bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 8 19:20:15 2020 -0400
Reacting convergence updates (#1026)
This sets a small_x and updates the simplified SDC convergence script
Exec/reacting_tests/reacting_convergence/convergence_simplified_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_strang.sh
Exec/reacting_tests/reacting_convergence/probin
commit 5d17ff316122b225c18baf9fd0df993e07228826
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 8 10:51:14 2020 -0700
Move simplified SDC burn into CTU advance (#1023)
Since the simplified SDC burn was happening right after do_advance_ctu, this change simplifies the logic so it happens just inside instead.
Source/driver/Castro_advance_ctu.cpp
commit 313543eafb9b11d4374c7b2fa3bd9e61b6936b11
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 8 08:49:21 2020 -0700
Rework the Reactions_Type StateData (#927)
The first NumSpec components of Reactions_Type are rho * omegadot rather than omegadot; then, the NumAux auxiliary components are stored, if the network has any auxiliary variables; then, rho * enuc is stored (enuc itself is removed), and finally the burn weights are stored. The checkpoint version has been incremented.
Some reactions_max_solve_level code which was accidentally removed in #922 is restored.
The derives in the flame and toy_flame problems are updated -- it looks like they were not correct before, because we intended to integrate (rho omegadot) before but were only integrating omegadot.
PR motivation
This cleanup, where the calculation of the burn is separate from the application to the state, will help make it easier to do certain experimentation we'd like to do with the burning, such as doing a higher-order burn, and doing the burn in parallel on the CPU and GPU.
CHANGES.md
Exec/reacting_tests/toy_flame/Prob.cpp
Exec/science/flame/Prob.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/timestep_nd.F90
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
Source/sdc/sdc_util.cpp
commit ea94c22e53c8acab65cf62c4c9ec78a3abdc1e93
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 8 06:30:11 2020 -0700
Make Detonation inputs-collision.testsuite run faster (#1024)
Exec/science/Detonation/inputs-collision.testsuite
commit 6553e80c2da615debfc6e936f7b0a8c0f6f1efbb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 7 16:44:21 2020 -0700
Disable agglomeration and consolidation in diffusion MLMG (#1022)
The MLMG operator used in diffusion now has agglomeration and consolidation disabled. These were not relevant since we're just calling apply_op, not doing V-cycles, and it turns out that one of the functions (makeSubCommunicator()) does not scale well to O(10k) ranks on Summit.
Source/diffusion/Diffusion.cpp
commit e677c0445dd2a8cf7995d1f71a879488901f6806
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 7 13:25:06 2020 -0700
Add fluxes consistently between simplified SDC and CTU (#1018)
At the end of the CTU hydro loop, we store the local Fab data from the fluxes and pressure into fluxes, mass_fluxes, and P_radial. This is done as an add because in general we subcycle the CTU advance, and we want the fluxes at the end of the timestep to be the sum of the fluxes from all subcycles. Then this data is reused later in the reflux.
Previously, for simplified SDC, we were copying the data instead of adding it, because we didn't want to add for each simplified SDC iteration, and when retry subcycling was added, it didn't work for simplified SDC. However we can now retry with simplified SDC, so we make it consistent with the CTU advance by adding fluxes as well, but only on the last SDC iteration.
In order to do this we modify Castro_advance_ctu.cpp slightly so that sdc_iters is directly modified on a retry (so that we can read its current value in the hydro advance).
We also correct the fact that P_radial was being stored inconsistently; we stored it always for non-Cartesian geometries, which was different from the logic we used for calculating the local pradial_fab update.
CHANGES.md
Source/driver/Castro_advance_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
commit 2362f0edbe99c5f3570faf159d30b3b7bcb51a5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 5 20:05:39 2020 -0700
Add README for SC20 setups (#1017)
Exec/hydro_tests/Sedov/scaling/sc20/README.md
Exec/science/wdmerger/science/sc20/README.md
commit 1dc4062cfb46ea810840f086e223c4757ddde26b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 2 13:22:27 2020 -0400
fix perturbation in 3-d (#1016)
The perturbation should be centered in the lateral directions in 3-d
Exec/science/flame_wave/Prob_nd.F90
commit feaaf2a20943ad1a96991fff236016b970a9815e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 2 09:34:19 2020 -0400
fix an FPE from uninitialized state with SDC (#1014)
we were not initializing the weights in the reactions_type state
Source/sdc/sdc_util.cpp
commit 67fd2bcecd26d39980940b79a4ade6ebf0993b6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 1 17:58:09 2020 -0400
convert enforce_minimum_density to C++ (#1011)
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Make.package
Source/hydro/advection_util.cpp
Source/hydro/advection_util_nd.F90
Source/hydro/hybrid_advection_nd.F90
commit f471d9697788f2750f964bcadc47a2e4b0353fcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 1 12:46:29 2020 -0400
some README updates (#1012)
README.md
commit adc552c21942232ba05531c27b1fffe2fccf61d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 1 09:42:26 2020 -0700
Update README to reflect PR-only model (#1013)
README.md
commit 577e0d95e369b9085e78807a7495d5ebba3d606e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 1 08:34:17 2020 -0400
port the MOL consup and the 2nd order diffusion to C++ (#996)
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/Make.package
commit 25780bc017ff9b1d774f7b507e0cf1ce0f458198
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 1 08:33:50 2020 -0400
fix some linting errors (#1008)
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
commit f5ae79e6fab04c3d5682b9f0d5df732946ce3494
Merge: 46365d92d c6a9471e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 1 08:28:23 2020 -0400
Merge branch 'development'
commit 46365d92d1df2825b736f709258316f513977d51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 1 08:28:08 2020 -0400
update AMReX and Microphysics to 20.06
external/Microphysics
external/amrex
commit c6a9471e5e14ff5d0f6a85906a30401fed125a2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 31 13:45:28 2020 -0400
update the docs on boundary conditions (#1010)
Docs/source/creating_a_problem.rst
Docs/source/software.rst
commit f28835165f1809b6a448c2e752fbbe93dbd815e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 30 13:20:18 2020 -0400
docs: add MHD to list of capabilities + some minor tweaks (#1009)
Docs/source/Introduction.rst
Docs/source/Preface.rst
commit c7128a91a43e7d1b54a1efce908a428cd67f87d8
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri May 29 18:48:59 2020 -0400
Example yt notebook (#1007)
This provides an example jupyter notebook demonstrating how to use yt for visualization of plot files. This notebook is embedded in the documentation.
Docs/Makefile
Docs/source/_static/theme_overrides.css
Docs/source/conf.py
Docs/source/visualization.rst
Docs/source/yt_example.ipynb
requirements.txt
commit 0a06e4545b9702a2e676d729c8d5d1058611c25d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 29 13:15:04 2020 -0400
some fixes to getting started docs (#1006)
Docs/source/getting_started.rst
commit f32390a61cf5858d0a50a47f675b48247ac45408
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu May 28 22:12:43 2020 -0400
remove the print in initializing magnetic fields (#1005)
also rename the Prob_mhd_nd.F90 in the merger directory
since it had another name, it was using the generic initialization
Exec/mhd_tests/BrioWu/Prob_mhd_nd.F90
Exec/mhd_tests/DaiWoodward/Prob_mhd_nd.F90
Exec/mhd_tests/FastRarefaction/Prob_mhd_nd.F90
Exec/mhd_tests/OrszagTang/Prob_mhd_nd.F90
Exec/mhd_tests/RT/Prob_mhd_nd.F90
Exec/mhd_tests/species/Prob_mhd_nd.F90
Exec/science/wdmerger/Prob_mhd_nd.F90
Source/problems/Prob_mhd_nd.F90
commit 53240552e25c73f0b5455120316d7c172f5990ad
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu May 28 12:28:10 2020 -0400
change remaining max to amrex:max (#1004)
Source/mhd/mhd_plm.cpp
commit 68e33d4f19955b8d21ab435f17c0d07165b80a88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 28 11:06:01 2020 -0400
port MHD to GPU (#993)
Source/driver/Castro.cpp
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/mhd_util.H
Source/problems/Castro_bc_fill_nd.cpp
Source/sources/Castro_thermo.cpp
commit df6e35715812537733d86d2f9ef6240e91668353
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 26 18:28:34 2020 -0400
add artifical viscosity and normalize species fluxes for MHD (#1001)
Source/mhd/Castro_mhd.cpp
commit 7ac62a088d0ec568ddcc2859169d7852e33d790d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 26 13:14:11 2020 -0400
start of the MHD docs (#983)
This also fixes some gravity formatting issues and updates the FAQ.
Docs/source/FlowChart.rst
Docs/source/Hydrodynamics.rst
Docs/source/build_system.rst
Docs/source/debugging.rst
Docs/source/faq.rst
Docs/source/gravity.rst
Docs/source/index.rst
Docs/source/mhd.rst
Docs/source/refs.bib
Source/driver/_cpp_parameters
commit 7d5cc3e14f44e52bd79af2645b21d874fb3b6cc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 26 12:26:45 2020 -0400
prevent UsL/UsR density from being <= 0 (#999)
Source/mhd/hlld.cpp
commit 282df547288a839a98dcacef33d57fcad7d8ae83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 25 16:10:52 2020 -0400
port the 4th order avisc and diffusion to C++ (#995)
Source/hydro/Castro_fourth_order_nd.F90
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/fourth_order.cpp
commit ac0843d29564010a37ba07277dd6aabd66026c39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 25 15:33:58 2020 -0400
fix some abs -> std::abs (#997)
Source/hydro/trace_plm.cpp
commit 2cb562a5bfd08a625f311b6fdbcdfdbb06470676
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 25 14:46:57 2020 -0400
New flame wave inputs (#991)
This updates the inputs to the versions being used for paper II
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.250Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.250Hz
commit ac7dd853a0f284d7be21e4b12546eb376d7defa9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 25 14:39:08 2020 -0400
convert the fourth order reconstruction to C++ (#994)
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/fourth_order.cpp
Source/hydro/fourth_order_nd.F90
commit 878bdc226ac69412df149b5b61131a7965f1725e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 24 15:53:18 2020 -0700
Simplify enforce minimum density by always resetting to small_dens (#989)
When the density is < small_dens, we unconditionally reset it to small_dens. castro.density_reset_method is removed.
The methodology we chose for how to do a reset arguably mattered when we were relying on it for cleaning up bad advances that resulted in a negative density. But now we are relying on retries to handle this (#796). So enforce_min_density should only be cleaning up two cases: when a FillPatch generates a negative density (which is pretty unlikely), and when a reflux generates a negative density (possible, but we'll need to address that separately (#341).
This also avoids the issue discussed in #985 since now a reset is a fully zone-local operation.
CHANGES.md
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/_cpp_parameters
Source/hydro/advection_util_nd.F90
commit 0013b1aebd0da38d125075649455998d412b0cad
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sun May 24 15:19:05 2020 -0400
mhd tests - alfven and mhd waves (#992)
alfven and magnetosonic waves test as in MM section 3.1
Exec/hydro_tests/Sedov/probin.3d.mhd
Exec/mhd_tests/Alfven/Prob_mhd_nd.F90
Exec/mhd_tests/Alfven/Prob_nd.F90
Exec/mhd_tests/Alfven/README
Exec/mhd_tests/Alfven/_prob_params
Exec/mhd_tests/Alfven/inputs-1_0_1d
Exec/mhd_tests/Alfven/inputs-1_0_2d
Exec/mhd_tests/Alfven/inputs-1_1
Exec/mhd_tests/Alfven/probin-1_0
Exec/mhd_tests/Alfven/probin-1_1
Exec/mhd_tests/MagnetosonicWaves/GNUmakefile
Exec/mhd_tests/MagnetosonicWaves/Make.package
Exec/mhd_tests/MagnetosonicWaves/Prob_mhd_nd.F90
Exec/mhd_tests/MagnetosonicWaves/Prob_nd.F90
Exec/mhd_tests/MagnetosonicWaves/README
Exec/mhd_tests/MagnetosonicWaves/_prob_params
Exec/mhd_tests/MagnetosonicWaves/inputs-1_0_2d_fast
Exec/mhd_tests/MagnetosonicWaves/inputs-1_1_slow
Exec/mhd_tests/MagnetosonicWaves/probin-1_0_fast
Exec/mhd_tests/MagnetosonicWaves/probin-1_1_slow
commit e0659d99c01a9b42fa3b9f87b886ee8a2019f4eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 24 14:18:25 2020 -0400
port the MHD HLLD solver to C++ (#990)
CHANGES.md
Source/driver/Castro_F.H
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/Make.package
Source/mhd/hlld.cpp
Source/mhd/hlld.f90
Source/mhd/mhd_state.F90
Source/mhd/mhd_util.H
commit 16d5aae151a8fe8a1b319d38c4d19c462871a4cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 23 15:05:45 2020 -0400
port the MHD PLM reconstruction to C++ (#987)
Source/driver/Castro.H
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/Make.package
Source/mhd/mhd_eigen.H
Source/mhd/mhd_plm.cpp
Source/mhd/mhd_plm_3d.f90
Source/mhd/mhd_sizes.H
Source/mhd/mhd_slope.H
Source/mhd/mhd_util.H
commit aee6a9e02da1d2e2e84c19142586020e9a3baf7d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 23 10:10:33 2020 -0700
Avoid possible sqrt of negative number in circvel (#988)
Source/driver/Derive.cpp
commit ad01d7cc398c4db56ab7a75e495d24080dd7f12a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 22 15:41:43 2020 -0400
Port MHD flattening to C++ and address box sizes (#984)
Now the flattening is done over the same size box as we do reconstruction on. Previously we were not computing the flattening coefficient in all the zones where we applied it. This also reuses the C++ flattening routine.
Note: this adds QPTOT to the primitive variable state so we can flattening on that.
Source/driver/_variables
Source/hydro/advection_util.cpp
Source/mhd/Castro_mhd.cpp
Source/mhd/Make.package
Source/mhd/flatten_mhd.F90
commit 9a87a85bde5439a8e0e8a7acddd0fb48321c4445
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 22 11:42:10 2020 -0400
we don't need NHYP in Fortran, so just define NUM_GROW in C++ (#982)
this also increases some domain sizes so the coarse grid n_cell > NUM_GROW
Exec/mhd_tests/Alfven/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-x-inv
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.briowu.test
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/OrszagTang/inputs
Exec/mhd_tests/OrszagTang/inputs.test
Exec/mhd_tests/RT/inputs_3d
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/meth_params.template
Source/mhd/Castro_mhd.cpp
commit 0f589525b365c40de32f778f147373951f852e55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 22 08:53:00 2020 -0400
fix some MHD array limits (#981)
Source/mhd/Castro_mhd.cpp
Source/mhd/flatten_mhd.F90
Source/mhd/mhd_plm_3d.f90
commit 02f7aca9470b75e076fdaaa4f1b5358721c70d74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 21 14:24:25 2020 -0400
tighten up the boxes for MHD half step (#980)
Lupe pointed out that for the half step we can use the same box size as
the final flux computation
Source/mhd/Castro_mhd.cpp
commit 55eaef1c347b49e797f3c92cf55e38800846298a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 21 09:25:03 2020 -0400
port the MHD CT upwind routines to C++ (#979)
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Make.package
Source/mhd/ct_upwind.cpp
Source/mhd/ct_upwind.f90
Source/mhd/mhd_state.F90
Source/mhd/mhd_util.H
commit 4072a62108c935bc6d7ed2c5a98ac96f80afc590
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 20 20:42:27 2020 -0400
Port the MHD electric routines to C++ (#978)
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Make.package
Source/mhd/electric.cpp
Source/mhd/electric.f90
Source/mhd/mhd_util.H
commit c6f823493b39c68dd16e5e86a466fa39ec5cfcd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 20 18:17:33 2020 -0400
port primtocons and prim_half to C++ (#977)
Source/driver/timestep.cpp
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/Make.package
Source/mhd/ct_upwind.f90
Source/mhd/mhd_sound_speed.H
Source/mhd/mhd_util.H
Source/mhd/mhd_util.cpp
commit 1b7f64bc8f7672a0800bc297709f7b3a614f230d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 20 13:04:32 2020 -0400
clean up some memory in the MHD driver (#976)
we were allocating two versions of E and flux
Source/mhd/Castro_mhd.cpp
commit acc38a02d94c967edf1da1ee5e0e65ba1e922a5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 20 10:58:40 2020 -0400
MHD ct_upwind port to C++ (#975)
This moves all of the ct_upwind driver into the main MFIter loop in C++. Now all of the allocations are done there. This makes it easier to port all of the remaining kernels to C++.
This closes #889
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/ct_upwind.f90
Source/mhd/electric.f90
Source/mhd/hlld.f90
Source/mhd/mhd_plm_3d.f90
commit 9def4e07ed554ff1d2404a338a9c30079cb52690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 19 21:12:55 2020 -0400
condense some interfaces to save on memory (#974)
this updates some MHD interfaces to eliminate temporary arrays
Source/mhd/ct_upwind.f90
commit 0624e080cfdfdfbec47dfc684c0ffcc65b359dff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 19 13:03:45 2020 -0400
shift the MHD interface states so left and right are indexed the same (#973)
Previously for the MHD solver, we were storing q_{i+1/2,L} as qleft(i,j,k) and q_{i-1/2,R} as qright(i,j,k). This shifts the indexing so (i,j,k) for an interface state always means {i-1/2,j,k}. This makes the convention consistent with the other hydro solvers.
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/ct_upwind.f90
Source/mhd/hlld.f90
Source/mhd/mhd_plm_3d.f90
commit c417aaaede4d025c542a7813012fdfd3d10dca30
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 18 12:36:37 2020 -0700
Add dtnuc_T burning timestep limiter (#972)
Similar to dtnuc_e and dtnuc_X, a timestep limiter dtnuc_T is added which restricts the burning from updating the temperature by more than the factor dtnuc_T * T / dT/dt.
CHANGES.md
Source/driver/_cpp_parameters
Source/driver/timestep_nd.F90
commit 3b2aee32ec8732c710c85df7538b31eeb3a99bd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 18 15:23:45 2020 -0400
start making interfaces more explicit (#971)
For PLM, we now pass in a different box for each direction. This also adds comments to the mag updates and adds an epsilon_ijk function.
Source/mhd/Castro_mhd.cpp
Source/mhd/ct_upwind.f90
Source/mhd/mhd_plm_3d.f90
Source/mhd/mhd_state.F90
commit e3e42142c0dcd2fdbb4ddedba26471cbae7434b2
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Sun May 17 17:45:02 2020 -0700
Asyncout (#936)
There are two changes in this PR. First, some prefetch calls are removed because they are done now in AMReX's I/O functions. Second, add support for using async out. It can be turned on with amrex.async_out=1. On up to 64 processes, it should work without any other changes. For more than 64 processes, one must compile with MPI_THREAD_MULTIPLE=TRUE if amrex.async_out is on.
Source/driver/Castro_io.cpp
commit 84b7663d2fe0b455aaf7f285456c677438de731f
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sun May 17 19:42:30 2020 -0400
correct signs in ctu (#970)
we are correcting for the signs issues in eq. 38 and eq. 45 MM
Source/mhd/ct_upwind.f90
commit d416f61218760ba8142f061405d95bc959046132
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 17 14:25:54 2020 -0400
clean up the HLLD Riemann solver (#969)
remove some unnecessary initialization
get rid of an EOS call for each state
Source/mhd/hlld.f90
commit 7c4ef203d053aa849531ab0bef77c3e4f8bcbf32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 16 20:34:59 2020 -0400
some more MHD cleaning (#968)
This simplifies the logic in the corner_couple routine. I also finished a read through the electric_edge_z and updated some comments. Finally, we don't need to initialize the interface states to 0 in mhd_plm.
This also removes some old Fortran files that are no longer used.
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd_F.H
Source/mhd/Make.package
Source/mhd/ct_upwind.f90
Source/mhd/electric.f90
Source/mhd/mhd_plm_3d.f90
commit d7e3c0480ef244d5fee6012bb7ab5ca737af8056
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 16 06:34:57 2020 -0700
Add a return if timestep validity check fails (#967)
This adds an immediate return if the timestep validity check fails, which makes it consistent with the other advance failures.
Source/driver/Castro_advance_ctu.cpp
commit 630f7d8f3e1c4c0e91f03b9a8a4bda4f1f6d0ac3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 16 09:30:27 2020 -0400
convert MHD consup to C++ and some GPU prep (#966)
this converts the MHD consup routine to C++ and adds elixirs to prep for
GPUs. It also removes the unused bcc array.
Source/hydro/Castro_hydro.H
Source/hydro/advection_util.cpp
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/mhd_util.cpp
commit b3d1cbdad34a08409fd8c163744c5736d6a0e4f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 16 09:29:52 2020 -0400
some cleaning of check_for_cfl_violation (#963)
we were returning before the error messages could be issued
now we compute dtdx, ... outside of the MFIter loop
Source/hydro/Castro_hydro.cpp
commit 8c58d1f45e6c9cc24c6ddba6b9661b46f64b4e0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 15 20:25:30 2020 -0400
port check_for_mhd_cfl_violation to C++ (#964)
This gets rid of the cs[AMREX_SPACEDIM] FABs for the sound speeds and instead computes them on the fly in check_for_mhd_cfl_violation as needed.
It also adds some comments to electric_edge_y as I took a pass reading through and checking it.
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/electric.f90
Source/mhd/mhd_util.cpp
commit 8c9c00b3ba7b6c25c069803539bed3cd52cc2ddd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 15 17:42:41 2020 -0400
use qaux instead of calling the EOS in each of the eigensystem routines (#965)
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/mhd_plm_3d.f90
commit afb44ba1dcbe91cbf1980dbd8bbfdaf04c0c9c10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 15 14:01:41 2020 -0400
new flame_wave inputs (#957)
This fixes BCs to the new HSE/upper BC and this sets up the 30 cm H/He burn
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.500Hz
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_boost/probin.boost_10_10
commit 63b182a053d0091e0a693d1d7df03d23093506ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 14 21:58:04 2020 -0400
add some comments to the electric field routines (#961)
This also makes a module to define UMAGX, UMAGY, and UMAGZ and it removes the initialization of E in the electric routines.
Source/mhd/Make.package
Source/mhd/ct_upwind.f90
Source/mhd/electric.f90
Source/mhd/hlld.f90
Source/mhd/mhd_state.F90
commit 87a6a104702bdf978e290dc09b72f73fa486d6ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 14 13:51:28 2020 -0400
some documentation fixes (#960)
Docs/source/faq.rst
Docs/source/io.rst
commit c1c5ed46503c1b071dba8dc6ee3190b2b952464d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 14 11:57:06 2020 -0400
add domain_is_plane_parallel option (#959)
this makes the radvel in the plotfile be in the x-y plane. This PR
also adds a circumferential velocity.
Docs/source/io.rst
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/_cpp_parameters
commit 0143c6da6be5b83d82c97379a25b20afa31f05d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 13 12:29:04 2020 -0400
clean up the corner coupling interfaces (#956)
This simplifies some of the corner coupling interfaces. We can infer the magnetic field
directions from the input states.
Source/mhd/ct_upwind.f90
commit 8f714637fd7856b2aab4c8dfb417aca79381cde0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 13 08:57:37 2020 -0400
start working on the sizes of the input states (#954)
This makes the sizes of the intermediate primitive and conservative state arrays more explicit. It also greatly reduces the amount of memory needed in the corner transport routines.
Source/mhd/ct_upwind.f90
Source/mhd/hlld.f90
commit 00e35d17c414ecf4f73abb4e888fe0914f3cc9ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 12 14:23:38 2020 -0400
make explicit the size of the boxes needed in the corner routines (#953)
There are many intermediate flux arrays in ct_update.F90. Now they are all explicitly sized. This will allow us to better optimize the box sizes needed.
Source/mhd/Castro_mhd.cpp
Source/mhd/ct_upwind.f90
commit ee94b1fef57463cdf252514599d10ed840f37174
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon May 11 17:12:22 2020 -0400
Slack notification for pushes to PRs (#949)
This will create a slack notification when there are pushes to pull requests.
.github/workflows/200px-Octicons-git-pull-request.png
.github/workflows/slack-notify.yml
commit b3aa42c0a3d525d6083f6370c307e847578db410
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 11 12:13:42 2020 -0400
an attempt at making the left and right states clearer (#947)
There are a few issues in how the left and right states are named. In mhd_plm, Ip is used for the left state and Im for the right. These are then stored in qp and qm in the driver. But this is opposite the convention that we use in the rest of the code. To make things clearer, qp is now qleft and qm is now qright.
I propagated this naming convention into ct_upwind. There however, there was more confusion as the names uL and uR were opposite their inferred meanings, so this was also fixed.
Source/mhd/ct_upwind.f90
Source/mhd/hlld.f90
Source/mhd/mhd_plm_3d.f90
commit f6cb585f5e965842e51a6b1c4e4dda786ac7af18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 11 11:15:55 2020 -0400
use gamma_law_general for the MHD problems (#950)
There are some thermodynamic derivatives needed in qflux that
are not provided by gamma_law
This also fixes species initialization
Exec/mhd_tests/Alfven/GNUmakefile
Exec/mhd_tests/BrioWu/GNUmakefile
Exec/mhd_tests/DaiWoodward/GNUmakefile
Exec/mhd_tests/FastRarefaction/GNUmakefile
Exec/mhd_tests/OrszagTang/GNUmakefile
Exec/mhd_tests/RT/GNUmakefile
Exec/mhd_tests/species/GNUmakefile
Exec/mhd_tests/species/Prob_nd.F90
Exec/mhd_tests/species/_prob_params
commit 012332ddea5eb16de309fb49f0a6fd740a4c045a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 11 09:13:29 2020 -0400
fix merge issue + remove unneeded Fortran file (#946)
Source/mhd/Castro_mhd.cpp
Source/mhd/Make.package
Source/mhd/mhd_sound_speed.f90
commit 98f79775efa3dcfe2992e1c07d82aef94f7c6020
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 10 16:10:31 2020 -0400
port magup to C++ (#945)
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
commit be8746981d4c78a09be6fd03aee0ffaefa51d7dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 10 15:42:15 2020 -0400
clean-up of mhd_plm (#944)
This reduces the 3 separate sweeps into a single interface routine that takes an idir argument. It also uses new integer keys to help make sense of the subset of variables that participate in the eigensystem.
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/mhd_plm_3d.f90
commit d8db77e5f9597f0d5a54aba997eb3709a7c72a7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 10 15:29:48 2020 -0400
fix the time centering of the thermo source (#943)
The driver handles the time centering of the thermo source by calling fill_thermo_source with the appropriate state and then combining the old and new sources to produce 1/2 (S_new - S_old)
which is the form of the source corrector. This fixes this implementation.
Source/sources/Castro_sources.H
Source/sources/Castro_thermo.cpp
commit 2a28ce3cab582c074f7063c5ca1c62d52c4019ac
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sun May 10 11:12:38 2020 -0400
mhd sources to plm (#934)
This adds the primitive state sources to the predicted interface states
Source/mhd/Castro_mhd.cpp
Source/mhd/mhd_plm_3d.f90
commit 53555084b792e7f40d4f402037dd3532959ff5c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 10 09:21:19 2020 -0400
more lint fixes (#941)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Derive.cpp
Source/problems/Castro_bc_fill_nd.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sponge.cpp
commit 86339ad34f35d1e785f65ddf13ee6751c9a542a0
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sun May 10 09:20:57 2020 -0400
remove ghost cells from B and extra from state (#928)
this fixes the ghost cells for the internal energy source to allow us to eliminate ghost cells for the state.
Source/driver/Castro_setup.cpp
Source/sources/Castro_thermo.cpp
commit d90cd8d4339a7a287ffde0d61d2f4b932dc93de3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 9 21:41:29 2020 -0400
use the hydro ctoprim (#931)
MHD now uses the same ctoprim as hydro
Source/hydro/Castro_hydro.H
Source/hydro/Make.package
Source/hydro/advection_util.cpp
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Make.package
Source/mhd/mhd_util.cpp
commit 2c6d83a9e1d9f56aa45d3f00b7e3c43e760d4396
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 9 18:50:41 2020 -0400
fix some virtual / override lint issues (#940)
this addresses some linter issues
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_ctu.cpp
commit 3cd3087030fbfc4f0bfdc6744ff6647d25ec76de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 9 18:32:10 2020 -0400
some if/for {} (#938)
some lint issues fixed
Source/driver/Castro_advance.cpp
Source/driver/Castro_setup.cpp
Source/hydro/slope.cpp
commit 2789b9743cf6cefbf1065a12a88d4ee8bf6a01d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 8 14:41:53 2020 -0400
Bugfix (#933)
fix 1-d compilation
Source/driver/Derive.cpp
commit 2b4b8d86fa838fb8a2b4e899c04b8b7be638a393
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 7 23:55:10 2020 -0400
switch to amrex::ParallelFor (#910)
this gives use better backtraces
Source/driver/Castro.cpp
Source/driver/Derive.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/edge_util.cpp
Source/hydro/flatten.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/slope.cpp
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/hydro/trans.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit cf1de386fa777b443e42c77556ef23bf6d380488
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 7 21:46:05 2020 -0400
make Array4 pass as reference (#926)
we now pass Array4 as a reference in all hydro routines
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol.cpp
Source/hydro/advection_util.cpp
Source/hydro/edge_util.cpp
Source/hydro/flatten.cpp
Source/hydro/fourth_center_average.H
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/slope.cpp
Source/hydro/trace_plm.cpp
Source/hydro/trace_ppm.cpp
Source/hydro/trans.cpp
Source/radiation/trace_ppm_rad.cpp
commit fb2ae08f0a552db57f01642e336093dfab24ffd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 7 21:45:15 2020 -0400
fix some unused variables warned by the linter (#932)
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/Derive.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/trace_plm.cpp
Source/reactions/Castro_react.cpp
commit 060ac939174bdb65ec6f7e7078baf00a56c5cfb5
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Thu May 7 17:10:01 2020 -0700
Save integrator stats in the Reactions_Type weights for Simplified SDC (#930)
This PR saves n_rhs + 2*n_jac from the integrator into the Reactions_Type variable weights for simplified SDC as is currently done for Strang.
To see this in the plotfiles requires first merging #929
CHANGES.md
Source/reactions/React_nd.F90
commit 26543e6cfb945819b39e65e0429ab9f572c588d7
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Thu May 7 16:05:46 2020 -0700
For Simplified SDC, in Castro::react_state, do not overwrite R_new with R_old after the burn. (#929)
This PR will ensure new Reactions_Type data is saved after the burn properly so enuc will be saved into the plotfiles correctly, corresponding to the value at the last SDC iteration. It should not change the estimated timestep because we aren't currently using Reactions_Type to do so.
To elaborate:
Currently in Simplified SDC, Castro::react_state() sets the new Reactions_Type data (R_new) in ca_react_state_simplified_sdc.
There we update Unew using the results of the burn, however, right before returning from react_state() we overwrite the burn results in R_new with the old values in Reactions_Type in R_old in the MultiFab::Copy().
This was done in 3460254 because at that time the burning timestep estimator required the Reactions_Type data to be defined. (Although even then it seemingly makes more sense to save R_new back into R_old after the burn instead of vice versa?).
As of 37e048c the timestep checking logic no longer requires the Reactions_Type data in the deprecated ca_check_timestep. We are just calling the actual_rhs to get an instantaneous value for d(Enuc)/dt. Although in Castro::estTimeStep() we are passing R_new into ca_estdt_burning, it remains unused there.
Source/reactions/Castro_react.cpp
commit d18b6ca57e081366e7972e41e370511360370a30
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu May 7 11:22:23 2020 -0400
action for running clang-tidy, clang-format and cppcheck (#914)
This adds an action which runs clang-tidy, clang-format and cppcheck on PRs.
.github/workflows/c-linter.yml
Docs/source/debugging.rst
commit 7c1177aff0888f36493ed579cf2b48d1667c4547
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 22:10:21 2020 -0400
fix compilation of sdc (#925)
Source/hydro/Castro_mol_hydro.cpp
commit 5934a5a4804cb178af307a51f5f186fc72489cf0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 22:09:56 2020 -0400
fix some tidy issues (#924)
Source/driver/Castro_util.H
Source/hydro/Castro_hydro.H
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
commit 232b8d2a7fd902eeb319a6e5f19557429daaaa15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 22:09:36 2020 -0400
standardize the header guards (#915)
Source/diffusion/Diffusion.H
Source/diffusion/diffusion_util.H
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Castro_error_F.H
Source/driver/Castro_generic_fill.H
Source/driver/Castro_util.H
Source/driver/Derive.H
Source/driver/MGutils.H
Source/driver/castro_limits.H
Source/gravity/Castro_gravity_F.H
Source/gravity/Gravity.H
Source/gravity/Gravity_F.H
Source/hydro/Castro_hydro_F.H
Source/hydro/hybrid.H
Source/hydro/riemann.H
Source/mhd/Castro_mhd_F.H
Source/mhd/mhd_sound_speed.H
Source/problems/Castro_bc_ext_fill_nd.H
Source/problems/Castro_bc_ext_fill_nd_F.H
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd_F.H
Source/radiation/HABEC_F.H
Source/radiation/HypreABec.H
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreMultiABec.H
Source/radiation/MGRadBndry.H
Source/radiation/NGBndry.H
Source/radiation/RAD_F.H
Source/radiation/RadBndry.H
Source/radiation/RadSolve.H
Source/radiation/RadTypes.H
Source/radiation/Radiation.H
Source/radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/_interpbndry/RadBoundCond.H
Source/radiation/_interpbndry/RadInterpBndryData.H
Source/radiation/fluxlimiter.H
Source/radiation/rad_util.H
Source/reactions/Castro_react_F.H
Source/rotation/Castro_rotation_F.H
Source/scf/scf_relax_F.H
Source/sdc/Castro_sdc.H
Source/sdc/Castro_sdc_F.H
Source/sources/Castro_sources_F.H
commit fba073963cff7d42143a23c5c993688c093794eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 6 12:58:29 2020 -0700
Clean up Strang interface (#922)
The Strang interface to react_state is cleaned up: rather than having an entry point in strang_react_first_half and strang_react_second_half, react_state is called directly.
The mask that was used to avoid burns on ghost zones is also removed.
Source/driver/Castro_advance_ctu.cpp
Source/reactions/Castro_react.H
Source/reactions/Castro_react.cpp
Source/reactions/Castro_react_F.H
Source/reactions/React_nd.F90
commit e2566b116adad30839e190b558d861c15ce7182f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 14:09:31 2020 -0400
use the CTU src_to_prim (#920)
this makes the MHD solver use the C++ src_to_prim, shared with hydro
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
commit a1e1f07181a4153610a9bbbbfb15ad1649189d8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 13:24:38 2020 -0400
store UEINT flux, initialize UTEMP and USHK flux to 0 (#921)
This fixes a floating point exception in the flux storage loops in Castro_mhd.cpp
Source/mhd/Castro_mhd.cpp
commit a85c95b7e72c9f2d15a0e382b5e0158b83a185c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 11:18:30 2020 -0400
move the fourth order center <-> average stuff to C++ (#884)
All of the averaging routines are now available in C++
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance_sdc.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/fourth_center_average.H
Source/hydro/fourth_center_average.cpp
Source/hydro/fourth_order_nd.F90
Source/sdc/Castro_sdc.cpp
commit 324682d5a37b823a1b9092f8046c81b002aca2f7
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue May 5 14:54:57 2020 -0400
add github pages status badge (#919)
README.md
commit 1257241a2011c4998d773f9590ae61282addee5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 5 08:28:56 2020 -0400
split out the MHD Initialization so we can run MHD on any problem (#909)
This gives us a separate Prob_mhd_nd.F90 that initiializes the magnetic field to 0. Problems can implement their own version of this. By providing this default we can run the MHD solver on any problem setup.
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/_prob_params
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sedov/_prob_params
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/mhd_tests/Alfven/Prob_mhd_nd.F90
Exec/mhd_tests/Alfven/Prob_nd.F90
Exec/mhd_tests/BrioWu/Prob_mhd_nd.F90
Exec/mhd_tests/BrioWu/Prob_nd.F90
Exec/mhd_tests/DaiWoodward/Prob_mhd_nd.F90
Exec/mhd_tests/DaiWoodward/Prob_nd.F90
Exec/mhd_tests/FastRarefaction/Prob_mhd_nd.F90
Exec/mhd_tests/FastRarefaction/Prob_nd.F90
Exec/mhd_tests/OrszagTang/Prob_mhd_nd.F90
Exec/mhd_tests/OrszagTang/Prob_nd.F90
Exec/mhd_tests/RT/Prob_mhd_nd.F90
Exec/mhd_tests/RT/Prob_nd.F90
Exec/mhd_tests/species/Prob_mhd_nd.F90
Exec/mhd_tests/species/Prob_nd.F90
Exec/science/wdmerger/Prob_mag_nd.F90
Exec/science/wdmerger/Prob_nd.F90
Source/problems/Make.package
Source/problems/Prob_mhd_nd.F90
commit 314e6ef43748129ea0ff228f7c0f71a0cf0e0c37
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon May 4 12:52:33 2020 -0400
Mhd density and pressure check in plm and riemann (#912)
Don't let the predicted states go lower than small_dens or small_press
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/hlld.f90
Source/mhd/mhd_plm_3d.f90
commit ed35de024c5825a907ad217666d51ea70ec8896e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 3 20:09:48 2020 -0400
fix the first computeTemp after init (#911)
since the initialization does not operate over ghost cells, the ghost
cell data is invalid, so we should not try to computeTemp there
Source/driver/Castro.cpp
commit 8fc8fcc1d43a0a3d9497ca5a3fd1ec910b944e1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 3 15:36:07 2020 -0400
we don't need QDPDE or QDPDR in qaux anymore for mhd (#907)
we compute these on the fly as needed
Source/driver/_variables
Source/mhd/Castro_advection_mhd_3d.F90
commit f2df0e3ff74d7072a780f98862a8339fb2d4c867
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 3 11:47:24 2020 -0400
run for the full Sod time so we can compare to analytic (#906)
This also increases the resolution to 128 zones
Exec/mhd_tests/BrioWu/inputs.sod.test
commit ec4ec8f7b2b1d8914ca8784489b7bf4bd3444579
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 3 11:46:49 2020 -0400
port main MHD driver to C++ (#904)
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/ct_upwind.f90
Source/mhd/electric.f90
Source/mhd/flatten_mhd.F90
Source/mhd/hlld.f90
Source/mhd/mhd_plm_3d.f90
commit 9efb689af3984cea54f4a392e6d5d9b3256bb6a0
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Sun May 3 09:31:01 2020 -0400
Github action for building docs (#899)
This defines a github action for building the documentation. It is triggered by pushes to the master and development branches
.github/workflows/gh-pages.yml
.travis.yml
deploy_docs_action.sh
commit 26563c0d4175f5a007d9461913775d43953589ae
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Sun May 3 08:44:52 2020 -0400
changed the limits in ctu routines calls (#905)
to be in terms of lo and hi, rather than the array limits
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/ct_upwind.f90
commit 7a8602e71ae3a3c79612c114b6c6b7ac846d68d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 15:04:28 2020 -0400
MHD cleaning (#901)
* fix spelling
* remove unimplemented option
Exec/mhd_tests/Alfven/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-x-inv
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.briowu.test
Exec/mhd_tests/BrioWu/inputs.sod.test
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/OrszagTang/GNUmakefile
Exec/mhd_tests/OrszagTang/Make.package
Exec/mhd_tests/OrszagTang/Prob_nd.F90
Exec/mhd_tests/OrszagTang/_prob_params
Exec/mhd_tests/OrszagTang/inputs
Exec/mhd_tests/OrszagTang/inputs.test
Exec/mhd_tests/OrszagTang/probin
Exec/mhd_tests/OrszagTang/probin.test
Exec/mhd_tests/species/inputs
Exec/mhd_tests/species/inputs.test
commit 0b9e24f13a50c718fe84d66cd430f4bef4475431
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 14:50:41 2020 -0400
convert the MHD soundspeed check to C++ (#902)
This ports estdt_mhd to C++
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/timestep.cpp
Source/driver/timestep_nd.F90
Source/mhd/mhd_sound_speed.H
commit 174a02c345e73498d57a281e21543b9a80652ccb
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Fri May 1 12:29:29 2020 -0400
MHD (#307)
This is a first implementation of a contrained transport, corner transport upwind MHD solver based on Miniati & Colella 2011. At the moment, it is not tested with AMR.
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/_prob_params
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_mhd_test
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_mhd_test
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sedov/_prob_params
Exec/hydro_tests/Sedov/inputs.3d.mhd
Exec/hydro_tests/Sedov/probin.3d.mhd
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/_prob_params
Exec/hydro_tests/Sod_stellar/inputs-test1-helm_mhd
Exec/mhd_tests/Alfven/GNUmakefile
Exec/mhd_tests/Alfven/Make.package
Exec/mhd_tests/Alfven/Prob_nd.F90
Exec/mhd_tests/Alfven/_prob_params
Exec/mhd_tests/Alfven/inputs-sod-x
Exec/mhd_tests/Alfven/probin-sod-x
Exec/mhd_tests/BrioWu/GNUmakefile
Exec/mhd_tests/BrioWu/Make.package
Exec/mhd_tests/BrioWu/Prob_nd.F90
Exec/mhd_tests/BrioWu/_prob_params
Exec/mhd_tests/BrioWu/inputs-briowu-x
Exec/mhd_tests/BrioWu/inputs-briowu-y
Exec/mhd_tests/BrioWu/inputs-briowu-z
Exec/mhd_tests/BrioWu/inputs-sod-x
Exec/mhd_tests/BrioWu/inputs-sod-x-inv
Exec/mhd_tests/BrioWu/inputs-sod-y
Exec/mhd_tests/BrioWu/inputs-sod-z
Exec/mhd_tests/BrioWu/inputs.briowu.test
Exec/mhd_tests/BrioWu/inputs.sod.test
Exec/mhd_tests/BrioWu/probin-briowu-x
Exec/mhd_tests/BrioWu/probin-briowu-y
Exec/mhd_tests/BrioWu/probin-briowu-z
Exec/mhd_tests/BrioWu/probin-sod-x
Exec/mhd_tests/BrioWu/probin-sod-x-inv
Exec/mhd_tests/BrioWu/probin-sod-y
Exec/mhd_tests/BrioWu/probin-sod-z
Exec/mhd_tests/BrioWu/probin.briowu.test
Exec/mhd_tests/BrioWu/probin.sod.test
Exec/mhd_tests/DaiWoodward/GNUmakefile
Exec/mhd_tests/DaiWoodward/Make.package
Exec/mhd_tests/DaiWoodward/Prob_nd.F90
Exec/mhd_tests/DaiWoodward/_prob_params
Exec/mhd_tests/DaiWoodward/inputs
Exec/mhd_tests/DaiWoodward/probin
Exec/mhd_tests/FastRarefaction/GNUmakefile
Exec/mhd_tests/FastRarefaction/Make.package
Exec/mhd_tests/FastRarefaction/Prob_nd.F90
Exec/mhd_tests/FastRarefaction/_prob_params
Exec/mhd_tests/FastRarefaction/inputs
Exec/mhd_tests/FastRarefaction/probin
Exec/mhd_tests/OrzagTag/GNUmakefile
Exec/mhd_tests/OrzagTag/Make.package
Exec/mhd_tests/OrzagTag/Prob_nd.F90
Exec/mhd_tests/OrzagTag/_prob_params
Exec/mhd_tests/OrzagTag/inputs
Exec/mhd_tests/OrzagTag/inputs.test
Exec/mhd_tests/OrzagTag/probin
Exec/mhd_tests/OrzagTag/probin.test
Exec/mhd_tests/RT/GNUmakefile
Exec/mhd_tests/RT/Make.package
Exec/mhd_tests/RT/Prob_nd.F90
Exec/mhd_tests/RT/_prob_params
Exec/mhd_tests/RT/inputs_3d
Exec/mhd_tests/RT/inputs_3d_mhd
Exec/mhd_tests/RT/probin
Exec/mhd_tests/RT/probin_3d_mhd
Exec/mhd_tests/species/GNUmakefile
Exec/mhd_tests/species/Make.package
Exec/mhd_tests/species/Prob_nd.F90
Exec/mhd_tests/species/_prob_params
Exec/mhd_tests/species/inputs
Exec/mhd_tests/species/inputs.test
Exec/mhd_tests/species/probin
Exec/mhd_tests/species/probin.test
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/tests/wdmerger_mhd/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_mhd/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_mhd/probin_test_wdmerger_3D
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Make.package
Source/driver/_cpp_parameters
Source/driver/_variables
Source/driver/filfc.f90
Source/driver/meth_params.template
Source/driver/timestep_nd.F90
Source/mhd/Castro_advection_mhd_3d.F90
Source/mhd/Castro_mhd.H
Source/mhd/Castro_mhd.cpp
Source/mhd/Castro_mhd_F.H
Source/mhd/Make.package
Source/mhd/ct_upwind.f90
Source/mhd/electric.f90
Source/mhd/flatten_mhd.F90
Source/mhd/hlld.f90
Source/mhd/mhd_plm_3d.f90
Source/mhd/mhd_sound_speed.f90
Source/mhd/notes/mhd_jacobian.ipynb
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Castro_bc_fill_nd_F.H
Source/problems/bc_fill_nd.F90
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
Source/sources/Castro_thermo.cpp
commit bd259f85fda9c8ba8abaee5a95990d23f1777c1f
Merge: 3eef784fb dd52aba5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 12:14:37 2020 -0400
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit dd52aba5cded02cb6ed907cb32315f51b3f714ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 12:14:00 2020 -0400
update submodules for 20.05 tagging (#897)
external/Microphysics
external/amrex
commit 3eef784fb053ddcabba818286102ac793c904ca9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 12:02:16 2020 -0400
update to 20.05
external/amrex
commit 42c55cc7b618afbfcb65aa41233035d14c28210e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 08:55:42 2020 -0400
update amrex and Microphysics
external/Microphysics
external/amrex
commit b2d0f26bcc983e24e6f9e4ba6212aaa8f280ba15
Merge: ab4ada857 7d89c9044
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 30 09:50:25 2020 -0400
Merge branch 'development' of github.com:amrex-astro/Castro into development
commit ab4ada85734f3479940d89b0817df44d036617af
Merge: dbd54d55e b86b52449
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 30 09:50:04 2020 -0400
Merge branch 'development' of github.com:zingale/Castro into development
commit 7d89c90449931c8ebe7332d6412df8604d86cb45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 30 09:28:02 2020 -0400
fix a copy for SDC -- wrong number of ghost cells were assumed (#885)
Source/driver/Castro_advance_sdc.cpp
commit dbd54d55e3096f13657f67bc15aae61e463f7aaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 29 18:45:37 2020 -0400
have castro handle burning failures
Exec/science/Detonation/probin-det-x.simplified_sdc
commit b86b524493d4bcf20cedb41b8cde1224d2ddf063
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 29 18:45:37 2020 -0400
have castro handle burning failures
Exec/science/Detonation/probin-det-x.simplified_sdc
commit 25c7e7331d17649cf8584990080ff4a3dbcc8700
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 28 15:20:42 2020 -0400
latest SDC test
Exec/science/rotating_star/inputs_2d.sdc_test
Exec/science/rotating_star/probin.sdc_test
commit 6b194325924014d68cfe12a99caec581622e5795
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 26 06:38:48 2020 -0700
Remove an unnecessary estTimeStep call (#881)
When use_post_step_regrid was added, logic was added to force subcycling if we were just coming off of a post-timestep regrid. But now we always use the subcycling driver and we check the timestep for validity at the end of the step, so this is no longer necessary. Also, it seems to cause segfaults in certain cases, though I don't know why.
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit bbb5c2eb6c83e8cb96f31627244516e11eec034c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 26 09:38:05 2020 -0400
if we are running simplified SDC, we need to use the numerical (#882)
Jacobian for now, since the analytic Jacobian is not yet in terms
of the proper state
Source/driver/Castro.cpp
commit 68e4f026efea7f3d68ebf41de53924ca35d7657f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 25 15:07:13 2020 -0700
Add a max level for explicitly doing burns (#878)
Above this max level, we interpolate from reactions data on the coarse level.
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probin-collision
Exec/science/Detonation/probin-collision.testsuite
Source/driver/_cpp_parameters
Source/reactions/Castro_react.cpp
commit 37e048ccface1579c09632c49182f2dbcf3b0ea1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 25 15:06:12 2020 -0700
Replace check_timestep with call to estDt (#880)
As noted in #879, check_timestep had a few issues, including that it didn't cover diffusion or simplified SDC. We replace that custom code with a call to estDt, which evaluates the new data. Then we can automatically get the new-time timestep limiter, and compare to see if it's within change_max of the old timestep. If not, we consider the step to have failed.
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance_ctu.cpp
Source/driver/timestep_nd.F90
commit 8edb76ccea97cea388a4897de38560106ec75e74
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 24 17:20:16 2020 -0700
Remove burn load balancing functionality (#877)
This functionality was not used much and makes maintenance of the reactions harder; plus, it does not make as much sense on accelerator-based architectures as it did on CPU-only architectures.
CHANGES.md
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Source/driver/_cpp_parameters
Source/reactions/Castro_react.cpp
commit dfd5a8212493e1e0f4a76ec571a1a67f6ad4f022
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 24 16:42:25 2020 -0400
finish porting derives to C++ (#875)
This moves the diffusion derives over to C++. That is the last of the standard Fortran derives. Note, some problems, like diffuse_test, still have Fortran derives, so those headers remain for now.
Source/diffusion/Castro_diffusion.H
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Castro_diffusion_F.H
Source/diffusion/Diffusion_nd.F90
Source/diffusion/Make.package
Source/diffusion/diffusion_util.H
Source/diffusion/diffusion_util.cpp
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
Source/driver/Make.package
Source/hydro/Castro_mol_hydro.cpp
commit d1fe02f7f5998e2f48f110a020986d3c0797a59e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 24 12:58:40 2020 -0700
Switch reduce_add to atomics for safety (#876)
reduce_add used a combined block level reduce plus atomics. This is generally unsafe inside an amrex::ParallelFor() or a #pragma gpu, but it works often enough that I didn't consider it a serious issue. But now I'm hitting some cases for small boxes where this is generating wrong answers so we need to fix it (see also #858). We should be switching this remaining code to C++ using ReduceOps soon (or pure atomics, where it makes sense) so this will become less of an issue. But until then we should fix the Fortran code.
Source/driver/reduction_nd.F90
commit c3c151204c85ba79800e6bac51905946d733c3cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 24 02:45:13 2020 -0700
Fix namespace
Source/reactions/Castro_react.cpp
commit 88afc1a991b093dc01f242dbf15624f16406396f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 24 03:42:08 2020 -0400
port some util functions to C++ (#867)
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util_nd.F90
commit 14b55c48e38300dfc0be4fe7cfaaf9c7b4984d82
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 23 03:13:41 2020 -0400
Check in collision test case
Exec/hydro_tests/Sedov/scaling/sc20/plot.py
Exec/science/flame_wave/science/sc20/probin
Exec/science/wdmerger/science/sc20/collision_ml0/inputs
Exec/science/wdmerger/science/sc20/collision_ml0/probin
Exec/science/wdmerger/science/sc20/collision_ml0/run_script.sh
Exec/science/wdmerger/science/sc20/collision_ml1/inputs
Exec/science/wdmerger/science/sc20/collision_ml1/probin
Exec/science/wdmerger/science/sc20/collision_ml1/run_script.sh
Exec/science/wdmerger/science/sc20/collision_ml2/inputs
Exec/science/wdmerger/science/sc20/collision_ml2/probin
Exec/science/wdmerger/science/sc20/collision_ml2/run_script.sh
commit 1914dd0edb34c70e05fde08993c328b33a8a031d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 22 08:52:41 2020 -0400
move runtime parameters into a namespace as globals (#873)
All runtime parameters are now globals, but in a namespace, castro::, ::gravity::, or diffusion:: (and radiation:: and radsolve:: for radiation). To make life easier, the castro namespace is used in Castro.H, so we can drop the namespace qualifier for them. But for the others, we cannot (we can't load all into the default namespace because of name collisions). This change allows us to use the runtime parameters in lambda functions on GPUs.
CHANGES.md
Exec/Make.auto_source
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/Make.package
Source/diffusion/diffusion_params.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Make.package
Source/driver/_cpp_parameters
Source/driver/castro_limits.H
Source/driver/parse_castro_params.py
Source/driver/runparams_defaults.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Make.package
Source/gravity/gravity_params.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/radiation/Make.package
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/radiation_params.cpp
commit 3dda71bb8b5b2d901316a000b701162e860c933e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 22 01:39:45 2020 -0400
Update Sedov plot script
Exec/hydro_tests/Sedov/scaling/sc20/plot.py
commit 1d0c67b31f4e21429a8f1345a4275baebfca0081
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 21 12:43:00 2020 -0400
continue -> return for lambda captures (#872)
Source/hydro/advection_util.cpp
Source/hydro/slope.cpp
commit a3f2a0425e77f3d02b9b191a2ec86615e228874f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 20 08:15:06 2020 -0700
Disable velocity limiter
This interferes with the small density limiter, which is more important
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 3a8247ce953dcd478863ef54eaed62bd8d5157e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 20:19:37 2020 -0700
Move burn weightings into Reactions_Type (#863)
We currently have a scheme for storing reactions weightings, which are a measure of the number of RHS evaluations during the burn and therefore a proxy for the difficulty of the burn. These weights were added as separate StateData depending on the runtime option use_custom_knapsack_weights.
This change instead places the weights directly in the Reactions_Type StateData as a new component. Now that we always store the weights, load balancing and other future changes that depend on the weights are easier to manage.
The only thing we have to be careful of now is that code that previously zeroed out all of the reactions components cannot be applied until after the weights have been used for their intended purpose. (For load balancing purposes, we want the minimum weight to be one, not zero.) For safety, then, we now don't zero out the reactions components in the strang_react functions, but instead handle the setting of those components directly in the react_state loop.
The parameter use_custom_knapsack_weights is now renamed use_burn_load_balancing so that it is clearer what is does.
In anticipation of future PRs, and because we burn on some ghost zones (the physical boundaries and coarse-fine boundaries), the number of ghost zones in Reactions_Type is increased to 4.
The checkpoint version has now been incremented; this version of the code will not be able to restart from a checkpoint generated by earlier versions of the code.
CHANGES.md
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/timestep_nd.F90
Source/reactions/Castro_react.H
Source/reactions/Castro_react.cpp
Source/reactions/Castro_react_F.H
Source/reactions/React_nd.F90
commit 1446cab773198e53e763b0102b9de1b3b949aef9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 19 19:42:19 2020 -0400
more derives porting (#864)
This moves all of the EOS-specific derives to C++
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit 947049960509f011b5b716de063bd160064ca062
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 19:06:38 2020 -0400
Update submodules
external/Microphysics
external/amrex
commit 78bc8776eb58a57dfc6d391ae8ba9cdd6bad1e86
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 19:00:07 2020 -0400
Check in run script
Exec/science/flame_wave/science/sc20/GNUmakefile
Exec/science/flame_wave/science/sc20/inputs
Exec/science/flame_wave/science/sc20/probin
Exec/science/flame_wave/science/sc20/run_script.sh
commit 412e912c42e28cfbe368c8a0f64aa971cbee1bfe
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 18:47:41 2020 -0400
Higher react boost
Exec/science/flame_wave/science/sc20/probin.boost_10_10
commit 11252d1963ff1461ae2dc336432557a619d3e247
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 18:47:23 2020 -0400
Sedov scaling updates
Exec/hydro_tests/Sedov/scaling/sc20/GNUmakefile
Exec/hydro_tests/Sedov/scaling/sc20/inputs
Exec/hydro_tests/Sedov/scaling/sc20/plot.py
Exec/hydro_tests/Sedov/scaling/sc20/run_scaling.sh
commit 53ee88431b3f35ad2c67b179fa9cdfbf1f4049fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 14:58:09 2020 -0700
Set dt_cutoff as fraction of current simulation time (#865)
The meaning of dt_cutoff has changed: it is now the fraction of the current simulation time which dt may be no smaller than, instead of being an absolute measure. We now have set a non-zero default (1.e-12) as well.
CHANGES.md
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/StarGrav/inputs_3d
Exec/gravity_tests/code_comp/inputs_2d.sdc4
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/inputs_3d.sdc4
Exec/gravity_tests/evrard_collapse/inputs
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/inputs_1d.well_balance
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
Exec/gravity_tests/hydrostatic_adjust/inputs
Exec/gravity_tests/hydrostatic_adjust/inputs-subchandra
Exec/hydro_tests/HCBubble/inputs-sod-x
Exec/hydro_tests/HCBubble/inputs.L0
Exec/hydro_tests/KH/inputs.2d
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/inputs.3d
Exec/hydro_tests/Noh/inputs_3d
Exec/hydro_tests/RT/inputs.dungeon
Exec/hydro_tests/RT/inputs_2d
Exec/hydro_tests/RT/inputs_2d.particles
Exec/hydro_tests/RT/inputs_3d
Exec/hydro_tests/Sedov/inputs.1d.cyl
Exec/hydro_tests/Sedov/inputs.1d.sph
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/inputs.3d.sph
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sedov/inputs.mini-Castro
Exec/hydro_tests/Sedov/inputs.mini-Castro.gpu_test
Exec/hydro_tests/Sedov/scaling/sc20/inputs
Exec/hydro_tests/Sod/Figure1/inputs-sod-1d
Exec/hydro_tests/Sod/Figure2/inputs-test2-1d
Exec/hydro_tests/Sod/Figure3/inputs-test3-1d
Exec/hydro_tests/Sod/inputs-double-rarefaction
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test1-helm
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-test2-helm
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-helm
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test4-helm
Exec/hydro_tests/Vortices_LWAcoustics/inputs.2d
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc2.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.2d.128
Exec/hydro_tests/acoustic_pulse/inputs.2d.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.512
Exec/hydro_tests/acoustic_pulse/inputs.2d.64
Exec/hydro_tests/acoustic_pulse/inputs.2d.64.sdc_ml
Exec/hydro_tests/acoustic_pulse_general/inputs.128
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.256
Exec/hydro_tests/acoustic_pulse_general/inputs.512
Exec/hydro_tests/acoustic_pulse_general/inputs.64
Exec/hydro_tests/double_bubble/inputs_2d
Exec/hydro_tests/double_bubble/inputs_2d.single
Exec/hydro_tests/double_bubble/inputs_2d.single.equal
Exec/hydro_tests/double_bubble/inputs_2d.test
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/inputs.2d.test
Exec/hydro_tests/gamma_law_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/inputs_2d_MAESTRO.big
Exec/hydro_tests/gresho_vortex/inputs.2d
Exec/hydro_tests/heating_verification/inputs
Exec/hydro_tests/oddeven/inputs.2d
Exec/hydro_tests/oddeven/inputs.3d
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
Exec/hydro_tests/symmetry/inputs.1d
Exec/hydro_tests/symmetry/inputs.2d
Exec/hydro_tests/symmetry/inputs.3d
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/toy_convect/inputs_2d
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/inputs.1d.test
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadSlope/inputs
Exec/radiation_tests/RadSourceTest/inputs-cooling
Exec/radiation_tests/RadSourceTest/inputs-heating
Exec/radiation_tests/RadSourceTest/inputs-heating-mg
Exec/radiation_tests/RadSphere/inputs
Exec/radiation_tests/RadSuOlson/inputs
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadThermalWave/inputs.1d
Exec/radiation_tests/RadThermalWave/inputs.1d.test
Exec/radiation_tests/RadThermalWave/inputs.2d
Exec/radiation_tests/RadThermalWave/inputs.2d.test
Exec/radiation_tests/RadThermalWave/inputs.3d
Exec/radiation_tests/RadThermalWave/inputs.3d.test
Exec/reacting_tests/bubble_convergence/inputs_1d.well_balance
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/inputs_2d.well_balance
Exec/reacting_tests/nse_test/inputs
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.128.testsuite
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
Exec/reacting_tests/reacting_convergence/inputs.64.testsuite.simplified_sdc
Exec/reacting_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/reacting_tests/toy_flame/inputs.1d
Exec/reacting_tests/toy_flame/inputs.1d.testsuite
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.regrid
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/Detonation/inputs-det-x.sdc2
Exec/science/Detonation/inputs-det-x.simplified_sdc
Exec/science/Detonation/inputs-det-x.subch
Exec/science/Detonation/inputs-det-x.test
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.big.template.strang
Exec/science/Detonation/nse_runs/inputs.template.sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/sdc_tests/inputs.1d.sdc
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/inputs.3d.test
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame/inputs.1d
Exec/science/flame/inputs.1d.aprox13
Exec/science/flame/inputs.1d.aprox13.boost
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.512
Exec/science/flame/inputs.1d.sdc.map
Exec/science/flame/inputs.1d.sdc.map.avg
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/old/inputs.boost_25_4
Exec/science/flame_wave/old/inputs/inputs_2d
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/science/flame_wave/old/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/flame_wave/science/sc20/inputs.boost_10_10.3d
Exec/science/nova/inputs_2d
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/rotating_star/inputs_1d
Exec/science/rotating_star/inputs_2d
Exec/science/rotating_star/inputs_2d.sdc_test
Exec/science/rotating_star/inputs_2d.strang_test
Exec/science/subchandra/inputs_2d
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/science/sc20/inputs_collision
Exec/science/wdmerger/science/sc20/inputs_merger
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/xrb_mixed/inputs_2d
Exec/unit_tests/diffusion_test/inputs.1d
Exec/unit_tests/diffusion_test/inputs.1d.sph
Exec/unit_tests/diffusion_test/inputs.2d
Exec/unit_tests/diffusion_test/inputs.2d.sph
Exec/unit_tests/diffusion_test/inputs.3d
Exec/unit_tests/particles_test/inputs.2d
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
commit 502da63c5d7a0f6c8d1addf7fb0834566f8135ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 09:27:38 2020 -0700
Add test coverage for custom knapsack weights (#869)
Enable test suite coverage of castro.use_custom_knapsack_weights.
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
commit e2d1b07023524da640cdc0ded6bb75001c7f1131
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 18 23:09:44 2020 -0700
wdmerger problem updates
Exec/science/wdmerger/science/sc20/GNUmakefile
Exec/science/wdmerger/science/sc20/inputs_collision
Exec/science/wdmerger/science/sc20/probin_collision
commit c25cd9a06675bd4f37c1c7c27059f3f62615d1c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 18 23:50:04 2020 -0400
move some more derives to C++ (#861)
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit 6fed713d90ab419c9c21a288579913d6968fc800
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 18 23:49:29 2020 -0400
Remove unused functions (#868)
Source/driver/Castro_util_nd.F90
commit 3d323741046d4b6b2dbb31f28e2427b4e769b8f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 18 20:45:36 2020 -0700
Add Detonation problem for SC20 paper
Exec/science/Detonation/science/sc20/GNUmakefile
Exec/science/Detonation/science/sc20/inputs
Exec/science/Detonation/science/sc20/probin
commit d5d341bf1f30e7be38655dc270037ddd6ac3a8c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 18 18:25:56 2020 -0700
Update the PR template (#866)
This change updates the PR template so that it has a section where the author can describe why the change should be implemented, since such discussion is inappropriate for the squash merge commit message (which should just be a factual description of what has changed).
.github/PULL_REQUEST_TEMPLATE.md
commit ee02bd0b18556a88d247e90f084fe2f5e663e91b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 18 10:53:40 2020 -0700
Remove obsolete parameter allow_small_energy
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
commit 79d200047b7c4d6c2704d87ae119a103ed5feee3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 17 19:01:41 2020 -0700
Disallow restarting from old checkpoints (#860)
We have maintained a checkpoint versioning system for a few years, and strove to maintain backward compatibility so that we could restart from an old checkpoint. This adds significant programmer overhead for dubious gain, since we are not aware of examples of people actually trying to use a new version of the code to restart from an old checkpoint. I propose removing this backward compatibility so that we are more free to make changes to StateData in the future without having to worry about corner cases in how this affects restarting.
CHANGES.md
Source/driver/Castro_io.cpp
commit 5db74e83058da453a514a4702cd3da01823ae519
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 17 21:03:25 2020 -0400
update changes
CHANGES.md
commit 4bfe8bd57423a8d969d3953c823bd4476a7a788b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 17 17:54:43 2020 -0700
Add option to do CTU reactions in C++ (#836)
A compile flag USE_CXX_REACTIONS is added which switches to the C++ integrator in Microphysics. Since we will be doing a phased implementation of the networks in Microphysics, this is opt-in for now.
Exec/Make.Castro
Exec/science/flame_wave/science/sc20/GNUmakefile
Exec/science/wdmerger/science/sc20/GNUmakefile
Exec/science/wdmerger/science/sc20/inputs_collision
Exec/science/wdmerger/science/sc20/inputs_merger
Exec/science/wdmerger/science/sc20/probin_collision
Exec/science/wdmerger/science/sc20/probin_merger
Source/driver/Castro.H
Source/driver/Castro_setup.cpp
Source/reactions/Castro_react.cpp
commit 01fc23cf2bcc94c80cab52062efcf92ca8ea9564
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 17 20:26:14 2020 -0400
port the sponge to C++ (#857)
This ports the sponge to C++, but it leaves the update_sponge_params routine in Fortran.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources_F.H
Source/sources/Castro_sponge.cpp
Source/sources/sponge_defaults.H
Source/sources/sponge_nd.F90
Source/sources/sponge_params.H
commit c7befda4a2eb243c1d5142837030b73139a0e399
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 17 17:02:41 2020 -0700
Turn off post-step regrid
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 3cb89eaa8922db94b60a305e69aba9865ca35485
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 17 18:44:44 2020 -0400
port some routines to C++ (#853)
This ports the hydro and diffusion timestep limiters and the thermo source to C++. We now use the reduceops stuff for the reduction.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Make.package
Source/driver/timestep.cpp
Source/driver/timestep_nd.F90
Source/sources/Castro_sources_F.H
Source/sources/Castro_thermo.cpp
Source/sources/Make.package
Source/sources/thermo_nd.F90
commit bc0cad7a15a7ad1abd7bcc5f9c1e0888179f2ec4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 16 19:46:35 2020 -0700
Switch to AMReX ReduceOps reduction approach (#858)
The original approach to reductions in the CUDA Fortran code was to use AMREX_MFITER_REDUCE_SUM, combined with a call to reduce_add, reduce_min, etc. When we switched to C++ with amrex::ParallelFor, we kept the same approach but called the equivalent C++ call from AMReX instead of reduce_add et al. I recently discovered that there were some edge cases where this is broken, and switched entirely to using atomics in commit b881808. While the safety issue was fixed, performance of reductions dropped enough that it is now a relevant factor.
So we are now switching (hopefully for good) to the AMReX reducer implementation that uses ReduceOps, ReduceData, and ReduceTuple. Some examples can be seen in amrex/Tutorials/GPU/ParallelReduce. In this approach we define a tuple of data to reduce over, along with associated reduction operations for each member in the tuple, and then our lambda function returns the data to reduce instead of being a void. The lambda function is evaluated by the reduce operation, and then we get the data at the end with amrex::get(). This operation is thread-safe, so in CUDA we don't need any special handling (that is done by AMReX) and for OpenMP we don't need to do a reduction (it is done atomically behind the scenes in AMReX; this is less efficient but probably doesn't matter for us).
Going forward, all new conversions to C++ that involve reductions should use this approach.
Source/driver/Castro.cpp
Source/driver/sum_utils.cpp
Source/hydro/Castro_hydro.cpp
commit 2469b749677c48e2ddc44f80f76ee85b49a8a2b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 12:03:10 2020 -0400
update BCs
Exec/science/flame_wave/science/sc20/inputs.boost_10_10.3d
commit 41f55a2042f4318d5a71807e275d00126f6fbb65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 10:53:17 2020 -0400
fix compilation
Exec/science/wdmerger/Prob.cpp
commit dfa6360e8f04d9f63d425ebc5cc45684ba10e432
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 10:23:44 2020 -0400
fix compilation
Source/scf/scf_relax.cpp
commit e8eedaa1a407fe5214be6700c0f63b18b1a5b364
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 15 20:12:54 2020 -0400
eliminate the intiial model from the BCs (#849)
This removes the initial model arrays from the boundary condition routines. The option of an interpolated boundary is now gone, and in its place we use the ambient state BCs. The motivation for this change is to reduce the memory footprint on the GPU.
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_1d.hse_test
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Source/driver/meth_params.template
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/bc_ext_fill_nd.F90
commit 7574386ca004a05c13ca293c68d940a9caa6f8eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 15 12:30:14 2020 -0700
Namespace
Source/gravity/Gravity.cpp
commit 9dd5ea2fc2c411e382ddc131673df518552525b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 14 17:18:32 2020 -0400
switch the weighting/unweighting to C++ (#854)
Source/diffusion/Diffusion.cpp
Source/driver/MGutils.H
Source/driver/MGutils.cpp
Source/driver/MGutils_nd.F90
Source/driver/Make.package
Source/gravity/Gravity.cpp
commit 33dfa9b80d6f272fb311a469a1b37608b7eea44e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 13 22:31:21 2020 -0700
Switch to rotating frame
Exec/science/wdmerger/science/sc20/inputs
Exec/science/wdmerger/science/sc20/probin
commit b881808bbd1f518c60123b8b195c0d18b8bfff36
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 13 22:31:06 2020 -0700
Fix reduction safety issues
Source/driver/Castro.cpp
Source/driver/sum_utils.cpp
Source/hydro/Castro_hydro.cpp
commit 1032bccf842289a3e831f16cfa66d466918a4543
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 13 22:12:21 2020 -0700
Fix typo
Source/hydro/Castro_hydro.cpp
commit 0cbab0eaa700450cbf17a73dda3fd14febce7749
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 12 18:51:38 2020 -0400
fix compilation with latest AMReX
Source/diffusion/Diffusion.cpp
commit 0cd7e28cd39a9895c8d47dc8b5b759ed54c8c397
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 12 14:21:02 2020 -0400
Ambient outflow velocity (#848)
This adds a new parameter to the ambient BCs, ambient_outflow_vel. If this is 1, then we set the normal velocity to outflow (using a min/max to enforce it is outgoing).
Source/driver/_cpp_parameters
Source/problems/bc_fill_nd.F90
commit 783e97b38cd6ecedcda9d35f266888e526e4dd40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 12 14:19:13 2020 -0400
allow the ambient stuff to apply only in certain directions (#847)
A new parameter, ambient_fill_dir, is introduced to allow the ambient BCs to only apply to outflow in a particular direction. -1 means all directions, while 0=x, 1=y, 2=z.
Source/driver/_cpp_parameters
Source/problems/bc_fill_nd.F90
commit 6232cf500612c1023351a4c7a63076632c4c8160
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 12 07:52:02 2020 -0700
Account for multiple edges in the flux limiters (#846)
It is possible even for limited fluxes to cause a negative density when multiple fluxes are summed, since we are only individually limiting fluxes. This PR accounts for that by increasing the effective floor for each flux by a factor of 6 (in 3D; lower in 1D/2D) to ensure that even if all six fluxes are evacuating at a large rate, the final density will still be > small_dens.
Source/hydro/advection_util.cpp
commit eef9a51ae98df9c509219f96a6bf434cfdc08ef4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 11 17:25:35 2020 -0700
Fix an ordering issue for flux limiter
Source/hydro/advection_util.cpp
commit 339d67986a31bb2caedd1f95709670bce8d3bde2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 11 17:14:42 2020 -0700
Provide a reason when an advance fails (#845)
The current code says "advance was unsuccessful" when it is rejected for a retry, but does not tell you why. This code adds a reason for each of the possible failure modes so that you have some idea of what went wrong.
To make the logic simpler to follow, check_timestep is moved into the main advance function.
Source/driver/Castro.H
Source/driver/Castro_advance_ctu.cpp
commit ae991c116a8ab7655ab050a361e12a4ef0f3f829
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 11 17:43:57 2020 -0400
update changes
CHANGES.md
commit f565bfd3bae6d65764e5c4e7dba31d211c7fe9db
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 11 14:32:42 2020 -0700
Switch over generic_fill/hypfill to AMReX implementation (#837)
AMReX provides CpuBndryFuncFab and GpuBndryFuncFab which are very similar to what generic_fill and hypfill did. The AMReX implementations are now used. We still have a hypfill and denfill function, so that existing problems are not broken, but the main one in Source/ no longer calls amrex_filcc (it only has the ambient code now). The problems that do override bc_fill_nd.F90 are thus no longer required to call amrex_filcc, although I have left them alone for now (they will just redundantly do it a second time).
Source/driver/Castro_generic_fill.H
Source/driver/Castro_generic_fill.cpp
Source/driver/Castro_generic_fill_F.H
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/generic_fill_nd.F90
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/bc_fill_nd.F90
commit e978bc6772134c99ee12def392ca149fe1c30613
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 10 15:24:37 2020 -0400
implement a density cutoff for pslope (#838)
Source/driver/_cpp_parameters
Source/hydro/slope.cpp
commit 73527e5be886501d4b02f8da8c3e6f6ba638b15e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 10 10:37:07 2020 -0700
Check in a first attempt at SC20 wdmerger test case
Exec/science/wdmerger/science/sc20/GNUmakefile
Exec/science/wdmerger/science/sc20/inputs
Exec/science/wdmerger/science/sc20/probin
commit 681bdde0daeaef23ef51f4b1ca4d0c29ac191282
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 10 10:28:05 2020 -0700
Always retry if the density is small or negative (#796)
The current code only initiates a retry if the density was updated by enforce_min_density from a sufficiently negative number to a sufficiently positive one. This made sense at the time of its implementation but a simpler method is now available: we check whether the minimum value of the density is less than small_dens after the advance, and if so we reject the timestep and retry the step.
The parameter castro.retry_neg_dens_factor is removed.
CHANGES.md
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit dbff42b446fc8810d5be123c7f26b1530ef0613a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 9 22:19:14 2020 -0700
Apply fake gravitational acceleration to BCs
Exec/science/Detonation/bc_fill_nd.F90
commit bfedf2fb6d48350882ed9d1aeeba9c99d8f0f4e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 9 22:05:39 2020 -0700
Switch to Castro fill_ambient_bc parameter
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/_prob_params
Exec/science/Detonation/bc_fill_nd.F90
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probin-collision
Exec/science/Detonation/probin-collision.testsuite
commit 835e5ade921f0b2a64e86f59372370a058bfdef3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 9 18:22:49 2020 -0700
Rework check_timestep to be based on change_max (#844)
check_timestep is currently effectively useless for CFL violations that
occur as the result of an advance, since it only refers to old data, and
for burning timestep limiting it uses an average of the old and new data.
With this change, we unify how they are used so that they both refer to
only the new data, and reject any timestep that would cause dt to shrink
by more than a factor of change_max. check_timestep is now effectively the
inverse operation of how change_max is used in estdt: whereas in estdt,
change_max allows the timestep to grow by no more than that factor, in
check_timestep it allows the timestep to shrink by no more than that factor
without doing a retry. In effect, this prevents the state from changing too
much in either direction in a single timestep.
CHANGES.md
Source/driver/Castro_F.H
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
Source/driver/timestep_nd.F90
commit 935550af144235c79a3cf2e1bfca1013906a5b99
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 9 11:19:07 2020 -0700
Enable stopping criterion for all problems
Exec/science/wdmerger/Prob.cpp
commit 76786d1049b7567414d63f8f1ec945d657b24a4c
Author: jmsexton03 <jmsexton@lbl.gov>
Date: Thu Apr 9 10:49:41 2020 -0700
C++ derive kineng, angmomx, angmomy, angmomz (#843)
This addresses issue #841 for the 4 derive variables used in sum_integrated_quanities. The kineng follows the Fortran version closely. The angular momenta functions draw from previous C++ conversions elsewhere in Castro, and could be modularized further if necessary. Since other C++ functions in Castro don't use a cross-product function, I did not reproduce the math_nd.F90 function in C++ for these methods.
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit cc6b123df88e49100b5551b2505f2081f0bf2448
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 9 07:54:58 2020 -0700
Convert hydro flux limiters to C++ (#842)
limit_hydro_fluxes_on_small_dens and limit_hydro_fluxes_on_large_vel are converted to C++. I have chosen to use GpuArrays rather than raw C arrays everywhere, which necessitated some changes in existing interfaces to do the same
Source/driver/Castro_util.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/advection_util_nd.F90
Source/hydro/hybrid.H
Source/hydro/riemann_util.cpp
Source/rotation/Castro_rotation.cpp
commit cec6e526cd28b3bd731147a4daaf7d7fd65ed9f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 9 09:49:42 2020 -0400
script to analyze profiles
Exec/gravity_tests/hse_convergence_general/profile.py
commit 45daeb51a8eede7d56f1792a47b685408f848457
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 17:32:03 2020 -0400
fix output
Exec/gravity_tests/hse_convergence_general/hse.py
commit 230afeecdf58a9cf8190bde6e22ab79c5b3d8dc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 9 04:19:37 2020 -0700
Scale dt_cutoff appropriately in the retry logic
Source/driver/Castro_advance_ctu.cpp
commit 37ff4b1b0fc1c24c2aa035afcaa631cb7b831d33
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 8 23:35:38 2020 -0700
Machine epsilon test on dt needs to be scaled appropriately
Source/driver/Castro.cpp
commit e3941e5c997202425c14c05ba1024d8ad4b376a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 8 15:26:12 2020 -0400
ppm_reference_eigenvectors is no longer an option
Exec/science/Detonation/sdc_tests/setup_runs.sh
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
commit bf96395f9baf662261b5c8127b3a4b2b1ae7d367
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 8 08:06:29 2020 -0700
Initialize some string values
Source/driver/_cpp_parameters
commit ac5a45c088537db9d3ca4d37cd720d3e598baec5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 7 21:38:38 2020 -0700
Set a job name
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit a85e80342a322c8fce51633a8adb98bb19ee2fb2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 21:56:16 2020 -0400
fix reflected states
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_mol.cpp
commit 42a7b6347410c76dc733586c3422f3b25b12e18d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 17:01:53 2020 -0400
take an argument
Exec/gravity_tests/hse_convergence_general/hse.py
commit a1c6de8383eccb16d3d5d5da0ef05d1bf4445dcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 16:51:50 2020 -0400
add an analysis script
Exec/gravity_tests/hse_convergence_general/hse.py
commit 509d16b8216274926749c2c024feb263bde72329
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 15:54:09 2020 -0400
update
Exec/gravity_tests/hse_convergence_general/README.md
commit 2a6b4d224654fc59bbc2e702c4cbf8f3b5195078
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 15:48:44 2020 -0400
better initial atmosphere
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
Exec/gravity_tests/hse_convergence_general/probin.hse_test
commit c6b51e5c8628b7c5a1e349ef6a9fe7b7d70c86d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 15:10:49 2020 -0400
a convergence suite
Exec/gravity_tests/hse_convergence_general/inputs_1d.128.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.256.hse_test
Exec/gravity_tests/hse_convergence_general/inputs_1d.512.hse_test
commit ba4dddb864d31daa2a9ae270bbaa7c9a4a4b3c3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 7 14:57:09 2020 -0400
a test problem for a real HSE atmosphere (based on flame_wave)
Exec/gravity_tests/hse_convergence_general/GNUmakefile
Exec/gravity_tests/hse_convergence_general/Make.package
Exec/gravity_tests/hse_convergence_general/Prob_nd.F90
Exec/gravity_tests/hse_convergence_general/README.md
Exec/gravity_tests/hse_convergence_general/_prob_params
Exec/gravity_tests/hse_convergence_general/initial_model.F90
Exec/gravity_tests/hse_convergence_general/inputs_1d.hse_test
Exec/gravity_tests/hse_convergence_general/probin.hse_test
commit 2d1dd428429a6fcf50c1fed3847fd52387d1e333
Author: jmsexton03 <jmsexton@lbl.gov>
Date: Tue Apr 7 10:17:07 2020 -0700
Sdc cxx conversion for non-f_rhs sdc_util.F90 functions (#797)
Make transition sdc_util.F90 and sdc_vode.F90 counterparts
Update convergence bash scripts to match current flags
Convert non-f_rhs and burn_state depending sdc fortran functions
Exec/hydro_tests/acoustic_pulse/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4_outflow.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_rk4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc4.sh
Exec/reacting_tests/bubble_convergence/converge_test.sh
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
Exec/science/flame/test_conv.sh
Exec/science/flame/test_sdc2.sh
Exec/science/flame/test_sdc4.sh
Source/driver/Castro_advance_sdc.cpp
Source/hydro/Castro_hydro_F.H
Source/sdc/Castro_sdc.H
Source/sdc/Castro_sdc.cpp
Source/sdc/Castro_sdc_F.H
Source/sdc/Make.package
Source/sdc/sdc_util.F90
Source/sdc/sdc_util.cpp
Source/sdc/sdc_util_nd.F90
Source/sdc/sdc_vode_nd.F90
commit b8b6214ce8b6c308a4739884fd826db10da73a39
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 6 16:15:36 2020 -0700
Convert normalize_species and compute_cfl to C++ (#839)
Some Castro class functions are moved from protected to public since that's necessary for CUDA.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/advection_util_nd.F90
commit 625eca5daf974095bdfc32b43568538b862e5091
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 6 01:43:02 2020 -0700
Give Shestakov + Bolstad a small but non-zero temperature
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
commit f0892a0f44f979675a7b7d8d47fbb4d2fd0432ad
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 6 01:38:00 2020 -0700
Lower small_temp
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit 58e7143289568b330e6335d89a93ad13f8e05f15
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 6 01:30:19 2020 -0700
Radiation RunOn
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGRadBndry.cpp
Source/radiation/RadBndry.cpp
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.cpp
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/_interpbndry/RadBndryData.cpp
Source/radiation/_interpbndry/RadInterpBndryData.cpp
commit 932444be1ef805848cea30977de5abed0cd9ea7b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 6 00:52:56 2020 -0400
Sedov scaling script for Summit
Exec/hydro_tests/Sedov/scaling/sc20/inputs
Exec/hydro_tests/Sedov/scaling/sc20/plot.py
Exec/hydro_tests/Sedov/scaling/sc20/probin
Exec/hydro_tests/Sedov/scaling/sc20/run_scaling.sh
Exec/hydro_tests/Sedov/scaling/sc20/run_script.sh
commit e7426bb831527aaffecaf6580ecf0032365efd0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 5 22:11:25 2020 -0400
first cut at SC20 files
Exec/science/flame_wave/science/sc20/inputs.boost_10_10.3d
Exec/science/flame_wave/science/sc20/probin.boost_10_10
commit d04721601b998c3a91be8e42fdb9cf8157b150ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 5 17:59:44 2020 -0400
Print per-rank FOM at end of run
Source/driver/main.cpp
commit 72c96d9906b88212d554cda0141b84f3b6e76a52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 5 10:56:35 2020 -0400
remove plm_well_balanced and update use_pslope (#831)
now use_pslope always uses zone i for the HSE reference point. pslope now works with sdc-2 as well and gives great results on the hse_convergence test problem. It essentially does what plm_well_balanced did before but now works for non-constant gravity. plm_well_balanced has been removed, as it is redundant.
CHANGES.md
Exec/gravity_tests/hse_convergence/convergence_sdc.sh
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/slope.cpp
commit c88d05fc4ca81392cff7dd6ab9b9de96f61084f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 4 19:37:07 2020 -0700
Make the oversubscription test stricter
Source/hydro/Castro_ctu_hydro.cpp
commit a3e5353b99f5d4c0af45a618a6ce7981f76ed3ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 4 14:07:16 2020 -0400
add hsereflect case
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit 941cb535eb87282d4718828359fd4f0a05f29574
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 4 13:40:23 2020 -0400
add a no pslope hse-reflect case
Exec/gravity_tests/hse_convergence/convergence_plm.sh
commit 4f1750a15725da8c07d14e79d9fa679013e304b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 4 11:14:37 2020 -0400
add hse_reflect
Exec/gravity_tests/hse_convergence/convergence_plm.sh
commit 88693b2abe886e751c7d746d1707f23a0e98475f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 3 07:05:30 2020 -0700
update executable name
Exec/reacting_tests/bubble_convergence/job_scripts/cori.bubble_convergence.slurm
commit bbafff06d6766bae1c497bbcc9d7934a69e1cf68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 3 09:39:32 2020 -0400
small_temp and small_dens check (#822)
This adds a check just after initialization that ensures that the problem setup did not try to set the temperature or density too close to the small cutoff values.
CHANGES.md
Source/driver/Castro.cpp
commit 70f1ed5fa132516234d88285aa09489e57e30dd8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 2 19:24:09 2020 -0400
update stored variables
Docs/source/Hydrodynamics.rst
commit 97039b4d9e836b5cd07e0bc2563f2a5918ef4217
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 2 12:08:42 2020 -0400
bring over from ppm_onesided
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit 2c816d26c27f9aa6858af8fdc1873d9acf2da191
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 21:00:57 2020 -0400
add variation on HSE
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit bea829fd211517b3131f6a1b631323a4c12bf3be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 15:34:26 2020 -0400
add sdc2 + ppm tests and fix some of the plm ones
Exec/gravity_tests/hse_convergence/convergence_sdc.sh
commit e12b7eb93ee2a59b23dda2f480f39a74f9d301ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 13:41:34 2020 -0400
port from pslope
Exec/gravity_tests/hse_convergence/convergence_plm.sh
commit bbd7616cbdc02a137b92243df6e17f1659ad7b3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 13:41:12 2020 -0400
just ppm
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit e2882dd85a975edfbca9d4a97d71b1757896aec5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 10:56:13 2020 -0400
more SDC tests
Exec/gravity_tests/hse_convergence/convergence_sdc.sh
commit a510317c4b481cca514179ce1cacc64164f13a94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 09:20:01 2020 -0400
update changes
CHANGES.md
commit 4e00d22ed8f7560bc29911770cff35eb6cc4acbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 08:53:02 2020 -0400
update changes
CHANGES.md
commit 5d5951d753ac34060ef1e240a0c7b0cc940e4561
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 09:17:28 2020 -0400
Remove src q (#829)
This removes the src_q multifab and instead converts the conserved state sources to primitive state sources FAB by FAB just before they are needed (in the creation of the interface states). This saves on memory from the MF as well as allows us to eliminate two entries in qaux (QDPDE and QDPDR). The trade-off is we now do an EOS call.
Answers may change because of the additional EOS call.
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/_variables
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util.cpp
commit a48e25a8ae709fb9dd55b0c0cb7376161fb71594
Merge: 5a142ef14 342de10c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 09:04:50 2020 -0400
Merge branch 'development'
commit 5a142ef14c0d1bf83382ef8f8a5f0ba047a4d3bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 09:03:45 2020 -0400
update AMReX and Microphysics to latest dev
external/Microphysics
external/amrex
commit 342de10c15bbc664831ca8ba1119d362521490a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 31 15:17:24 2020 -0400
last commenting
Source/hydro/slope.cpp
commit 62339b96213c2d0fc21cf084de2c628cbdb4f8a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 31 14:02:41 2020 -0400
more comments
Source/hydro/slope.cpp
commit 9b6d8c0f85711da94ac551600c8661eb6c3a8a88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 31 13:23:32 2020 -0400
some comments
Source/hydro/slope.cpp
commit 0dd066c13cfe6bf31b10447f767d1f30190a89c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 23:39:19 2020 -0400
fix typo
Source/hydro/slope.cpp
commit 7f342a0b158945b7d473505b04aac3762a6653a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 18:48:00 2020 -0400
add a convergence test for SDC
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
Exec/gravity_tests/hse_convergence/convergence_sdc.sh
commit 280c0833644f353c1e45dfda4116639321ce5a8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 15:02:53 2020 -0400
update the convergence script
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit 8bf3bc4ad2a2de6ee2bbc1030ab615c2fbe38300
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 12:54:41 2020 -0400
add plm + reflect
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit d6ffb317d5674ada83905f4e2c786a04065bd7a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 10:40:24 2020 -0400
fix time_integration_method check
Exec/gravity_tests/hse_convergence/initial_model.F90
commit 500ad933fc89d97befbc25b3fc0720707f0fd7e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 10:21:03 2020 -0400
fix time_integration_method check
Exec/reacting_tests/bubble_convergence/initial_model.F90
commit ab5f921ff4404be6b5591943d5e9833dcb0e0d2a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 30 08:42:06 2020 -0400
remove Fortran docs build
Docs/add_doxy_headers.py
Docs/make_api.py
Docs/preprocess_files.py
Docs/source/conf.py
requirements.txt
commit 8b61899069457d5c9068dcdf030ce905549cac54
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 30 08:09:05 2020 -0400
update sphinx and breathe versions
requirements.txt
commit b2b16f0cd5c33d78bcc60e07d4164a53130c28fe
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 30 07:51:09 2020 -0400
pin sphinxfortran version instead
requirements.txt
commit 926aa39c942912d77cf28e230f2d70316dfa3378
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 30 07:44:16 2020 -0400
pin version of sphinxcontrib-websupport
requirements.txt
commit c6002b11a26c0e5f41a60588b7e179e0795609f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 20:37:31 2020 -0400
we don't need QGC if we are doing CTU (#827)
Source/driver/_variables
Source/hydro/advection_util.cpp
commit ebd6ab6c471fcd87543916e3057cedd8185784b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 20:34:11 2020 -0400
fix the fix
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit 2d9e9a613acaae3c7b4c7c3aca90b7660ae2478a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 20:27:01 2020 -0400
store output
Exec/reacting_tests/bubble_convergence/converge_test.sh
commit c274dabbfe7f96e349857e2b28b73e2e61e1063d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 20:25:34 2020 -0400
fix the energy
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit fa78c1bfb0f9cb2c469a9d44c099a701cacf3e24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 16:34:09 2020 -0400
automate the convergence testing + lots of tests
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit 52bf7393b4f347c97fb1ffc81563ca7017acaac9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 16:00:46 2020 -0400
a more automated convergence test
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
commit b15b3f479a0c651cfc2f6edc00e3eb9cb81657df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 15:44:42 2020 -0400
update the convergence
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
commit 3acbad789b2aa16f43496d9b485fbf4344887337
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 15:24:06 2020 -0400
use_reconstructed_gamma1 = true only makes sense for SDC/MOL
Source/hydro/riemann_solvers.cpp
commit 4d7bffd36a568fd4cf632b50c60ee7816cfb6ec3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 13:56:18 2020 -0400
add convergence test
Exec/gravity_tests/hse_convergence/convergence_ppm.sh
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
commit 980243527b1e214f717841bffbd63a5b5b21ca47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 13:48:25 2020 -0400
new inputs files
Exec/gravity_tests/hse_convergence/inputs.ppm.128
Exec/gravity_tests/hse_convergence/inputs.ppm.256
Exec/gravity_tests/hse_convergence/inputs.ppm.512
Exec/gravity_tests/hse_convergence/inputs.ppm.64
Exec/gravity_tests/hse_convergence/probin.128
Exec/gravity_tests/hse_convergence/probin.256
Exec/gravity_tests/hse_convergence/probin.512
Exec/gravity_tests/hse_convergence/probin.64
commit 421bdcd212525bb919b1cf45cd72a2ec5a40c5e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 13:28:25 2020 -0400
fix scaling of rho X when we perturb
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit 68e8a3ef2ac4b48c3b731795d36e600fc6873e98
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 13:24:52 2020 -0400
new test problem
Exec/gravity_tests/hse_convergence/GNUmakefile
Exec/gravity_tests/hse_convergence/Make.package
Exec/gravity_tests/hse_convergence/Prob_nd.F90
Exec/gravity_tests/hse_convergence/README.md
Exec/gravity_tests/hse_convergence/_prob_params
Exec/gravity_tests/hse_convergence/initial_model.F90
Exec/gravity_tests/hse_convergence/inputs
Exec/gravity_tests/hse_convergence/inputs_1d.well_balance
Exec/gravity_tests/hse_convergence/network_properties.F90
Exec/gravity_tests/hse_convergence/probin.256.nopert
commit 112deb0fa114799ca65e9122047e0918b9c62069
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 12:26:30 2020 -0400
smarter choosing of the HSE integration
Exec/reacting_tests/bubble_convergence/initial_model.F90
commit 4739f834b9047a4bbf02d6a4aac9456e3c4f6fc6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 12:15:32 2020 -0400
merge perturbation into the main loop
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit eaab9c0f86c11c9714eddf7b23fd7a5a5d97842e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 11:04:02 2020 -0400
remove allow_negative_energy
this option no longer exists
Exec/hydro_tests/acoustic_pulse_general/inputs.128
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.256
Exec/hydro_tests/acoustic_pulse_general/inputs.512
Exec/hydro_tests/acoustic_pulse_general/inputs.64
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.128.testsuite
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
Exec/reacting_tests/reacting_convergence/inputs.64.testsuite.simplified_sdc
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.512
Exec/science/flame/inputs.1d.sdc.map
Exec/science/flame/inputs.1d.sdc.map.avg
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame_wave/old/inputs.boost_25_4
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
commit 403f5fc4746bbf25ab5e78ee938278f239f48d7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 10:22:09 2020 -0400
fix tiling issue
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit d09a07a4896e2040cc096952c4342734eeb0659e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 10:02:42 2020 -0400
update README
Exec/reacting_tests/bubble_convergence/README.md
commit 0633e42b1c91255114c589678baa69e3629619f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 29 09:17:08 2020 -0400
add note
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
commit 3846dfe6931abe92abd65052ba676c877dcb030b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 20:52:26 2020 -0400
update executable name
Exec/reacting_tests/bubble_convergence/converge_test.sh
commit a37ff8de74b6eceb8697862d7f2a938557267e4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 20:51:10 2020 -0400
update executable name
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
commit 713606dd8092e42918c6f1b4dd7c7aa40d5b17c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 15:31:38 2020 -0400
add some scaling nums
Exec/science/flame_wave/scaling/3lev/scaling-2020-03-18.txt
Exec/science/flame_wave/scaling/3lev/scaling-2020-03-21.txt
commit ebcad7d57879ce2d6d016be0c731dc89d9784d20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 15:19:03 2020 -0400
reorganize
Exec/science/flame_wave/scaling/1lev/scaling-2019-11-18.txt
Exec/science/flame_wave/scaling/2lev/scaling-2020-02-19.txt
Exec/science/flame_wave/scaling/2lev/scaling-2020-03-08.txt
Exec/science/flame_wave/scaling/2lev/scaling-2020-03-17.txt
commit eb401eb70a20c055687f866323fb1d7e331e50b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 15:38:39 2020 -0400
thin out output + convergence script
Exec/gravity_tests/evrard_collapse/convergence_test.sh
Exec/gravity_tests/evrard_collapse/inputs
commit 0d9eedbe65d6d17e087b454897a5a0c57161fca1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 14:36:27 2020 -0400
add a readme giving implementation refs
Exec/gravity_tests/evrard_collapse/README.md
commit bc7c2e66c3b901d772b6db028c467611a88d5579
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 22 17:28:31 2020 -0700
Switch over to the new Fab interface for BC fills (#819)
This is in preparation to use the new fab_filcc in AMReX.
generic_single_fill and generic_multi_fill are merged into one function, generic_fill, since the Fab interface has no notion of separate single and group interfaces. Similarly, the calls to denfill and hypfill are now both done in one function (though the functions are not merged, to preserve user-facing code).
The source fill routines are also merged into the generic fill routines.
Finally, instead of locally overriding the BCs in the boundary fill routine, we now globally override any inflow boundary conditions (for the non-State_Type data) to become FOEXTRAP. So this is the same result but with code that is a little simpler and will be easier to link up to AMReX later.
Source/driver/Castro_generic_fill.H
Source/driver/Castro_generic_fill.cpp
Source/driver/Castro_generic_fill_F.H
Source/driver/Castro_setup.cpp
Source/driver/Castro_source_fill.H
Source/driver/Castro_source_fill.cpp
Source/driver/Castro_source_fill_F.H
Source/driver/Make.package
Source/driver/generic_fill_nd.F90
Source/driver/source_fill_nd.F90
Source/problems/Castro_bc_ext_fill_nd.H
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
commit c4c173583ec5f19044801864f29c7e0c8f35bc1c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 22 08:52:52 2020 -0700
Fix check_for_nan ghost cell check
Source/driver/Castro.cpp
commit afd7eccf1da8a7cb0d7d042860b2ca15a1e03b9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 21 13:39:42 2020 -0400
have the HLL solver modify the flux passed in (#823)
this fixes a bug where we may have an uninitialized flux
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
commit 76bf77f5dcf8a10023dd88d189f6537edd17570a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 21 12:23:13 2020 -0400
fix non-rotation compilation
Source/hydro/advection_util.cpp
commit a97a3dd1c87cd795af2ff83a09c2d9bf8158043b
Merge: 7925c25a8 f47b5f502
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 21 12:19:27 2020 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit f47b5f502d276c2430764e9b097b04563521d731
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 21 11:44:40 2020 -0400
seems GpuArray is const on the GPU but not on CPU
Source/hydro/advection_util.cpp
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
commit cccb93a95219f8e496d1de21b95b28d6e8ffad10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 21 10:18:57 2020 -0400
update chages
CHANGES.md
commit 8ed7cfd897a74a36720ffe50475ad99bd2752404
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 20 21:35:30 2020 -0400
convert ctoprim to C++ (#804)
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/wdmerger_util.F90
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/advection_util.cpp
Source/hydro/advection_util_nd.F90
Source/radiation/Make.package
Source/radiation/rad_util.F90
Source/radiation/rad_util.H
Source/radiation/rad_util_nd.F90
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation.cpp
Source/rotation/Castro_rotation_F.H
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.F90
Source/rotation/rotation_sources_nd.F90
commit 3c3089022c47c9f7321a121e1a6b888645bcfec4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 00:38:46 2020 -0700
Update to new Jacobian parameter interface
Source/sdc/sdc_util.F90
commit 23c5d279ffb4d6c3ee3b5f63cb8fb683baabe755
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 21:53:02 2020 -0400
fix indexing into vode_state % y(:)
Source/sdc/sdc_vode.F90
commit 43cfd09a5e2da6dd007caf7c9e00f134d9e60b64
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 19 10:38:53 2020 -0700
Add some RunOns
Exec/science/wdmerger/Prob.cpp
Source/hydro/Castro_hydro.cpp
commit 9efc3d929052edd9f39e128232baccb127c013aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 10:33:42 2020 -0400
get this compiling
Source/sdc/sdc_util.F90
commit 1ea89e5550f6b9d9c08bfefaad3b422b2697ec80
Merge: ace1cb6cb c82c281d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 09:48:28 2020 -0400
Merge branch 'development' into vode_opts
commit c82c281d5db61357e836aeb2711451f6984c68e3
Merge: 3c4ed386d 2ea951043
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 09:39:03 2020 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 3c4ed386d537bc8ea3cd66556893b4626ceed696
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 09:38:53 2020 -0400
fix irp_spec
Source/sdc/sdc_util.F90
Source/sdc/sdc_vode.F90
commit 2ea9510435c2633ce6b49760bdcfd0ead177d248
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 21:54:35 2020 -0700
Update to new dvode interface
Source/sdc/sdc_util.F90
commit fa3c5b44c6b040cf637edc94951b5c1ca0510e4a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 19:34:12 2020 -0700
IOPT is no longer in dvode interface
Source/sdc/sdc_util.F90
commit d7e5527c044c238c00dd1b959e550f3ef0de62d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 19:16:23 2020 -0700
ITASK is no longer in dvode interface
Source/sdc/sdc_util.F90
commit 5add074db59e7c80fc31bff19b8fd38f994fd6c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 17 11:03:59 2020 -0400
lowest GPU count #s
Exec/science/flame_wave/scaling/scaling-2020-03-17.txt
commit 41f5329e08a2f89502955846523ecfd6f2334038
Merge: b95af8417 4daf8bcd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 17 10:47:57 2020 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b95af84174bd5bd8bbc63343bbb2f6cc9160b3bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 17 10:47:18 2020 -0400
add newest scaling
Exec/science/flame_wave/scaling/scaling-2020-03-17.txt
commit 4daf8bcd120455564376c48f9f1a70290262e70b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 17 09:46:03 2020 -0400
std::max -> amrex::max
Source/hydro/trace_plm.cpp
commit 7925c25a8bc5cfe83b3d4a3b330d7b92434aa3c4
Merge: 5447454c4 a64a57fd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 17 09:28:08 2020 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit a64a57fd69502a2bdd9daba0658d030e9e82838b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 16 17:51:10 2020 -0700
Convert wdmerger to use the auto prob params script (#818)
This moves all wdmerger data except the initial models to the auto prob params script.
In order to get the tests to work, I modified the prob params script to search for _prob_params in a directory named PROBLEM_DIR which the problem can specify.
Exec/Make.Castro
Exec/Make.auto_source
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/_prob_params
Exec/science/wdmerger/binary.F90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/problem_derive_nd.F90
Exec/science/wdmerger/problem_io.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_util.F90
commit ed630e5fd191212b1858bd192564bcf0eb92eff7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 16 19:05:56 2020 -0400
update changes
CHANGES.md
commit 3adf1a47bc2e7e74851e5102502ec53b778e6ef2
Merge: 2eb4a6ccc fc7bf8d1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 16 18:12:32 2020 -0400
Merge pull request #812 from AMReX-Astro/source_corrector
Presently if use_retry is enabled we make a pre-emptive copy of the StateData right at the beginning of the timestep. We then back up to that copy of the state if a retry is triggered, and try again with a shorter timestep. Since use_retry was so useful, we made it the default, but this meant that we were always doubling the memory requirement of the state, and on GPUs this is a problem due to the limited memory capacity. To avoid this problem we placed the backup state in CPU pinned memory. This meant that making the backup was relatively expensive (as the bandwidth is now the bandwidth of the CPU-GPU interconnect, which is much lower than the bandwidth of GPU DRAM), but at the time we did it (commit 0a95b63) the cost of the advance on the GPU was much larger than the cost of the copy. However, our recent C++ ports have made the advance so fast that saving the backup state is now the single largest cost in the timestep. So we need a strategy that does not require saving the backup state on every step.
The proposed solution is to only backup when we detect that a retry is needed. This means that we first attempt the advance and then we make the backup of the state if the advance failed. The backup state (called prev_state in the code) is thus a copy of the failed advance, but this is actually acceptable because we don't ever need the new data* from the backup (just the old data), and the old data should be approximately the same independent of whether we retry with a smaller timestep. In fact, this approach is actually better than the status quo. At present, if we have to retry, we're backing up to a copy of the state made before any advance was done. Now, the reason we have to make a backup of the old data at all is that we want the old data at the end of the timestep, after all subcycles have been completed, to be the data at the start of the whole timestep, not the start of the last subcycle (this is necessary for valid time interpolations on the fine level). But by backing up to the old data before any advance was done, we actually lose out on the reset of the old data that happens in the first subcycle, which is something we want to happen so there's fully valid old-time data (that is, for the same reason we have an old-time update to begin with in the timestep, rather than just accepting the new-time data from the last step). This does mean we will see changes in the test suite for problems with retries.
A second benefit is that we no longer need to back up all the way to the beginning of a step when we hit a retry. We simply retry the same subcycle with a shorter timestep. This is valid as long as the CTU advance is written in an idempotent way where doing it multiple times in a row doesn't result in unintended results, and that is true given the way we have written it: the old source term data simply gets recomputed and overwritten, and the new data gets copied from the old data and then added to. The only exception is the aforementioned source term corrector, which has been dealt with.
The only caveat with this approach is that there is one piece of data that actually depends directly on data from the last timestep, which is the source term predictor in CTU, or the last iteration's correction term in simplified SDC. The strategy above would not give us a valid way to restore the source term predictor after a retry, since we've already erased the data from the last timestep. So what we do now for CTU is to save off the source term predictor into a separate array (source_corrector) in the first pass through the timestep. The saved source corrector is established before any changes are made to the StateData, so it is indeed the data we want. If we do a retry, we just refer back to that saved data rather than recalculate it (which would now be impossible). This does add some additional memory requirements, but we can make up for it later (for example, sources_for_hydro doesn't really need to be stored for the full timestep anymore). For simplified SDC, we cannot quite do this because the failure could occur in the second SDC iteration, at which point we'd have lost the lagged solution from the previous timestep, and the lagged solution from the failed advance cannot be trusted. So the solution is to zero out the lagged sources and then take an extra SDC iteration to compensate.
*This does mean we're saving more data than we need. As an optimization for later we can just save the old data.
commit fc7bf8d1a3c2e576244f3ed77c19475e53680af0
Merge: 33ec40ffe 2eb4a6ccc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 16 13:30:11 2020 -0400
Merge branch 'development' into source_corrector
commit 2eb4a6ccca45b3acdb07c5145d4ad333b29ef4a1
Merge: 403f4f98b ab48e4f49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 15 15:22:29 2020 -0400
convert the PLM routines to C++ (#814)
As part of the conversion from Fortran to C++, we merged the separate x, y, and z slope computations with a dimension-agnostic version. This actually fixed a bug in the plm_well_balanced code as well as did the proper symmetry BCs in all directions for the well-balanced. We also now do the reflecting BCs to the interface states correctly (previously, our test for the domain lo/hi was wrong).
commit ab48e4f496fa68d57f3be5f1dd34e898748d01aa
Merge: 5dfe833f0 403f4f98b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 15 15:08:48 2020 -0400
Merge branch 'development' into cxx-plm
commit 403f4f98be4b3cea25d3da7328d25c9087f008bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 10:12:15 2020 -0700
Move all wdmerger data out of probdata
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/binary.F90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/problem_derive_nd.F90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.F90
commit 67c41988190f3ae2ca0d17d409de734dac3203b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 09:40:48 2020 -0700
Compute polytrope K offline to avoid C++/Fortran conflicts
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/probin
commit 5dfe833f05b927764cf69c448a5ab871d8cffad8
Merge: f79266d57 fafa17023
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 15 11:58:55 2020 -0400
Merge branch 'development' into cxx-plm
commit fafa170232d0300dd4047cb374b7403790b910e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 08:58:35 2020 -0700
Convert reset_internal_energy to C++ and simplify the algorithm (#817)
We now simply evaluate the eint corresponding to small_temp, and reset eint (and eden) as needed to be at least that large. We then apply the dual energy criterion. This makes the behavior corresponding to allow_small_energy == 0 the default, and removes that parameter.
CHANGES.md
Docs/source/Hydrodynamics.rst
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/driver/Castro_util_nd.F90
Source/driver/_cpp_parameters
Source/hydro/Castro_hydro.cpp
commit f79266d5794e5d6e5637abb8ae3b09c2ffe6df79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 15 10:59:54 2020 -0400
a bunch of fixes from the PR review
Source/hydro/Castro_mol.cpp
Source/hydro/trace_plm.cpp
commit da588012e0bf1f7f779e81c08f5aeaea8cde5a1d
Merge: bb9bf9869 022bdc141
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 15 09:23:23 2020 -0400
Merge branch 'development' into cxx-plm
commit 022bdc1410579f9a4029a11a9e88f0f888c498e1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 06:12:48 2020 -0700
Remove BC fill routines other than for State_Type (#815)
This PR removes all boundary fill interfaces other than hypfill and denfill (gravity, rotation, reactions, radiation). The existence of these routines creates substantial maintenance overhead relative to the value they add, since none of the problems actually use them to update the boundaries. As an example of the problem this complexity adds, not all of the routines were addressing inflow boundaries consistently (in particular, some override an inflow boundary to do first-order extrapolation so that there's meaningful data, and some don't, leading to garbage data for e.g. the reactions). The only one of these that a user would be likely to touch was the radiation fill, but we have no problem setups demonstrating this (they all use radiation.lo_bc and radiation.hi_bc instead), and it's also hard to see how a user could have effectively used the radiation fill for a multigroup problem, since you don't come in with information about which group you're in.
CHANGES.md
Docs/source/radiation.rst
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
Exec/hydro_tests/double_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/gamma_law_bubble/bc_ext_fill_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Source/driver/Castro_setup.cpp
Source/problems/Castro_bc_ext_fill_nd.H
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/problems/Castro_bc_ext_fill_nd_F.H
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Castro_bc_fill_nd_F.H
Source/problems/bc_ext_fill_nd.F90
Source/problems/bc_fill_nd.F90
commit d1b490506d19c72664701d39f0c3248a2fa9ef4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 03:15:39 2020 -0700
Make Problem.H includes public
Source/driver/Castro.H
commit 73aedd963a1c1618109d7328b56eb6778f5701e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 01:36:51 2020 -0700
Fix default rotation case
Exec/science/wdmerger/ext_src_nd.F90
commit 01ddc4d84caeed2a861440aecd51c9c48fc8e6fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 15 00:19:11 2020 -0700
Handle relaxation source for state_in_rotating_frame = 0
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/wdmerger_util.F90
commit bb9bf9869889104e79b21baabb38ea456fbcc92e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 19:35:40 2020 -0400
fix compilation of MOL + PLM
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
commit f0561b7a15e7118b3147ab97b25801b1124cacbf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 18:08:47 2020 -0400
first pass at the MOL PLM
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_nd.F90
commit 451b4816d30162c895cf6d1aab0c68fef79ae18d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 14:42:05 2020 -0400
amrex::min
Source/hydro/slope.cpp
commit 438299538c8f4fef49345e343dd5a94ba82c444c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 12:05:33 2020 -0400
fix some shadows
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/trace_plm.cpp
commit 03dc9ee62407bd1623577c65892916bcca13fe18
Merge: 0310ec930 4c7bddbc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 11:00:59 2020 -0400
Merge branch 'development' into cxx-plm
commit 4c7bddbc28893ceb669be0068566af523e340c90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 11:00:25 2020 -0400
move diffusion to C++ (#811)
We now use the C++ interfaces to the conductivities in StarKiller Microphysics. There are small differences due to optimization (O(1.e-10)).
Source/diffusion/Castro_diffusion.H
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Castro_diffusion_F.H
Source/diffusion/Diffusion_nd.F90
Source/diffusion/Make.package
Source/driver/Derive.cpp
commit 0310ec93039a5b32e8c8f575265b69917e73c0c7
Merge: 8868104e0 b205f6590
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 14 10:59:01 2020 -0400
Merge branch 'development' into cxx-plm
commit ace1cb6cbd8ec680a1e7e70d1c11f18d5777e9f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 22:22:01 2020 -0400
get SDC compiling with vode_opts2 in Microphysics
Source/sdc/sdc_vode.F90
commit b205f6590ca34d41a45f2d4fa281388446e39fcf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 22:20:30 2020 -0400
Revert "get more SDC stuff compiling"
This reverts commit 4fc9f35405725313ec5687e9ddbeb1187bbc71a1.
Source/sdc/sdc_vode.F90
commit 4fc9f35405725313ec5687e9ddbeb1187bbc71a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 22:16:48 2020 -0400
get more SDC stuff compiling
Source/sdc/sdc_vode.F90
commit 8868104e0dd0f26aaac1cbcfb2fbeb8e1583df7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 17:36:44 2020 -0400
fix GPUing
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/slope.cpp
commit 33ec40ffe5734b443deb19962ba59b02a41bcbb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 12:06:13 2020 -0700
Fix some logic
Source/driver/Castro_advance_ctu.cpp
commit fa587b2c1581a86c93ec9dc6003c49bb8c58fd80
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 10:09:50 2020 -0700
Add a period. For my sanity.
Source/driver/Castro_advance_ctu.cpp
commit 5447454c4e490932f7e4972f1bdc880d2a478083
Merge: d49dfbcfb 8791c437f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 13:00:55 2020 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 75db9ce689cffb77cc7ef8c7b3ce1eb1f8fbf96a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 09:45:48 2020 -0700
Add an SDC iteration after a retry
Source/driver/Castro_advance_ctu.cpp
commit 4211d0a53dd62ea19992a897ff18250c0b396772
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 12:23:06 2020 -0400
fix compilation
Source/hydro/trace_plm.cpp
commit 380b29b5e0b2a6dacd4edd40b6ac8f03cb4d9487
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 12:16:34 2020 -0400
need to mark this public
Source/gravity/Gravity.H
Source/hydro/slope.cpp
commit bad3457841a6cde97fc734e03a1983af9db6f2dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 11:47:37 2020 -0400
failed attempt at getting access to const_grav
Source/gravity/Gravity.H
Source/hydro/slope.cpp
commit ba49c05552dcabc0dae0b1739a1a62daa417ba79
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 08:36:00 2020 -0700
Add an ifdef
Source/driver/Castro_advance_ctu.cpp
commit 56ee025f8278c305bbf9487bcc169216aa075c1a
Merge: e0b1f4c78 8791c437f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 08:35:33 2020 -0700
Merge branch 'development' into source_corrector
commit 8791c437f2c7d3091072bbe437c673b03a6241ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 08:14:56 2020 -0700
Check in simplified SDC convergence test
Exec/reacting_tests/reacting_convergence/convergence_simplified_sdc.sh
commit e903dadcd2ccb24fe4fed85943894cb164acd4d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 08:14:41 2020 -0700
Fix CUDA compile
Source/hydro/advection_util.cpp
commit 5e8e3d516a7d8c07550f0aa1ef521997004b6113
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 11:11:01 2020 -0400
add the trace
Source/hydro/trace_plm.cpp
commit fc86c1bebe3465c132cef5d08edc26e9ae88828b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 10:45:20 2020 -0400
no longer needed
Source/hydro/trace_plm_nd.F90
commit c93f0cdad2615a22a4076311fb5826ce10c33665
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 10:45:05 2020 -0400
this compiles but doesn't yet run
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Make.package
Source/hydro/slope.cpp
commit e0b1f4c78b238ab077e5d791b3b0664710f81c37
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 13 07:07:43 2020 -0700
Zero out lagged source terms after a failed advance
Source/driver/Castro_advance_ctu.cpp
commit dc21f833fba191bb041f69cde7c0589caa63e6a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 21:29:49 2020 -0700
Re-fix source corrector
Source/driver/Castro_advance_ctu.cpp
commit 3534d514aba734e0467b1867eeea3b0e12fd181c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 20:06:21 2020 -0700
Fix corrector condition for simplified SDC
Source/driver/Castro_advance_ctu.cpp
commit fb0c7e165f5f9641d69c765c9773fd9b1dd04b3e
Merge: a3d54ae47 af8b9cf44
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 19:56:39 2020 -0700
Merge branch 'development' into source_corrector
commit af8b9cf4416c999927895a3aabfc9ddc75370eb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 19:55:28 2020 -0700
Store reactions data in new StateData
Source/reactions/Castro_react.cpp
commit 1037a3c556944043982a48e0c4d4e8f08f4ff5bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 21:50:18 2020 -0400
add to the build system
Source/hydro/Make.package
Source/hydro/slope_nd.F90
commit cf190820a7d9a2b33d0712aec2fcf3e531678405
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 21:48:29 2020 -0400
unify the directions in the slope construct + move to C++
Source/hydro/slope.cpp
commit 8ebf15f1e8ad307a1f5d4f3c5e8fba1a3170bbe5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 20:01:04 2020 -0400
start moving PLM to C++
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_nd.F90
commit a3d54ae47e00d52d3efecc7549ec95a9faf70ae5
Merge: c69021a7d 99ddacaa1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 10:08:26 2020 -0700
Merge branch 'development' into source_corrector
commit 99ddacaa1e10a6de13727cbc6791308fbba61395
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 10:00:12 2020 -0700
Turn on verbosity
Exec/science/Detonation/inputs-collision.testsuite
commit a2b199595863856ff1cd2839a775527d380073af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 09:04:23 2020 -0400
remove unused var
Source/hydro/riemann_solvers.cpp
commit d5a5dd75a53db93d18a401de905e38c534bac99c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 00:51:26 2020 -0700
Move some Riemann functionality into headers
Source/hydro/riemann.H
Source/hydro/riemann_util.cpp
commit c69021a7d2bbb1554d7b7d31de65e2e7c66bdf8b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 22:26:59 2020 -0700
We don't need to reset the iteration count on a retry
Source/driver/Castro_advance_ctu.cpp
commit 23a29146424d9faa9a0805729fcba64c382f4ee8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 20:02:38 2020 -0700
Move the source corrector save up in case the burn fails
Source/driver/Castro_advance_ctu.cpp
commit 3e82e8c6f9b562e24372a3bc60e5d5cbb14f30a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 19:16:45 2020 -0700
Only save the state if we're doing a retry
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit abf4788b2983bae28315354d475792b262d11677
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 18:33:34 2020 -0700
Remove unused data
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit 29f463cd55a2829cd75c39fbcb48bbc0d910ac37
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 18:13:12 2020 -0700
Don't recalculate on a retry
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit 53f66fbe0932096f17603e5cb76793d67dfbde48
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 13:18:47 2020 -0700
Revert "Don't need to store the MultiFab"
This reverts commit 1d1cd5c34e62ca09c8e8565dd61a1872f0a0cbf9.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit bd3dd411b174e960627ebe0b28688e8ab63a2d03
Merge: 1d1cd5c34 fb91dbf5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 13:18:34 2020 -0700
Merge branch 'development' into source_corrector
commit fb91dbf5f618b08be9be59471e766c0a76252352
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 08:41:48 2020 -0400
fix more shadowing
Source/driver/Castro.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
commit be715337582ac633b6808a7cf08021796ce2e842
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 08:36:36 2020 -0400
address some static analysis warnings
Source/hydro/riemann_solvers.cpp
commit 1d1cd5c34e62ca09c8e8565dd61a1872f0a0cbf9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 9 22:25:02 2020 -0700
Don't need to store the MultiFab
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit 177aba31bf3c6f3f175e41fdd19be8ae0951e1b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 9 21:43:03 2020 -0700
Do the source corrector after the swap
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit 469c9b4f7f619dd07def8c4f87b8dea902f466b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 9 19:40:34 2020 -0700
Clear memory
Source/driver/Castro_advance.cpp
commit 5ad751062d103a3ba64de1c4b68f9b6d995c8b81
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 9 17:45:36 2020 -0700
Merge SDC source and source_term_predictor
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
commit a58b415227ab473d10a42365886f081a7a350b66
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Mon Mar 9 12:57:46 2020 -0700
prepare for upcoming amrex changes in BaseFab (#806)
This prepares Castro for upcoming changes in AMReX. It is expected to work with both development and basefab_runon branches of AMReX. I have done some tests, but there might still be something that needs to be fixed for AMReX basefab_runon branch. I had to mark sumDerive public so that CUDA host device lambda can be used in that function.
Co-authored-by: Max Katz <maxpkatz@gmail.com>
Source/driver/Castro.cpp
Source/gravity/Gravity.cpp
commit c71a814379cc4fe3e5beb40e0f6e877febb57543
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 9 09:24:09 2020 -0700
Transverse optimizations (#810)
trans_single and trans_final are split into the individual qm and qp loops, and then we drop the local arrays of edge data. This helps for larger networks. We also create inline function versions of upass_map and qpass_map.
Source/driver/Castro_util.H
Source/hydro/Castro_hydro.H
Source/hydro/trans.cpp
commit 849738083dd37b7c0ea29024f1cb051d813be08a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 8 16:43:50 2020 -0700
Fill in valid initial temperature data for Sedov
Exec/hydro_tests/Sedov/Prob_nd.F90
commit 2782a5d8fd1a4af6c8977f463a59e3cb2ac6d82e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 8 10:42:30 2020 -0700
Convert sums to C++ (#800)
The functions used by sum_integrated_quantities() now write their reductions in C++ instead of Fortran. Some unused functions are removed.
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Make.package
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit b19f804bf02e378d30a777758b4d48a06db2a13f
Merge: 774748ada 140af6548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 13:01:57 2020 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 774748ada3fb195b687d6a4baaddfd40864c1be8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 13:01:49 2020 -0400
more scaling
Exec/science/flame_wave/scaling/scaling-2020-03-08.txt
commit 140af65489c57522c305e0aba58924ca8ae9ad29
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 8 09:08:14 2020 -0700
Make mom_flux_has_p an on-demand function (#807)
mom_flux_has_p is now an on-demand function rather than an array. This avoids some issues with the CUDA build.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_util.H
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/riemann.cpp
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/trans.cpp
commit dd80165a84f9ea82a1944e80d7aa40773dce610b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 11:57:18 2020 -0400
std::max/min -> amrex::max/min
Source/hydro/riemann_solvers.cpp
commit 447d552a592ea6283067a074f2d43ff1aa86f15c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 10:53:56 2020 -0400
update changes
CHANGES.md
commit a00bac177b6e459451817f3b6b2d55d6c1d274fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 21:03:36 2020 -0500
convert the Riemann solvers to C++ (#801)
All of the Riemann solvers are now in C++.
Co-authored-by: Max Katz <maxpkatz@gmail.com>
Exec/Make.Castro
Source/driver/Castro.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/riemann.H
Source/hydro/riemann.cpp
Source/hydro/riemann_nd.F90
Source/hydro/riemann_solvers.cpp
Source/hydro/riemann_util.cpp
Source/hydro/riemann_util_nd.F90
commit a0963ab4177378231626240c2fc2e893b82bdbc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 15:43:29 2020 -0500
fix compilation
Source/gravity/Gravity.cpp
Source/scf/scf_relax.cpp
commit 9bb41a89c16b3b47cb4c0e79867fab2d87f78ae2
Merge: bf80febf3 12db38fe4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 14:36:54 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit bf80febf3408cbbdcac5a1620e29caa649d38516
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 14:35:34 2020 -0500
update sphinx docs location
.gitignore
commit 12db38fe424dcfbecd7f6f63353ebb8e6b1f9329
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 7 10:56:18 2020 -0800
Remove MPI bits from radiation code
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.cpp
commit 6f613b32acdb874b929c910a193600104f2969a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 13:53:18 2020 -0500
convert radiation PPM tracing to C++ (#803)
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Make.package
Source/hydro/ppm_nd.F90
Source/hydro/trace_ppm.cpp
Source/radiation/Make.package
Source/radiation/trace_ppm_rad.cpp
Source/radiation/trace_ppm_rad_nd.F90
commit e2b892d1e6677629d27eb0c8d50ab6f32052adce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 13:10:21 2020 -0500
don't need get_grav_const
Exec/science/wdmerger/Prob.cpp
commit 3b323e3189cc49b6d81a0779fc2a7c096f1c7fa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 12:06:05 2020 -0500
inline -> AMREX_FORCE_INLINE
Source/hydro/ppm.H
commit 917f7caa9c1805a38d925832479b3a329e840da8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 7 08:53:21 2020 -0800
Convert hybrid hydro to C++ (#805)
Hybrid hydro is converted to C++. Some of the Fortran routines remain since they are still used in certain places like the Riemann solver and the MOL hydro, but CTU is updated for the new interfaces.
Note: sometimes we use this in problems where there is no radial momentum, it's all angular momentum, but because the radial momentum is zero, numerical roundoff error can cause apparently large changes

Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util.H
Source/driver/Make.package
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Make.package
Source/hydro/hybrid.H
Source/hydro/hybrid_advection_nd.F90
commit e361ca0d15f0210a5e343e1b4e0594e1e743ca44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 09:31:01 2020 -0500
get constants from the C+= header now (#802)
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/scf/scf_relax.cpp
Source/scf/scf_relax_F.H
Source/scf/scf_relaxation.F90
commit 871f3bb6d576bec0cebf04467c73db82c235292b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 5 17:16:09 2020 -0500
fix more shadowing
Source/hydro/Castro_ctu.cpp
Source/hydro/advection_util.cpp
Source/hydro/trans.cpp
commit 56c94dc82cbbec578d9b5f935ffdb7b414b8ff8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 5 13:16:20 2020 -0500
block off radiation var
Source/hydro/trans.cpp
commit 5b6d404e88d6b0002a21c96809ddb7f9b01aa12e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 5 13:08:47 2020 -0500
fix some shadowing
Source/hydro/advection_util.cpp
Source/hydro/trace_ppm.cpp
Source/hydro/trans.cpp
commit f6860227ccaa1801d2feeca608fbc1c1f7c5971d
Merge: ab0fe1ba4 5537fe701
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 19:58:26 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ab0fe1ba43b847549c51d58024c7a4b96ee7c42c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 19:58:08 2020 -0500
max -> amrex::max; min -> amrex::min
Source/hydro/flatten.cpp
commit 5537fe701d1b0fe4792038ccb2d82d0ab96eb7ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 19:17:26 2020 -0500
pstar_bisection was an infinite loop
now we limit it to 5*cg_maxiter
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util_nd.F90
commit 6a5d70220cb17f3283a791815f5b8b9c82a3a6cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 13:47:30 2020 -0500
reset small_{temp,pres_dens,ener} to be tiny but positive
this syncs up with Fortran
Source/driver/Castro_setup.cpp
commit e5f34a5e64d9286ba8c96dc56a3dcc040ab5f889
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 08:23:32 2020 -0500
Convert the transverse routines to C++ (#783)
Co-authored-by: Max Katz <maxpkatz@gmail.com>
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Make.package
Source/hydro/trans.cpp
Source/hydro/trans_nd.F90
commit d49dfbcfb35b8dc4a2acc7043bf627dbebcbac08
Merge: df9145f53 d7b3d606e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 3 17:32:28 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d7b3d606e70884f34dd29e0419afed74a4cc4274
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 3 13:33:10 2020 -0800
Add capability to call the EOS in C++ (#788)
We can now call the EOS from C++. ca_compute_temp is converted to C++ (except for the part dealing with clamp_ambient_temp, which is deferred for now), as well as reset_edge_state_thermo.
Exec/Make.Castro
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Castro_util_nd.F90
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/edge_util.cpp
Source/hydro/edge_util_nd.F90
commit df9145f5364482abd1989fd98373403bcbcfbc6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 3 15:38:07 2020 -0500
fix executable name
confirmed that this still gives 4th order convergence
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
commit e9a966eb633944eeb002bf40e11ffea0c9045a4d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 3 13:09:03 2020 -0500
add separate master & dev branch docs builds, add section on continuous integration to the development best practice page
.travis.yml
Docs/source/_static/theme_overrides.css
Docs/source/_templates/dev_layout.html
Docs/source/_templates/layout.html
Docs/source/conf.py
Docs/source/development.rst
deploy_docs.sh
commit bd99479361eaa68738d6a8281f4dbc588f90fd0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 2 20:39:10 2020 -0500
update README -- we shouldn't use the script anymore, now that we
use submodules.
README.md
commit 6fa478af6a809ec364afa4b6c7329c273097fe20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 2 14:23:47 2020 -0500
remove accidental commit
Source/hydro/riemann.cpp
commit 8b0f7d4933672537d922808e58ac2dd82543125c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 2 13:28:03 2020 -0500
convert to C++
Source/hydro/riemann.cpp
commit c477a95fe1f38eab88111c7d279c033b240571b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 2 12:37:21 2020 -0500
update to 20.03
external/amrex
commit 43e6849c18e951eb7c5c5f97c6ebe1780075b56f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 2 10:14:53 2020 -0500
use agg to let this work headless
Exec/science/flame_wave/analysis/slice_multi_crop.py
Exec/science/flame_wave/analysis/slice_multi_crop_H_He.py
commit 8d67c6c43ffbd1bfad494a6e07ae0cbd9ce4419c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 2 06:57:27 2020 -0800
Implement Edd_factor in C++ (#799)
Since we don't have an easy way to access limiter and closure in device code, these are parameters to the function (for now, at any rate). Also, those variables are made static members of the Radiation class so that we can make local copies of them for lambda captures.
Source/radiation/Make.package
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/fluxlimiter.H
commit dd2e1e9b1724a95e6a75bc86d750cc2f940cb85c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 2 00:20:24 2020 -0800
Fix bug in large velocity limiter
Source/hydro/advection_util_nd.F90
commit ad0fda06fb44053debe7fdb160f4493378436cf7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 20:14:29 2020 -0800
Limit fluxes on small density
Exec/hydro_tests/rotating_torus/inputs_3d
commit 3dbd9d5e72781cb88024afdf325aaa199c82c7d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 20:12:00 2020 -0800
Print out moment of inertia every step
Exec/hydro_tests/rotating_torus/Prob.cpp
Exec/hydro_tests/rotating_torus/Problem.H
commit 44ef8e3018526d8121695e74c84385ac75a33ee1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 20:11:02 2020 -0800
Add option to calculate radial moment of inertia
Source/driver/Castro_F.H
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
commit c5a917bbca81bcc65c29df1794ea2860d0067aa4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 13:50:44 2020 -0800
rotating_torus now supports state_in_rotating_frame = 0
Exec/hydro_tests/rotating_torus/Prob_nd.F90
external/Microphysics
commit 3fb5c14cadaf26609e12124958c8a926de8f7e0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 1 14:23:53 2020 -0500
Update Microphysics to release 20.03
external/Microphysics
commit bfda8601dafcc0f9af401e9ea68edae743e583bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 29 15:19:44 2020 -0500
update changes
CHANGES.md
commit 76123a0e45eedb780e33b2ea510497715be9b435
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 27 21:54:18 2020 -0500
remove unused cmpflx interface (#792)
Source/hydro/riemann_nd.F90
commit 15ac032b14d25b8d57ba41aea4556e64d820fc8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 27 21:46:52 2020 -0500
convert PPM reconstruction to C++ (#786)
the ppm reconstruction and tracing routines have been converted to C++ for the CTU and MOL solvers.
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/Make.package
Source/hydro/edge_util_nd.F90
Source/hydro/ppm.H
Source/hydro/ppm_nd.F90
Source/hydro/trace_ppm.cpp
Source/hydro/trace_ppm_nd.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 43d506c2ec1fcfd566986e6b7dd5e4992a0dc2ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 27 21:41:32 2020 -0500
add the logo to the docs
Docs/source/castro_logo_hot_200.png
Docs/source/conf.py
commit a014c86263dc7df24efd25276c575df1d1ad33e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 26 10:55:27 2020 -0500
don't need domlo/hi in trace_plm
Source/hydro/Castro_ctu_nd.F90
Source/hydro/trace_plm_nd.F90
commit 253460618caa7ef71d0061f6348d0434d50f4a04
Merge: b019a5277 81cf2e8c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 25 12:51:41 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b019a527753b13e4786c1e70ad1b06c442448c19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 25 12:51:17 2020 -0500
castro.fourth_order hasn't existed for a while
we get the order directly from the sdc order
Exec/hydro_tests/Sod/compare_methods.sh
Exec/hydro_tests/Sod_stellar/compare_methods.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc2.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
commit f0781c12b6d31fb7010ea7a322c84a44e24763bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 25 12:51:07 2020 -0500
we no longer have rk4 integration
Exec/hydro_tests/acoustic_pulse/convergence_rk4.sh
commit 81cf2e8c91791c7e3f895b4c9788547cbe0c55f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 25 06:42:21 2020 -0800
Avoid the singularity in cylindrical coordinates
Source/hydro/hybrid_advection_nd.F90
commit 1cf8511ef806ea593c013030ed60a04491564862
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 14:41:15 2020 -0500
remove GDGAME -- it is no longer used
Source/driver/_variables
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util_nd.F90
Source/hydro/trans_nd.F90
commit dfe7657c2ddfb45179c6a12c41d1d37e60be491a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 10:32:31 2020 -0500
make a testsuite version to get the right gamma
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.testsuite
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords.testsuite
commit 1030a194270a342601ca1855f990abc03b695cdb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 10:17:46 2020 -0500
remove gammae inputs
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/hydro_tests/Sod_stellar/inputs-test1-helm.gammae
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
commit df8d3c10f975dc1f46dd3628c943c6a7f2cb7c31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 18:22:35 2020 -0500
update changes
CHANGES.md
commit c2a0a678e2c790799d82cb11525ec176f937dd82
Merge: d28042e9e d6c04b87a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 16:11:08 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d28042e9e2cd27883b4dadb64aaed2cf9d4fa084
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 16:08:22 2020 -0500
add iso_c_binding
Source/driver/extern_probin.template
commit d6c04b87af5828fa0f873703159d9ceb3595a5cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 09:40:07 2020 -0500
remove the reconstruction of gamma_e on interfaces (#780)
This drops the alternative to (rho e) on interfaces -- reconstructing gamma_e. They both are about the same, so there's no need to support both
Note: as a consequence of this, we will be removing the ppm_temp_fix = 1 option from CTU (since apparently it was never coded into the default rhoe reconstruction for some reason). See issue #781
Docs/source/Hydrodynamics.rst
Source/driver/_cpp_parameters
Source/driver/_variables
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/advection_util_nd.F90
Source/hydro/edge_util_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_nd.F90
Source/radiation/trace_ppm_rad_nd.F90
commit e3e7f70371ef92e81631d2390d0570fbbc3e6c8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 22 23:34:11 2020 -0800
Quiet compiler warnings
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/gravity/Gravity.cpp
commit ce41950fdfd6ebc1769aa5c454655afbc2ccd6ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 13:35:49 2020 -0500
update changes
CHANGES.md
commit de469e8c63abfd4c13b307de5f741c1066d38a25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 12:38:04 2020 -0500
initialize the extern parameters in C++
Source/driver/Castro.cpp
commit 082e707dc1885c5007052c96fe39c83827c62e3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 12:25:37 2020 -0500
hook in the C++ parameters
Exec/Make.auto_source
Source/driver/extern_probin.template
commit 5ae777b02328b7d2f5b8fd28871d9d38fb512030
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 11:55:43 2020 -0500
fix net location
Util/exact_riemann/GNUmakefile
commit 9dbbdfc69d27bea9ba9b2396a204d03ae07f7bf3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 22 08:53:58 2020 -0800
Depend on Microphysics fundamental constants (#787)
To avoid redundancy, we remove Castro's copy of the fundamental constants and rely directly on Microphysics.
Exec/Make.Castro
constants/Make.package
constants/constants_cgs.f90
external/Microphysics
commit 745fd8722cb1043e0297bfc4547a7be295281f91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 10:59:37 2020 -0500
remove refs to other diffusion
Docs/source/diffusion.rst
commit 72a35453bf9ed8ba309d78a712b1a66d724bd7b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 08:18:47 2020 -0500
get the aux_names from the C++ header (#784)
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
commit 45994be97da27894d74f3f887fd644e51c873b59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 21 15:43:36 2020 -0500
merge the transverse routines (#768)
This consolidates the various transverse routines, using mini-Castro as a guide.
* 2-d axisymmetric pure hydro will have roundoff diffs because we now include the area factors in the z-direction (previously it was only in the r direction)
* we are slower by about 10% -- this is likely because the compiler cannot do cache optimization. We will address this with templating when we convert to C++
* for radiation, in 2-d we now use the general geometry form for the radiation pressure in the transverse flux
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Make.package
Source/hydro/edge_util.F90
Source/hydro/trans_nd.F90
commit 972b99dc84cfbf90d629898a1deac4f8d89eaceb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 12:25:35 2020 -0800
Rename Fortran files to end with _nd.F90 (#785)
As we convert things to C++, we will have intermediate states where some parts of a file are in Fortran and others in C++. To make this easier, we should maintain the convention that the C++ file has the normal name (e.g. advection_util.cpp) and the Fortran file has a _nd suffix (e.g. advection_util_nd.F90). This PR converts several files to abide by this convention to make the porting easier later.
Exec/Make.auto_source
Exec/Make.cuda_rules
Source/driver/Castro_error_nd.F90
Source/driver/Castro_util_nd.F90
Source/driver/Make.package
Source/driver/amrinfo_nd.F90
Source/driver/check_for_nan_nd.F90
Source/driver/generic_fill_nd.F90
Source/driver/interpolate_nd.F90
Source/driver/io_nd.F90
Source/driver/math_nd.F90
Source/driver/parse_castro_params.py
Source/driver/prob_params_nd.F90
Source/driver/reduction_nd.F90
Source/driver/set_variables.py
Source/driver/source_fill_nd.F90
Source/driver/timestep_nd.F90
Source/gravity/GR_Gravity_1d.F90
Source/gravity/GR_Gravity_2d.F90
Source/gravity/GR_Gravity_3d.F90
Source/gravity/Gravity_1d.F90
Source/gravity/Gravity_2d.F90
Source/gravity/Gravity_3d.F90
Source/gravity/Make.package
Source/hydro/Castro_fourth_order_nd.F90
Source/hydro/Make.package
Source/hydro/fourth_order_nd.F90
Source/hydro/riemann_util_nd.F90
Source/hydro/trace_plm_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_nd.F90
Source/problems/Make.package
commit fbe29b6e413b30360a4214554d3af2f5179fd7d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 21 08:49:06 2020 -0500
reorganize the makefiles (#782)
This splits up the makefiles and uses Make.Microphysics_extern from Microphysics directly.
submodule update Microphysics to bafff355959ce1226beb51e0b2f04a3a5e337e91
Exec/Make.Castro
Exec/Make.auto_source
external/Microphysics
commit ee46fbb6639287a316b66555b313cfa6ff209c57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 20 10:29:35 2020 -0500
new scaling numbers
Exec/science/flame_wave/scaling/scaling-2020-02-19.txt
commit 1d33d0943d159cdd40e4f1bede64352844cfe975
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 15:01:47 2020 -0500
add single-level note
Exec/science/flame_wave/scaling/scaling-2019-11-18.txt
commit 84944e2c424db2df79cc31e10e2fc34a4b69bd05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 14:13:24 2020 -0500
add the probin
Exec/science/flame_wave/scaling/probin.boost_10_10
commit 1a66395dff3f477cccd7a460f91528d2f9fd0240
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 14:05:13 2020 -0500
rename with date
Exec/science/flame_wave/scaling/scaling-2019-11-18.txt
commit 8da7f5bc65039637d41fe23be43b2ac976302014
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 13:47:52 2020 -0500
VODE90 -> VODE
Exec/reacting_tests/nse_test/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/rotating_star/GNUmakefile
Exec/science/subchandra/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_collision/GNUmakefile
Exec/unit_tests/model_burner/GNUmakefile
Exec/unit_tests/reactions_driver_test/GNUmakefile
Exec/unit_tests/reactions_driver_test/README.md
commit d8276b32c752eef092c7cfd2df14cff48bdf97fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 13:45:49 2020 -0500
fix VODE check
Exec/Make.Castro
commit 3b995bec77d18daa6ab76f63e591ae5250379d7c
Merge: 546c5042a 743ec90ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 11:27:03 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 546c5042a728b195edb96fd1911f4025a9ef68cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 19 11:26:05 2020 -0500
remove vestiges of viscosity
Exec/Make.Castro
commit 743ec90adc3bd7cf9c65ba88cd945cac5e0ddc65
Author: Alice Harpole <harpolea@login2.summit.olcf.ornl.gov>
Date: Wed Feb 19 10:41:17 2020 -0500
submit scripts and inputs files for XRB scaling test
Exec/science/flame_wave/scaling/inputs.scaling_384.3d
Exec/science/flame_wave/scaling/inputs.scaling_576.3d
Exec/science/flame_wave/scaling/submit_flame.sh
Exec/science/flame_wave/scaling/submit_flame_384.sh
Exec/science/flame_wave/scaling/submit_flame_576.sh
commit 6989075b32bf0183b883053110e6647b34323358
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 18 14:27:07 2020 -0800
Update AMReX
external/amrex
commit 51c2dd384b19dd016d232a682515cd673ce9976a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 17 16:28:53 2020 -0800
Set up rotating_torus to run on GPUs
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
commit 0c2f4e58a1b470f1f292dff620651ebf59629274
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 17 15:48:18 2020 -0500
fix executable name
Docs/source/getting_started.rst
commit 9900caa9dd1d71436a4a129c494dee5d501a3d94
Merge: 0dbcbdc41 7cf92d50e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 17 15:04:52 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 0dbcbdc416880c9baac90bbeefae88d950f1a2fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 17 15:04:39 2020 -0500
a pass through getting started
Docs/source/getting_started.rst
commit 7cf92d50ef8abd03bd5f63160bf30953b63c8069
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 17 09:50:30 2020 -0500
update email
.mailmap
commit 76548b4921a076bc209bd4e65daee82767561aa3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 17 09:47:43 2020 -0500
update mailmap to catch more dupes
.mailmap
commit be353f584f9d00b9b1ade4b87520d32f478eb1be
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 17:22:26 2020 -0800
Revert "Use gray acceleration for the Mach 5 test"
This reverts commit d371bec3d9eb257bb07f2d563b90da8f6787c5d9.
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
commit c0a6e40f42f15929d82b29c5f903e292b9546f20
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 16:33:28 2020 -0800
Update Microphysics (for network autogeneration). Again.
external/Microphysics
commit f5e6334e334ca722a0c5cd456e1f7941ed694270
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 15:20:44 2020 -0800
Update Microphysics (for network autogeneration)
external/Microphysics
commit d371bec3d9eb257bb07f2d563b90da8f6787c5d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 15:11:36 2020 -0800
Use gray acceleration for the Mach 5 test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
commit d26e4ae3b5a42e1e9c3cc44ec0fdf3703a21dc05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 16 15:13:23 2020 -0500
Autogen network_properties.{F90,H} (#774)
This is done together with starkiller-astro/Microphysics#253 to store the autogenerated network_properties.{F90,H} in the castro_source_dir/ build directory.
Exec/Make.Castro
commit ea2a8fec9a4e8dd779151406deed3af5a05fe2d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 12:00:39 2020 -0800
Treat HypreExtMultiABec as its own class member
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
commit 99e202179ddd495fd876e6247ae1bfec778f6b97
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 08:56:40 2020 -0800
Fix an illegal array access issue
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/Radiation.H
commit 5ba31e9d478771f54a6db558cf26e7c08d56ce23
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 06:24:17 2020 -0800
Add analytic solution for the radiating sphere to the plotfile (#759)
The Python analysis routine is also updated to take advantage of this, rather than relying on a fixed output (which could only be used at a specific simulation time and distance from the origin).
Diagnostics/Radiation/rad_sphere.cpp
Exec/radiation_tests/RadSphere/Problem_Derive.H
Exec/radiation_tests/RadSphere/Problem_Derive.cpp
Exec/radiation_tests/RadSphere/Problem_Derive_F.H
Exec/radiation_tests/RadSphere/Problem_Derives.H
Exec/radiation_tests/RadSphere/Tools/GNUmakefile
Exec/radiation_tests/RadSphere/Tools/analytic.f90
Exec/radiation_tests/RadSphere/problem_derive_nd.F90
Exec/radiation_tests/RadSphere/python/RadGroup.py
Exec/radiation_tests/RadSphere/python/paper.py
Exec/radiation_tests/RadSphere/python/phys.py
Exec/radiation_tests/RadSphere/testsuite_analysis/radsphere.py
Exec/radiation_tests/RadSphere/testsuite_analysis/radsphere_analytic.out
commit 83a904be4d0b06205bb125d439f44b92f90fc9d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 16 06:00:30 2020 -0800
Fix a potential square root of a negative number (#773)
Although lambda is limited to be no smaller than 1/3, due to roundoff
error the factor (1 - 3 * lambda) may evaluate negative, in which case
sqrt(1-3*lambda) will fail. So we force it to be no smaller than 0.
Source/radiation/fluxlimiter.F90
commit f940a8035382f5a7706411f3c1a10a978edba324
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 19:54:54 2020 -0800
Remove unused DumpModel code
Docs/source/build_system.rst
Source/driver/main.cpp
Source/radiation/DumpModel1d.H
Source/radiation/DumpModel1d.cpp
Source/radiation/Make.package
commit 04f0cc0a1c2990c942f55746389dfada93609a41
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 19:48:57 2020 -0800
Remove a couple neutrino references
Docs/source/build_system.rst
Docs/source/radiation.rst
commit 8aa1b7aa4efea3f625ac810d2716723c2b725b9e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 19:39:43 2020 -0800
Merge coding conventions into development
Docs/source/coding_conventions.rst
Docs/source/development.rst
Docs/source/index.rst
commit 392bde72f781fc18947af4c584a4986c480410cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 19:28:38 2020 -0800
Rename releases -> development best practices
Docs/source/development.rst
Docs/source/index.rst
commit 834e853cc1d18fbeb36c4a2cef4d156074b7a735
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 17:41:19 2020 -0800
Fix a VLA issue
Source/driver/Castro_F.H
Source/driver/Castro_setup.cpp
commit 753f0a0724ee82725ded2db0685851f17dd1ffbd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 15 17:47:30 2020 -0500
fix type of dt
Source/hydro/Castro_hydro.H
Source/hydro/advection_util.cpp
commit df53baa5bdccf391400d5b5fb374197b1df09fd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 15 17:18:48 2020 -0500
change .array() syntax
Source/hydro/Castro_ctu_hydro.cpp
commit 1ec14a6556c60bf2570e6b65bda83588609011a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 15 16:57:19 2020 -0500
use the C++ network species names
Exec/science/flame/Prob.cpp
commit b1bb2df82e0c525ef288f404215169500db5c11a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 15 11:46:16 2020 -0500
move more routines over to C++ (PR 3/∞) (#761)
This converts normalize_species_fluxes, scale_flux, and scale_rad_flux to C++
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/advection_util_nd.F90
commit 1a4f0e7dad674eb51b1941a9b891c9454ed0d146
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 14 15:21:18 2020 -0500
add cron to job type
.travis.yml
commit 3a19ce5f853d59c9735f50db3de6a154ed31534c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 14 13:10:14 2020 -0500
plotting script for H/He runs
Exec/science/flame_wave/analysis/slice_multi_crop_H_He.py
commit 539aab061a3863611d7d50cbc310a5d2e0a10ecb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 06:44:41 2020 -0800
std::min -> amrex::min
Source/hydro/advection_util.cpp
commit f8655ff98e1b342742c485f9458a219e0306a074
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 05:35:39 2020 -0800
Place general_null network files in tmp_build_dir (#770)
Exec/Make.Castro
commit 2da69cc76269625e046e2c7e2c654cc68b472c78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 14 08:32:16 2020 -0500
species names are now in the C++ header so we no longer need Fortran gets (#769)
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
commit 3300798c0a485cf35f2f00ed72e206eb0a2fae1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 19:37:30 2020 -0500
clean up some headers
Source/driver/Castro.H
Source/hydro/Castro_hydro.H
commit 9cbc824f81c6fe50aef85c52fb0ece7b6c889375
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 18:13:04 2020 -0500
remove some unused function prototypes
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
commit a15af99a2efade281e2ca2725a573634f188e90a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 17:56:32 2020 -0500
more shadowing fixes
Source/hydro/advection_util.cpp
commit 622672f9d0d72380286630b247309c48962d055b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 16:13:22 2020 -0500
fix more shadowing
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/scf/scf_relax.cpp
commit 8d64f1b5f3172be5440e855f64abda63403a524f
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Feb 13 15:45:44 2020 -0500
fixed travis pr script
Util/code_checker/pr_tab_remover.sh
commit 9833ef5ed0b14b01d401800c96842d0d4f5c61af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 15:24:35 2020 -0500
fix some shaddowing highlighted by the static analyzer
Source/driver/Castro.cpp
Source/gravity/Gravity.cpp
Source/hydro/flatten.cpp
commit 9e85b04c5c40843460b8166650e2726452f67c83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 11:42:18 2020 -0500
reorg outputting
Docs/source/io.rst
Docs/source/vis_tools.rst
Docs/source/visualization.rst
commit c2991041fd0e0940beff8ca4008831f39e23f6b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 11:27:53 2020 -0500
merge chapters
Docs/source/index.rst
Docs/source/retry.rst
Docs/source/timestepping.rst
commit 4ab7f57fe0a70a92b72e19df5b42d7b51d55b9ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 10:12:21 2020 -0500
move more routines to C++ (PR 2/∞) (#756)
This converts ca_shock, apply_av, apply_av_rad to C++
Source/driver/Castro.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/advection_util.cpp
Source/hydro/advection_util_nd.F90
commit 9d0d4dbcffba784d2f0026648b233e7681ef7b02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 13 09:28:40 2020 -0500
move the EOS reset on states outside of the trans loop (#767)
This puts the reset_edge_state_thermo calls outside of the trans loops. Note that the reason we chose to do this is because it removes the EOS from the transverse routines, which allows us to move the transverse routines to C++ independently of the implementation of the EOS in Microphysics in C++ (which is happening over a longer timescale). However, in the long run when we have got that all done, we will want to look at moving this back to be a zone-by-zone implementation.
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/trans.F90
commit 001643721612faa8275124b59b9d66d0eda5f52d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 19:58:37 2020 -0500
update changes
CHANGES.md
commit b6bf050a656ac84905ead7c6b49eaba419b46f0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 15:35:31 2020 -0500
convert some CTU hydro routines to C++ (#731)
This converts the CTU consup for hydro (not radiation) , the flattening routines, and src_to_prim to C++
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/hydro/Castro_ctu.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
Source/hydro/advection_util.cpp
Source/hydro/advection_util_nd.F90
Source/hydro/flatten.cpp
Source/hydro/flatten_nd.F90
Source/hydro/hybrid_advection_nd.F90
commit d14bf5ab83bfd361093d224f72b58e08c76200e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 12 11:04:03 2020 -0800
Add AMReX as a git submodule (#762)
.gitmodules
CHANGES.md
Docs/source/getting_started.rst
Docs/source/releases.rst
Exec/Make.Castro
external/amrex
commit 78b847e4f4d5084575ee1d05a1d3392d9886a79e
Merge: fd3ccf442 2bfe12889
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 13:16:06 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit fd3ccf442f2d9917d93fed16b536d7f3798b7580
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 13:09:37 2020 -0500
switch blocking_factor to 8
Exec/radiation_tests/RadSuOlson/inputs
commit 2bfe12889c76ad89fc236a49a22a2c2c3b3cda2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 12 07:21:36 2020 -0800
Update mini-Castro inputs for only single grid
Exec/hydro_tests/Sedov/inputs.mini-Castro
commit dbece54e6252229960f6a803c8aa251ec5a6017e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 10:09:47 2020 -0500
remove ppm_temp_fix = 3 (T based eigensystem) (#764)
CHANGES.md
Docs/source/Hydrodynamics.rst
Source/hydro/trace_ppm.F90
commit 29a67b4a2e420e3821c2810ad96b6bdde14c8bfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 09:08:09 2020 -0500
more docs updates
Docs/source/FlowChart.rst
Docs/source/getting_started.rst
Docs/source/inputs.rst
Docs/source/refs.bib
Docs/source/timestepping.rst
commit 28dbd87e620e679fb22cea033cd280a8f0a0fe1d
Merge: 4f3782fb9 0a24b2ab6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 08:12:11 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 0a24b2ab6d585d28cb89077c68873992375d7339
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 12 05:11:45 2020 -0800
Move Microphysics to a new external subdirectory (#765)
This PR proposes to adopt a trend where external dependencies of Castro all live in the external/ subdirectory, and moves Microphysics there.
.gitmodules
Docs/source/getting_started.rst
Docs/source/software.rst
Exec/Make.Castro
external/Microphysics
commit 4f3782fb95eabd92e6aaec6d3de6261f9184cc17
Merge: d9ba1467a 4372488f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 12 08:04:09 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 4372488f2d13b554bc922eeeb3005f2e3f335ceb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 11 18:41:15 2020 -0800
Update Microphysics
Microphysics
commit d9ba1467a7f55fa69fbba8fa1f539376ab1c40dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 20:49:37 2020 -0500
some more docs updates + a new release doc
Docs/source/AMR.rst
Docs/source/Hydrodynamics.rst
Docs/source/Introduction.rst
Docs/source/Preface.rst
Docs/source/index.rst
Docs/source/radiation.rst
Docs/source/releases.rst
Docs/source/retry.rst
Docs/source/sdc.rst
commit ff16935764f1dd71e279d6ca3b3bf62a30581fa7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 11 13:41:00 2020 -0800
Handle the plotfile case where a derived variable has multiple components (#758)
In this case, the plotfile logic would only plot the first component of the derived
variable. Now, if a derived variable has multiple components, we plot all components.
The name of each is appended with an integer variable indicating which one it is.
This issue also exists in AMReX, where this plotfile code presumably originally came from.
CHANGES.md
Source/driver/Castro_io.cpp
commit 4ea1e5120eaaf46397be927f4d26ccd97ce0871d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 16:12:22 2020 -0500
move sphinx_docs -> Docs
Docs/Doxyfile
Docs/Makefile
Docs/add_doxy_headers.py
Docs/converting_docs.txt
Docs/make_api.py
Docs/pandoc.sh
Docs/preprocess_files.py
Docs/rp.py
Docs/source/AMR.rst
Docs/source/ConvertCheckpoint.rst
Docs/source/EOSNetwork.rst
Docs/source/FlowChart.rst
Docs/source/Hydrodynamics.rst
Docs/source/Introduction.rst
Docs/source/LineQueryPlot_0_t_magvel.png
Docs/source/MAESTRO_restart.rst
Docs/source/OffAxisProjection_density.png
Docs/source/Particles.rst
Docs/source/Preface.rst
Docs/source/Profile2D_1_Density_magvel_kineng.png
Docs/source/RT_ppm_type.png
Docs/source/Slice_z_pressure.png
Docs/source/Verification.rst
Docs/source/_static/theme_overrides.css
Docs/source/build_system.rst
Docs/source/center.png
Docs/source/coding_conventions.rst
Docs/source/conf.py
Docs/source/corner.png
Docs/source/creating_a_problem.rst
Docs/source/debugging.rst
Docs/source/diffusion.rst
Docs/source/domain-tile.png
Docs/source/faq.rst
Docs/source/fluid_motion.png
Docs/source/getting_started.rst
Docs/source/gpu_porting.rst
Docs/source/gravity.rst
Docs/source/index.rst
Docs/source/index_grid2.png
Docs/source/inputs.rst
Docs/source/io.rst
Docs/source/isocontours.png
Docs/source/mathsymbols.tex
Docs/source/mpi_plus_x.rst
Docs/source/rad.rst.old
Docs/source/radiating_source.png
Docs/source/radiating_sphere.png
Docs/source/radiation.rst
Docs/source/refs.bib
Docs/source/regridding.rst
Docs/source/retry.rst
Docs/source/rotating_torus_00000_density.png
Docs/source/rotating_torus_00200_density.png
Docs/source/rotating_torus_hybrid_00200_density.png
Docs/source/rotation.rst
Docs/source/rp_intro.rst
Docs/source/sdc.rst
Docs/source/sedov_cyl.png
Docs/source/sedov_sph.png
Docs/source/self_consistent_field.rst
Docs/source/sod_3d.png
Docs/source/sod_3d_ppm0.png
Docs/source/software.rst
Docs/source/sponge.rst
Docs/source/test2_3d.png
Docs/source/test3_3d.png
Docs/source/test_suite_day.png
Docs/source/test_suite_main.png
Docs/source/tframes.png
Docs/source/timestepping.rst
Docs/source/tracer_trajectory.png
Docs/source/vis_tools.rst
Docs/source/visualization.rst
Docs/source/volume.png
Docs/source/zreferences.rst
deploy_docs.sh
commit 0ce616d53a5d2a4ee10d37b6734f2677e0fc9717
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Feb 11 14:25:56 2020 -0500
fixed rsa keys
Util/code_checker/pr_tab_remover.sh
commit f08a875002a4302548edb925d8f80c0b563b389d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 11 11:12:44 2020 -0800
Replace Castro microphysics with starkiller-astro Microphysics (#760)
This implements the Microphysics part of #651. We replace the local Castro Microphysics directory with a dependence on the main starkiller-astro Microphysics directory. This means that obtaining Microphysics is now a requirement for using Castro. If the user sets MICROPHYSICS_HOME as before, then their workflow does not change. A new path is that Microphysics is a git submodule of Castro, so if the user does git submodule update --init --recursive then they will obtain the version of Microphysics that we specify in the repo, and if they do not have MICROPHYSICS_HOME set then this submodule will be used. The repo is now updated with git pull --recurse-submodules, so that updates to Microphysics come along when you pull.
A minor associated change is that we've standardized on NETWORK_INPUTS in all of the makefiles, instead of using GENERAL_NET_INPUTS with the hardcoded path.
.gitmodules
CHANGES.md
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/double_mach_reflection/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/heating_verification/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/nova/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/science/rotating_star/GNUmakefile
Exec/science/subchandra/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/model_burner/GNUmakefile
Exec/unit_tests/particles_test/GNUmakefile
Exec/unit_tests/reactions_driver_test/GNUmakefile
Microphysics
Microphysics/EOS/Make.package
Microphysics/EOS/README
Microphysics/EOS/_parameters
Microphysics/EOS/composition.F90
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/EOS/rad_power_law/Make.package
Microphysics/EOS/rad_power_law/_parameters
Microphysics/EOS/rad_power_law/rad_power_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/conductivity/constant_opacity/Make.package
Microphysics/conductivity/constant_opacity/_parameters
Microphysics/conductivity/constant_opacity/constant_conductive_opacity.F90
Microphysics/conductivity/powerlaw/Make.package
Microphysics/conductivity/powerlaw/_parameters
Microphysics/conductivity/powerlaw/powerlaw_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/gammalaw_aux.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
Microphysics/opacity/Readme
Microphysics/opacity/breakout/Make.package
Microphysics/opacity/breakout/opacity_table_module.F90
Microphysics/opacity/rad_power_law/Make.package
Microphysics/opacity/rad_power_law/_parameters
Microphysics/opacity/rad_power_law/opacity_table_module.F90
Microphysics/viscosity/constant/Make.package
Microphysics/viscosity/constant/_parameters
Microphysics/viscosity/constant/constant_viscosity.f90
sphinx_docs/source/getting_started.rst
commit 58771cbc3305186fd29df3de2cf91c4703eeca52
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Feb 11 12:19:47 2020 -0500
added script to travis build to run tab exterminator script on PRs and push changes
.travis.yml
Util/code_checker/clang_static_analysis.py
Util/code_checker/pr_tab_remover.sh
commit 137acb0eb9838d393bdc479c4a00353619462785
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 12:15:29 2020 -0500
some splitting
sphinx_docs/source/index.rst
sphinx_docs/source/inputs.rst
sphinx_docs/source/io.rst
sphinx_docs/source/regridding.rst
sphinx_docs/source/timestepping.rst
commit f485d76081270d6a6180fe2780cde410ca251090
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 11:49:57 2020 -0500
some docs cleaning
sphinx_docs/source/Introduction.rst
sphinx_docs/source/Preface.rst
sphinx_docs/source/inputs.rst
commit e9a02de547334b917df25055856c8004509ffa43
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 10 20:18:19 2020 -0800
Revert eos_on_host; always use normal EOS call
The intended direction for this change is no longer needed,
as we will switch to attributes(host,device) eventually
instead. Since this method is extremely expensive on GPUs,
it did not make sense to keep doing it.
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/hydro_tests/HCBubble/Prob_nd.F90
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/heating_verification/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/RadFront/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/toy_flame/Prob_nd.F90
Exec/science/Detonation/Prob_nd.F90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/flame/Prob_nd.F90
Exec/science/flame_wave/initial_model.F90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/wdmerger_util.F90
Exec/unit_tests/diffusion_test/Prob_nd.F90
commit fd39921c0c9887b116747c84ec963803eb06a3b6
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Feb 10 13:04:06 2020 -0500
convert tabs to spaces (#763)
Source/diffusion/Diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/CastroBld.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/main.cpp
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/gravity/Castro_gravity.H
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/particles/CastroParticles.cpp
Source/problems/Prob_nd.F90
Source/radiation/Castro_radiation.cpp
Source/radiation/HABEC_F.H
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGRadBndry.H
Source/radiation/MGRadBndry.cpp
Source/radiation/NGBndry.H
Source/radiation/RAD_F.H
Source/radiation/RadBndry.H
Source/radiation/RadBndry.cpp
Source/radiation/RadMultiGroup.cpp
Source/radiation/RadPlotvar.cpp
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
Source/radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/_interpbndry/RadBndryData.cpp
Source/radiation/_interpbndry/RadBoundCond.H
Source/radiation/_interpbndry/RadInterpBndryData.H
Source/radiation/_interpbndry/RadInterpBndryData.cpp
Source/reactions/Castro_react.H
Source/reactions/Castro_react.cpp
Source/scf/scf_relax_F.H
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.H
Source/sources/Castro_sources.cpp
Source/sources/Castro_thermo.cpp
commit c4a55e4cd5ee22a20a4a255ac98974bc910c0c93
Merge: ce89ddcbc b39bc029d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 10 12:06:01 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ce89ddcbc9c75b110b8141f3fa137a566db768a4
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 10 12:05:44 2020 -0500
script to convert tabs to spaces
Util/code_checker/tab_exterminator.sh
commit b39bc029d3221315e7ca6f1042fcbcd004b08fe2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 10 10:15:26 2020 -0500
split okay_to_burn into two functions
Source/driver/timestep.F90
Source/reactions/React_nd.F90
Source/reactions/react_util.F90
commit 144117c02f68dfe6119361a5d3238ffe76b153de
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 23:20:23 2020 -0800
Add intent(in) to pure function
Source/reactions/react_util.F90
commit aed6b91f643dfbc9b41d584f5271a003a7a425d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 22:52:31 2020 -0800
Fix group indexing in emissivity
Source/radiation/Rad_nd.F90
commit 7ee7f81b8ead7ebe52a331b2d335229d07579f84
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 22:16:46 2020 -0800
Dimension agnostic dcoefs
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit b6b97cc81cbf725f456ad845c418bcc0a84b7516
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 21:45:33 2020 -0800
Dimension agnostic lacoefmgfld
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 7ccc82c813aa7bf164a2d00520deefd25581c78c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 21:32:04 2020 -0800
Dimension agnostic multrs
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 39a237bc283319eff00f6d790271ca0670b4bc4c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 20:51:05 2020 -0800
Dimension agnostic rhstoer
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 5a90639ff76410a7601c3e4af2140e130e2d1453
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 12:51:02 2020 -0800
Merge two versions of okay_to_burn
Microphysics/networks/burner.F90
Source/driver/timestep.F90
Source/reactions/React_nd.F90
Source/reactions/react_util.F90
commit 708811843a5fafd3c47254c34903ed9c2ea0932e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 10:50:21 2020 -0800
Check in missing file
Source/problems/emissivity_override.F90
commit e7b6081a8c4346c1dd21ff4077bc71a74bd821ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 09:45:28 2020 -0800
C++ extern files go to the tmp_build_dir
Exec/Make.Castro
commit 1fa9a3287f9ff4a5785471c901330655c22d03c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 09:17:42 2020 -0800
Merge the single-group emissivity into the multi-group case
Source/radiation/Rad_nd.F90
commit 6711cf8d23f282f276a1ac98f6f59529093b1de8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 09:01:44 2020 -0800
Avoid special cases in emissivity with override subroutine
This has been applied to RadShestakovBolstad (to implement the Wien's
law emission) and RadSuOlsonMG (to implement the picket-fence model).
Exec/radiation_tests/RadShestakovBolstad/emissivity_override.F90
Exec/radiation_tests/RadShestakovBolstad/inputs-Tf0.1
Exec/radiation_tests/RadShestakovBolstad/inputs.Planck
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadSuOlsonMG/emissivity_override.F90
Source/problems/Make.package
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/blackbody.F90
commit 8e64659a75f67a4c53098d283a9d24a788e2af8b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 08:01:55 2020 -0800
Fix compilation
Source/radiation/RadMultiGroup.cpp
Source/radiation/Radiation.cpp
Source/radiation/energy_diagnostics.cpp
commit 9bcb2bcdc026c96be3d0764c430b23fe07787eab
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 23:52:14 2020 -0800
Use normal geometric group growth for RadSphere
Exec/radiation_tests/RadSphere/inputs
Source/radiation/Make.package
Source/radiation/RadMultiGroup.cpp
Source/radiation/RadTests.H
Source/radiation/Radiation.cpp
commit 541d6428f94e85c4b0a8b239de73331b99d1381c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 23:05:21 2020 -0800
Remove neutrino code
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/radiation/RadMultiGroup.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/energy_diagnostics.cpp
commit 339f9b5fc9aed26ee68ec07f503622fa77629b93
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 22:49:22 2020 -0800
Remove no longer used do_thermal_wave_cgs parameter
Source/radiation/RadTests.H
Source/radiation/Radiation.cpp
commit 331fe7f078c98b7f04579d382e9f7ed945369bf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 20:33:02 2020 -0500
actual_network.H -> network_properties.H
Microphysics/networks/general_null/Make.package
Source/driver/set_variables.py
commit a35f2c82dbdf1515f1071d0fcd3eb0e02168373f
Merge: 7f37218be f6639a6aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 17:46:31 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 7f37218bebb23a8381c4451bbf740676b33bc57c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 17:46:20 2020 -0500
fix namelist
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit f6639a6aacd0d15c79e523e497e1249d8295388f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 14:16:03 2020 -0800
Avoid divide-by-zero error
Source/radiation/HABEC_nd.F90
commit 88c9e5e0d13c56cd1ed633f3ba8e66bf17735731
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 13:34:50 2020 -0800
Update CHANGES for C++ variable name change
CHANGES.md
commit 0fd65b68f2a65ffd5b77fd7219d1cd158a7e87f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 16:27:14 2020 -0500
sync the conserved state names between C++ and Fortran (#757)
Now we use URHO for density in both C++ and Fortran (and same for the other conserved state indices). This still sets the only state names for backwards compatibility.
Exec/hydro_tests/gamma_law_bubble/Problem_Derives.H
Exec/radiation_tests/RadThermalWave/Problem_Derives.H
Exec/reacting_tests/reacting_bubble/Problem_Derives.H
Exec/science/wdmerger/Problem_Derives.H
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/unit_tests/diffusion_test/Prob.cpp
Exec/unit_tests/diffusion_test/Problem_Derives.H
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/_variables
Source/driver/set_variables.py
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/fourth_order.F90
Source/particles/CastroParticles.cpp
Source/radiation/DumpModel1d.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/Radiation.cpp
Source/radiation/energy_diagnostics.cpp
Source/reactions/Castro_react.cpp
Source/scf/scf_relax.cpp
Source/sources/Castro_sources.cpp
commit 568aeafc2458212525cd6413c06f396d4cfe99fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 03:35:37 2020 -0800
Mark up EOS for OpenACC
Microphysics/EOS/composition.F90
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_override.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Source/driver/Castro_nd.F90
commit 55a6a3919863bc46fbf753a54c11d558555f74fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 05:52:20 2020 -0500
switch Fortran state indices to parameters (#755)
Exec/Make.Castro
Source/driver/Castro_nd.F90
Source/driver/Make.package
Source/driver/meth_params.template
Source/driver/set_variables.py
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trans.F90
Source/radiation/rad_params.F90
Source/radiation/trace_ppm_rad_nd.F90
sphinx_docs/source/build_system.rst
commit a35a6c2334ee6ee5779313f09244fb2b74342e60
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 8 02:22:11 2020 -0800
Add dLogArea
Source/driver/Castro_util.F90
commit ac4b66173d34cd4910809fe641b666ef8d818d08
Merge: 410b09411 c8b19bab8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 7 21:09:31 2020 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit c8b19bab879b0be6c8293537b161e840402ba32e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 7 20:44:30 2020 -0500
remove unused functions
Source/driver/Castro_nd.F90
commit 410b09411f033cc0aa1294b0e37e37b915dae4b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 7 20:33:34 2020 -0500
fix compilation
Source/radiation/RAD_F.H
commit 14096680c251c2f04b316a23b3f7f4edcf94e0f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 7 19:46:43 2020 -0500
move flatten_pp_threshold to _cpp_parameters
Source/driver/_cpp_parameters
Source/driver/meth_params.template
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit 96e4c0777cb1c8d010f1f328c7429bd58bfd3361
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 7 14:20:20 2020 -0500
get rid of the coord_type check in ca_shock
we clearly have implemented the other geometries
Source/hydro/advection_util_nd.F90
commit 2a2609397832f618a883c7c156ffef07ea54f43d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 6 14:47:31 2020 -0500
Variable cleanup cxx (#754)
This switches the initialization of the C++ state indices (e.g. Density, QRHO, ...) to constexprs. This let's the work with the lambda-capture GPU offloading. Note: the Fortran indices are still handled the same way as before. This is an alternative to #747
As part of this change, the general_null network writes out a C++ header.
Exec/Make.Castro
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
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_generic_fill.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Castro_source_fill.cpp
Source/driver/Make.package
Source/driver/_variables
Source/driver/set_variables.py
Source/problems/Castro_bc_fill_nd.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit e4910112e42d6a7b9af25cf7e2651e1c04c5bba9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 21:53:09 2020 -0500
switch to prob params
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/Make.package
Exec/radiation_tests/RadSuOlsonMG/Prob_nd.F90
Exec/radiation_tests/RadSuOlsonMG/_prob_params
Exec/radiation_tests/RadSuOlsonMG/probdata.F90
commit e3ea493ebf4985be2ec6301d00b9297f1c137bf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 20:29:30 2020 -0500
switch to prob params
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSphere/Make.package
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/radiation_tests/RadSphere/_prob_params
Exec/radiation_tests/RadSphere/probdata.F90
commit 70539d241ce252215a90524a9cccbe9a315dcf31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 20:19:13 2020 -0500
switch to prob params
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSourceTest/Make.package
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/_prob_params
Exec/radiation_tests/RadSourceTest/probdata.F90
commit 08459dfa803a179da827a2d91848fe667ac6ef1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 20:09:10 2020 -0500
update to prob params
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSlope/Make.package
Exec/radiation_tests/RadSlope/Prob_nd.F90
Exec/radiation_tests/RadSlope/_prob_params
Exec/radiation_tests/RadSlope/probdata.F90
commit c4f4df02e6013a175d84cc3bbd7c166dba28cf3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 17:12:44 2020 -0500
switch to prob params
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/Make.package
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
Exec/radiation_tests/RadShestakovBolstad/_prob_params
Exec/radiation_tests/RadShestakovBolstad/probdata.F90
commit 6973e9927e074d1fcb162d5a1bf7fe55398cfa71
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 5 07:12:56 2020 -0800
Ambient state (#595)
* Add an ambient state module
* Call EOS on ambient state
* Add option to fill BCs with ambient material
* Make ambient_state available on the GPU
* Fix compilation for 1D/2D
* Fix namelist inconsistency
* Reset changes to probin
* Add option to clamp ambient temperature
* Fix ambient_state indexing
* Mark get_ambient_eos for GPU
* Add new ambient parameters to wdmerger_3D test
* Don't change Roche factor
* Fix merge issue
* Apply temperature clamping as part of clean_state
* Clamp internal energy in addition to temperature
* Make the clamping safety factor a runtime parameter
* Fix a GPU loop
* Rename a parameter
* Be more careful with X
* Set initial ambient state completely
* Merge clamp_ambient_temp into compute_temp
* Fix another X
* Remove ambient_eos
* Fix a comparison
* Also reset total energy
Co-authored-by: guadabsb15 <guadabsb15@gmail.com>
Co-authored-by: Michael Zingale <michael.zingale@stonybrook.edu>
Exec/science/flame_wave/inputs_H_He/probin.H_He.1000Hz
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/wdmerger_util.F90
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Castro_util.F90
Source/driver/_cpp_parameters
Source/problems/Make.package
Source/problems/ambient.F90
Source/problems/bc_fill_nd.F90
commit 576ce2c27ecf55541088431fc1149ca4ee1d57b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 4 12:05:25 2020 -0800
More conservative tagging
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/probin
commit 443723779d6c54f044bcaffaa16bad0880d1345a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 4 12:00:15 2020 -0500
address compiler warnings (#750)
This cleans up some compiler warnings. Most are shadowing.
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit d45a5c3a0f38dead8a0a042cf1b821ab118a317d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 3 20:40:57 2020 -0800
More subcycles
Exec/science/wdmerger/tests/tde/inputs
commit 2241d465053cdeb8b1888cd24890481e0e7f690c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 3 16:10:34 2020 -0800
Fix another CUDA reduction issue (#753)
Extension of #745. I missed that the Fortran cycle statements result in some threads failing to execute the reduction, so the reduction was sometimes generate NaNs.
Source/reactions/React_nd.F90
commit 984d72c66c79d4206ada07c06a81290c33006465
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 1 15:48:31 2020 -0500
update docs
sphinx_docs/source/build_system.rst
commit a6c1c2ee7b09a49521b4f5921f9c25ccb74fb781
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 1 15:47:21 2020 -0500
fix error message
Util/scripts/write_probdata.py
commit 3c84692eb260819619ff7a608f9de8dd1cf85496
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 1 15:45:54 2020 -0500
fix error message
Microphysics/networks/general_null/write_network.py
commit 4c9a23ca48893f033f6a4a0bd33fc02a110d3ffe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 1 14:34:22 2020 -0500
update changes
CHANGES.md
commit 7e2a124af8a114f25931cb9012a39b301d6721da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 31 15:58:25 2020 -0500
remove unneeded trailing index in interface states to Riemann (#751)
* remove unneeded trailing index in interface states to Riemann
* a few more Riemann fixes
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/riemann_nd.F90
commit a4da59544f8bac35ca9de972fcd00d18dcf629fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 28 19:49:51 2020 -0500
remove unused modules
Source/hydro/trans.F90
commit ca880189fad92cef4ec838ad286ef0dd6f6d0c75
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 13:48:55 2020 -0500
only match warnings for cpp files
.travis.yml
Util/code_checker/clang_static_analysis.py
commit b03022e06c8c14807f087c9765f08182f3872215
Merge: cb6353627 c5e57a25c
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 12:23:58 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit cb63536270d888f6da9299262ffea2e2120a2147
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 12:21:44 2020 -0500
only print out unique warnings, ignore pragma gpu warnings
.travis.yml
Util/code_checker/clang_static_analysis.py
commit c5e57a25c1b1d6a4284b2f4c60ed08419d58360b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 28 12:18:08 2020 -0500
make auxillary variables know to C++ (#746)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_variables
Source/driver/set_variables.py
commit 9ad0ca475dcb3b12dfd16692fe1207164af49343
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 28 12:17:21 2020 -0500
2nd order MOL/SDC cleaning (#749)
This reduced the memory needed for the interface states by doing all of the state reconstruction / flux solve in a loop over dimensions. Addresses #741
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
commit 4d58cb4ae5b6ff5363bccdc644d1d0adef873aae
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 11:38:00 2020 -0500
added python script to travis build
.travis.yml
commit d57f8589c0c7b89dac0a27c15c21d7ed54e1a8a2
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 11:18:50 2020 -0500
added a script to extract Castro-only warnings from scan-build and print them out after compilation
Util/code_checker/clang_static_analysis.py
commit 212f770d7ea41da120031adf30bf0b66aa62f3fd
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 10:28:49 2020 -0500
turn AMReX and Microphysics back on, save output to file
.travis.yml
commit be93c669d2dc4194f2e4081da0214b402ea38d6d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 09:35:20 2020 -0500
only run on pull requests and ignore all AMReX and Microphysics files from static analysis
.travis.yml
commit 63cc4a5885f5191a5acc8adc8fe717e314a40ca3
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 08:40:20 2020 -0500
turn off OMP, CUDA and MPI in travis build
.travis.yml
commit 2f16c992fc37d6cda4086cda1dfe1942e5c2ddd5
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 08:37:35 2020 -0500
left out an underscore
.travis.yml
commit 338446047f7b569b9f88a9d3c3e60615d7ef3e4d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 08:32:46 2020 -0500
left out the include keyword
.travis.yml
commit b33032ca58fd263de1bf1ed909f843e40489b40e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Jan 28 08:27:20 2020 -0500
added clang static analyzer to travis build
.travis.yml
commit 144520b03fc319ecc0a2cf45934a897508560f7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 15:07:09 2020 -0500
add a 2nd order 2-d test
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc2.testsuite
commit 1d49f9be9b314cdee1da33f1850fe688fa120ec0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 13:15:10 2020 -0500
store the archiving script
Exec/science/flame_wave/job_scripts/summit/summit_gpu.submit
Exec/science/flame_wave/job_scripts/summit/summit_hpss.submit
commit 5335ad04feba9ba2c932e2307b9d666af33ae4f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 13:14:52 2020 -0500
move
Exec/science/flame_wave/job_scripts/chainbsub.sh
commit 8af74f046c1b93ad9f3da5cc121a34986dbcc576
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 13:13:04 2020 -0500
update jobs stuff
add .submit files
Exec/science/flame_wave/job_scripts/summit/chainbsub.sh
Exec/science/flame_wave/job_scripts/summit/process.xrb
commit cb8206c0a054b20865eef0865c282dc42732e875
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 10:23:05 2020 -0500
update changes
CHANGES.md
commit d3d7bd712c5b61bc31f2c9e3eb09051a041ac42e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 26 13:12:56 2020 -0800
Point to main wdmerger inputs
Exec/science/wdmerger/tests/tde/inputs
commit 1ba7bb5c0624ada20b1e9b2a521955aba27bc3cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 25 17:31:22 2020 -0500
add guards
Source/diffusion/Castro_diffusion_F.H
Source/gravity/Castro_gravity_F.H
Source/reactions/Castro_react_F.H
Source/rotation/Castro_rotation_F.H
Source/sdc/Castro_sdc_F.H
Source/sources/Castro_sources_F.H
commit 5fcd2ce308f99a6194b90f15d5a311b008e4f84b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 25 15:41:11 2020 -0500
split up headers (#744)
This splits the main headers up based on what directory the source implementation lives.
Source/diffusion/Castro_diffusion.H
Source/diffusion/Castro_diffusion_F.H
Source/diffusion/Make.package
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/gravity/Castro_gravity.H
Source/gravity/Castro_gravity_F.H
Source/gravity/Make.package
Source/hydro/Castro_hydro_F.H
Source/reactions/Castro_react.H
Source/reactions/Castro_react_F.H
Source/reactions/Make.package
Source/rotation/Castro_rotation.H
Source/rotation/Castro_rotation_F.H
Source/rotation/Make.package
Source/sdc/Castro_sdc.H
Source/sdc/Castro_sdc_F.H
Source/sdc/Make.package
Source/sources/Castro_sources.H
Source/sources/Castro_sources_F.H
Source/sources/Make.package
commit 5163fb6b6d415e2e8c4461293812121f0592ca0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 25 12:27:50 2020 -0800
Fix some reduction race conditions and thread-safety issues (#745)
Source/driver/timestep.F90
Source/gravity/pointmass_nd.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/advection_util_nd.F90
Source/reactions/React_nd.F90
commit 2024771c61496ebeaa99964c5f276198d076b256
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 25 11:04:50 2020 -0500
add inputs files for SDC comparison test
Exec/science/rotating_star/inputs_2d.sdc_test
Exec/science/rotating_star/inputs_2d.strang_test
commit 76299cab22cb5dfd78fc712a040d2b3d9da1c2c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 25 10:52:27 2020 -0500
move the 4th order driver to C++ (#742)
This switches the driver for the 4th order SDC solver to C++ and removes redundant code by implementing a loop over coordinate direction.
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
commit a1d535bc7a2013db12b8775bec17b50226f462b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 23 10:51:37 2020 -0500
remove unused prototypes
Source/driver/Castro.H
commit 9f194ca1a8c34d7dfa3728f60a2ca2c4f589eb51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 23 07:59:18 2020 -0500
Statedata (#743)
Automate the avgDown of state data to work on all components. This will help as need solvers are merged.
Also, ifdef out the simplified SDC statedata type, to be consistent with how we ifdef out other types.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/hydro/Castro_hydro.cpp
Source/sources/Castro_sources.cpp
commit 9f4841e7210df91e6b6fa6ba489111db77aef358
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 22 13:32:35 2020 -0500
fix potential race condition making directory with parallel builds
Source/driver/set_variables.py
commit ba861847f81a4bb20d42e5c4dd154573341fb85e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 18:33:15 2020 -0800
Update OpenACC directives for meth_params
Source/driver/Castro_nd.F90
Source/driver/meth_params.template
Source/driver/prob_params.F90
commit 558dbd9b224f2039412fcb2f681dd36f1f375675
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 12:34:39 2020 -0800
Generalize SuOlsonMG source term
Exec/radiation_tests/RadSuOlsonMG/rad_source.F90
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
Source/radiation/rad_source.F90
commit 708958169c542b6c7caa7cedec0a730e0975aee7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 12:03:53 2020 -0800
Dimension agnostic compute_rhs
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit f12377779710276850b4f1046dc62146aba41b52
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 12:03:36 2020 -0800
Fix some GPU syntax issues
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
commit f203768d2c8af43d11597d64b2fb931e8d71a53d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 20 13:36:05 2020 -0500
Fourth cleanup 3 (#738)
The merges the calls to normalize_species_fluxes between the 2nd and 4th order code paths + adds the density flux limiter to the 4th order (even though it won't be 4th order). Finally, it reorganizes the construction of the fluxes so that each direction's code is together. This will make it easy to move this to C++ as a single loop over dimension.
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_hydro.cpp
commit cc2d0f667d3d06cdde198f90e32221b76074e580
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 08:01:38 2020 -0800
Remove integrate_Planck option, always integrate by default (#740)
There existed an option to turn off the normal behavior of integrating
the Planck function to get the blackbody spectrum at each group center.
This was only used in the RadSphere test, and the alternative was to
evalute the Planck function as piecewise constant within each energy
group. This introduces code complexity without any obvious gain; we still
get reasonable results using the more general expression, and reduce
the number of code paths to maintain.
CHANGES.md
Exec/radiation_tests/RadSphere/inputs
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit a4cfa3aed688eba1725d997d72e6ec35a231e272
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 00:43:28 2020 -0800
Dimension agnostic accel routines
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit 63898006ece113c8c4562d016f1d56bdb3d6dbb6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 19 23:16:06 2020 -0800
More dimension agnostification
Also, remove some more neutrino code and clean up interfaces
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit 8d63a2aef0503196edebba01dd24f7ff38a14cb0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 19 22:02:07 2020 -0800
Dimension agnostic convergence checks
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
commit 6b3f31949922da619ea286506142695312f8d781
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 19 13:32:03 2020 -0800
Add comments for blackbody radiation routines
Source/radiation/blackbody.F90
commit 36ddfad36782ea178f383f855d9b4ca89628d2af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 19 15:42:41 2020 -0500
initialize all StateData new time data to 0 in the Castro constructor (#739)
commit 1cf5bcdc439d83e4faedd60458b68fab497bad14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 19 15:42:03 2020 -0500
initialize all StateData new time data to 0 in the Castro constructor (#739)
Source/driver/Castro.cpp
commit c3a9ed49354eac33d04bdf528e33e440383ffaa5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 19 10:01:49 2020 -0800
Dimension agnostic compute_emissivity
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit bb66bd8e0cd8475fe6cdf8f2d6d61d0f413f88cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 19 09:32:08 2020 -0800
Fix RadSuOlsonMG initialization
Exec/radiation_tests/RadSuOlsonMG/Prob_nd.F90
commit c76caa887a0786a7894161d0594374a7c4864170
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 19 08:59:58 2020 -0800
Generate Castro param files at compile time (#736)
Castro runtime parameter files are now generated at compile time. This removes the need to run mk_params.sh whenever you update _cpp_parameters.
Exec/Make.Castro
Source/driver/meth_params.F90
Source/driver/mk_params.sh
Source/driver/param_includes/Make.package
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/diffusion_defaults.H
Source/driver/param_includes/diffusion_job_info_tests.H
Source/driver/param_includes/diffusion_params.H
Source/driver/param_includes/diffusion_queries.H
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_job_info_tests.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/driver/param_includes/particles_defaults.H
Source/driver/param_includes/particles_job_info_tests.H
Source/driver/param_includes/particles_params.H
Source/driver/param_includes/particles_queries.H
Source/driver/param_includes/radiation_defaults.H
Source/driver/param_includes/radiation_job_info_tests.H
Source/driver/param_includes/radiation_params.H
Source/driver/param_includes/radiation_queries.H
Source/driver/param_includes/radsolve_defaults.H
Source/driver/param_includes/radsolve_job_info_tests.H
Source/driver/param_includes/radsolve_params.H
Source/driver/param_includes/radsolve_queries.H
Source/driver/parse_castro_params.py
sphinx_docs/source/build_system.rst
sphinx_docs/source/rp_intro.rst
commit 26bc3d5bd9e1875fbb57448f703fa631bf74f3ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 18 19:31:27 2020 -0800
Remove unused MGFLD code
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
commit 8f477a32171751a5d29d648e800f3439f08f90bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 20:51:14 2020 -0500
fix some bounds issues
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_hydro.cpp
commit df248d4c410334389a0dbc3024e7f3a8126973f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 19:48:28 2020 -0500
fix interface that typecheck flagged
Exec/science/Detonation/bc_fill_nd.F90
commit 2464c7fc33e69dbdb3e2afe220e89c228e89bbfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 19:40:35 2020 -0500
fix some array sizes
Source/hydro/Castro_mol_hydro.cpp
commit badd4d3b7b86ffffc1b38b18e71d4984dd284f40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 19:27:58 2020 -0500
some restructuring -- we were never actually dealing with qe or the fluxes
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
commit 57799cdbe391bae06b84cb14cc50ae4ac70f3076
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 17:52:42 2020 -0500
disable retry
Exec/science/Detonation/inputs-det-x.sdc.test
commit 28313d50adf612a8bc4f267b011a5f5f532f928a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 12:34:51 2020 -0500
more clean-ups of the 4th order hydro solver (#732)
This reuses the flux scaling and consup routine from the 2nd order solver for the 4th order code path.
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
commit db5a964852085277c9e5805c35d41261d13633d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 18 08:46:12 2020 -0800
Some I/O cleanup
Source/radiation/MGFLDRadSolver.cpp
commit 3a4053f091c06e1ac440156b2f5f844abdbae9cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 18 08:21:32 2020 -0800
Fix a bug in the volume function
Source/driver/Castro_util.F90
commit 3074b477515f7a59222dde63610d1458d29f0f7b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 18 07:24:26 2020 -0800
Remove more neutrino code
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGFLDneut_1d.f90
Source/radiation/MGFLDneut_2d.f90
Source/radiation/MGFLDneut_3d.f90
Source/radiation/Make.package
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 1e5eab3d22c139f5251664cabec9d43fc056385a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 18 08:29:18 2020 -0500
some cleanups of the fourth order reconstruction (#649)
This does some basic cleanups of the fourth-order reconstruction to eliminate arrays in prep for GPUing. It also reuses the shk and flatn computation done in C++ for MOL.
Exec/hydro_tests/acoustic_pulse/convergence_sdc4_outflow.sh
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/fourth_order.F90
commit 9a0f3afc29a44be6d18cdfce65c4121b4f99368f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 17 18:22:24 2020 -0500
update changes
CHANGES.md
commit 3460254fc9d66772e90538e60ef11edda545a8ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 17 07:38:35 2020 -0500
fix nuclear burning dt estimator with simplified SDC (#733)
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/timestep.F90
Source/reactions/Castro_react.cpp
commit bb03878a56d293c12e20eb6d289297c9ca498207
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 17 00:50:20 2020 -0500
Improve hydro performance when oversubscribed
Source/hydro/Castro_ctu_hydro.cpp
commit 3cc68e26b8f7d8dd67b5db33521d04ff97d62fc5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 13 23:49:28 2020 -0800
Fix ifdefs for acc device updates
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
commit 69df55197d0a466f2d855509a27b7ebff974b4a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 13 13:57:44 2020 -0500
update changes
CHANGES.md
commit 623b190ed280dbea6ad225e641d08d6d926e5487
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 12 15:18:09 2020 -0500
simplified SDC can use the same hydro timestep constraint as CTU+Strang (#727)
Source/driver/timestep.F90
commit 1d2ee51edc7c1706f2b640597eb5b6702b679095
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 9 18:59:24 2020 -0500
use jacobian = 2 for now, until we fix up the SDC analytic jac
Exec/science/rotating_star/probin
commit 7d9445e0e31f4e5f3e0e53eb67eb69693a853092
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 8 21:06:00 2020 -0500
define EXTRA_THERMO even for simplified SDC
this is needed for the analytic Jacobian
Exec/Make.Castro
commit 6253ee415c3dc78cf88bbf6d6881d276155efe9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 5 23:11:40 2020 -0500
Add some BL_PROFILE
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.cpp
commit dad5dc91c03b75e80cbff3fd2c28f29e223a626b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 21:18:53 2020 -0500
switch to auto prob params
Exec/science/xrb_mixed/GNUmakefile
Exec/science/xrb_mixed/Make.package
Exec/science/xrb_mixed/Prob_nd.F90
Exec/science/xrb_mixed/_prob_params
Exec/science/xrb_mixed/probdata.F90
commit 1a1c1132234b2df337ffe44921dd17e7254da9c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 20:50:23 2020 -0500
switch to auto prob params
Exec/science/planet/GNUmakefile
Exec/science/planet/Make.package
Exec/science/planet/Prob_nd.F90
Exec/science/planet/_prob_params
Exec/science/planet/probdata.F90
commit c74487d5ed288f20ae8bbd6dc9941349ab121146
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 19:39:37 2020 -0500
update to auto prob params
Exec/science/rotating_star/GNUmakefile
Exec/science/rotating_star/Make.package
Exec/science/rotating_star/Prob_nd.F90
Exec/science/rotating_star/_prob_params
Exec/science/rotating_star/probdata.F90
commit 34616880ad3b32e150084c87a99da32ac1cbe42d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 19:32:29 2020 -0500
update to auto prob params
Exec/science/nova/GNUmakefile
Exec/science/nova/Make.package
Exec/science/nova/Prob_nd.F90
Exec/science/nova/_prob_params
Exec/science/nova/probdata.F90
commit aaebe0b0cba27d2fa60042ec171863966a120879
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 19:18:19 2020 -0500
switch to auto prob params
Exec/science/flame/GNUmakefile
Exec/science/flame/Make.package
Exec/science/flame/Prob_nd.F90
Exec/science/flame/_prob_params
Exec/science/flame/probdata.F90
commit 9d80ea0148fcba3fc154ca9a6b82853a7e4bdca6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 5 14:14:29 2020 -0500
Remove an incorrect boundary type check
Source/radiation/HABEC_nd.F90
commit 3456e065183100178746ffa13a971345a6c8ae4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 12:24:33 2020 -0500
switch to auto prob params
Exec/science/Detonation/GNUmakefile
Exec/science/Detonation/Make.package
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/_prob_params
Exec/science/Detonation/probdata.F90
commit 1e0b271b4035283cb853968e1a4159c9aa827b88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 11:23:44 2020 -0500
switch to auto prob params
Exec/science/convective_flame/GNUmakefile
Exec/science/convective_flame/Make.package
Exec/science/convective_flame/Prob_nd.F90
Exec/science/convective_flame/_prob_params
Exec/science/convective_flame/probdata.F90
commit c862e2b13573a731da0c8ece7d7fc9837f38707b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 10:02:02 2020 -0500
switch to auto prob params
Exec/scf_tests/single_star/GNUmakefile
Exec/scf_tests/single_star/Make.package
Exec/scf_tests/single_star/Prob_nd.F90
Exec/scf_tests/single_star/_prob_params
Exec/scf_tests/single_star/probdata.F90
commit 793a6b7e95936badd70a55ad22ab7398cfba6123
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 4 23:29:18 2020 -0800
Port more HABEC to the GPU
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.cpp
commit 592498cb0481fce477d1a5f9837bef13ab25e127
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 4 23:27:03 2020 -0800
Avoid a divide-by-zero
Exec/radiation_tests/RadThermalWave/problem_derive_nd.F90
commit a21a0344a622200a276ed5a98cc1173e8f74fc26
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 4 19:57:30 2020 -0800
GPU compatible problems also do radiation init on GPU
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Source/driver/Castro.cpp
Source/driver/Castro_F.H
commit bb1644d1c02ad84c70784647765c6f72686ea9cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 4 19:31:49 2020 -0800
Move RadThermalWave to the GPU
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/probdata.F90
commit 93bf0580bee6ee1e739c1b03452783129a79d141
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 22:46:13 2020 -0500
fix compilation
Exec/reacting_tests/toy_flame/Prob_nd.F90
commit bf9d051c84ee9d7ee17d2e4a014eddbdc0b13113
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 22:37:54 2020 -0500
switch to auto prob params
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/reacting_tests/toy_flame/Make.package
Exec/reacting_tests/toy_flame/Prob_nd.F90
Exec/reacting_tests/toy_flame/_prob_params
Exec/reacting_tests/toy_flame/probdata.F90
commit 3c118880be957994acaf52f0b65b514ff4f1499c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 22:24:02 2020 -0500
remove unneeded vars
Exec/reacting_tests/nse_test/Prob_nd.F90
commit 3bad4c2fdca6250f4b9af1ab8a09ed463288cf71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 22:23:39 2020 -0500
switch to auto prob params
Exec/reacting_tests/reacting_convergence/GNUmakefile
Exec/reacting_tests/reacting_convergence/Make.package
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/reacting_convergence/_prob_params
Exec/reacting_tests/reacting_convergence/probdata.F90
commit 0c2dc22f8dc0557aa351cb18e0c1966bfd5a450d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 22:11:57 2020 -0500
switch to auto prob params
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/reacting_bubble/Make.package
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/_prob_params
Exec/reacting_tests/reacting_bubble/probdata.F90
commit 60a29c88e60fb77c4121eb699ade457b0b2852a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 22:02:05 2020 -0500
switch to auto prob params
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/nse_test/Make.package
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/nse_test/_prob_params
Exec/reacting_tests/nse_test/probdata.F90
commit a1caac57af28fc7c8515c13ddb3499c8f5096407
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 21:48:53 2020 -0500
remove probdata
Exec/reacting_tests/bubble_convergence/probdata.F90
commit f5780825b55a95ee673f233a8dc3f8ea94d5e9e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 21:48:22 2020 -0500
switch to auto prob params
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/bubble_convergence/Make.package
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/_prob_params
commit 3728c987783268a7fcc6b0d893374e1d4827db31
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 4 18:15:20 2020 -0800
Move power law opacity into its own module (#725)
This PR unifies the approach to opacities in the radiation code, so that ca_compute_planck, ca_compute_rosseland, and ca_compute_scattering are the only entry points to getting the opacities. These work for single-group or multi-group problems. To do this, we moved the power-law opacity to its own module in Castro/Microphysics, rad_power_law, replacing the powerlaw-example case, and now have the problems point to the new opacity directory rather than null. (The null directory has been removed, to prevent people from accidentally trying to continue using the old setup.) All of the corresponding inputs parameters for the power law opacity have been moved to the probin file (in the extern namelist).
We now always expect the user to pick a specific opacity implementation, so the parameter radiation.use_opacity_table_module has been removed.
The multigroup solver was previously forcing the Rosseland opacity to be equal to the Planck opacity if the latter was set but the former was not. There was similar unintuitive behavior for the behavior of the scattering parameter. Now you will get exactly what you ask for in the probin file, given the defaults in the _parameters file for the rad_power_law opacity. By default the constant coefficients for both are negative, which is invalid, so both must be set to a non-negative value for the code to work. Problems that were previously setting const_kappa_p but not const_kappa_r should set the latter equal to the former to maintain the same code behavior. The analogous thing should be done for the exponents (kappa_p_exp_m, kappa_p_exp_n, and kappa_p_exp_p).
CHANGES.md
Exec/Make.Castro
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/Rad2Tshock/probin.M2
Exec/radiation_tests/Rad2Tshock/probin.M5
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadFront/probin
Exec/radiation_tests/RadFront/probin1d
Exec/radiation_tests/RadFront/probin2d
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadShestakovBolstad/probin.common
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSlope/inputs
Exec/radiation_tests/RadSlope/probin
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSourceTest/inputs-cooling
Exec/radiation_tests/RadSourceTest/inputs-heating
Exec/radiation_tests/RadSourceTest/inputs-heating-mg
Exec/radiation_tests/RadSourceTest/probin-cooling
Exec/radiation_tests/RadSourceTest/probin-heating
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSphere/inputs
Exec/radiation_tests/RadSphere/probin
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlson/inputs
Exec/radiation_tests/RadSuOlson/probin
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadSuOlsonMG/probin.common
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/radiation_tests/RadThermalWave/Problem_Derive.H
Exec/radiation_tests/RadThermalWave/Problem_Derive.cpp
Exec/radiation_tests/RadThermalWave/Problem_Derive_F.H
Exec/radiation_tests/RadThermalWave/Problem_Derives.H
Exec/radiation_tests/RadThermalWave/inputs.1d
Exec/radiation_tests/RadThermalWave/inputs.1d.test
Exec/radiation_tests/RadThermalWave/inputs.2d
Exec/radiation_tests/RadThermalWave/inputs.2d.test
Exec/radiation_tests/RadThermalWave/inputs.3d
Exec/radiation_tests/RadThermalWave/inputs.3d.test
Exec/radiation_tests/RadThermalWave/probin.1d
Exec/radiation_tests/RadThermalWave/probin.2d
Exec/radiation_tests/RadThermalWave/probin.3d
Exec/radiation_tests/RadThermalWave/problem_derive_nd.F90
Exec/science/bwp-rad/GNUmakefile
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
Exec/science/bwp-rad/probin
Exec/science/bwp-rad/probin.dens_sponge
Exec/science/planet/GNUmakefile
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/planet/probin
Microphysics/opacity/null/opacity_table_module.F90
Microphysics/opacity/powerlaw-example/Make.package
Microphysics/opacity/powerlaw-example/opacity_table_module.F90
Microphysics/opacity/rad_power_law/Make.package
Microphysics/opacity/rad_power_law/_parameters
Microphysics/opacity/rad_power_law/opacity_table_module.F90
Source/driver/Castro.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
sphinx_docs/source/radiation.rst
commit d0883f6e790edbca19dfb963da28bff813c17368
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 4 11:12:22 2020 -0500
add some docs on MPI+OpenMP and MPI+GPU
sphinx_docs/source/index.rst
sphinx_docs/source/mpi_plus_x.rst
commit 8744bab2eca3261810a0362263079d217cf4d379
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 3 17:45:26 2020 -0500
put the files created a build time in their own build-specific dirs (#726)
this addresses #359 and also fixes the issue with state sizes if
we do a CTU/Strang build followed by a simplified-SDC build without
an intermediate clean
Exec/Make.Castro
sphinx_docs/source/build_system.rst
commit eebd40692d3bdbba2654b2b8b7d86a49d88a61d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 3 11:17:49 2020 -0500
for true SDC, disable retry and ensure that abort_on_failure = T
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
sphinx_docs/source/retry.rst
commit b28807edc9bc9c1d8ad2602567f4231eb77d1fb1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 3 09:55:24 2020 -0500
do_real_eos has been removed
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
commit eca769c2fa657b2f8243e4fe16d1350912b3b093
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 3 06:45:40 2020 -0800
Replace do_real_eos = 0 with an actual EOS (#722)
This PR adds an EOS, rad_power_law, which replaces the functionality previously provided by radiation.do_real_eos = 0. The EOS defines c_v as before, and can only be called in (rho, T) and (rho, e) modes. It does not define hydrodynamic variables like pressure, so it cannot be used in conjunction with castro.do_hydro = 1. This sets us up for merging the radiation and non-radiation EOS interfaces.
CHANGES.md
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test.multid
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/inputs.1d.test
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadShestakovBolstad/probin.common
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSlope/inputs
Exec/radiation_tests/RadSlope/probin
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/radiation_tests/RadSphere/inputs
Exec/radiation_tests/RadSphere/probin
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlson/Make.package
Exec/radiation_tests/RadSuOlson/Prob_nd.F90
Exec/radiation_tests/RadSuOlson/inputs
Exec/radiation_tests/RadSuOlson/probdata.F90
Exec/radiation_tests/RadSuOlson/probin
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadSuOlsonMG/probin.common
Microphysics/EOS/rad_power_law/Make.package
Microphysics/EOS/rad_power_law/_parameters
Microphysics/EOS/rad_power_law/rad_power_law.F90
Source/driver/Castro.cpp
Source/driver/Castro_util.F90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/radiation_defaults.H
Source/driver/param_includes/radiation_job_info_tests.H
Source/driver/param_includes/radiation_params.H
Source/driver/param_includes/radiation_queries.H
Source/radiation/Castro_radiation.cpp
Source/radiation/MGFLD.cpp
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
sphinx_docs/source/radiation.rst
commit bce975b7f93521f673735f5f83de174488bd5f2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 3 09:11:49 2020 -0500
Turn on castro.use_retry by default (#724)
This enables Castro's retry (as suggested in #211). It also overrides Microphysics's integration abort_on_failure to be false, so Castro can retry for burn failures.
CHANGES.md
Microphysics/networks/_parameters
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
sphinx_docs/source/inputs.rst
sphinx_docs/source/retry.rst
commit b4d39ac5c20ef4205762250408816efb55041321
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 2 08:47:03 2020 -0800
Remove hard_cfl_limit (#723)
This removes the parameter hard_cfl_limit. It's not a safe parameter to use.
CHANGES.md
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/inputs.2d_good
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_1d.hse_test
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/old/inputs.boost_25_4
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/science/flame_wave/old/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/rotating_star/inputs_2d
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 1f17181d8c7da54cd967a0e1988b1113c81e6d34
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 2 00:57:17 2020 -0800
Add NGROUPS to makefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
commit 11122c4b9e6d6e150662c1f96b8b883c64d7fb81
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 21:09:59 2020 -0800
Remove incorrect abort
Source/radiation/Radiation.cpp
commit d311fdde22c675be5f5f939ff55ef660b3b0923a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 1 21:31:54 2020 -0500
update changes
CHANGES.md
commit 575ca10b957b24f6430c040bfccc3f5302886dfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 1 21:29:55 2020 -0500
remove unnecessary clean_states (#721)
There are a few places where we do clean_states successively that are unnecessary. This PR removes these extra clean_state's.
This also moves some SDC-specific code into the SDC advance function.
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
commit 1604f107479a2b1d3a99d9da86ec8662b440ecb4
Merge: d9f2c853f 1c285d7a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 1 17:14:51 2020 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d9f2c853f0af0e982a6dc6115eafc1c306908d83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 1 17:14:39 2020 -0500
reduce blocking factor for suite
Exec/science/flame_wave/inputs_3d.testsuite.gpu
commit 1c285d7a8d8025be9b6e8e70057e1ba54cf3d8d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 14:03:26 2020 -0800
Some more do_real_eos == 0 cleanup
Source/driver/Castro.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
commit c8b8a5fd0bea8f7066f9adeea186365c35764c47
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 13:24:44 2020 -0800
Turn some parameter changes into asserts
Source/radiation/Radiation.cpp
commit 2c1dc0f5ca737a70ed764dc799b32220d41ea760
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 12:20:45 2020 -0800
Merge last function in SGFLD.cpp into Radiation.cpp
Source/radiation/Make.package
Source/radiation/Radiation.cpp
Source/radiation/SGFLD.cpp
commit 55e8eee20d95ed62badf0c233ee4b640754fd6bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 1 16:31:54 2020 -0500
drop max_grid_size back down to fit in memory on groot
Exec/science/flame_wave/inputs_3d.testsuite.gpu
commit 203c2222204d09d02487c791b679eceb7feeb271
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 11:37:38 2020 -0800
Remove neutrino code from makefiles
CHANGES.md
Exec/Make.Castro
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/planet/GNUmakefile
Source/driver/set_variables.py
commit 2a66663d37446378b6f1f0ad8678295dc3d2fbdd
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 11:34:24 2020 -0800
Add a missing pragma back
Source/radiation/Radiation.cpp
commit 0bac4148ae1c35480969d2c2957ea3f40c7dee3a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 1 00:03:34 2020 -0800
Merge real and artificial EOS together
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/radiation_defaults.H
Source/driver/param_includes/radiation_job_info_tests.H
Source/driver/param_includes/radiation_params.H
Source/driver/param_includes/radiation_queries.H
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit 23a3bdeea0c5e3dbe1e418289e2827906e988d7e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 23:45:58 2019 -0800
Group EOS calls together
Source/radiation/Castro_radiation.cpp
Source/radiation/Radiation.cpp
commit 59c07e8db1796087049302a26450ddc14d153c8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 23:22:46 2019 -0800
Move some EOS parameters to the params script
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/radiation_defaults.H
Source/driver/param_includes/radiation_job_info_tests.H
Source/driver/param_includes/radiation_params.H
Source/driver/param_includes/radiation_queries.H
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit d04e2b1cf5650c6b27dd8af57245f93efbf980c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 22:49:51 2019 -0800
gtemp is redundant
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit c6e255ced6b276cac15c539d73efb26652beca37
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 20:52:36 2019 -0800
Move some work to the GPU
Source/driver/Castro.cpp
Source/radiation/HypreABec.cpp
commit d9de91eb2416275083b77c67861e39f25dd6d54f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 20:22:54 2019 -0800
cexch
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 9276a6f6368d488cee54febf794e45db83668fe0
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 19:36:29 2019 -0800
ca_update_matter
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/rad_params.F90
commit ef7eacab34c1afc4bd3d3e4fe3ce303136d78168
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 15:53:48 2019 -0800
Finish up working on state_update
Source/driver/Castro.cpp
Source/radiation/MGFLD.cpp
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
commit 4c613a8fbc0191910922408feff4583808cbb6c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 00:39:43 2019 -0800
Dimension agnostic, GPU-friendly put_radial_phi
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit b386f6f38d81407d1e8834e2e9e1d352d9a4cc29
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 00:21:10 2019 -0800
Dimension agnostic, GPU-friendly compute_radial_mass
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit f3723970094c5dba81519f93040dee74e3df0be4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 31 00:20:54 2019 -0800
Add option to do a pure atomic sum reduction
Source/driver/reduction.F90
commit b1773caf5650ae6d8259a548af244a0581dd560d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 30 22:41:21 2019 -0800
GPU compatible DustCollapse setup
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/DustCollapse/Prob_nd.F90
commit 943ed1e5ae382b5c10025c19afae851c30525e74
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 30 03:37:13 2019 -0500
Check valid bounds in all three dimensions
Source/radiation/HABEC_nd.F90
commit 231de25a9835708f1013e7b7e5b601c55a40dee2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 30 00:21:08 2019 -0800
Fix an index validity check
Source/radiation/HABEC_nd.F90
commit ea7d3b5d90cf2b00ee5e08b9a1789a6f24d8c979
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 23:46:48 2019 -0800
Remove some incorrectly placed error catching statements
Source/radiation/RadSolve.cpp
commit 2d71f6be9f89a196a815f84330d4fa3312c7b96c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 21:49:49 2019 -0800
Remove synchrony requirement
Source/radiation/Radiation.cpp
commit 80881c71635f2475def9664e98a8b8d9b508ff0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 21:44:07 2019 -0800
Merge Fab version into update_rosseland_from_temp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit 39fb56b260db6da4d63a6d3ed03308e5370598a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 19:31:48 2019 -0800
Port hbvec, hbvec3
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.cpp
commit 132f15f7e21d6880716efaf03aa35f425fc6b96f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 17:14:48 2019 -0800
Rename riemann_speed_limit, remove it from Riemann solver (#714)
riemann_speed_limit is renamed speed_limit. It is removed from the Riemann solver, and is only applied for the flux limiter. The Riemann speed limit was always a stopgap solution until the flux limiter was developed.
CHANGES.md
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
commit 5d2b7f26f68a5132dfed102cf1a82961a09882ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 15:07:17 2019 -0800
RadSolve needs to be instantiated after a restart
Source/driver/Castro_io.cpp
commit dfd9ecc5f821f23f995760b9edc0e9c64633a3a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 14:43:52 2019 -0800
Add some elixirs
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.cpp
commit 18c1d4a6d47752b4542b76c7ea133e02226c0b65
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 14:37:37 2019 -0800
Port hbmat, hbmat3
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.cpp
commit 3b565768c6dd025033bfe57ef419891284753ac2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 14:16:28 2019 -0800
Port hacoef and hbcoef
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/HypreABec.cpp
commit c07b938ed4ced17c682f8a0a79f2bfa2be70eb91
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 13:41:35 2019 -0800
Place metrics in HABec module
Source/radiation/HABEC_nd.F90
Source/radiation/Rad_nd.F90
commit 3d73479bf46d3e4f5c17e651e08a5e1eeb79af79
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 13:39:29 2019 -0800
Remove some unused ABec code
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
commit b2c6d07161c6609f8025e616d7f7757475779b81
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 05:48:24 2019 -0800
Dimension agnostic, GPU-friendly bclim
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit fc9be7ea2bd35d203d2e0677844af28982af6c05
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 05:01:42 2019 -0800
Dimension agnostic, GPU-friendly set_abec_flux
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_F.H
Source/radiation/HABEC_nd.F90
Source/radiation/Make.package
Source/radiation/RadSolve.cpp
commit 3176bafcfb9e0c38e2cdca031f19a12e369a809f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 04:38:06 2019 -0800
Dimension agnostic, GPU-friendly ceup
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 7fb91c8ae3e7fd9def6e2ac4c08e6c6105d9804f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 04:13:19 2019 -0800
Dimension agnostic, GPU-friendly levelRhs
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 45282cf258ce611425a6529d520fb2864b628102
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 12:32:54 2019 -0800
Set compute_new_dt_on_regrid by default (#720)
The AMR parameter amr.compute_new_dt_on_regrid is now on by default; closes #356. This avoids crashes that result from the CFL number being too large after regridding, because we update the timestep after seeing that larger velocity.
The user can still opt to set this off if they want to, since the location where we're setting it in Castro occurs before the Amr ParmParse of this parameter.
CHANGES.md
Source/driver/Castro.cpp
commit 9138fd4ae89596d68189346b11af7735dafd6f80
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 11:34:54 2019 -0800
Remove self-gravity define, use GRAVITY always (#719)
This PR closes #157 by removing the SELF_GRAVITY ifdef -- we revert back to the previous behavior where GRAVITY is the only relevant define.
Also, I'm including a centralization on the approach for grav_source_type = 4 based on g, not phi. The mechanism based on phi is slightly better at conservation in the presence of coarse-fine boundaries, but the difference between the two methods is quite small in absolute terms -- both are very good -- and it is better to only have one method so that we don't have to worry when switching between different gravity implementations (not all of them define phi).
Exec/Make.Castro
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Make.package
Source/gravity/gravity_sources_nd.F90
commit 2802125d2bc4a4098146f5aff541b618f4845e6e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 03:38:16 2019 -0800
Store RadSolve in Castro instead of creating on demand
The prior approach of creating a RadSolve object on demand allowed for
maximum flexibility but is not optimal for performance, since creation
and destruction of all of the array data is very expensive, especially
on GPUs (relative to the compute phase). Now we store the RadSolve
object in Castro, similar to other Castro-owned data, and it is filled
on Castro construction (which occurs at initialization or after a regrid).
As a result, for a single-level solve (or a multi-level solve with no
regrids), we only pay the cost of array initialization once, allowing us
to amortize the cost over many timesteps and effectively make it free.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/SGRadSolver.cpp
commit e8dfaea86255deb5f1c6c61ba3bba809dfa0fbd9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 29 02:51:55 2019 -0800
Avoid some VLA issues
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
commit be6aa6da5ae45f51f65223c1f6c1dd063c56965e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 28 23:15:11 2019 -0800
Move RadSolve params to _cpp_params
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/radsolve_defaults.H
Source/driver/param_includes/radsolve_job_info_tests.H
Source/driver/param_includes/radsolve_params.H
Source/driver/param_includes/radsolve_queries.H
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.cpp
commit 0c018054c43ac583378cb27f47a42168aaeae5f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 28 21:41:57 2019 -0800
Fix some Box declarations
Source/problems/Castro_bc_fill_nd.cpp
commit b71c46b48dbbb0927ff541daf902460518cb89eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 28 20:28:33 2019 -0500
update blocking_factor
Exec/science/flame_wave/inputs_3d.testsuite.gpu
commit ebbfb541f77b92375ddd7b6d656d60808c17dc93
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 28 15:38:04 2019 -0800
Fix an interface bug
Exec/science/wdmerger/wdmerger_util.F90
commit fa4932ff84a16a0b5c5846c66f303834ff50cf33
Merge: c2f4174b9 2893f20db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 28 11:31:44 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit c2f4174b9583a3c2bbcab4c5425c4ab6f132ab22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 28 11:31:32 2019 -0500
bump up blocking_factor for GPU performance
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_3d.testsuite
commit 2893f20dbf99689f026fdef2a4cc2e1a5a042a89
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 28 03:44:12 2019 -0800
Effectively disable tiling when using CUDA
Source/driver/Castro.cpp
commit 6195dee5c96735c240b099c9d0d521b49654dda4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 28 03:01:30 2019 -0800
Make some GPU pragmas box loops
Source/driver/Castro.cpp
Source/driver/Castro_generic_fill.cpp
Source/driver/Castro_source_fill.cpp
Source/driver/Derive.cpp
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/problems/Castro_bc_fill_nd.cpp
commit 8a7f97c03a5d98eed5114313dfb72ceb959c728d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 28 00:29:04 2019 -0800
Dimension agnostic, GPU-friendly flux limiter
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 9622543144bd4b05c55fd964a0242d2c61dc55c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 23:53:39 2019 -0800
Dimension agnostic, GPU-friendly scaled gradient
scgrd1 and scgrd2 are merged since scgrd2 is a generalization of the former
that includes gradients in the orthogonal directions. scgrd3 is not implemented
since it was not handled in any test case.
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit a6f32d9221af323b5b71697824dce058f133aee7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 20:10:33 2019 -0800
Dimension-agnostic, GPU friendly level A coefficients
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadSolve.cpp
Source/radiation/Rad_nd.F90
commit 6a3bb521f78d3e98156eb1b4c1b93f04ea847ff7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 18:52:00 2019 -0800
Use existing integrate_grav for make_radial_phi (#717)
make_radial_phi had a simple approach for integrating the mass distribution to get the gravitational acceleration, which was then integrated to get the gravitational potential. This PR uses the existing ca_integrate_grav to do the first step. Since the algorithm is different (more sophisticated) answers will change. This step is in preparation for offloading the radial gravity routines.
Source/gravity/Gravity.cpp
Source/gravity/Gravity_nd.F90
commit e89d71856c253d779fa9e209b66782d495a1b9d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 15:11:06 2019 -0800
compute_eta on device
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
commit b5c831ca740fa68443dd438e6e20a79a4ae499b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 14:10:00 2019 -0800
get_planck_and_temp on device
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 2123501714d403b2eb3f010d71cedd679bb9c2b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 13:18:19 2019 -0800
Add option for rad compute_temp to update state
Source/radiation/MGFLD.cpp
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit 0db05626fca9e2ba89aef595e1b1c0b54bc37e14
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 12:57:38 2019 -0800
Remove Fab interface for get_frhoe
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
commit 8b1e1c930dbb39b573d8f102366670ebf89736ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 12:35:44 2019 -0800
Dimension agnostic, GPU-friendly compute_rosseland
Source/radiation/MGFLD.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
Source/radiation/SGFLD.cpp
commit 6fd0b6c88c024775993d8236214eb0f97c76bc49
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 12:35:00 2019 -0800
opacity f90 -> F90
Microphysics/opacity/breakout/Make.package
Microphysics/opacity/breakout/opacity_table_module.F90
Microphysics/opacity/null/Make.package
Microphysics/opacity/null/opacity_table_module.F90
Microphysics/opacity/powerlaw-example/Make.package
Microphysics/opacity/powerlaw-example/opacity_table_module.F90
commit 9ba6e704cbd5fed8d1584c4b2a8a42bb6f7fe355
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 12:10:06 2019 -0800
Note new minimum Hypre version requirement
CHANGES.md
sphinx_docs/source/radiation.rst
commit ff4e65e27ab4f3781f38506dfe84fb2daa0b7aa2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 11:41:23 2019 -0800
Dimension-agnostic, GPU-friendly rad EOS
Source/driver/Castro.cpp
Source/radiation/MGFLD.cpp
Source/radiation/Make.package
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit c1cd9b91a0b2c8e5a6d3c43f9e8d2b0e20b0f576
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 00:18:35 2019 -0800
Dimension-agnostic, GPU-friendly rosse1, rosse1s
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit a908d0017a0bca8d0a1e1f907b31a7355f770100
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 27 00:06:40 2019 -0800
Put in a synchronize for now
Source/radiation/Radiation.cpp
commit c0e4471e3412f71136a869c67cbe3308213b7299
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 26 22:43:27 2019 -0800
Update radiation build instructions
sphinx_docs/source/radiation.rst
commit 9eb8a140716d4f5e22eaf9d25387583b1be3d296
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 26 22:08:46 2019 -0800
Simplify to only one HYPRE env var
Exec/Make.Castro
commit b0cb6a3fd1cd0e126da801b6e65e9b692953c230
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 26 22:02:26 2019 -0800
Add in some temporary synchronizes to avoid race conditions
Source/radiation/HypreABec.cpp
commit d8773635ec1e63453613d82ebc9bb3ca63bfd0a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 26 18:33:02 2019 -0800
Move a copy out of a loop for safety
Source/radiation/SGRadSolver.cpp
commit 346a5d789d1694919bfc4e1a50de29d55433633c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 26 16:08:22 2019 -0800
Must initialize/cleanup Hypre
Exec/Make.Castro
Source/driver/main.cpp
commit 8fce7846928293b2959344f1eccec5757521627d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 26 18:07:35 2019 -0500
inputs files from summit
note: for the 2000 and 1000 Hz cases, I changed dx_model from 10 to 20 here
Exec/science/flame_wave/inputs_H_He/inputs.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/inputs.H_He.500Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.1000Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.2000Hz
Exec/science/flame_wave/inputs_H_He/probin.H_He.500Hz
commit 9e8ff6a74a1b3d7c35ebc46211d8dc62a48cc864
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 26 17:36:02 2019 -0500
these are the inputs/probins for the pure He, no boost runs on Summit
Exec/science/flame_wave/inputs_noboost/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/inputs.noboost.500Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.1000Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.2000Hz
Exec/science/flame_wave/inputs_noboost/probin.noboost.500Hz
commit afada956011e5ba996b170c345a5a2a122ce6893
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 26 13:16:45 2019 -0800
Fix grav extrapolation for external BCs
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
commit 232b757b69da8fe7734fc4f24e8880b34d1854b8
Merge: e2988a313 78650e711
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 26 15:37:44 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit e2988a313107aa53570ce6eee2b6bc128425b073
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 26 15:37:31 2019 -0500
get this working in 1-d
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/inputs_1d.hse_test
commit 3b5ed4eb319dee214dbadb9b339551ddc6440155
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 26 15:31:51 2019 -0500
add 1-d hse test
Exec/science/flame_wave/inputs_1d.hse_test
Exec/science/flame_wave/probin.hse_test
commit 78650e711cb19af67032140d19278f0e042ba03f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 22:30:15 2019 -0800
Make gravity vectors non-static
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit 8b7272b2a5eb005bfd18c99c288d6f80e13dc845
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 16:02:07 2019 -0800
Switch to gravity vectors that are GPU-friendly
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit 91eec8837a6737133353ea522b40c53c5b417caa
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 14:05:52 2019 -0800
Don't initialize multipole gravity if we're not using it
Source/gravity/Gravity.cpp
commit f4fd2adfbd7e04ffdea271c2674c7b958d80218e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 13:31:33 2019 -0800
Offload direct sum BCs onto the GPU
Source/gravity/Gravity.cpp
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
commit a1313176db0a3e1c1bde01291442ea07e2998573
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 12:55:26 2019 -0800
Fix some invalid math operations
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
commit 26feb8e22320a04e1868af8af27478c365179273
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 10:33:58 2019 -0800
Fix typo
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
commit 6e307defe022020658874306c85888083384036b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 01:56:09 2019 -0800
Add missing module use
Exec/science/wdmerger/Problem.f90
commit 0175f0776afa688e2a265ca05cbf3adb787d60c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 01:46:52 2019 -0800
Print out uniform cube/sphere error at runtime
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
Exec/gravity_tests/uniform_cube_sphere/inputs
commit 6bf357eef7e7e651b76881d161be0f5a0a73482d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 25 01:22:52 2019 -0800
Handle an edge case where the block size is less than a warp
Source/driver/reduction.F90
commit 12bbc2239920bf7b42534d996af690847e818a6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 24 22:21:17 2019 -0500
update changes
CHANGES.md
commit 5f2d40ec4dedae0ef34a00bff95b1a224d639d5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 24 22:17:15 2019 -0500
address some precision issues (#711)
This is a run of the dpconvert.py script to make sure precision is done correctly.
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.F90
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/analytic.f90
Exec/radiation_tests/RadSourceTest/planck.f90
Exec/radiation_tests/RadSphere/Tools/fradsphere.f90
Exec/science/convective_flame/Prob_nd.F90
Exec/science/convective_flame/initial_model.f90
Exec/science/convective_flame/probdata.F90
Exec/science/flame_wave/initial_model.F90
Exec/science/planet/ext_src_nd.F90
Exec/science/planet/probdata.F90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.F90
Exec/unit_tests/particles_test/Prob_nd.F90
commit f33888cece4bcbeabd26faf587dffef8688f273e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 24 19:10:34 2019 -0800
Add option for using monopole BCs in 3D (#716)
By setting gravity.max_multipole_order to a negative number, you can use monopole gravity to fill the boundary conditions, rather than the multiple BCs. This is useful for debugging purposes.
To make the behavior consistent, we now use multipole BCs by default in 2D as well.
Source/gravity/Gravity.cpp
commit 596631d07a22b579a1d551fc8ab4cc33acb2797e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 24 16:49:59 2019 -0800
Do some more wdmerger operations on the GPU
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/wdmerger_util.F90
commit f9f0bc279b4798e7fa214fe3687160b27fd40f9d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 24 15:12:06 2019 -0800
uniform_cube_sphere on GPU
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
commit 4c2655fee296edbea1f260d072acca61b4fab1e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 24 04:30:03 2019 -0500
Do some initializations on the GPU
Source/gravity/Gravity.cpp
commit acd2d4321d79e97c60d1737023f6622112ad0c5e
Merge: c3018e4b8 2317bfa9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 24 01:48:21 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2317bfa9fc3e6902b47bc6e3aeadf140959a66c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 22 11:37:51 2019 -0800
Set hard_cfl_limit to 1 since we are doing retries
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit cb163085da427fe95f868a15ccc83d84f5c61dad
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 22 11:05:46 2019 -0800
Disable tiling on the GPU on several loops
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/sum_utils.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/scf/scf_relax.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_thermo.cpp
commit aa51c53e2d9fdbd69c0f34cb2f6c63d67dee7475
Merge: 9fd3efac6 76c6d265a
Author: Alice Harpole <harpolea@login2.summit.olcf.ornl.gov>
Date: Fri Dec 20 16:32:10 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 9fd3efac6bb04aeb228e1c014c868edf04bc1831
Author: Alice Harpole <harpolea@login2.summit.olcf.ornl.gov>
Date: Fri Dec 20 16:31:55 2019 -0500
inputs files for running rotating star with retries
Exec/science/rotating_star/inputs_2d
Exec/science/rotating_star/probin
commit 76c6d265a11069a43455f800ff903014225b6cb0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 19 19:38:14 2019 -0800
Update variable name to avoid confusion
Exec/science/wdmerger/Prob.cpp
commit 7d736f7b23f722f90488fedbe669a72694a664a6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 19 19:23:40 2019 -0800
Remove restriction that we cannot be subcycling while relaxing
Exec/science/wdmerger/Prob.cpp
commit 3d68db1a4ab5d3ef86186ad06ea2d4f777ddfb8b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 19 19:19:47 2019 -0800
Use gravity predictor at new time for rotation frequency update
Exec/science/wdmerger/Prob.cpp
commit ce8a5c1b64bcc3629d11bd6e8c66ec46f440322f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 19 18:40:17 2019 -0800
Enable velocity flux limiter
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 316c38be9855aa78143f8cc549d93124e812822a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 19 18:39:43 2019 -0800
Re-enable density flux limiter
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 77c14fa58920138bdbcd10491bedb94fdeb106d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 19 13:39:39 2019 -0800
Add a flux limiter based on large velocities (#712)
This new flux limiter uses the same algorithm as the existing flux limiter that prevents small densities, but uses it to prevent large velocities (specifically, larger than riemann_speed_limit). This is useful for situations where large speeds are being generated in low-density material due to a large momentum flux from an adjacent high density zone.
CHANGES.md
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/advection_util_nd.F90
commit 12602b6357bdfcd1074e48ba20380262a00553d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 19 13:54:20 2019 -0500
update a comment
Source/sources/sponge_nd.F90
commit 5df4d8864fe0b170c98f7450851cda02d18e6121
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Wed Dec 18 14:36:09 2019 -0800
Alias GradPhiPhysBCFunct to amrex::PhysBCFunctNoOp (#713)
Instead of defining our own no-op class derived from amrex::PhysBCFunctBase to be used by FillPatch, we can use amrex::PhysBCFunctNoOp.
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit 80d7076983c2af5b3c78feb9a71c6a42abb12ad9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 18 17:12:12 2019 -0500
remove the perturbation
Exec/science/rotating_star/Prob_nd.F90
commit 108cef4a14f49b4621e3bf056de5b269201f5d2e
Merge: a1472fe32 d1e0f7384
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 16 15:08:19 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit a1472fe32bb9b653e7d231d1a771b6144e751514
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 16 15:08:00 2019 -0500
updated version of the script that doesn't add unnecessary modules
Util/scripts/dpconvert.py
commit d1e0f7384f7f38d5b0a089c3ad58d512fef6ac0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 16 08:20:35 2019 -0800
Dimension agnosticize cfrhoe
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/Rad_nd.F90
Source/radiation/Radiation.cpp
commit af11337fc15a962bb5aed8442fa31b219c7643cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 16 08:19:34 2019 -0800
Fix header grouping
Source/radiation/Make.package
commit a10889133d8658e9051aa64ebfcc3f02826d37f8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Dec 16 11:03:56 2019 -0500
this should fix the docs
sphinx_docs/preprocess_files.py
commit c3018e4b8b615f832665e6776fbf8dddda21021c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 15 22:24:51 2019 -0500
Rename turn_off_relaxation
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/wdmerger_util.F90
commit 635f0416170fca33ef572b857f8627bc7f89be0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 15 22:14:31 2019 -0500
Don't disable sponging when relaxation is disabled
Exec/science/wdmerger/wdmerger_util.F90
commit d9cc0a79a783fae750203b6b973dfe59c14e641d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 15 22:11:58 2019 -0500
Move a print from Fortran to C++
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/wdmerger_util.F90
commit 7c170717fa3c9b640006e34ad141b98f03b48820
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Sun Dec 15 15:10:54 2019 -0500
missed parentheses
sphinx_docs/preprocess_files.py
commit 6b3572c4032c46edde167cddc6894d8a96185b8d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Sun Dec 15 15:09:10 2019 -0500
added line to strip out any dimension descriptions from fortran files before processing them using sphinx fortran
sphinx_docs/preprocess_files.py
commit e506f94c60df0cf5c4307a226c2f07da17899e8f
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Sun Dec 15 15:02:53 2019 -0500
updated rotating star inputs files
Exec/science/rotating_star/inputs_2d
Exec/science/rotating_star/probin
Util/code_checker/fortran_checker.py
commit 35f1c507d20d9e922b1cd552e47efd555ac2eac4
Merge: 033a9682d 9e9127a70
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Sun Dec 15 15:02:29 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 9e9127a70a9c4e51631faf0d7a6bde072324842d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 15 02:43:04 2019 -0500
Rewrite some conditional logic
Source/driver/Castro_advance_ctu.cpp
commit 7fd868f489a960906e7539518e1d67d118a1d510
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 15 01:41:15 2019 -0500
Turn on sponge by default
Exec/science/wdmerger/probin
commit cf065e46fb6eb193a77d75177cbf091de7f496b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 14 23:45:24 2019 -0500
Print out initial wdmerger orbital speed
Exec/science/wdmerger/wdmerger_util.F90
commit 249290018c7a7cd3d1a6b1dab04809666ff5d8f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 14 20:50:41 2019 -0500
Formatting
Source/hydro/advection_util_nd.F90
commit 51240dc5f6825f52a45d3715a78b5a6ed96eacba
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 14 17:55:54 2019 -0700
Add option to apply sources consecutively (#710)
This new option allows you to add sources to the state as they are calculated, rather than grouping them together at the end. Its purpose is to allow sources that come at the end, in particular the sponge and the external source term, to act on the state after the actual physics source terms have already been applied.
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/sources/Castro_sources.cpp
commit 753f45f1f839354fa444ce9c82a510667275b8de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 14 16:18:34 2019 -0500
add a sparse Jac stuff
Microphysics/networks/burn_type.F90
commit a1607ec721661a5dd473a9f6e18fb75c590101f4
Merge: bec958d09 d7ac90f2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 13 12:47:03 2019 -0500
Merge branch 'development' into jac
commit d7ac90f2b6ed1edaa4c11f81f02e2fd41f70b356
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 13 10:37:51 2019 -0700
Add an option for implicit external source terms (#709)
The external source terms are currently only implemented as an explicit predictor-corrector scheme. This is incompatible with how wdmerger implements its relaxation source term, so wdmerger is currently not working as intended. This PR introduces a new option, castro.ext_src_implicit (defaulting to 0) which, if turned on, changes the handling of the external source terms to allow an implicit solve. This is done by subtracting the full old-time source and adding the full new-time source in the corrector, rather than -0.5 and +0.5 of each, respectively. It would still be up to the individual problem to make sure they are consistent with this scheme if they turn the option on. Even if they don't, the source term ends up being a simple time-advanced source term at n+1 which is not a serious problem.
CHANGES.md
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/sources/Castro_external.cpp
commit 45cebcb87fe4c89d9e4b5f1521e2c7b678474747
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 13 11:05:17 2019 -0500
Use relaxation in wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
commit f72e31ee5657b8ee31db5db0097caaf5ec7d91f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 12 16:50:27 2019 -0700
Reorder sources so external is last (#708)
This PR reorders the listing of the source terms so that the external source terms are last. This currently enables nothing new, but is in anticipation of later changes. Answers will change to roundoff since we're adding the sources in a different order now.
Source/driver/Castro.H
commit c6f7365fb662106fba80710b9b21063a90445fb0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 17:38:55 2019 -0800
Convert LAPACK to a module
Source/radiation/RadHydro_nd.F90
Util/LAPACK/Make.package
Util/LAPACK/dgtsv.f
Util/LAPACK/lapack.F90
Util/LAPACK/xerbla.f
commit 4c53b165534903588000d050764f650e2cf8dba9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 17:09:23 2019 -0800
Fix a use statement
Source/radiation/Rad_nd.F90
commit af7efcc61cab6066c7caa18e1dc07209c2b3a52d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 17:06:22 2019 -0800
Mark up more Edd_factor on GPU
Source/hydro/Castro_ctu_nd.F90
Source/hydro/trans.F90
commit f67edb2b0b35697838eeef5467bc14ba726b09b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 17:03:26 2019 -0800
RadHydro_nd on GPU
Source/radiation/RadHydro_nd.F90
commit 1059c529395ec39b756582804f1c952367e75f0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 17:00:22 2019 -0800
Put some radiation params on the GPU
Source/radiation/Rad_nd.F90
Source/radiation/rad_params.F90
commit 1ea0cdd5444107b2594a2beea81033896db9a019
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 16:40:02 2019 -0800
RadDerive_nd.f90 -> .F90
Source/radiation/Make.package
Source/radiation/RadDerive_nd.F90
Source/radiation/RadDerive_nd.f90
commit 618bb9527e7a2ef7b71d1fcd38a38ecd9c7bce5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 16:21:50 2019 -0800
blackbody.f90 -> .F90
Source/radiation/Make.package
Source/radiation/blackbody.F90
Source/radiation/blackbody.f90
commit bff3b893da051502cdaff1942b52873b6764ba2e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 14:04:38 2019 -0800
filter_nd.f90 -> .F90
Source/radiation/Make.package
Source/radiation/filter.F90
Source/radiation/filter.f90
commit d70dbb16aad1681e4a17e051f630ebfc73b4b07b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 13:52:07 2019 -0800
RadHydro_nd.f90 -> F90
Source/radiation/Make.package
Source/radiation/RadHydro_nd.F90
Source/radiation/RadHydro_nd.f90
commit 3ce56f631754928cb0e79b97c7b2d25072432e7d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 13:37:17 2019 -0800
trace_ppm_rad cleanup
Source/radiation/trace_ppm_rad_nd.F90
commit cc966ae94b0e88ae41df6b4b9ed207ee40f9451f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 13:33:13 2019 -0800
Rad_nd.f90 -> .F90
Source/radiation/Make.package
Source/radiation/Rad_nd.F90
commit 0de6d506d94584e3efef21a2ebf67de6a82f88ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 13:26:24 2019 -0800
rad_params.f90 -> .F90
Source/radiation/Make.package
Source/radiation/rad_params.F90
commit 2a487a05900d17a717420c8ce1946105ee37c4bf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 13:11:44 2019 -0800
rad_util on GPU
Source/hydro/advection_util_nd.F90
Source/radiation/Make.package
Source/radiation/rad_util.F90
commit 1c98c63130e112176840d9028bd6082780bfc9a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 12:51:47 2019 -0800
edd_factor marked up for GPU
Source/hydro/riemann_util.F90
Source/radiation/Make.package
Source/radiation/fluxlimiter.F90
Source/radiation/fluxlimiter.f90
commit 698cc16b540b8fc15c1e1826ad5072c60960bf15
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 12:47:31 2019 -0800
Put some radiation parameters on the GPU
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 67a6b058e6647cdfdf9209d690ee7e80bc8cefa2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 8 12:37:31 2019 -0800
Syntax cleanup in riemann_util
Source/hydro/riemann_util.F90
commit 93f4a7c37f73dc5cb4dd8213b8c028df6930f86b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 7 17:04:10 2019 -0500
fix one of the regex to avoid false positives
Util/scripts/dpconvert.py
commit fde8438cb9f80601c29e2aed3cf0a027989f64c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 7 14:08:00 2019 -0500
some robustification
Util/scripts/dpconvert.py
commit bec958d09e9024698aca07662d6279590d1dbbc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 5 10:07:31 2019 -0500
get this compiling with the new interface
Microphysics/networks/burn_type.F90
Source/driver/timestep.F90
Source/reactions/react_util.F90
commit 23c62b43f51de0f0a79353037a981208044b1fab
Merge: 1ad4fb323 8643bd314
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 17:08:36 2019 -0500
Merge branch 'development' into jac
commit 36c14f498a655f59129ec76eeea92f686748c064
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 14:19:34 2019 -0500
update for VODE90 -> VODE
Source/sdc/sdc_util.F90
commit 8643bd31439ec71dbf61c25bed39eb80b1e655c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 13:03:23 2019 -0500
address compiler warnings (#703)
* clean up some compiler warnings
* block off some SDC stuff
* more unused variable fixes
* more unused variables
* remove unused variables
Exec/science/flame_wave/Prob_nd.F90
Microphysics/EOS/composition.F90
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/main.cpp
Source/gravity/Gravity_nd.F90
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
Source/problems/bc_ext_fill_nd.F90
Source/reactions/React_nd.F90
commit fb7713899538a66ecdf22e5d1126ba96b2ce5d84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 2 09:18:41 2019 -0500
update for 19.12
CHANGES.md
commit cc2aa6182045841aac81d59ddfa60b072de8d0f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 1 18:44:53 2019 -0500
fix precision issue:
Exec/science/flame_wave/initial_model.F90
commit b8d98dc01eb4558a3d1696f84e38d81db077f2a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 1 08:36:08 2019 -0500
fix ext_src size
Source/hydro/hybrid_advection_nd.F90
commit f831670e00bd0b9d99070255976e8ac9e38a51be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 1 08:35:18 2019 -0500
fix source size
Source/hydro/advection_util_nd.F90
commit 34d2bd199624c62e48548c1ab770cbd58e36f480
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 1 08:21:30 2019 -0500
fix size of ext_src
Exec/gravity_tests/code_comp/ext_src_nd.F90
Exec/gravity_tests/hydrostatic_adjust/ext_src_nd.F90
Exec/hydro_tests/heating_verification/ext_src_nd.F90
Exec/hydro_tests/test_convect/ext_src_nd.F90
Exec/hydro_tests/toy_convect/ext_src_nd.F90
Exec/science/Detonation/ext_src_nd.F90
Exec/science/planet/ext_src_nd.F90
Exec/science/wdmerger/ext_src_nd.F90
commit daae0de8dc9a32e79cc7a462f89b85a87b8ee1c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 1 08:18:24 2019 -0500
fix size of ext_src
Source/sources/ext_src_nd.F90
commit 9a20fec297fa5537f5e46d1a71c4908b2710f857
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 20:48:44 2019 -0500
fix srcU dimensions
Source/hydro/Castro_mol_nd.F90
commit 319a8e61a4e75241a15fdf3a0035e24910eda297
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 30 16:57:32 2019 -0800
Use the subcycling-enabled retry CTU advance for simplified SDC (#695)
The retry mechanism can be used for the simplified SDC advance as well as the standard CTU advance.
I've made some changes to improve this and make it quite simple. Now we simply do the SDC iterations inside the outer while loop that does retries.
I've also made some cosmetic changes to the return values of the CTU advance and react_state to return bools, indicating whether or not they were successful (unsuccessful meaning we either abort or retry).
CHANGES.md
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
commit 584c1f3fcb0dfeff59d3941dd78576361f167872
Merge: 783bad270 29cfa9940
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 18:24:57 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 783bad2701292c0730fdf440e05f51a94fc67d3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 18:24:43 2019 -0500
add some compiler notes
sphinx_docs/source/FlowChart.rst
commit 29cfa9940a18b79ca32fe123206a80c0a9d42d16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 14:10:38 2019 -0500
add status to sdc_t
Microphysics/networks/sdc_type.F90
commit 4578cf13b9e7f7f38ccfe71c932922c739641482
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 29 17:38:41 2019 -0800
Lengthen the last subcycle timestep to avoid very small dt (#701)
Due to roundoff issues, it is possible for the current algorithm to divide the main timestep into N smaller dt's that, when summed up, so not exactly equal the desired target time. We already have protection against the case where the final time is slightly larger than the target time (in which case we shortened that timestep) but we had no protection against the case where we would end up slightly short of the target time, in which case we'd have to take a very short last timestep. This PR resolves that issue by making that last timestep slightly longer.
CHANGES.md
Source/driver/Castro_advance_ctu.cpp
commit 4f70657f615debb3406b6f73d628e906d893e00b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 29 18:04:23 2019 -0500
add changes
CHANGES.md
commit 799174f2a4995a475e2404c96fe97ea5ef20b3e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 29 18:02:25 2019 -0500
reduce memory usage for conserved-state sources (#699)
This change removes the species from the conserved state sources. Closes #698
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_variables
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/source_fill.F90
Source/gravity/gravity_sources_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/rotation/rotation_sources_nd.F90
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_thermo.cpp
Source/sources/sponge_nd.F90
Source/sources/thermo_nd.F90
commit 049883f03da0ca1ba98d052e63a236c5e2710b86
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 27 23:59:27 2019 -0800
Increase stop_time to account for the pure C/O case
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
commit 3d1593c7749e8a65a7d2f65e824f29d9ee8f5485
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 27 23:45:16 2019 -0800
Mark up ext src for GPU
Exec/science/Detonation/ext_src_nd.F90
commit 034945a1c270baff1f26e347d32373f33783b9f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 27 23:36:48 2019 -0800
Replace real gravity in the collision problem with a mockup
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/ext_src_nd.F90
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probdata.F90
Exec/science/Detonation/probin-collision
Exec/science/Detonation/probin-collision.testsuite
commit 0a95b632ab1cec929df8b5b8f83df922828002b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 26 22:27:22 2019 -0800
Store the retry state in pinned memory
Source/driver/Castro_advance.cpp
commit 26c6f1c6d6183d77a086da85df90db8e370b1dd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 25 11:06:50 2019 -0500
some SDC solver safety (#692)
This adds a little protection to the input state for the SDC solve and better error output
Source/sdc/Castro_sdc.cpp
Source/sdc/sdc_util.F90
commit 033a9682dec54e0422eff78743f698aa57e2fba7
Merge: ebd813969 817a6baf8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Nov 25 08:35:53 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 817a6baf85faf903179377a579d7cc30e6e2db19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 25 08:11:29 2019 -0500
fix some more uninitialized variables
Exec/hydro_tests/gamma_law_bubble/problem_derive_nd.F90
commit e59c59629e236bcb3ad34c3fff70529019640dbe
Merge: b3b07b7bc 194a8460a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 23 18:55:02 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b3b07b7bc516ed3f29530b708f1276d30855cf64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 23 18:54:54 2019 -0500
add the logo
README.md
commit 194a8460a156d183bee1e122c145046c43d80c22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 23 14:38:15 2019 -0500
fix uninitialized e in derive
Exec/hydro_tests/gamma_law_bubble/problem_derive_nd.F90
commit 1ad4fb32361ea10feda8fb53814946bb3c5ab3f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 21 15:40:50 2019 -0500
revert change
Exec/science/flame_wave/probin.testsuite
commit e9132d7902eef70b7c12a01c0e9c42de3f4d7a36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 21 15:39:57 2019 -0500
do away with the jac in burn_t
Exec/science/flame_wave/probin.testsuite
Microphysics/networks/burn_type.F90
Source/reactions/react_util.F90
commit 32e93c959cf43907a96f894ca2f848e3d3d147ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 20 14:17:09 2019 -0500
increase max_grid_size
Exec/science/flame_wave/inputs_3d.testsuite.gpu
commit dc3c09ecf3b41a7dada1c7b014719ab47218ac23
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 20 13:23:03 2019 -0500
Print out per-level FOM
Source/driver/Castro_advance.cpp
commit 1b592c525ad9b9fcabba47c7ed0381ba317f5784
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Tue Nov 19 17:37:59 2019 -0800
When using simplified SDC, define SDC_EVOLVE_ENERGY for StarKiller Microphysics. (#696)
Exec/Make.Castro
commit ebd813969e3bfa8741a4d746e0c66b86ce3c4a6e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Nov 19 11:55:56 2019 -0500
added a check to make sure Fortran variables that are initialized at definition include the save parameter
Util/code_checker/fortran_checker.py
commit b21dead7d468031ce870c6b78f49abdd02306521
Merge: 2f6520c13 df6ac9489
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 19 11:02:54 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2f6520c1370f4ef6d53a908c0914fe2106a65512
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 19 11:02:40 2019 -0500
add a GPU test
Exec/science/flame_wave/inputs_3d.testsuite.gpu
commit df6ac94892c017e5e78753c50cbc62b5c5aea725
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Nov 19 10:41:57 2019 -0500
Update requirements.txt
requirements.txt
commit 89a67796db290d282bcc03ad68468a72102b4d9d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Nov 19 10:37:09 2019 -0500
hopefully fixed docs build
requirements.txt
sphinx_docs/preprocess_files.py
commit fe6db26e5ca45c354b439b3f1237c97f70a807d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 18 20:52:15 2019 -0500
Make collision test problem harder with smaller ode_max_steps
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probin-collision.testsuite
commit eccdea4079df5cec6dfe948eb637718417e1d56b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 18 17:01:58 2019 -0500
use named indices to make the code clearer
Source/reactions/react_util.F90
Source/sdc/sdc_util.F90
commit 9a7a10587001a2527140cb1f7b2f940e5ddf6948
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 18 14:51:42 2019 -0500
fix comment
Source/reactions/react_util.F90
commit 31f78e9ef38a5e946baf62cde2d62c3e9d029f50
Merge: 2bf4a9453 8551cde85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 18 13:04:48 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2bf4a94539a1d69882cdf256193902bca2a4a0f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 18 13:04:30 2019 -0500
fix sign on dw/dU(E) Jacobian for the KE term
Source/sdc/sdc_util.F90
commit 8551cde85d65b3a8fba8657594d56386f3f9d4c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 17 18:34:27 2019 -0500
Add a Detonation collision problem for the test suite
Exec/science/Detonation/inputs-collision.testsuite
Exec/science/Detonation/probin-collision.testsuite
commit 2b7e12960cf7b5275296626bec799576a8fd64d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 17 15:25:59 2019 -0500
burn_failed should have an OMP reduction
Source/reactions/Castro_react.cpp
commit 37e1df2bd544f1d1c991811560f3a4fae3c7982e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 12:13:10 2019 -0500
switch from xenial to bionic (18.04)
.travis.yml
commit 2c890249a1a30bceeb39c956fb3f1fadaad5f280
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 12:08:05 2019 -0500
sync requirements up with MAESTROeX
requirements.txt
commit f8265798f09a87d0b92c1da7012f064b8776184c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 11:52:57 2019 -0500
fix index issues
sphinx_docs/source/build_system.rst
commit d8aafadfe36af7e3f997e4ac3dc7b3b93eecb1d3
Merge: 9dcde6a00 f98a148b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 09:52:20 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 9dcde6a00c724ea5da28df4986a589f911d5a1f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 09:52:11 2019 -0500
a little updating
sphinx_docs/source/build_system.rst
commit f98a148b55c9c5d47b5cb93a68d84d61eedba0db
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 17 09:35:48 2019 -0500
Move fill_ambient to bc_fill_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Exec/science/Detonation/probdata.F90
commit 677cbee2bc630f230f88b4bd9ce15ae23dbf8ec1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 17 09:33:11 2019 -0500
Fix managed attribute syntax
Exec/science/Detonation/probdata.F90
commit acd09084d2e8f37c9143621f6a03b768c973d5eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 09:13:44 2019 -0500
add rendered logos
Util/logo/castro_logo_hot_100.png
Util/logo/castro_logo_hot_1600.png
Util/logo/castro_logo_hot_200.png
Util/logo/castro_logo_hot_400.png
Util/logo/castro_logo_hot_800.png
Util/logo/variations/castro_logo_PuBuGn.svg
Util/logo/variations/castro_logo_RdPu.svg
Util/logo/variations/castro_logo_YlGr.svg
commit 9c6c56abe98a9b02676149b19083349e88db66e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 16 15:15:42 2019 -0500
Fix what we pass to okay_to_burn
Source/reactions/React_nd.F90
commit 364e8c9d587cc963dfefd334e535d564453758e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 16 15:12:12 2019 -0500
Enable simplified SDC driver if CUDA is used
Source/driver/Castro_advance.cpp
commit bb77166b6516c1767ea18a56e6f44a617b6253e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 16 12:22:04 2019 -0500
Don't check for NaNs on the GPU
Source/driver/Castro_advance.cpp
commit a4dc760ef77b247a8a969f029b219d4ca40b238b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 16 12:19:21 2019 -0500
Mark up simplified SDC react_state for GPUs
Source/driver/Castro_F.H
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
commit 2c6982acc11d97926bb396bb3dc8a16d63b1e88b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 16 12:07:47 2019 -0500
Fix typo in error message
Source/driver/Castro.cpp
commit 13758652174260047ad7dc9131ceacf2e9ac5fd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 15 10:16:59 2019 -0500
undo some accidental changes
Exec/science/Detonation/GNUmakefile
commit f2576af41c646272ea6c64f4b578c23e1f44334e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 14 11:29:12 2019 -0500
add model_burner
CHANGES.md
Exec/science/Detonation/GNUmakefile
commit fc4f57ff207e816de3ae1fb4d33ca242b59abc98
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 14 11:16:06 2019 -0500
switch network
Exec/unit_tests/model_burner/GNUmakefile
commit 3534e1a1ae3f588e6a8b59209b829a4ef1a6110f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 14 11:04:58 2019 -0500
add a new model_burner unit test
Exec/unit_tests/model_burner/15m_500_sec.hse.6400
Exec/unit_tests/model_burner/GNUmakefile
Exec/unit_tests/model_burner/Make.package
Exec/unit_tests/model_burner/Prob_nd.F90
Exec/unit_tests/model_burner/README.md
Exec/unit_tests/model_burner/_prob_params
Exec/unit_tests/model_burner/inputs
Exec/unit_tests/model_burner/probin
commit f92922a66d3671dd1ad03802cabcfb8e77b415c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 12 14:08:27 2019 -0600
Fix ca_apply_metric for GPUs (#694)
ca_apply_metric was wrong on the GPU for two reasons. First, it was launching work over a cell-centered box but updating two nodal Fabs, so it was missing zones. Second, the memory access pattern is bad, since it is not strided in memory. Probably this is suboptimal for CPUs too, there's not enough work involved in saving r that it makes sense to invert the loop order.
Source/driver/MGutils_nd.F90
Source/gravity/Gravity.cpp
commit cbc22dfb65f06c63e36636645cc86cc803555f9b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 21:36:33 2019 -0800
Don't tile y dimension in 2D on GPUs
Source/driver/Castro.cpp
commit 5c68a181ede058ced73295b6408a7c5b70238ac0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 20:54:04 2019 -0800
Add BL_PROFILE to various Gravity functions
Source/gravity/Gravity.cpp
commit 181cf7eb884cac00b4742dff405736fb778d898d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 23:24:57 2019 -0500
Check in a 2D collision setup
Exec/science/wdmerger/tests/wdmerger_collision/inputs_2d_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_2d_collision
commit ec0fb0c1ba0695167007c0bc19b8922fb8ff0d34
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 23:19:09 2019 -0500
Add function markup for the GPU script
Source/driver/timestep.F90
Source/rotation/Rotation_nd.F90
commit f13986b8956d9ac730964df46f54d2e6d56169eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 23:07:41 2019 -0500
2D gravity terms on the GPU
Source/driver/Castro_F.H
Source/gravity/Gravity.cpp
commit 29ebe02da926814d1865a9e9b112e083fe08b6ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 22:54:26 2019 -0500
Mark up some reactions code for the GPU
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/timestep.F90
Source/reactions/react_util.F90
commit 8e1befd581842c6910670c32b1fbf9ad27c0ccb4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 20:33:21 2019 -0500
Mark up fill_rotation_psi for device
Source/rotation/Rotation_nd.F90
commit ccf2112b701d4fa2f24e950627ac85ec4fb9ad85
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 20:28:46 2019 -0500
Mark up conducteos for the GPU
Microphysics/conductivity/conductivity.F90
commit 8ec93577fed64d867f027db7eda3dab0560accbf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 20:26:57 2019 -0500
Factorial does not need to be evaluated on the device
Source/gravity/Gravity_nd.F90
commit 6feba691728bc436e9ee02f916f556eb6b4e7a67
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 16:43:56 2019 -0500
Roll back change to not use host version
Exec/Make.Castro
commit 4bc1170fa636d8f311998bef48549797844fe559
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 16:38:37 2019 -0500
Allow code to compile for either old or no-host builds
Microphysics/EOS/eos.F90
Source/driver/reduction.F90
commit 2c89d0bab35676612cb024994b4d8030ff343260
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 16:34:52 2019 -0500
Specify return values for area, volume
Source/driver/Castro_util.F90
commit 7da29386ea22b28dd2467a9caa1b2d22ef634cf6
Merge: cbbfebbe7 325789417
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 11 14:53:12 2019 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit cbbfebbe79261a6aa9cf0c8e8579d40b6b7b2103
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 11 14:52:58 2019 -0500
less frequent outputting when we are not boosting
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
commit 325789417e0c1b19a6d38ce16171e42bb8fb7696
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 11 14:16:57 2019 -0500
fix istate check from VODE90
Source/sdc/sdc_util.F90
commit 6cdc939d02b6b97d9f583f52b3f555caecb87060
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 11 13:25:41 2019 -0500
add O14/O15 + disable burner retry to let Castro retry work
Exec/science/flame_wave/probin.H_He
commit 042ad48b3d0cf317cbcc01a2a57c000cf4e6e741
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 11 12:36:39 2019 -0500
add some safety checks
Source/driver/Castro.cpp
commit d8205a31162951773cf6297954b77ef4ef3c3bc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 11 12:32:05 2019 -0500
if-def out a check on sdc_order
Source/driver/Castro.cpp
commit 84c60e6310453ccaa9a001d8254b8c52bce21317
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 11:25:12 2019 -0500
Put enforce_consistent_e back in
Source/driver/Castro.cpp
commit 80b24cec702c7e095dda482afb7093d6749194cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 11:03:51 2019 -0500
Call ca_unweight_cc on the GPU
Source/gravity/Gravity.cpp
commit ab04d8a8afe7a9ccd427f9f10af93e6c7ac0ca78
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 11:03:34 2019 -0500
ifdef out SDC for CUDA builds
Source/driver/Castro.cpp
commit bcb07901f16ab4466c467f53d68b12569a8195f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 10:54:25 2019 -0500
Don't include SCF if using CUDA
Source/scf/Make.package
commit 70d6383924fa23192287e78c80f4bd09f514b62d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 09:57:53 2019 -0500
Missed another SDC ifdef
Exec/unit_tests/diffusion_test/Prob.cpp
commit 867d133f6ec37c48fceece3e9a01fefd68d88142
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 21:36:37 2019 -0800
Only build a device version of pragma gpu functions
Exec/Make.Castro
Microphysics/EOS/eos.F90
Source/driver/reduction.F90
commit 59b168ca15c9dedca73565ff19077c8f43558c01
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 20:28:00 2019 -0800
Update to new GPU pragma syntax
Exec/Make.cuda_rules
commit 930ea851cd60615d5729b7539095a100767d148a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 20:24:48 2019 -0800
Fix typo
Source/hydro/riemann_util.F90
commit a8084885f80ac066aa38109ed64682f142297f68
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 20:10:16 2019 -0800
Move max reduction into Castro
Source/driver/reduction.F90
Source/hydro/advection_util_nd.F90
commit c8626403a45a49a310bd985c184e3bd2f24c9a3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 19:53:08 2019 -0800
Add gpu markup to a few functions
Source/driver/Castro_util.F90
Source/hydro/riemann_util.F90
commit 7d62ba280a428735b5afdba3d5c8e5c569db3ff9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 19:32:26 2019 -0800
Remove unused filcc_nd
Source/driver/Make.package
Source/driver/filcc_nd.F90
commit b053a851d301f553066d85d8e15a45f265408ee9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 19:03:25 2019 -0800
Implement alternate ctoprim on the device
Source/hydro/Castro_hydro.cpp
commit 74fc102326bfcfc130b15cf0bf49fe3e9fe3bd71
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 19:03:07 2019 -0800
Wrap another SDC call in an ifdef
Source/driver/Castro.cpp
commit f45f30be43091dc6eebba06828ff0d73037e1b0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 17:19:42 2019 -0800
Check in reduction.F90
Source/driver/reduction.F90
commit 4e75210cd580d111b4c050c024ee672881d7695e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 15:11:30 2019 -0800
Fix use statements
Exec/science/wdmerger/wdmerger_util.F90
commit 38dd11c1aa9a58f9dc74dcbdd3dc59d29af0b123
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 14:46:30 2019 -0800
Move min reduction into Castro
Source/driver/timestep.F90
Source/hydro/advection_util_nd.F90
commit 452ccb499317f41076e5bb5cb418a57281559388
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 14:34:48 2019 -0800
Move add reduction into Castro
Exec/science/wdmerger/wdmerger_util.F90
Source/driver/Make.package
Source/driver/sums_nd.F90
Source/gravity/Gravity_nd.F90
Source/hydro/Castro_ctu_nd.F90
commit c2c1665f1a67f792fa1343f4b12b2310f701f08e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 14:30:11 2019 -0800
Wrap more hydro in TRUE_SDC
Source/driver/Castro.cpp
Source/hydro/Castro_hydro.cpp
commit e2abf271691ab7d5515efd1afd4f33add5ef4568
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 13:26:20 2019 -0800
Wrap some hydro in USE_TRUE_SDC
Source/hydro/Make.package
commit 764661f1bda6b12de68430b92c01fee2052ce32f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 12:23:44 2019 -0600
Call EOS on host explicitly in probinit (#693)
In preparation for future GPU changes, when we call the EOS in probinit, call it explicitly from the host, which for CUDA builds will call the EOS on a single GPU thread. (Slow, but functional.)
CHANGES.md
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/hydro_tests/HCBubble/Prob_nd.F90
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/heating_verification/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/RadFront/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/initdata_others.f90
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/toy_flame/Prob_nd.F90
Exec/scf_tests/single_star/Prob_nd.F90
Exec/science/Detonation/Prob_nd.F90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/convective_flame/initial_model.f90
Exec/science/flame/Prob_nd.F90
Exec/science/flame_wave/initial_model.F90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/wdmerger_util.F90
Exec/unit_tests/diffusion_test/Prob_nd.F90
commit 1dfc88576b984a5af5d9cc2164ff7a68b0156569
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 9 13:49:47 2019 -0500
bl_error -> castro_error
Exec/science/wdmerger/wdmerger_util.F90
commit f2d54f2da5bc343cd4e610e8361cbeda06f6cb88
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 9 02:28:09 2019 -0500
Add a wrapper that calls the device EOS from the host
Microphysics/EOS/eos.F90
commit 4fc7eef2bf073816940806f7bbf8d265c4b50d81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 8 18:50:34 2019 -0500
define the composition stuff
Microphysics/EOS/composition.F90
commit 4007127e071e6e1b2aa454961b87f7b30d575d52
Merge: b7772161a 973eb19a3
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Nov 7 13:54:33 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b7772161ae038d402b23201ad1bec0da4c2ec749
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Nov 7 13:54:30 2019 -0500
improved timestep limiter diagnostic routine to avoid memory issues
Diagnostics/timestep_limiter/main.cpp
commit 973eb19a39a9cbff78af0f23d7c687545ff3371a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 6 14:21:29 2019 -0500
fix compilation for the case where we don't have the Microphysics repo
Microphysics/EOS/Make.package
Microphysics/EOS/composition.F90
commit 6714052088e07fcb9b84e3f99e137feddeb2493c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 5 13:11:01 2019 -0500
more docs
sphinx_docs/source/index.rst
sphinx_docs/source/retry.rst
commit 941790cf0edc39942af55e41b6ff1e3a36bf1690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 5 12:52:52 2019 -0500
some fixes
sphinx_docs/source/EOSNetwork.rst
commit 5529b182cfc4875e873c1ca533dd8a43dfc999e3
Merge: 7fe3d77e5 8c72c225b
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Nov 5 11:10:17 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8c72c225b666e179eb17a72d4a097e9fff757ad7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 4 16:34:11 2019 -0500
split the X derivatives from eos_t (#691)
This PR coordinates with starkiller-astro/Microphysics#207 to remove the composition derivatives from eos_t to boost GPU performance.
Exec/Make.Castro
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
Source/sdc/sdc_util.F90
Source/sdc/sdc_vode.F90
commit 199dc677e5ef9409a5ed3107e6b8080b18e9ffee
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 3 08:23:01 2019 -0800
Inline pdivu (#689)
There is no need to store a fab for pdivu, it can just be calculated on demand on a per-zone basis in the update.
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/advection_util_nd.F90
commit ad296b7f952d77e6a4d1014c849509d780b78984
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 19:32:45 2019 -0400
a bunch of small optimizations (#688)
This is a bunch of optimizations -- mainly getting rid of divides
There is also one bug fix here to the 4th order artificial viscosity -- we were not doing the 3-d terms correcrly.
Source/diffusion/Diffusion_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trans.F90
commit 2a060a2aba6f4e39ca7923b700cad80242ad04e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 19:24:37 2019 -0400
only true SDC needs the extra thermo defined
Exec/Make.Castro
commit 1a172010b821c98fe5f0e7364a7b73b28873f0be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 13:43:21 2019 -0400
update changes
CHANGES.md
commit f39aa2a25d0be4ade764a917224c1fb5ec040ecf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 12:40:11 2019 -0400
Vode90 sdc (#677)
This switches the new SDC ODE integrator to VODE90.
To allow this, we now need to compile as make USE_TRUESDC=TRUE. The old Simplified SDC method is now built as make USE_SIMPLIFIED_SDC=TRUE.
The default integrator used by Castro is now VODE90. This is done for GPU support.
This removes support for the original VODE integrator. This requires StarKiller PR starkiller-astro/Microphysics#194 to be merged first
closes #547
Exec/Make.Castro
Exec/reacting_tests/nse_test/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/rotating_star/GNUmakefile
Exec/science/subchandra/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_collision/GNUmakefile
Microphysics/networks/Make.package
Microphysics/networks/burner.F90
Microphysics/networks/general_null/Make.package
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Make.package
Source/reactions/React_nd.F90
Source/reactions/react_util.F90
Source/sdc/Castro_sdc.cpp
Source/sdc/Make.package
Source/sdc/sdc_util.F90
Source/sdc/sdc_vode.F90
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/build_system.rst
commit 2cf79beaf2b471f61eba0d5b9833a28ed360a3e3
Merge: a1cbf69be a6b652b4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 1 19:09:39 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit a1cbf69be4dc823ff31af8515e54f9fc9d2872b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 1 19:09:27 2019 -0400
add a 4th fuel mass fraction input
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/_prob_params
commit a6b652b4c6ad9f60d1351bf60a29d59c7693b68c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 1 07:38:55 2019 -0400
update for 19.11
CHANGES.md
commit 68e4bd11d7c310bff3be73d46c5ce2b96fde99ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 14:13:56 2019 -0400
a mixed H/He burst
Exec/science/flame_wave/inputs.H_He
Exec/science/flame_wave/probin.H_He
commit 07872a4f3806484a0bf846c2f0c90ad65d7f6e39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 13:46:05 2019 -0400
move the boost inputs to their own directory
for the most part these were used for paper I and we are now moving
to no boosting
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/inputs_boost/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/inputs.boost_5_5
Exec/science/flame_wave/inputs_boost/probin.boost_10_10
Exec/science/flame_wave/inputs_boost/probin.boost_10_10.sdc
Exec/science/flame_wave/inputs_boost/probin.boost_10_10_slow
Exec/science/flame_wave/inputs_boost/probin.boost_5_5
commit c87f753326a1d813adffd63680dd62d04dffa301
Merge: c3bac37b7 81e6ad80a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 13:35:08 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 81e6ad80a08c4b602072ecd528fa9be847779d91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 10:50:59 2019 -0400
sync up with the main version
Exec/gravity_tests/code_comp/inputs_3d.sdc4
commit af958e6ee5ed2c5e27b8b99a993faeddfb7dbe3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 10:46:35 2019 -0400
remove gravity.drdxfac = 2
Exec/gravity_tests/code_comp/inputs_3d
commit 4541e0a2b668917ce17b431cd8cf109c19c309ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 10:17:34 2019 -0400
a little organization
sphinx_docs/source/creating_a_problem.rst
commit a9603406bdd6c0daff4df1d9518678c87e39dc50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 10:09:24 2019 -0400
update the creating a problem section
sphinx_docs/source/creating_a_problem.rst
commit fc132c153115f6e93b30ce9cfaec2fb325c58846
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 08:46:01 2019 -0400
switch to auto prob params
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadFront/Make.package
Exec/radiation_tests/RadFront/Prob_nd.F90
Exec/radiation_tests/RadFront/_prob_params
Exec/radiation_tests/RadFront/probdata.F90
commit c119f2844f2f2d5d2900eab68189a2dc4288bfed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 08:36:23 2019 -0400
switch to auto prob params
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/Rad2Tshock/Make.package
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/_prob_params
Exec/radiation_tests/Rad2Tshock/probdata.F90
commit 59e6ad104202de8462fea6e7df99abb05bdb8677
Merge: 276a377b3 d3d5a3658
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 08:11:03 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d3d5a36589d90408c5fb1a49e1fae2e1e2ffe18b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 30 19:26:56 2019 -0700
Fix ifdef/endif typo.
Source/hydro/advection_util_nd.F90
commit c3bac37b75e4e491d86cc095280040b3d6bb3b57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 30 19:36:02 2019 -0400
fix compilation
Source/hydro/advection_util_nd.F90
commit 276a377b38da1a781d91658380929a3a160f334d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 30 15:23:13 2019 -0400
emdif -> endif
Source/hydro/advection_util_nd.F90
commit f73e0a2910813c1ce3797910a03e39c46847853f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 30 11:17:18 2019 -0400
ifdef out the species sources rather than check at runtime
Source/hydro/advection_util_nd.F90
commit 1a1b59f1b934432c4d8863cd2b21f6a20fa0a951
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 29 18:13:37 2019 -0400
no idea how this compiled before...
Source/reactions/react_util.F90
commit 470256eee3af12b699463b13fb7b62a3160cb22f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 29 18:04:07 2019 -0400
a simplified SDC 2-d test problem
Exec/reacting_tests/reacting_convergence/inputs.64.testsuite.simplified_sdc
commit 7fe3d77e52b966c5dfccba38557043b679f5bfba
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Oct 29 11:14:30 2019 -0400
code_comp fixes
Diagnostics/timestep_limiter/GNUmakefile
Diagnostics/timestep_limiter/limiter_util.F90
Diagnostics/timestep_limiter/main.cpp
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.F90
Exec/science/rotating_star/inputs_1d
Exec/science/rotating_star/inputs_2d
commit 02eccb92454d2f3c457ee1925a0665b774b73aa9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 28 14:10:58 2019 -0400
some fixes
Exec/hydro_tests/heating_verification/GNUmakefile
Exec/hydro_tests/heating_verification/ext_src_nd.F90
Exec/hydro_tests/heating_verification/inputs
Exec/hydro_tests/heating_verification/probin
commit 7ad21015384df64c6a0db5d3c4552827151fc64e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 28 13:41:45 2019 -0400
initial heating test problem
Exec/hydro_tests/heating_verification/GNUmakefile
Exec/hydro_tests/heating_verification/Make.package
Exec/hydro_tests/heating_verification/Prob_nd.F90
Exec/hydro_tests/heating_verification/_prob_params
Exec/hydro_tests/heating_verification/bc_ext_fill_nd.F90
Exec/hydro_tests/heating_verification/ext_src_nd.F90
Exec/hydro_tests/heating_verification/inputs
Exec/hydro_tests/heating_verification/probin
commit 44d5d9cfaf582570bfe7e0993415860f42b4ca49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 28 10:36:47 2019 -0400
remove ppm_reference_eigenvectors
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/code_comp/inputs_2d.sdc4
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/inputs_3d.sdc4
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm.gammae
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test4-helm
Exec/hydro_tests/double_bubble/inputs_2d.single
Exec/hydro_tests/double_bubble/inputs_2d.single.equal
Exec/hydro_tests/gresho_vortex/inputs.2d
Exec/hydro_tests/test_convect/inputs_2d
Exec/reacting_tests/nse_test/inputs
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.regrid
Exec/science/Detonation/inputs-det-x.simplified_sdc
Exec/science/Detonation/inputs-det-x.subch
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.big.template.strang
Exec/science/Detonation/nse_runs/inputs.template.sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/convective_flame/inputs.2d_good
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame/inputs.1d
Exec/science/flame/inputs.1d.aprox13
Exec/science/flame/inputs.1d.aprox13.boost
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.512
Exec/science/flame/inputs.1d.sdc.map
Exec/science/flame/inputs.1d.sdc.map.avg
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame_wave/inputs.boost_10_10
Exec/science/flame_wave/inputs.boost_10_10.3d
Exec/science/flame_wave/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs.boost_5_5
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/inputs.noboost.3d
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/old/inputs.boost_25_4
Exec/science/flame_wave/old/inputs/inputs_2d
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/science/flame_wave/old/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
Exec/science/flame_wave/scaling/inputs.scaling.3d
Exec/science/nova/inputs_2d
Exec/science/rotating_star/inputs_1d
Exec/science/rotating_star/inputs_2d
Exec/science/subchandra/inputs_2d
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit ab3d3aec731e7d95561c02edbb63877366869386
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 27 08:07:44 2019 -0400
switch to markdown
CHANGES.md
commit 1ca52baf76f64f73ada2c24fbf7dd318e6b032fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 27 08:01:01 2019 -0400
update changes
CHANGES
commit 91745a854655a160d601ae4406df4bfd97c82196
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 27 04:22:08 2019 -0400
fix radiation compilation
Source/hydro/riemann_nd.F90
Source/radiation/trace_ppm_rad_nd.F90
commit fd8ef1c8a38979b5a75c01e760b5bc933b7ef522
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 27 04:19:04 2019 -0400
update changes
CHANGES
commit 35cb84ac93041b7794745f41f0b65a0fe2b72cd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 26 15:00:03 2019 -0400
some PPM optimizations (#642)
This implements various optimizations in the PPM solver
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/trace_ppm.F90
commit a7e36125aa40c2bd2924900d7629f4c3f5d5d5b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 25 08:12:48 2019 -0700
Make evrard_collapse a GPU compatible problem
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
commit e7736e0340ef33f02fb820adc99f203df107ea4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 23 15:25:34 2019 -0400
some potential logos
Util/logo/README.md
Util/logo/castro_logo_PuBuGn.svg
Util/logo/castro_logo_RdPu.svg
Util/logo/castro_logo_YlGr.svg
Util/logo/castro_logo_hot.svg
Util/logo/castro_logo_hot_offset.svg
Util/logo/logo.py
commit bc3ecb3db1d5c51aad9c23bf4f488245b3c85dad
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Oct 21 16:53:00 2019 -0400
added diffusion
Diagnostics/timestep_limiter/Limiter_F.H
Diagnostics/timestep_limiter/limiter_util.F90
Diagnostics/timestep_limiter/main.cpp
commit 8721cd6f5052384b52aae9b461126b69f05addf7
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Oct 21 16:13:27 2019 -0400
script that processes a plotfile to find the location where the timestep was limited
Diagnostics/timestep_limiter/GNUmakefile
Diagnostics/timestep_limiter/Limiter_F.H
Diagnostics/timestep_limiter/Make.package
Diagnostics/timestep_limiter/limiter_util.F90
Diagnostics/timestep_limiter/main.cpp
Diagnostics/timestep_limiter/probin
commit 5b97a6bdab085d6cd4650f773899cf72cd683951
Merge: cd52fb207 00aabb90c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 17 11:25:05 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit cd52fb207863a9b73244cdef9c7fe3435d914462
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 17 11:24:37 2019 -0400
fix burning timestep limiter with simplified SDC
Source/driver/timestep.F90
commit 00aabb90cffeaf2fcffa22372080f3c3d60b3fc5
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Oct 17 11:22:20 2019 -0400
added 15m initial model
Exec/science/rotating_star/15m_500_sec.hse.6400
commit c641ba602a42768e5a7ea75af45715774aa549a0
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Oct 16 15:43:18 2019 -0400
added 1d spherical rotating star problem
Exec/science/rotating_star/GNUmakefile
Exec/science/rotating_star/inputs_1d
Exec/science/rotating_star/inputs_2d
Exec/science/rotating_star/probin
commit ed43d27f56df0a05cf27e834790920430d47697f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 14 16:51:06 2019 -0400
swtich to auto prob params
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/Make.package
Exec/hydro_tests/Vortices_LWAcoustics/Prob_nd.F90
Exec/hydro_tests/Vortices_LWAcoustics/_prob_params
Exec/hydro_tests/Vortices_LWAcoustics/probdata.F90
commit 68c966b0c568e24fa37f9b60ecf6ebf30b3e8484
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 14 16:41:51 2019 -0400
switch to auto prob params
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/test_convect/Make.package
Exec/hydro_tests/test_convect/Prob_nd.F90
Exec/hydro_tests/test_convect/_prob_params
Exec/hydro_tests/test_convect/probdata.F90
commit a0b5855e05118fddaddd1658ab57cf0db70e6ea3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 14 16:34:19 2019 -0400
not needed
Exec/hydro_tests/symmetry/probdata.F90
commit 442462647d895854efbd68ba48a2191885eecde4
Merge: ba0bf2eec dfbd4db25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 14 16:32:33 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ba0bf2eec6d7245b6e3732bd8fdd41a9574df8e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 14 16:32:19 2019 -0400
switch to auto prob params
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/symmetry/Make.package
Exec/hydro_tests/symmetry/Prob_nd.F90
Exec/hydro_tests/symmetry/_prob_params
commit dfbd4db25e1ad4e2928cd3546dc9c4dd1e032b02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 14 15:05:36 2019 -0400
add a routine to make a pretty plot
Exec/unit_tests/diffusion_test/analysis/slice_grid.py
commit d4be3fa3c9dc3f865357ba9cd5afe6c635b25b28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 15:37:49 2019 -0400
define USE_SIMPLIFIED_SDC to match the new microphysics
Exec/Make.Castro
commit 93a790ed3db3cfe619bfbd7ca59f7c2ba1503d98
Merge: f06175f75 4acc574e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 12:43:00 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit f06175f75448004801abc988310e416f77438277
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 12:42:49 2019 -0400
define SIMPLIFIED_SDC
Exec/Make.Castro
commit 4acc574e3cfad65d758eed2272e449bee726670d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 09:09:50 2019 -0700
BL_PROFILE in gravity source
Source/gravity/Castro_gravity.cpp
commit 80cdbdcef4ebff9374334e05053d40dc1aa6b303
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 10 20:45:22 2019 -0400
explicitly fill shk instead of setVal (#681)
Source/hydro/Castro_ctu_hydro.cpp
commit e1ff682103b8bcafb7820e944d4fd895e8278bde
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 10 17:59:16 2019 -0400
switch to auto prob params
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/rotating_torus/Make.package
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/_prob_params
Exec/hydro_tests/rotating_torus/probdata.F90
commit 79779b789abc2e4ffa082c19fa196cab491a8718
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 10 17:33:22 2019 -0400
use auto prob params
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/riemann_test_zone/Make.package
Exec/hydro_tests/riemann_test_zone/Prob_nd.F90
Exec/hydro_tests/riemann_test_zone/_prob_params
Exec/hydro_tests/riemann_test_zone/probdata.F90
commit e44cca5670345220480c4dfa037d1feded43830f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 10 17:32:56 2019 -0400
allow / in the regex and escape the `-`
Util/scripts/write_probdata.py
commit 786843d3cee38b789f99664c5ce60ee1d2943058
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 10 08:40:28 2019 -0400
add auto prob params
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/KH/Make.package
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/KH/_prob_params
Exec/hydro_tests/KH/probdata.F90
commit 040ce967b90d1533075607895b7f65383630e80f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 10 08:31:24 2019 -0400
switch to auto prob params
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/HCBubble/Make.package
Exec/hydro_tests/HCBubble/Prob_nd.F90
Exec/hydro_tests/HCBubble/_prob_params
Exec/hydro_tests/HCBubble/probdata.F90
commit 99c095b39eb103ecefa414519f0964aba1269399
Merge: 182009e90 7f622ea42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 21:03:38 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 182009e90136ea8fdf604c91411dbe896b60d7d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 21:03:15 2019 -0400
add a 1000Hz no boost script
Exec/science/flame_wave/inputs.noboost.1000Hz
Exec/science/flame_wave/job_scripts/chainbsub.sh
Exec/science/flame_wave/probin.noboost.1000Hz
commit ff204efecc513296b1d4d2fb40490b403a8e71b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 20:55:54 2019 -0400
switch to 10 cm
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/probin.noboost
commit 7f622ea42f605bfc9757536d3a0abdd6c8f5f825
Merge: 21b6025f8 35a47d016
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 11:45:53 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 21b6025f8af22b8b3075eef7fefce4662a8729ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 11:45:34 2019 -0400
comment out a renormalization for now -- this causes trouble for some problems
Source/driver/sdc_util.F90
commit 35a47d016dfc681cbaa98fc80594ae66a2fecd5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 09:00:55 2019 -0400
use auto prob params
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/Make.package
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/_prob_params
Exec/gravity_tests/uniform_cube_sphere/probdata.F90
commit cebfd392ef5ab89350d704e4658c4b8e6fe70f59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 08:33:40 2019 -0400
switch to auto prob params
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/Make.package
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/_prob_params
Exec/gravity_tests/hydrostatic_adjust/probdata.F90
commit 896fd9d1d424dda5ed6661220e667cfbf2550698
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 9 08:15:25 2019 -0400
use auto prob params
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/evrard_collapse/Make.package
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
Exec/gravity_tests/evrard_collapse/_prob_params
Exec/gravity_tests/evrard_collapse/probdata.F90
commit 9eb39ad567b7788966f596d0c0088bc75f5a8e5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 8 22:05:39 2019 -0400
switch to auto prob params
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/DustCollapse/Make.package
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/_prob_params
Exec/gravity_tests/DustCollapse/probdata.F90
commit 48f2596b93b580745c808f399313480b90daf818
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 8 10:24:47 2019 -0400
make it easier to read
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
commit ad62429bc53dc533c97a134ac87ae33f217842e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 7 20:02:39 2019 -0400
switch to auto prob params
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/gresho_vortex/Make.package
Exec/hydro_tests/gresho_vortex/Prob_nd.F90
Exec/hydro_tests/gresho_vortex/_prob_params
Exec/hydro_tests/gresho_vortex/probdata.F90
commit 675a1bdc8efabc45302d85bbbeff26b31f439f12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 7 19:52:30 2019 -0400
switch to auto prob params
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/Make.package
Exec/hydro_tests/gamma_law_bubble/Prob_nd.F90
Exec/hydro_tests/gamma_law_bubble/_prob_params
Exec/hydro_tests/gamma_law_bubble/probdata.F90
commit aa821e88777ce7defd03d4ce345a97981f27af3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 7 19:41:37 2019 -0400
switch to auto prob params
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Sod_stellar/Make.package
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/_prob_params
Exec/hydro_tests/Sod_stellar/probdata.F90
commit 8ea4eb34d9758d050c7d109f14c288783462f1ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 7 19:12:07 2019 -0400
update changes
CHANGES
commit acb3154bf33ebb590c160e9cc4cdbca11f130578
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 7 13:01:38 2019 -0400
Radau quadrature for SDC (#666)
This implements Radau quadrature for the SDC integration. Addresses #664
Exec/science/Detonation/inputs-det-x.sdc2
Exec/science/Detonation/sdc_tests/inputs.1d.sdc
Exec/science/Detonation/sdc_tests/make_plots.py
Exec/science/Detonation/sdc_tests/probin.sdc
Exec/science/Detonation/sdc_tests/setup_runs.sh
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_sdc.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_util.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
commit 08d1a379a4e58a082951e8511f957541011c50a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 7 09:09:17 2019 -0700
PPM simplification (#678)
Various simplifications of ppm_reconstruct and ppm_int_profile.
Source/hydro/Castro_mol_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 4c261f94238fb6f643b735b63001004cda696cd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 7 08:56:56 2019 -0400
fix dimension
Source/hydro/trace_ppm.F90
commit afe626c26a512651a3e5314914f62499694ae169
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 6 22:46:39 2019 -0700
Set USE_OMP = FALSE for the two tests where it was TRUE
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/science/wdmerger/GNUmakefile
commit cd3fff6595f63547dd55a3cca89abbb8712098bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 6 01:39:34 2019 -0400
Simplify flux limiter to have single limiter per interface
This resolves the issue in #646. We were getting non-deterministic behavior
because we were mixing and matching updates from the left and right side of
the interface. By only applying the limiter to whichever side of the interface
would go negative, and thus only obtaining a single theta for the limiter,
we sidestep the issue and also simplify the code.
Source/hydro/advection_util_nd.F90
commit 0e31aa78aca84eaef740c70439926801ee460c36
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 6 00:14:40 2019 -0400
Simplify conditionals
Source/hydro/advection_util_nd.F90
commit a0c61e928cd3db0778ffada6df077f992f9dfb90
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 5 19:04:10 2019 -0400
Deal with roundoff issues in the flux limiter
Source/hydro/advection_util_nd.F90
commit c07533370d3a30f9b84d7d860a19ef7c5dcc840d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 5 19:00:28 2019 -0400
Generalize hydro flux limiter for non-Cartesian coordinates
Source/hydro/advection_util_nd.F90
commit 193dd58d980e241e89015ba82965ddb37b68d6c7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 5 17:00:51 2019 -0400
Zero out LF flux for variables that don't advect
Source/hydro/advection_util_nd.F90
commit 0fdcd061c3f3a2ef76f1bd44c0f5c668c9290255
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 5 16:53:28 2019 -0400
Fix a comment
Source/hydro/advection_util_nd.F90
commit d9a607d889f33ba2b7e835366966dc1ec5b300e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 5 16:46:52 2019 -0400
Disable hydro flux limiter due to bug #646
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
commit 0d70eb3d9643edca27a0705b51aaad646693c765
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 3 09:00:12 2019 -0400
switch to auto prob params
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/hydro_tests/toy_convect/Make.package
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/_prob_params
Exec/hydro_tests/toy_convect/probdata.F90
commit 5801b882708ae9eb0046b73a65bba1197359701c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 3 08:46:49 2019 -0400
switch to auto prob params
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/oddeven/Make.package
Exec/hydro_tests/oddeven/Prob_nd.F90
Exec/hydro_tests/oddeven/_prob_params
Exec/hydro_tests/oddeven/probdata.F90
commit d5a00d5fcd9fc23783ce19a2879720ee2a7fd6dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 3 08:30:56 2019 -0400
switch to auto prob params
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/RT/Make.package
Exec/hydro_tests/RT/Prob_nd.F90
Exec/hydro_tests/RT/_prob_params
Exec/hydro_tests/RT/probdata.F90
commit 71bc598065f18c2b3c2cf992ae6907716d53b122
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 1 09:33:01 2019 -0400
update release
CHANGES
commit d8dc9e81cad01957d13b4ce60dd7a16f76b4840b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 1 09:30:05 2019 -0400
update changes
CHANGES
commit bb0b1586cb5d72e46798a7c5b4fa5d302da81bb0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 30 23:44:03 2019 -0400
Fix some missing module use statements
Source/scf/scf_relaxation.F90
commit b7535f73d618d1dd8a86148b105783c84cce8978
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 30 18:06:54 2019 -0700
Disable CUDA compile verbosity
Exec/Make.Castro
commit 5c2a015d99585c9763fb4276e17d1cee5ddda9f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 30 16:40:08 2019 -0700
Add GPU information to job_info
Closes #675
Source/driver/Castro_io.cpp
commit ab273c5f3721d8fbb889896e69976f9794bf4651
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Sep 30 17:03:16 2019 -0400
updated parse_castro_params.py so that it generates reals with _rt (instead of x.xdx)
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
commit b9a0fc12c2bfb765ad1cd199aa8aaf6852dfa3a6
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Sep 30 16:33:40 2019 -0400
added _rt to some constants, initialized aux for some eos calls
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/gravity/Gravity_2d.f90
Source/hydro/fourth_order.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/reactions/React_nd.F90
Source/scf/scf_relaxation.F90
Source/sources/thermo_nd.F90
Util/code_checker/fortran_checker.py
commit 752958a69e784f1f1dcde21db5e49e8821a09c94
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Sep 30 15:43:26 2019 -0400
fixed a couple of bugs in regex
Util/code_checker/fortran_checker.py
commit 014447e73bbfe29fd507d87bb0c86b1e689c75db
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Sep 30 15:23:53 2019 -0400
added tests for eos and state vector
Util/code_checker/conftest.py
Util/code_checker/fortran_checker.py
commit 06ef5d19ceadf01324727c88eb2aa838a102ad7a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Sep 30 14:01:47 2019 -0400
started work on a code checker that checks source files for simple errors
Util/code_checker/conftest.py
Util/code_checker/fortran_checker.py
commit efda261cd0c870bccd11f1c620e455414138642f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 20:31:16 2019 -0400
add readme
Exec/science/flame_wave/job_scripts/summit/README.md
commit e3f9adee7e1d42f58c5b1323fb42cb76e43e9a36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 20:30:26 2019 -0400
add notes
Exec/science/flame_wave/job_scripts/cori/README.md
commit ea76269b44825c79c5265648dbb73246049c78c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 20:29:04 2019 -0400
transfer
Exec/science/flame_wave/job_scripts/cori/cori.xfer.slurm
commit 77e3bd140fe07168fa2e8d791859bac0003c35a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 20:27:46 2019 -0400
move
Exec/science/flame_wave/job_scripts/cori/cori_haswell.MPI.slurm
Exec/science/flame_wave/job_scripts/cori/edison.xfer.slurm
Exec/science/flame_wave/job_scripts/edison.MPI.slurm
Exec/science/flame_wave/job_scripts/summit/process.xrb
Exec/science/flame_wave/job_scripts/summit/summit_gpu.submit
commit 5892905638ce70fff7558f6cc31b41ff689ee1a8
Merge: 5d1ba6b46 fa03871f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 19:10:46 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 5d1ba6b469d638fa68f36dd24d595997d21bc3af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 19:10:32 2019 -0400
these are the version from summit
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/probin.noboost
commit fa03871f571beab127312eb60a89f5d251a23f91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:49:46 2019 -0400
update to python3
sphinx_docs/rp.py
commit 69310122cd43529cff49fa95b5d408357e619582
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 27 19:32:01 2019 -0400
switch to python3 and argparse and lots of cleaning
Microphysics/networks/general_null/write_network.py
commit 3d8bdd5c0d3e347aa51302b2907bac8b7a7bd043
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 27 18:54:50 2019 -0400
some linting
Source/driver/set_variables.py
commit bfb4a32f66b91eb728b4235685ea4673b01704eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 27 18:51:21 2019 -0400
switch to python3 + use set comprehensions
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
commit 959852eb9806e99ee55d9e789d11086251ffee7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 27 17:32:55 2019 -0400
no longer needed
Source/driver/sdc_plan.txt
commit 6356ea67afe883d995defbe5b81ada337ddc5b7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 27 17:15:47 2019 -0400
add some more recent changes
CHANGES
commit 4dc809334dc74e0a184a99039c49490d3d7bb608
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 26 22:36:38 2019 -0400
Add I/O time in seconds to job_info
Closes #365
Source/driver/Castro.H
Source/driver/Castro_io.cpp
commit e05c92ec88d787b3b39edf290581ca8a57f7a4d1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 26 11:32:42 2019 -0700
Remove an unnecessary print
Source/diffusion/Castro_diffusion.cpp
commit 7e3f06b6d5f9ea37a8c89e6821d2caa7367145ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 26 13:43:02 2019 -0400
generalize refinement to 3-d
Exec/science/flame_wave/problem_tagging_nd.F90
commit 627ca8df62c7e5f2990450d3715e9d07290ea6d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 26 09:52:48 2019 -0400
Add timings for individual source terms for v > 1
Source/diffusion/Castro_diffusion.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit bcbc8017f5d24b3646e9c208efa9cc6ca6d0015a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 21:41:53 2019 -0400
add some protection
Source/scf/scf_relax_F.H
commit d04f70db9b6de53631bdaba8e0d971f24a4c8a43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 20:10:53 2019 -0400
switch to auto prob params
Exec/hydro_tests/double_mach_reflection/GNUmakefile
Exec/hydro_tests/double_mach_reflection/Make.package
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/_prob_params
Exec/hydro_tests/double_mach_reflection/probdata.F90
commit a1db4fd640188448d332d2ab4881f95c8dbdd006
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 19:42:28 2019 -0400
switch to auto prob params
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/double_bubble/Make.package
Exec/hydro_tests/double_bubble/Prob_nd.F90
Exec/hydro_tests/double_bubble/_prob_params
Exec/hydro_tests/double_bubble/probdata.F90
commit 2e58b185732903e2c8ade64566c6d1226fa703e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 19:04:29 2019 -0400
switch to the auto prob params
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod/Make.package
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod/_prob_params
Exec/hydro_tests/Sod/probdata.F90
commit e82a0a0947abcec0b0c4f1d859b3eb7cc850d3bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 18:18:05 2019 -0400
switch to auto prob params
Exec/science/subchandra/GNUmakefile
Exec/science/subchandra/Make.package
Exec/science/subchandra/Prob_nd.F90
Exec/science/subchandra/_prob_params
Exec/science/subchandra/probdata.F90
commit d008747ca28a05b37c9389d29c2f8aa2b9db7b8a
Merge: b17f62d54 0c4395489
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 16:01:09 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit b17f62d54feb983acb34cd7647e6cca664c63baf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 16:00:05 2019 -0400
add Summit GPU script
Exec/science/flame_wave/job_scripts/summit_gpu.submit
commit 0c4395489a6f1b93ed8c4badc15552d5f5402707
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 15:30:53 2019 -0400
swtich tagging from integer(1) to c_int8_t (#674)
switch integer(1) -> c_int8_t
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Exec/hydro_tests/toy_convect/problem_tagging_nd.F90
Exec/science/convective_flame/problem_tagging_nd.F90
Exec/science/flame_wave/problem_tagging_nd.F90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/xrb_mixed/problem_tagging_nd.F90
Source/driver/Tagging_nd.F90
Source/problems/problem_tagging_nd.F90
commit f035160d467e090551e66e46891987694dd78956
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 15:29:02 2019 -0400
fix compilation
Exec/radiation_tests/RadBreakout/Prob_nd.F90
commit fcd38fc2429c7a990567f3b0cc7acaa01205af66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 15:21:36 2019 -0400
fix compilation
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
commit 0628e7902a85de8cf37f3aef3b330e4ab59c281c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 11:05:43 2019 -0400
remove prints
Util/scripts/write_probdata.py
commit ff5bced79e62a9d13fffd79cdab2822f2e965639
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 24 12:43:59 2019 -0400
update changes
CHANGES
commit f3faa0791706549502e0abb532b06a9abe96fde5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 24 12:37:39 2019 -0400
gpu compatible problems (#634)
This gets rid of the use of xlo in the Prob_nd.F90 files. This is a key step in the change to the GPU problem interface. This also converts a few problems over to the new auto prob_params
system.
Together these are enough to show how to convert a problem to GPU friendly.
Addresses #622
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/StarGrav/Make.package
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/gravity_tests/StarGrav/_prob_params
Exec/gravity_tests/StarGrav/probdata.F90
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Make.package
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/_prob_params
Exec/gravity_tests/code_comp/probdata.F90
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/hydro_tests/HCBubble/Prob_nd.F90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse/Make.package
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/_prob_params
Exec/hydro_tests/acoustic_pulse/probdata.F90
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/Make.package
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/_prob_params
Exec/hydro_tests/acoustic_pulse_general/probdata.F90
Exec/hydro_tests/oddeven/Prob_nd.F90
Exec/radiation_tests/RadBreakout/Prob_nd.F90
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/scf_tests/single_star/Prob_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/nova/Prob_nd.F90
Exec/science/rotating_star/Prob_nd.F90
Exec/science/subchandra/Prob_nd.F90
Exec/science/xrb_mixed/Prob_nd.F90
commit 0545a25d9fd5edeecde162eaf185e45f829db299
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 24 12:35:06 2019 -0400
automatically create the probin parameters and namelist (#673)
The automates the creation of the probdata variables, the namelist for reading them, setting them as managed for CUDA, and adds the ability to output the values to a file (like job_info)
This feature is opt-in. You need to set USE_PROB_PARAMS in your GNUmakefile and then
define the problem parameters in a file _prob_params in the problem directory.
For problems that opt-in, the values of the problem parameters are now output into the job_info file.
closes #234
closed #619
.gitignore
Exec/Make.Castro
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sedov/Make.package
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sedov/_prob_params
Exec/hydro_tests/Sedov/probdata.F90
Exec/science/flame_wave/GNUmakefile
Exec/science/flame_wave/Make.package
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/_prob_params
Exec/science/flame_wave/probdata.F90
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Util/scripts/prob_params.template
Util/scripts/write_probdata.py
commit f726a4ee6a876ca4ce5ace12ab201ac68fe91a50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 23 18:51:39 2019 -0400
add PR #s
CHANGES
commit 9a07076ddb486f206f53c78c11267df3cea9509e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 23 14:19:46 2019 -0400
fix merge issue
Source/driver/Castro_setup.cpp
commit eeaa8f13e4d162062c5f775742a9040bc9679cb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 23 14:04:30 2019 -0400
preserve the numerical meaning of the time integration in the enum
Source/driver/Castro.H
commit 82f51a318d2afd93ad6954b4475d96fd72389c77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 23 11:34:59 2019 -0400
some SDC improvements (#654)
Implements reflecting BCs for PLM reconstruction with SDC (issue #652)
Implements the density and temperature limits to burning for SDC (issue #598)
Fixes the weighting of the flux registers for SDC (#658)
Implements a well-balanced scheme for 2nd order PLM reconstruction (#294)
Also adapts the bubble_convergence problem to work as a test for the well-balanced method and can now do second-order or fourth order initial model generation.
Changes the meaning of the plm_iorder flag to now do 1 = piecewise constant, 2 = 2nd order MC limiter, and >= 3 for 4th order MC limiter
Adds support for HSE boundary conditions in +X and +Y
CHANGES
Exec/hydro_tests/acoustic_pulse/inputs.2d.64.sdc_ml
Exec/hydro_tests/acoustic_pulse/probin
Exec/reacting_tests/bubble_convergence/analysis/hse.gp
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/inputs_1d.well_balance
Exec/reacting_tests/bubble_convergence/inputs_2d.well_balance
Exec/science/flame_wave/inputs.boost_10_10.sdc
Exec/science/flame_wave/inputs.boost_10_10.sdc.small
Exec/science/flame_wave/probin.boost_10_10.sdc
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_util.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/slope_nd.F90
Source/problems/bc_ext_fill_nd.F90
Source/reactions/React_nd.F90
Source/reactions/react_util.F90
commit ea7da931a3a9bdea799231e1fc9760bd825472ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 23 09:14:32 2019 -0400
Remove MethodOfLines from time integration methods
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
Source/driver/timestep.F90
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_thermo.cpp
commit f96163ee3ebc9aa0d5e021657e0ac9bd8c212450
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 16:16:17 2019 -0400
get rid of all the remaining sphinx errors
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/Particles.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/rad.rst.old
sphinx_docs/source/refs.bib
sphinx_docs/source/rotation.rst
commit 7819f376cd4fd46bf52a88ead10c2d735ce39321
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 15:55:01 2019 -0400
up the font size
sphinx_docs/source/_static/theme_overrides.css
commit afa54717b0ed9b9e10054f979a1f6811ff77b3dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 15:40:28 2019 -0400
remove some padding
sphinx_docs/source/_static/theme_overrides.css
commit 40fd029c36eb97c811724f1d8faa9d8ef3a912f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 15:23:52 2019 -0400
remove the border and background from parameters in the html
sphinx_docs/source/_static/theme_overrides.css
commit 65ee807ba96644b4bd5bd89f2e5403607dfa13a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 14:31:27 2019 -0400
lots more reference fixing
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/Introduction.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/getting_started.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/radiation.rst
sphinx_docs/source/software.rst
commit c5eb5f3639e597161c50cd1fbf37f3fe21ebd662
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 14:25:05 2019 -0400
formatting
Diagnostics/Sedov/README.md
commit b923490b9e3c78e6a8c8b485aae3b55b99befaec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 13:53:24 2019 -0400
a bunch of fixes to reference + now let us ref tables and figs
sphinx_docs/source/conf.py
sphinx_docs/source/inputs.rst
sphinx_docs/source/io.rst
sphinx_docs/source/software.rst
commit b3a4c72a0ceba3de19e69418d7c0eb62b1c46bcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 22:40:00 2019 -0400
add SDC chapter
sphinx_docs/source/index.rst
sphinx_docs/source/sdc.rst
commit 1eaed1825e9b7336932b96891ab02230afa0e97c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 22:23:45 2019 -0400
another ref
sphinx_docs/source/FlowChart.rst
commit 4aa12effbf569eaaaae5454e86bf6ac9135b15a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 22:22:08 2019 -0400
some reference fixes
sphinx_docs/source/AMR.rst
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/diffusion.rst
sphinx_docs/source/gpu_porting.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/radiation.rst
sphinx_docs/source/rotation.rst
sphinx_docs/source/sponge.rst
commit c109527bbf270076b528764dc1c1e2ec98543580
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 21:52:41 2019 -0400
merge some loops
Source/driver/Castro_advance_sdc.cpp
commit 9e2f8c0db4aeef357e749696c11cbf71bd0dc1c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 20:53:52 2019 -0400
finish documenting the SDC flow
sphinx_docs/source/FlowChart.rst
commit 49d1d8fb0dff654a9d50cc56c76604ae36a7136b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 18:44:01 2019 -0400
a bit more flowcharting for SDC
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/mathsymbols.tex
commit 5d5b6de1d43eb2c9a3a5169022817d22d7f51402
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 17:50:01 2019 -0400
start working on SDC docs
sphinx_docs/source/FlowChart.rst
commit ad3469955ba7055c9655069b386fbbda0d682a71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 15:21:09 2019 -0400
remove test_react -- the reactions_test_driver replaces it
Exec/unit_tests/test_react/GNUmakefile
Exec/unit_tests/test_react/_parameters
Exec/unit_tests/test_react/inputs
Exec/unit_tests/test_react/main.cpp
Exec/unit_tests/test_react/probin
Exec/unit_tests/test_react/testburn.f90
commit b5f94bb97af1bed4fe2fa179bbc1a907389c9566
Merge: 358a6393b fd71addab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 15:21:45 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit fd71addabf9ad8921597ffe75b659c96ec8b5ad9
Merge: d953c0639 391a5f245
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 20 12:50:50 2019 -0400
Merge branch 'master' into development
commit 391a5f2459f98278f3df6080165e5fd63bbee8d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 20 12:21:57 2019 -0400
add AMReX badge
README.md
commit 358a6393bd810785d2b3271db2889baf1947f6f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 19 10:48:41 2019 -0400
update sdc
Exec/science/Detonation/sdc_tests/make_plots.py
commit d953c063943ee241b47b997f3ee2804ec5dbf5a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 17 17:00:50 2019 -0400
a script to make the plots
Exec/science/Detonation/sdc_tests/make_plots.py
commit 972c4a942f658ac2acc72dd7cb0a91c14d9d5d89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 17:32:58 2019 -0400
fix number of steps
Exec/science/Detonation/sdc_tests/inputs.1d.sdc
commit 76e44a682c57e1e390bce24a1e1ff8aaaff675d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 17:24:06 2019 -0400
remove mpi
Exec/science/Detonation/sdc_tests/setup_runs.sh
commit 5d26c4da4aaae89b5b9eaf4205e16a4ae0eff38b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 17:21:59 2019 -0400
fix names
Exec/science/Detonation/sdc_tests/setup_runs.sh
commit 7bc22b1152912e541ca833f2cb33ff23d139b85b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 17:18:29 2019 -0400
add a script to automate comparisons
Exec/science/Detonation/sdc_tests/inputs.1d.sdc
Exec/science/Detonation/sdc_tests/probin.sdc
Exec/science/Detonation/sdc_tests/setup_runs.sh
commit b784669b49e055eef24dc2ff7a35ff7707b1bfbd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 14:19:24 2019 -0400
fix index error
Exec/gravity_tests/code_comp/model_util.F90
commit 05cf2f0b8ef42f16f6fbaddad66a42854015375a
Merge: 2cd10da3f 0a0b24526
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 14:05:44 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2cd10da3f2065ab07220f99594a0c394fb10a40a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 14:05:29 2019 -0400
updated version of the comparison with the different quadrature types
Exec/science/Detonation/analysis/compare_plot.py
commit 0a0b24526c3659225fea6543f4b93abeac21c0eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 16 13:44:55 2019 -0400
move the code_comp initial model to probinit (#671)
This moves the generation of the initial model for code_comp to probinit, similar to how we do other problems. It is now managed by model_parser. The downside is that we need to specify the number of zones to use for the model generation, alteast until we deal with #669
* separate the initial model into a subroutine to make it easier to play with
* switch to model_parser to manage the model
* change coords
* fix allocates
* some conflicts
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_2d.sdc4
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/probdata.F90
commit bdd4c9189a4fba623fb1c8c80bd6ede145d0e383
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 15 18:22:24 2019 -0400
these are not used
Exec/reacting_tests/bubble_convergence/bc_ext_fill_nd.F90
Exec/reacting_tests/bubble_convergence/source_fill.F90
commit 778c0df184db0e90358046adaee6c558793db1f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 13 10:11:32 2019 -0400
Purge remaining references to mol_order
Exec/reacting_tests/bubble_convergence/bc_ext_fill_nd.F90
Exec/reacting_tests/bubble_convergence/source_fill.F90
Exec/unit_tests/diffusion_test/Prob.cpp
commit a8f2c3d0e2e458778ac40395e2fb06c2a0ce575a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 19:08:50 2019 -0400
add README.md
Exec/hydro_tests/Sod_stellar/README.md
commit 3cc87ac40f9db0c14fa845253bab83ce99f6ffad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 15:40:20 2019 -0400
remove MOL references
sphinx_docs/source/FlowChart.rst
commit 164111c48abd2a18130363f04188711b3d4a024c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 15:36:20 2019 -0400
update changes
CHANGES
commit 1a2ac12e9f2deef15f706474bf12f0950fc19763
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 15:29:04 2019 -0400
remove the RK-based MOL time integration method (#657)
it is not tested, still uses Strang, and doesn't have an easy path to AMR
SDC is the better option.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/Castro_mol_hydro.cpp
commit da3a73d603cafd74971e07480a8d049083a325a4
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 12:57:37 2019 -0400
made integrate_model GPU friendly
Exec/gravity_tests/code_comp/model_util.F90
commit 2153fa36b83f5d8c444cb9c2b7d16989fd3a4190
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 12:27:00 2019 -0400
prescribe_grav_nd f90-> F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.F90
Source/gravity/Make.package
Source/gravity/prescribe_grav_nd.F90
commit 626d3e675fc92c0bee5198e1bf89749fee6ef841
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 12:11:52 2019 -0400
made grav_zone compilable on the GPU
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.f90
commit 16d4a901d24788ec8a106db8b49541aa80e876a4
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 11:47:20 2019 -0400
add more !gpus to code_comp problem setup
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
commit 4efc39f6dc1cb418a4696a8f10a8471ef5563d8d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 11:34:41 2019 -0400
add !gpu to ca_initdata
Exec/gravity_tests/code_comp/Prob_nd.F90
commit 4308d77c291708d737593fa5730175a8a8ce3c11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 11:21:39 2019 -0400
switch interface to GPU compatible
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
commit 3c5d9c425bc3671db1b2c02ba80b78db6ad28bdf
Merge: 1f83d046d 002950482
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 11:15:55 2019 -0400
fixed merge conflicts
commit 1f83d046dc39bb252c090ee3cc498ee006482d76
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Sep 12 11:15:02 2019 -0400
made probdata variables managed so available on the GPU in code_comp problem
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/probdata.F90
commit 002950482ce4f329be8c6782b21068822f6b6a51
Merge: 2dbf313eb f4e43b304
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 07:50:56 2019 -0400
Merge branch 'master' into development
commit f4e43b30490375b5c1dd59f69ea4ba82ecccb3de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 12 07:45:07 2019 -0400
Code comp model (#668)
This separates the initial model generation into a subroutine
* use single gamma EoS for the initial data
* add a readme
* Code comp new (#667)
For 4th order runs, this constructs the code_comp initial model to 4th order accuracy
* fix dimensioning into grav array
* adjust plotfile output frequency
* added ! to code_comp files
* add an option to disable the perturbation
* set the default for do_pert
* fix the EOS call
add some comments
* separate the initial model into a subroutine to make it easier to play with
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/Problem_Derive.H
Exec/gravity_tests/code_comp/Problem_Derive.cpp
Exec/gravity_tests/code_comp/Problem_Derive_F.H
Exec/gravity_tests/code_comp/Problem_Derives.H
Exec/gravity_tests/code_comp/README.md
Exec/gravity_tests/code_comp/ext_src_nd.F90
Exec/gravity_tests/code_comp/inputs_2d.sdc4
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/inputs_3d.sdc4
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.f90
Exec/gravity_tests/code_comp/probdata.F90
Exec/gravity_tests/code_comp/probin
Exec/gravity_tests/code_comp/problem_derive_nd.F90
commit 2dbf313eb588fa47fee023077d87716a8486cc54
Merge: eebf0eb07 44608bb94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 11 17:32:57 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 44608bb94c69ef7cc721568794b7bbdf51be2c16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 11 14:14:41 2019 -0400
fix the EOS call
add some comments
Exec/gravity_tests/code_comp/model_util.F90
commit 5deddae70664b781724bcc0d1e15af26506d20ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 11 13:43:45 2019 -0400
set the default for do_pert
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_2d.sdc4
commit 85c97be06bfa2fcbb0e2b269d4e462267d8b4cd6
Merge: 22efbb452 531cad87c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 11 13:40:53 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 22efbb4521f1cb918ea03d44d2010a56eff039ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 11 13:40:39 2019 -0400
add an option to disable the perturbation
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/probdata.F90
commit eebf0eb079f1b6237b2b1d06de4ca04794685411
Merge: fe0b79257 531cad87c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 11 10:26:05 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 531cad87c57b0a381cb98d8b12b35a23f6d60280
Merge: 88cf8a449 0d13f48c8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Sep 10 16:48:37 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 88cf8a44986a70019e57b2782ddadb8512193505
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Sep 10 16:48:28 2019 -0400
added ! to code_comp files
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/Problem_Derive.H
Exec/gravity_tests/code_comp/Problem_Derive.cpp
Exec/gravity_tests/code_comp/Problem_Derive_F.H
Exec/gravity_tests/code_comp/Problem_Derives.H
Exec/gravity_tests/code_comp/ext_src_nd.F90
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/probin
Exec/gravity_tests/code_comp/problem_derive_nd.F90
commit 0d13f48c840952e18da2411181d332c1ed72b8a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 10 10:48:54 2019 -0400
adjust plotfile output frequency
Exec/gravity_tests/code_comp/inputs_2d.sdc4
Exec/gravity_tests/code_comp/inputs_3d.sdc4
commit 213551215cc2cf57ef04ee09363e72912fe4b3ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 10 10:30:14 2019 -0400
fix dimensioning into grav array
Exec/gravity_tests/code_comp/prescribe_grav_nd.f90
commit b2c2a3990994807fe9be40c68b8017952d245a0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 10 10:28:25 2019 -0400
Code comp new (#667)
For 4th order runs, this constructs the code_comp initial model to 4th order accuracy
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_2d.sdc4
commit aee8296bac01cd0cae079352d6d8404febdb4f0b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 10 08:11:21 2019 -0400
add a readme
Exec/gravity_tests/code_comp/README.md
commit fe0b792572008db112c05d1cfd8e3c9418747ad2
Merge: 47f34c451 f3923199a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 3 15:36:30 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 47f34c451a69ddba23d9c7e8af938ff744db0240
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 3 15:29:47 2019 -0400
add the Radau quadrature -- not ready for use yet
Source/driver/Castro_setup.cpp
commit f3923199a429b0bcf6a6214be4d91f09a65dc714
Merge: f602888c8 72733c8da
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Sep 3 09:31:56 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit f602888c8902fc84a73e9ba45eddb865a500e3b5
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Sep 3 09:31:49 2019 -0400
use single gamma EoS for the initial data
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/probdata.F90
Exec/gravity_tests/code_comp/probin
commit 72733c8da9f7303c74584092b9df467121fdac2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 3 03:02:56 2019 -0400
update changes
CHANGES
commit e80400fb2cba9e53d1f8cda6572777fe3eaf1377
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 31 14:49:35 2019 -0400
fix compilation
Source/driver/Castro_advance.cpp
commit 719d5e9c2217413c1459b62682c80d07183e4137
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 31 13:36:05 2019 -0400
fix the new source fill patch
Source/driver/Castro_advance_sdc.cpp
commit 8a8f89ca23a32c07ff0639a78e29447d7c98ac43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 31 12:51:10 2019 -0400
update changes
CHANGES
commit 6a4195955dfda8069bc6a281f7b079afd7ace8b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 30 18:04:56 2019 -0400
store the Reactions_Type stuff a proper cell-averages to 4th order (#647)
Source/driver/Castro_advance.cpp
Source/driver/Castro_sdc.cpp
commit 24f0eb1cd59b9f6c8ff997deea7908b26ec66eff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 30 18:01:53 2019 -0400
some SDC optimizations for the last iteration (#662)
Source/driver/Castro_advance_sdc.cpp
commit 8daf94cd8feb0ccafc215a150c5a74e8eb96df8e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Aug 30 13:47:47 2019 -0400
use RK2 to integrate HSE in code comp problem
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/probin
commit 8177d1cec6ac8a8b5d91eb736b7f7f932db02f54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 29 09:16:44 2019 -0400
make the gravity its own function (#663)
This removes the redundant computations of g
* make the gravity its own function
* add a separate function for setting the species
Exec/gravity_tests/code_comp/Make.package
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/model_util.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.f90
commit ec7c35a42b3c1a9550cf4df6ca8422ed0227309e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 15:32:46 2019 -0400
use average(rho*g) to calculate HSE for code_comp problem
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_3d
commit dc639294dda0b9a5a2456a8ae7da564b4de57a0a
Merge: 3bc361627 80d1eda17
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 14:27:33 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 3bc3616273c0ced650029b0fcab564b8eafe156f
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 14:27:31 2019 -0400
fixed calculation of fg in code_comp problem
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/inputs_3d.sdc4
commit 80d1eda17fc95188b7e22d89f2457386cea0e313
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 28 13:18:00 2019 -0400
change output names
Exec/gravity_tests/code_comp/inputs_3d.sdc4
commit 86dea442d2bbf0df3a2d563c9b470c297f9c3ce0
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 12:53:03 2019 -0400
got rid of model input file
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/probdata.F90
Exec/gravity_tests/code_comp/probin
commit e1273f3aa9d3d8bf9ff34ee1cf4b917ff36151d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 28 12:41:55 2019 -0400
SDC version
Exec/gravity_tests/code_comp/inputs_3d.sdc4
commit 65462d832f94758149b965955964cad6e98c61db
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 12:22:58 2019 -0400
removed hcore.dat
Exec/gravity_tests/code_comp/hcore.dat
commit 6c423486e6fd11e0ccabff162fcf266e0f5f99a4
Merge: 50affd6e1 656ddb6a9
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 12:15:12 2019 -0400
Merge branch 'code_comp' into development
commit 50affd6e1d2fcd167226f81e624c5b374bf37835
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 28 11:51:14 2019 -0400
update for C++ Plotfile utils
Exec/hydro_tests/Sod/testsuite_analysis/sod.py
commit 2b757c93f9919a9f3ab173a328354d73a283f3c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 28 11:49:47 2019 -0400
update to C++ Plotfile util routines
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test1-helm.py
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test2-helm.py
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test3-helm.py
commit 656ddb6a90b0c6a00bfd9d444275506c666fff33
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Aug 28 10:22:32 2019 -0400
added species
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/simple.net
commit d1dae561738f7374de0eba684f2b47d5ddc61bd2
Merge: 44a6742dc d9483b61c
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Aug 27 16:59:20 2019 -0400
Merge branch 'code_comp' of github.com:AMReX-Astro/Castro into code_comp
commit 44a6742dc28010c092b0fc6b9e2160943d69cd9a
Merge: 493174507 f591e2cbc
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Aug 27 16:59:04 2019 -0400
new code comparison problem
commit f591e2cbcb13152e861e226c0a1ff8fb4734f5d8
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Tue Aug 27 08:41:30 2019 -0400
Updates to flame wave analysis scripts (#661)
* Updates to flame wave analysis scripts
Completely rewrote the front tracking script. The output and methods are now
configurable through command line arguments, and it should have a much
smaller memory footprint. The script for processing the data file was
updated accordingly.
Also updated the plot generator script with the bug fixes / new
additions that I've made over the past year or so.
* Added README, updated image animators
Added a faster image animator script, and shifted the old one into
mpl_image_animator.py. Also added a README.
Exec/science/flame_wave/analysis/README.md
Exec/science/flame_wave/analysis/flame_speed.py
Exec/science/flame_wave/analysis/front_tracker.py
Exec/science/flame_wave/analysis/image_animator.py
Exec/science/flame_wave/analysis/mpl_image_animator.py
Exec/science/flame_wave/analysis/plot_generator.py
commit 4c60747407d836d9bf100147104e033cffff935d
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Aug 26 17:47:02 2019 -0400
Add --describe command line option (#660)
Source/driver/Castro.H
Source/driver/Castro_io.cpp
Source/driver/main.cpp
sphinx_docs/source/faq.rst
commit 557dfde12ddc315c326c2f2b6c2b1ee223ec80e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 21 11:25:03 2019 -0400
extend this to work in 1-d too
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit 6495a0d12005b3da98a44607c636c69c33bfbbb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 19 20:02:33 2019 -0400
use abs() for velerror tagging (#655)
CHANGES
Source/driver/Tagging_nd.F90
commit 975ebfe9238f3ffd255df8be14e1e0411d6aba30
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 19 10:19:14 2019 -0400
add an SDC inputs
Exec/science/flame_wave/inputs.boost_10_10.sdc
commit c8ab8488997b6bcd3832882659ffb41c65277fef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 17 14:13:17 2019 -0400
add overview script
Exec/science/flame_wave/analysis/overview.py
commit efa48b6028462aef819547fd3f81b909f7988fd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 14 21:21:40 2019 -0400
updated version
Exec/science/flame_wave/analysis/time_series.py
commit 80e735cb593c2b70768cf597c690954d2599b1aa
Merge: 2e2172f1b 66c41145d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 14 20:34:32 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 2e2172f1b1032314310391077af373b61b844685
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 14 20:34:15 2019 -0400
add a time series plot
Exec/science/flame_wave/analysis/time_series.py
commit 66c41145d2f51e2cb47677cf342cf194041a0927
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 11 21:04:53 2019 -0700
Sync up diagnostic output
Source/hydro/Castro_ctu_hydro.cpp
commit 982b992aa709bb050aaa6b8f83f9c3cdd77286af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 8 11:21:12 2019 -0400
fix docs directory location
README.md
commit 56e94ffcc24a75479b5d8f35b0d41fe89e081ca1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 20:03:02 2019 -0400
fix 2-d power law stuff
I can't reproduce the old #s -- I suspect I ran without powerlaw
Exec/unit_tests/diffusion_test/README.md
commit 40faeb120e41e5d05e93b062853831fcea090ea5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 19:34:19 2019 -0400
use MPI
Exec/unit_tests/diffusion_test/README.md
commit 612014e023a9fb7ec079f686dc7bee0a5c24f9c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 15:47:30 2019 -0400
add notes on HSE convergence
Exec/reacting_tests/bubble_convergence/README.md
commit e863dae52e04b6d8e68bce122dccd7860b0f5ca5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 15:07:40 2019 -0400
add latex pretty stuff
Exec/unit_tests/diffusion_test/analysis/create_pretty_tables.py
commit 1c855d63375f5d477d7fb8a43f5573c8678bb2ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 15:07:05 2019 -0400
add convergence script
Exec/reacting_tests/bubble_convergence/README.md
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
commit ae88e199c6bf1d23207d77bf890d0e7a18fe8e9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 15:06:03 2019 -0400
pure HSE testing
Exec/reacting_tests/bubble_convergence/README.md
Exec/reacting_tests/bubble_convergence/converge_test_sdc4_nopert.sh
Exec/reacting_tests/bubble_convergence/probin.128.nopert
Exec/reacting_tests/bubble_convergence/probin.256.nopert
Exec/reacting_tests/bubble_convergence/probin.64.nopert
commit 58607d113498bc8be0195c79a1a4262eee30edd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 14:16:47 2019 -0400
don't do slipwall
Exec/hydro_tests/Sod_stellar/compare_methods.sh
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
commit 2ec266418acb2c58a88f30f1332052c245d403f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:56:30 2019 -0400
update style
Exec/reacting_tests/bubble_convergence/analysis/slice_multi.py
commit 56ca91281da399e4670f9ca0846fd0159537c698
Merge: 94e21a642 1e1d47c9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:31:54 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 94e21a642f8a3be2cb5cb91021cb76103b5e9579
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:31:46 2019 -0400
add plot tool
Exec/reacting_tests/bubble_convergence/analysis/slice_multi.py
commit 1e1d47c9f017ea6eb95575f5504e5d6f10300b5c
Merge: 165be45cd 34c66c217
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:30:58 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 165be45cd15784ddb25b493d327397f9a141cb2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:30:47 2019 -0400
add plot tools
Exec/hydro_tests/acoustic_pulse_general/analysis/slice_multi.py
Exec/reacting_tests/reacting_convergence/analysis/slice_multi.py
commit a8f49c233d8099c3d29d180d1ad5449e3279fffb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:28:41 2019 -0400
add plotting script
Exec/hydro_tests/acoustic_pulse/analysis/slice_multi.py
commit 34c66c217cb2ad2dd71cba400d2d5cbb4d964ab1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:27:24 2019 -0400
add convergence notes
Exec/reacting_tests/bubble_convergence/README.md
commit b26217ab510a9d06b0232c00c33ea10bd6fb0120
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:12:26 2019 -0400
add latex pretty script
Exec/reacting_tests/bubble_convergence/job_scripts/create_pretty_tables.py
commit b768b098e9836ff2706d4366663f89f1b26f1b45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:05:48 2019 -0400
add convergence notes
Exec/reacting_tests/reacting_convergence/README
Exec/reacting_tests/reacting_convergence/README.md
commit 9344fe24914191c8c08e10031306fed73c428016
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:04:03 2019 -0400
remove old file
Exec/hydro_tests/acoustic_pulse_general/README
commit 0631a9206ebfba83e53933aec43dadf8ab2abe44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 13:02:04 2019 -0400
add script to output latex tables
Exec/reacting_tests/reacting_convergence/analysis/create_pretty_tables.py
commit e08f27c6ea93a0491d488c93a398950e0173e683
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 12:40:45 2019 -0400
fix some convergence notes
Exec/hydro_tests/acoustic_pulse/README.md
Exec/hydro_tests/acoustic_pulse_general/README.md
commit 29a737934f763e904aa5e3b2835fbb802941c39d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 12:38:29 2019 -0400
add pretty table output
Exec/hydro_tests/acoustic_pulse_general/job_scripts/create_pretty_tables.py
commit bd73dd92eb54da534705acdffebfbd3b6c535661
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 12:31:13 2019 -0400
add convergence instructions
Exec/hydro_tests/acoustic_pulse/README
Exec/hydro_tests/acoustic_pulse/README.md
commit 505a15c7a15cbaa7f5a968ee65db731d39c3e5ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 5 12:28:02 2019 -0400
add latex extraction script
Exec/hydro_tests/acoustic_pulse/job_scripts/create_pretty_tables.py
commit 19a4eb60a5f72d6f51391791ab220167ddcff6c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 4 19:50:22 2019 -0400
fix some formatting
sphinx_docs/source/inputs.rst
commit bf6e96c2bdc2f6629bd21f18d0b0302466329b92
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 3 16:45:48 2019 -0400
add a readme
Exec/reacting_tests/bubble_convergence/README.md
commit b7da738c1501ab6be7384c6c137a03ea63e63d1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 3 16:44:59 2019 -0400
default to the 4th order SDC
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
commit 24c63dee7eebc973fa590fc8e84148f78e37028a
Merge: 305cfa5b6 9f9e27913
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 15:05:42 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 305cfa5b602499ca437721831b95c7a00be00525
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 15:05:29 2019 -0400
remove old scripts -- use workflow now
Util/job_scripts/edison/chainslurm.sh
Util/job_scripts/edison/edison.MPI.OMP.slurm
Util/job_scripts/edison/edison.MPI.slurm
Util/job_scripts/edison/edison.xfer.slurm
Util/job_scripts/edison/process.xrb
Util/job_scripts/edison/slack_job_start.py
commit 9f9e279134123905a91a2ae6a76e419227c47039
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 07:55:24 2019 -0700
update changes
CHANGES
commit 591509773b74818c8c38e029232232a747f98837
Merge: 01f41f2d0 3ad0a3362
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 07:53:36 2019 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 01f41f2d01082e6fa92fe18def34430640754d7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 07:53:20 2019 -0700
remove slack
Exec/hydro_tests/acoustic_pulse/job_scripts/cori.acoustic_pulse_convergence.slurm
commit 3ad0a33626062ca32ae7f05049187619fda1eca9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 10:37:50 2019 -0400
get rid of the special BCs for this problem
Exec/science/flame/bc_fill_nd.F90
commit b62ec373fd8e2808f648be2992a7d0ed68962545
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 2 10:24:11 2019 -0400
don't modify the interface states at outflow for 4th order
this is not correct and not 4th order accurate.
Source/hydro/fourth_order.F90
commit 110dbc5a80250ba424cbd58e71e1eb961ef298b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 19:30:10 2019 -0700
fix inputs names
Exec/reacting_tests/bubble_convergence/job_scripts/cori.bubble_convergence.slurm
commit 50c3252b20b6f24af8053618a01b64dac863ed0d
Merge: a2a84598a 672749888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 17:21:07 2019 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit a2a84598a486174608fe3ddcc062d91dbf8a781c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 17:20:46 2019 -0700
update the flame job launch scripts
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc4.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.strang.slurm
commit 672749888238523df9a56ebd4bb12caf06fc7bc7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 1 17:10:50 2019 -0700
Cannot use AMREX_INT_ANYD without #pragma gpu
Source/driver/Castro.cpp
Source/hydro/Castro_hydro.cpp
commit 4a7a9d839b72c4674fbea0f19c7dc5ca790bfdf1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 15:47:02 2019 -0700
update the changes
CHANGES
commit 3c4c0409e331273188b25ba4a7d4958c75166870
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 13:23:13 2019 -0700
update some job scripts
Exec/hydro_tests/acoustic_pulse/job_scripts/cori.acoustic_pulse_convergence.slurm
Exec/hydro_tests/acoustic_pulse_general/job_scripts/cori.acoustic_pulse_convergence.slurm
commit 9e73ce3107ce4da309c375196a206369c074f495
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 13:20:01 2019 -0700
add some job scripts
Exec/reacting_tests/bubble_convergence/job_scripts/check_convergence.sh
Exec/reacting_tests/bubble_convergence/job_scripts/cori.bubble_convergence.slurm
commit 78aa8b908615a3bbb05bd80b6cf4ccda9f32ceb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 13:07:09 2019 -0700
update interpolation interface
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/bc_ext_fill_nd.F90
Exec/reacting_tests/bubble_convergence/source_fill.F90
commit 23aae048e10a14074fc6a25aaadf97cf929415e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 12:11:12 2019 -0700
more job scripts
Exec/hydro_tests/acoustic_pulse/job_scripts/cori.acoustic_pulse_convergence.slurm
Exec/hydro_tests/acoustic_pulse_general/job_scripts/check_convergence.sh
Exec/hydro_tests/acoustic_pulse_general/job_scripts/cori.acoustic_pulse_convergence.slurm
commit 37b1af9893435e832b45c1ae0aa4a355a2721700
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 12:02:15 2019 -0700
scripts to run convergence on Cori
Exec/hydro_tests/acoustic_pulse/job_scripts/check_convergence.sh
Exec/hydro_tests/acoustic_pulse/job_scripts/cori.acoustic_pulse_convergence.slurm
commit 2c5f4482a7243bc390021a9eddda1442b9b4348d
Merge: 8a2f7b4f6 a61f8aa5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 08:41:12 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8a2f7b4f683dd1c4b322f7a5844d0f75075925a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 08:40:58 2019 -0400
update CHANGES
CHANGES
commit a61f8aa5d25c0b2546da509bcabd4a8616ec29f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 1 00:39:17 2019 -0700
Merge dimension-specific cases in hydro flux limiter
Source/hydro/advection_util_nd.F90
commit 849f2a460ec21a6bfa503adb3a165e10e709202e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 1 00:35:56 2019 -0700
Fix indexing bug in hydro density flux limiter
Source/hydro/advection_util_nd.F90
commit ebee7c4d871ec664c8a715b8f6bb33ac9fb302e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 31 21:16:09 2019 -0400
switch to interior stencils at physical boundaries (#633)
This adopts the one-sided stencils from McCorquodale and Colella at physical boundaries. With this change we get 4th order convergence for hydrostatic atmospheres with reflecting BCs.
This closes #293
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/probin.128
Exec/reacting_tests/bubble_convergence/probin.256
Exec/reacting_tests/bubble_convergence/probin.512
Exec/reacting_tests/bubble_convergence/probin.64
Exec/unit_tests/diffusion_test/Prob.cpp
Exec/unit_tests/diffusion_test/README.md
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_sdc.cpp
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/fourth_order.F90
commit c086d2f81cc089d0de29e42d03d3bb057ee8fe6e
Merge: 568cb1925 00d3fe1f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 30 20:41:55 2019 -0400
Merge branch 'master' into development
commit 568cb19255c62b17cee4805078f79ceff6d9f528
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 30 20:40:27 2019 -0400
add some updates
CHANGES
commit 8a6d0a57110dba35aa4739ff3484718137f81b3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 24 23:21:13 2019 -0400
Cap registers for source_fill.F90
Exec/Make.cuda_rules
commit 8bedd185e312688fc18994faee37bf5cfeba0892
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 29 14:18:31 2019 -0400
switch to 4th order + analytic Jacobian
Exec/science/Detonation/inputs-det-x.sdc.test
commit 867017fdd242e3bc2a08cef0f50ec566b3390508
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 27 16:39:30 2019 -0700
Fix the double Mach reflection problem so it compiles for GPUs (#645)
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/inputs.2d.test
Exec/hydro_tests/double_mach_reflection/probdata.F90
commit 2137ca335a63c75f5c3441b56bc3fad887cb164b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 24 21:01:08 2019 -0400
Only do initial sums if sum_interval > 0
Exec/science/wdmerger/Prob.cpp
commit f16cfa403cdcdd0b438a51d994e0c6eb94379e3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 22 17:43:42 2019 -0400
Update StarLord to mini-Castro
Exec/hydro_tests/Sedov/inputs.mini-Castro
Exec/hydro_tests/Sedov/inputs.mini-Castro.gpu_test
Exec/hydro_tests/Sedov/probin.mini-Castro
commit 93e3e4333129db9626d3baade43771454ba631dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 20 20:53:26 2019 -0400
some flowchart cleaning
sphinx_docs/source/FlowChart.rst
commit 5a9d4c8711a427824c4386b02ec31ec75f91d0c7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 19 02:06:38 2019 -0400
Make number of ghost zones optional
Source/driver/Castro.H
commit e638a4584954ae050ea16256b3fa16eb99949cbc
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 19 02:00:29 2019 -0400
More hybrid momentum function renaming
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/hydro/Castro_hybrid.cpp
commit 592352b501b286e03731d1f47c642052d34aac81
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 19 01:44:48 2019 -0400
Rename hybrid advection functions for consistency
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/hydro/Castro_hybrid.cpp
Source/hydro/hybrid_advection_nd.F90
commit 0db327c048044f4fe61e702acaad734cb30eaf41
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 19 01:31:46 2019 -0400
Use integer parameters for gravity types
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/gravity/gravity_sources_nd.F90
commit c5fb08f3051bfabb23615494e9b79a1a636b4cae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 18 16:30:25 2019 -0400
change the species tracing (#632)
we now just use the limit of the parabola if the wave moves away from the interface
Source/hydro/trace_ppm.F90
commit 86fdcaf94c5438806b56715641069ffa79b1f185
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 18 13:23:14 2019 -0400
remove the transverse velocities from the passive map (#641)
This removes QV and QW from the pass_map stuff for looping over passives. This makes the code overall more consistent. Note: in some places were we doing the same thing twice (overwriting the previous), with different floating point ops (multiplying by 1/rho instead of dividing by rho).
Source/driver/Castro_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
Source/radiation/trace_ppm_rad_nd.F90
commit e81dff7306e8ddee5eab8455dc3a116cec59cff6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 15 18:52:17 2019 -0400
remove unused variables
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/Tagging_nd.F90
Source/driver/sdc_util.F90
Source/hydro/advection_util_nd.F90
Source/reactions/react_util.F90
Source/scf/scf_relaxation.F90
commit fddbf3686f3499ad8d782a893339a14f66bae7b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 15 17:47:13 2019 -0400
eliminate arrays holding ppm integrals (#624)
This gets rid of the multidimension Ip and Im arrays that hold the integrals under the parabolas for each characteristic wave. Now, instead, we do the reconstruction and integration "on demand" in the trace routine. This saves considerable memory.
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit b3d31bc6df2b15623a402a52f9732ee05aaebdde
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 15 16:22:02 2019 -0400
Castro error wrapper (#637)
We now use castro_error() instead of amrex_error()
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/gravity_tests/evrard_collapse/probdata.F90
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
Exec/hydro_tests/HCBubble/Prob_nd.F90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/RT/Prob_nd.F90
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sod/Prob_nd.F90
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/double_bubble/Prob_nd.F90
Exec/hydro_tests/double_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/hydro_tests/gamma_law_bubble/Prob_nd.F90
Exec/hydro_tests/gamma_law_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/gresho_vortex/Prob_nd.F90
Exec/hydro_tests/oddeven/Prob_nd.F90
Exec/hydro_tests/riemann_test_zone/Prob_nd.F90
Exec/hydro_tests/symmetry/Prob_nd.F90
Exec/hydro_tests/test_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/RadBreakout/Prob_nd.F90
Exec/radiation_tests/RadFront/Prob_nd.F90
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
Exec/radiation_tests/RadSlope/Prob_nd.F90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
Exec/radiation_tests/RadSphere/Prob_nd.F90
Exec/radiation_tests/RadSuOlson/Prob_nd.F90
Exec/radiation_tests/RadSuOlsonMG/Prob_nd.F90
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/bc_ext_fill_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/initdata_others.f90
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/toy_flame/Prob_nd.F90
Exec/scf_tests/single_star/Prob_nd.F90
Exec/science/Detonation/Prob_nd.F90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/convective_flame/Prob_nd.F90
Exec/science/convective_flame/initial_model.f90
Exec/science/flame/Prob_nd.F90
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/initial_model.F90
Exec/science/nova/Prob_nd.F90
Exec/science/planet/Prob_nd.F90
Exec/science/rotating_star/Prob_nd.F90
Exec/science/subchandra/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/wdmerger_util.F90
Exec/science/xrb_mixed/Prob_nd.F90
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/particles_test/Prob_nd.F90
Exec/unit_tests/reactions_driver_test/Prob_nd.F90
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Microphysics/networks/burner.F90
Microphysics/networks/network.F90
Source/driver/Castro_error.F90
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/MGutils_nd.F90
Source/driver/Make.package
Source/driver/check_for_nan.f90
Source/driver/extern_probin.template
Source/driver/interpolate.F90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/sdc_util.F90
Source/driver/set_variables.py
Source/gravity/GR_Gravity_1d.f90
Source/gravity/GR_Gravity_2d.f90
Source/gravity/GR_Gravity_3d.f90
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_nd.F90
Source/gravity/gravity_sources_nd.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
Source/problems/Prob_nd.F90
Source/problems/bc_ext_fill_nd.F90
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
Source/radiation/rad_util.f90
Source/radiation/trace_ppm_rad_nd.F90
Source/reactions/react_util.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.F90
Source/rotation/rotation_sources_nd.F90
Util/conservative_interpolate/conservative_map.F90
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_support.f90
Util/model_parser/model_parser.F90
commit d75429cbd7d6e16d331ae8703b770abe4a9e4a67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 14 20:58:42 2019 -0400
add cori script
Exec/science/flame_wave/job_scripts/cori_haswell.MPI.slurm
commit e28fa137363fa38a45290b60914e97cc141f1a63
Merge: e24e4a0f1 015bce30a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 14 20:57:50 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit e24e4a0f13f3a2bcf350c7d4c4ff16b1ee2fdbaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 14 20:57:31 2019 -0400
remove some ancient code
Exec/hydro_tests/Sod/ColellaGlaz/Castro_2d.f
Exec/hydro_tests/Sod/ColellaGlaz/TODO
commit 015bce30a8213fc15d76a2f5ba5564378081e3b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 14 15:31:30 2019 -0400
don't enforce EXT_DIR for source_fill and generic_fill in setup (#639)
instead we leave it for the implementation to enforce, so it can be overridden.
remove redundant function prototypes
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Source/driver/Castro_setup.cpp
Source/problems/Castro_bc_fill_nd.H
commit 5f3ac8f5aae57dcb809f175d5c5deb4c6c0785a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 13 12:00:39 2019 -0400
update some locations
sphinx_docs/source/software.rst
commit b50445bd0eb15f20b72664a16d3e9d8b2c5ea581
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 13 11:57:17 2019 -0400
Prob_nd.F90
sphinx_docs/source/Introduction.rst
sphinx_docs/source/inputs.rst
sphinx_docs/source/rotation.rst
commit c674b1fa35cbe9cac7b700b7216d4344f1a0da6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 13 10:33:44 2019 -0400
fix name
Exec/science/flame/probin.sdc.3alpha
commit f65d4cdbe3d0ef184dae955de28dea4285fa3780
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 13 10:30:56 2019 -0400
new inputs for 3-alpha suite
Exec/science/flame/inputs.1d.sdc.test.3alpha
Exec/science/flame/probin.3alpha
commit ada49fda679d04e29acaccf7365e36b45efae7df
Merge: 73bb24041 9189be042
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 22:10:32 2019 -0400
Merge pull request #610 from AMReX-Astro/sdc_diffusion
Implement diffusion (including 4th order) for MOL and SDC + SDC solver fixes
This implements a flux-based thermal diffusion term for MOL and SDC in both 2nd and 4th order. It also cleans up the SDC solvers, uses a better error estimate for Newton, adds a multi-newton option, and various bug fixes.
commit 9189be042907229712ce375eca7efe7bc765c392
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 22:05:21 2019 -0400
fix some compilation
Source/hydro/Castro_mol_hydro.cpp
commit 6472790f1542ba556aee2416d9c8cbb5ce6e85cc
Merge: 78f431dae 73bb24041
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 21:25:14 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 73bb24041c2c96cfcb2ae7d59105540dc7edd7c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 21:24:26 2019 -0400
ifdef out some amrex_error for CUDA
Util/conservative_interpolate/conservative_map.F90
commit 78f431daeeae1943ac74c74a87652af5c7220a0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 12 14:55:37 2019 -0400
Fix comment
Source/driver/Castro.cpp
commit 29754774133cd9df861e2aa43e88eb5c3a083244
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 13:22:05 2019 -0400
ialways use sdc_newton_subdivide as the entry point
Source/driver/sdc_util.F90
commit fc9f099814612903c807b8bbdbe20e45b964b478
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 12:53:40 2019 -0400
remove comments
Source/driver/Castro_util.F90
commit 6ca7a103c380aa50d729eb5491a1c798556b3481
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 12:49:26 2019 -0400
remove redundant comment
Source/driver/Castro_util.F90
commit e71acc7d6ab6de9459c68cb1e0363b13cfdc01ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 12:42:58 2019 -0400
remove commented code
Source/driver/sdc_util.F90
commit c056a6ac22741e8273daa7fa3eae14d6ead9a0fd
Merge: 310fff2bb 3f06b41c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 12:38:28 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 310fff2bb8fc7238419682539188b8637eb8396d
Merge: e70f65b29 282573635
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 12 12:38:23 2019 -0400
Merge branch 'sdc_diffusion' of ssh://github.com/AMReX-Astro/Castro into sdc_diffusion
commit 3f06b41c5f3148d06ce8bd5aa46685636ce7821f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 11 11:56:54 2019 -0400
fix GPU compilation
Source/driver/interpolate.F90
commit 3fe4f8b63542cc3005a60856bbb62659712ab9b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 11 10:19:21 2019 -0400
explicitly mark public
Util/model_parser/model_parser.F90
commit a422cc57b3d7730a989c692ea82a827efe3e0b39
Merge: cb1545ef2 d74e20036
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 11 10:11:37 2019 -0400
Merge pull request #631 from AMReX-Astro/interp
move interpolate_sub into model_parser_module
commit d74e20036ce07cc8a916a671346051b1af3cc75d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 10 20:56:42 2019 -0400
separate inteprolate_sub out into model_parser_module
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/hydro_tests/gamma_law_bubble/problem_derive_nd.F90
Exec/hydro_tests/test_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/initdata_others.f90
Exec/reacting_tests/reacting_bubble/problem_derive_nd.F90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/nova/Prob_nd.F90
Exec/science/planet/Prob_nd.F90
Exec/science/rotating_star/Prob_nd.F90
Exec/science/subchandra/Prob_nd.F90
Exec/science/xrb_mixed/Prob_nd.F90
Source/driver/interpolate.F90
Source/problems/bc_ext_fill_nd.F90
commit ba2b6fb950a50d2f5bf56f1da3ed578ee97cf7d6
Merge: 24b290323 cb1545ef2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 10 20:21:14 2019 -0400
Merge branch 'development' into interp
commit cb1545ef23e5bf237cc69c02e8036b464b28344a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 10 20:19:02 2019 -0400
remove the backup hse_* arrays
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
Exec/gravity_tests/hydrostatic_adjust/probdata.F90
commit 24b290323443a0a9db8cb42a1dbb578c6d149037
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 10 20:01:40 2019 -0400
some work on the interpolation
Exec/gravity_tests/StarGrav/Prob_nd.F90
Source/driver/interpolate.F90
Util/model_parser/model_parser.F90
commit 2825736355c3eec293615180c44cab0d2a696bf2
Merge: 580a4b2d4 baea0b852
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 3 14:49:48 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 580a4b2d44dc69a0e46f1a80511562cc96a9f0df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 3 14:49:28 2019 -0400
add option to turn off pert + switch to reflect
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/probdata.F90
Exec/reacting_tests/bubble_convergence/probin.128
Exec/reacting_tests/bubble_convergence/probin.256
Exec/reacting_tests/bubble_convergence/probin.512
Exec/reacting_tests/bubble_convergence/probin.64
Exec/reacting_tests/bubble_convergence/source_fill.F90
commit baea0b8527cfa42beee63cde018c85397792bd42
Merge: aedeb43ed e3ba74e3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 2 14:12:18 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 00d3fe1f5ef5fba7432ebbe8034a6d77429989e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 1 02:36:37 2019 -0400
merge and update changes
CHANGES
commit aedeb43edcc09e2369a23234816dac507c0e0263
Merge: 7208383da bef13c21a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 15:45:28 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 7208383da4986b356f59f015a294a657d35761b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 15:45:13 2019 -0400
fix the source fill at the upper boundary to be 4th order
Exec/reacting_tests/bubble_convergence/source_fill.F90
commit bef13c21a5fe5002f19b166e59fbee5abd4a50d9
Merge: 96102b3ab 5f8b93169
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 15:06:00 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 5f8b93169b280b64d9c680aede05458336d14a4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 14:58:42 2019 -0400
make the HSE BCs 4th order-ish
Exec/reacting_tests/bubble_convergence/bc_ext_fill_nd.F90
Exec/reacting_tests/bubble_convergence/source_fill.F90
commit fbbfe0ae99cfce068f164629d03cb0524e679335
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 13:54:54 2019 -0400
add HSE source filling
Exec/reacting_tests/bubble_convergence/source_fill.F90
commit 96102b3ab4d8e457babb9775a0d2ada83c0bb357
Merge: cbf0e1e67 2b709080e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 13:54:28 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit e3ba74e3e9a00b228f0fd78d1aa42f20eb5d2fd3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 29 10:41:07 2019 -0700
Call ca_shock from C++
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
commit 329e6d090780229b257a14a0a423ded47154ff43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 11:34:41 2019 -0400
update changes
CHANGES
commit 2b709080e21bb1cdcfb65afbf21a31d0473d9f83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 29 09:20:07 2019 -0400
reduce stop time to avoid very nonlinear regime
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
commit bdc63baa1753307439c69656c1a9863fe76a146b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 28 18:11:13 2019 -0700
Move S_new into consup radiation ifdef
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro_F.H
commit cb0527338a7dce1bef80c919f40de789db4c368e
Merge: ceb178799 4b155ff1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 19:08:52 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit cbf0e1e6765d532932c20dfed4a779be8c1d0fca
Merge: 4b155ff1e 4fc0de398
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 18:57:43 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 4fc0de3982e60ced6480b841adf56d5b409b74e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 18:54:40 2019 -0400
fix double definitions of some functions
Source/driver/Castro_source_fill.H
Source/driver/Castro_source_fill.cpp
commit 4b155ff1e77c822529bef2334f4c013aa6ebaaee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 18:54:40 2019 -0400
fix double definitions of some functions
Source/driver/Castro_source_fill.H
Source/driver/Castro_source_fill.cpp
commit cf8ac60fb90d4a4ed10e39887a7c4efa7947e207
Merge: 66236ff00 37d824d16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 18:46:48 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 37d824d1660fca27493fca007d3ef1575f4c5149
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 19:46:24 2019 -0300
split source fill into its own routine (#627)
this splits the generic BCs into source and generic
and we now use the source for ... sources! This makes it
easier to override them. Also, add checks for external BCs
and set to outflow for all quantities.
Source/driver/Castro_setup.cpp
Source/driver/Castro_source_fill.H
Source/driver/Castro_source_fill.cpp
Source/driver/Castro_source_fill_F.H
Source/driver/Make.package
Source/driver/generic_fill.F90
Source/driver/source_fill.F90
Source/problems/Castro_bc_fill_nd.H
Source/problems/bc_ext_fill_nd.F90
commit 91eb1950de86e839e3fa84350a20241523390ab6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 18:26:08 2019 -0400
fix compilation
Exec/hydro_tests/gamma_law_bubble/bc_ext_fill_nd.F90
commit cc7e1e1a546f15603153b5b7a668d4b88f7852db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 18:24:06 2019 -0400
fix compilation
Exec/hydro_tests/double_bubble/bc_ext_fill_nd.F90
commit ceb17879963f576beeb4af53fcbdfb23be0c22c0
Merge: 66236ff00 97a7352f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 14:32:40 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 97a7352f8cbe3d1bee52e94ba2b8d10e030ea762
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 14:32:08 2019 -0400
rename adv -> grav
Source/problems/bc_ext_fill_nd.F90
commit 66236ff0016e30404853810889e287379e684411
Merge: 3f89bf159 caad481d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 14:25:30 2019 -0400
Merge branch 'development' into sdc_diffusion
commit caad481d0470fba41ac9dc630700e7acc4cca301
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 14:07:38 2019 -0400
add stubs for external filling of gravity
Source/problems/Castro_bc_ext_fill_nd.H
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/problems/Castro_bc_ext_fill_nd_F.H
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/bc_ext_fill_nd.F90
Source/problems/bc_fill_nd.F90
commit 3f89bf159e6ca0ef5ca57a44e4176e09077c97d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 28 12:52:41 2019 -0400
switch to a HSE BC
this involves integrating the initial conditions into buffer zones for the BC fill
the initial conditions here converge 4th order
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
commit 47decb54c614a6c5b17ef1c346d3e3bdc7a9194f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 27 22:44:25 2019 -0400
Add comment explaining total energy source term in the sponge
Source/sources/sponge_nd.F90
commit a335604a70dbb29e4ce92e7c210e540d0426119f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 21:25:59 2019 -0400
sdc-safe dts:
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
commit ed3d3a70978b8cccaa24d0ac4317b86692dad76f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 15:23:33 2019 -0400
this is the script for Strang
Exec/reacting_tests/bubble_convergence/converge_test.sh
commit 63b47252048eb737ea806f3deb657793f5bfe0ca
Merge: b76e4aaa2 5784043f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 15:19:42 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 5784043f893c01d9dd7a00b31b1852cf4e3407eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 15:11:27 2019 -0400
These inputs files give a good convergence test
for Strang, it should 2nd order convergence (for the high-res)
Exec/reacting_tests/bubble_convergence/inputs_2d.128
Exec/reacting_tests/bubble_convergence/inputs_2d.256
Exec/reacting_tests/bubble_convergence/inputs_2d.512
Exec/reacting_tests/bubble_convergence/inputs_2d.64
Exec/reacting_tests/bubble_convergence/probin.128
Exec/reacting_tests/bubble_convergence/probin.256
Exec/reacting_tests/bubble_convergence/probin.512
Exec/reacting_tests/bubble_convergence/probin.64
commit 0111fc8f2ef12185d421823a031e88cbd9a3463b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 15:11:10 2019 -0400
fix uninitialized issue
Exec/reacting_tests/bubble_convergence/initial_model.F90
commit e1e90a57bd474bdd6080fd9a6059b3fae135825a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 12:35:12 2019 -0400
turn back on perturbation
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit e13e7e4856c2686a8b9dec4b2c014d7226d4e5ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 12:25:46 2019 -0400
fix an O(dx) error in the HSE model
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/inputs_2d
Exec/reacting_tests/bubble_convergence/probin
commit b76e4aaa2aa43bf06733d06e39803a9e2775b538
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 08:41:56 2019 -0400
get rid of unnecessary copies
Source/driver/Castro_advance_sdc.cpp
commit 939d58a2efd5662be6b0bcd1f2863667a34a1a7e
Merge: 14a3e343d 28b1abeaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 27 08:36:35 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 28b1abeaa2d8a9eea80838f789ea897f333b9264
Merge: bbcdfdcbb aef138b88
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 26 23:44:01 2019 -0400
Merge branch 'development' into sdc_diffusion
commit aef138b880ffea5f06a93c947f9e561c4282c197
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 26 23:20:04 2019 -0400
Do not directly modify USHK in the hydro
Source/driver/Castro_advance.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
commit e16d6357b4436e08033d7f9bd8df9bc19d97ae0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 20:44:07 2019 -0400
this seems to be a good test problem now
Exec/reacting_tests/bubble_convergence/inputs_2d
Exec/reacting_tests/bubble_convergence/probin
commit df985d1d6754998a1c6a01165ec688686f0c402f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 20:35:45 2019 -0400
some better parameters
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/inputs_2d
Exec/reacting_tests/bubble_convergence/probin
commit 339897ebd69d3c1256b28d0f22c863a224bbb721
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 19:31:03 2019 -0400
bump up pert
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
commit 72ff2c29e9a99713267d182a8e443301c0319ae0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 17:36:09 2019 -0400
update the instructions on building a problem
sphinx_docs/source/creating_a_problem.rst
commit 14a3e343de5dfb44c7ae7bf4dbff7b6191b657ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 15:25:45 2019 -0400
update params for new flame
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.512
Exec/science/flame/probin.sdc.map.avg
commit 606adbe07765874bd68bb3df327d8e5a846c181a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 15:25:06 2019 -0400
update params
Exec/reacting_tests/bubble_convergence/inputs_2d
Exec/reacting_tests/bubble_convergence/probin
commit 6224db9d48b4a5f8eac55b26cf7e25e139b237ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 14:54:15 2019 -0400
this seems to do initialization correctly
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/bubble_convergence/Make.package
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/inputs_2d
Exec/reacting_tests/bubble_convergence/probdata.F90
Exec/reacting_tests/bubble_convergence/probin
commit 553e97fd16ceca3236b8aa9e4d48da4c01652afe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 26 12:55:50 2019 -0400
start of a bubble convergence test
Exec/reacting_tests/bubble_convergence/GNUmakefile
Exec/reacting_tests/bubble_convergence/Make.package
Exec/reacting_tests/bubble_convergence/Prob_nd.F90
Exec/reacting_tests/bubble_convergence/initial_model.F90
Exec/reacting_tests/bubble_convergence/inputs_2d
Exec/reacting_tests/bubble_convergence/probdata.F90
Exec/reacting_tests/bubble_convergence/probin
commit 649204e757ffe975a01d0462311e641d7877714f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 25 11:13:14 2019 -0400
add intents
Exec/science/convective_flame/Prob_nd.F90
commit bbcdfdcbb365a08409dc2777e674aa3efeb4f8cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 25 10:19:42 2019 -0400
comment out a code path if we are in simplified-SDC
Source/reactions/react_util.F90
commit d3b04ca5f5d5592747a6a4599d1a777a53ec831b
Merge: 2342e5596 ccd97265d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 25 10:12:45 2019 -0400
Merge branch 'development' into sdc_diffusion
commit ccd97265d4f3eeda467b0b3d3faf0366aa069c52
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 25 05:00:48 2019 -0700
Add method to determine whether oversubscribing GPU memory
Source/driver/Castro.H
commit 7dc898c3fee0821811463461fa6b780b72a41d44
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 25 04:16:07 2019 -0700
Tag Sborder
Source/driver/Castro_advance.cpp
Source/hydro/Castro_ctu_hydro.cpp
commit d8a38b0b0c13242c95edddfee853811dd1ae8766
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 25 03:59:37 2019 -0700
Simplify by having everything owned by AmrLevel
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit 4206eaed71be57254d1b422c29895c7309c14b28
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 25 03:53:52 2019 -0700
Fix bounds
Source/hydro/Castro_ctu_nd.F90
commit ae646290634fee984acb2d7cb1dc32eca342b51a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 25 06:33:26 2019 -0400
Fix typo
Source/hydro/Castro_ctu_hydro.cpp
commit 4df77019e1953c454b05c369236f8bd9aa6ed3ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 24 21:09:05 2019 -0400
tweak the coord computation
Exec/science/convective_flame/problem_tagging_nd.F90
commit 2342e559601b531eb8527a53f8b4cb8c8a75b938
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 24 21:04:50 2019 -0400
fix some dimensioning
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
commit a7c46b7e2b4f2159f274b0038a69209688a71b82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 24 20:56:33 2019 -0400
globally set DIMENSION_AGNOSTIC -- AMReX uses it.
This fixes some failures
Exec/Make.Castro
Exec/Make.cuda_rules
commit 0238466290355ab78eab107b1522ba73bd12a009
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 24 10:12:35 2019 -0700
Perform a GPU synchronization if running out of memory in the hydro
Source/hydro/Castro_ctu_hydro.cpp
commit ed8de7f2490f447a6a60627fb8f030aede552d08
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 24 09:58:51 2019 -0700
Add regiontag to Castro_advance
Source/driver/Castro_advance.cpp
commit 9ddb6d394a81e21a29ae8854e7bdeb537d48db6b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 24 08:15:06 2019 -0700
Add region tags
Source/driver/Castro.cpp
commit 7631c694228ed7cf122bc03b5b196a8c8ecbea99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 23 11:43:38 2019 -0400
move to markdow
Exec/science/flame/README
Exec/science/flame/README.md
commit 8c84fc455eedc4d66bcb4e4eabaa72bc16de435c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 22 16:11:20 2019 -0300
remove non-dimension agnostic stuff (#621)
This removes all traces of the old dimension-specific routines
CHANGES
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/double_mach_reflection/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/reacting_bubble/Prob_2d.f90
Exec/reacting_tests/reacting_bubble/Prob_3d.f90
Exec/reacting_tests/reacting_convergence/GNUmakefile
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/scf_tests/single_star/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/nova/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/science/rotating_star/GNUmakefile
Exec/science/subchandra/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/particles_test/GNUmakefile
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_error_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/problems/Castro_bc_fill.H
Source/problems/Castro_bc_fill.cpp
Source/problems/Castro_bc_fill_F.H
Source/problems/Make.package
Source/problems/Prob_1d.f90
Source/problems/Prob_2d.f90
Source/problems/Prob_3d.f90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_1d.F90
Source/problems/bc_fill_2d.F90
Source/problems/bc_fill_3d.F90
Source/problems/problem_tagging_1d.f90
Source/problems/problem_tagging_2d.f90
Source/problems/problem_tagging_3d.f90
Source/sources/Castro_external.cpp
Source/sources/Make.package
Source/sources/ext_src_1d.f90
Source/sources/ext_src_2d.f90
Source/sources/ext_src_3d.f90
commit b92f16cca44e8cb737162bc082618a44bab451ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 22 13:20:43 2019 -0400
add external source
Exec/science/planet/ext_src_nd.F90
commit 0d66f46e9e38517a2f757bdb4d3b7ea45044e1cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 22 13:20:12 2019 -0400
switch to dimension agnostic
Exec/science/planet/GNUmakefile
Exec/science/planet/Make.package
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/planet/Prob_3d.f90
Exec/science/planet/Prob_nd.F90
Exec/science/planet/bc_ext_fill_1d.F90
Exec/science/planet/bc_ext_fill_2d.F90
Exec/science/planet/bc_ext_fill_3d.F90
Exec/science/planet/bc_fill_1d.F90
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/bc_fill_3d.F90
Exec/science/planet/ext_src_3d.f90
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/planet/probdata.F90
commit 37aac5c1dd400c6bde99f2914a71fc2faed5e6cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 22 11:52:08 2019 -0400
fix bc check
Source/problems/bc_ext_fill_nd.F90
commit 291a948f1babe0d03592249c4699b410192e80c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 22 11:48:49 2019 -0400
implement HSE for 1-d
Source/problems/bc_ext_fill_nd.F90
commit cd6b1a471d9c7cfefe2edccd1306e8a5537cb4d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 22 10:20:34 2019 -0400
get rid of the loop over components
Source/problems/bc_ext_fill_nd.F90
commit 8ed5ca185017dc1d78ce5de95cd72f046593f208
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 20:53:41 2019 -0400
merge the RT_particles propblem with RT
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/RT/README.md
Exec/hydro_tests/RT/inputs_2d.particles
Exec/hydro_tests/RT/particle_file
Exec/hydro_tests/RT_particles/GNUmakefile
Exec/hydro_tests/RT_particles/Make.package
Exec/hydro_tests/RT_particles/Prob_nd.F90
Exec/hydro_tests/RT_particles/README
Exec/hydro_tests/RT_particles/probdata.F90
Exec/hydro_tests/RT_particles/probin
commit e2607cb8c3f7e91c01e5ece428fc1c0b90b36d3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 19:26:38 2019 -0400
a little cleaning
Exec/hydro_tests/RT/Prob_nd.F90
commit 254de61643cc9007c83f378cdabc66ccd753137e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 19:26:29 2019 -0400
siwtch to dimension agnostic
Exec/hydro_tests/RT_particles/GNUmakefile
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/Prob_nd.F90
commit 59746d93c9634f261b948dc073e375f24c6966a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 21 14:20:17 2019 -0700
Clarify comment
Exec/science/wdmerger/ext_src_nd.F90
commit d59316772a11a24ba2af58e19b64a18044c01d75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 16:27:30 2019 -0400
add closing mark
Exec/unit_tests/diffusion_test/README.md
commit 2312a5b61a3b1dcbed92f117e7bf0639e0b6e003
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 16:26:17 2019 -0400
add to the READM
Exec/unit_tests/diffusion_test/README.md
Exec/unit_tests/diffusion_test/convergence_powerlaw.txt
Exec/unit_tests/diffusion_test/convergence_sdc4.txt
Exec/unit_tests/diffusion_test/convergence_sph.txt
commit 3367aa40835254b0842e050f1d3e45f33964e8f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 13:32:39 2019 -0400
update lots of changes
CHANGES
commit 56a9907af7a4d9f3cd778bb8179b2405ba8f218b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 21 13:16:29 2019 -0400
fix the 2-d thermal diffusion with SDC
it is now 4th order accurate with non-constant conductivity
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/diffusion_test/convergence_powerlaw_sdc4.txt
Source/driver/Castro_advance.cpp
Source/hydro/Castro_fourth_order.F90
commit 4ee2aec39e5d58d21dcb54e6dc3d522f4a838fb2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 22:14:11 2019 -0400
first pass at 4th order multidimensional diffusion
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
commit 95b2528c47b7de8ac4d22fda3aa25d9609f31cd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 21:18:24 2019 -0400
a tool to plot the 1-d profiles
Exec/unit_tests/diffusion_test/analysis/profiles.py
commit 336d52426d4030e57a0c80341052db4870fd6947
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 20:51:00 2019 -0400
update the notes
Exec/unit_tests/diffusion_test/convergence_powerlaw_sdc4.txt
commit 3009a000f54ac7f51a04a98a4f351b5a13e37738
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 16:52:41 2019 -0400
a little cleaning
Source/driver/Castro_util.F90
commit a72ac9e83a5d8f5646879650c2fdfb4e498335ab
Merge: f333438c8 2f3cc0514
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 16:30:50 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit f333438c876ff903d7f14ba74c8f178789e41358
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 16:30:37 2019 -0400
add use_reconstructed_gamma1
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.512
commit 2f3cc051494d7b323d4a7867169628506f77997d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 15:01:45 2019 -0400
add a small_x to initialization
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
commit 423d3fc5faff887f20f48043657b8f4522e85a04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 12:30:43 2019 -0400
this file is not needed
Exec/science/flame/inputs.1d.sdc.conv.4096
commit 53a2ab34962cc2dc2743b2bfd50d6322df8d9665
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 10:49:53 2019 -0400
fix formatting
Source/driver/interpolate.F90
commit 5394194a9a545fa1e472c91757c57ebc15381e8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 16 07:58:32 2019 -0700
update for Cori
Exec/reacting_tests/reacting_convergence/job_scripts/cori.reacting_convergence.slurm
Exec/reacting_tests/reacting_convergence/job_scripts/edison.MPI.slurm
commit 55a254c1c68d7fabad54ad969c1402f5defe089f
Merge: 661edffeb 896955f1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 10:30:57 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 896955f1cbbf49822afceb01e1009c5edb090db0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 10:28:46 2019 -0400
Implement a conservative model mapping.
This reads in a model of the conserved variables (e.g. created by fextract)
and has routines to conservatively map it onto the grid. It assumes
that the model quantities represent averages and suitably coarsens those
averages onto the Castro grid.
Util/conservative_interpolate/Make.package
Util/conservative_interpolate/conservative_map.F90
commit 661edffeb1ffd6285b4270f4031c9479c3fb9212
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 10:20:59 2019 -0400
switch over to conservative map 3-alpha runs
Exec/science/flame/inputs.1d.sdc.conv.1024
Exec/science/flame/inputs.1d.sdc.conv.2048
Exec/science/flame/inputs.1d.sdc.conv.4096
Exec/science/flame/inputs.1d.sdc.conv.512
Exec/science/flame/test_conv.sh
commit e3afd9f40d2a156a1d50c1ce3674d3bdeca4cef2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 10:20:36 2019 -0400
remove old models
Exec/science/flame/flame_4096_sdc4_plt2100952.slice
Exec/science/flame/flame_4096_sdc4_plt323427.slice
commit 09b634cc63ee7af99eabe3ffccd0511b39214d06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 20 10:19:42 2019 -0400
switch models, setup for 3-alpha
Exec/science/flame/probin.sdc.map.avg
commit 8b030f0be75cffe6af3990f97cf80e8fd8aaa2d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 19 20:49:16 2019 -0700
sum_force_on_stars in CUDA
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/wdmerger_util.F90
commit e907b7b17469cc4eea7e576f0fdaefe346a04caa
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 19 20:36:23 2019 -0700
Perform sum reductions in a thread-safe way for CUDA
amrex_reduce_add should not be inside a conditional: every thread needs
to call it for the algorithm to make sense, since it does a within-block
reduction first. The solution is for every thread to call it, with a
multiplicative factor computed inside the conditional.
Exec/science/wdmerger/wdmerger_util.F90
commit c07886a9999ab8afc6c5f5661cf89d721ccf87e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 21:04:09 2019 -0400
make this dimension agnostic
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/Prob_nd.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/ext_src_nd.F90
Exec/hydro_tests/toy_convect/probdata.F90
Exec/hydro_tests/toy_convect/problem_tagging_2d.f90
Exec/hydro_tests/toy_convect/problem_tagging_nd.F90
commit 3212c63d9b4834792f3bfc9bca98f58581dd273c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 19 19:33:44 2019 -0400
Initialize single_star
Exec/science/wdmerger/wdmerger_util.F90
commit efadf0aafbf37e8c7068630e7c64af6403fa6958
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 15:19:00 2019 -0400
when castro.initialization_is_cell_average = 1, we still need to fiddle
with the energy
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util.F90
commit 918cc1e0e63a132878ab5d1b5d5530bb445e6dc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 10:24:12 2019 -0400
fix xcen
Exec/science/Detonation/Prob_nd.F90
commit 88986f9479a5d8e116e6b583c2483293e86bc8a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 10:09:17 2019 -0400
fix compilation
Exec/science/Detonation/probdata.F90
commit 5e8f7dfde2520c2a1ec51adeb9eb0ea00a30c685
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 09:59:53 2019 -0400
fix initialization
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
commit d9483b61c3c9a363a3ba6f52b92051f190f5d697
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 09:41:52 2019 -0400
turn on a ppm option
Exec/gravity_tests/code_comp/inputs_3d
commit e70f65b295efe1aebf2c600ea3ae3a36f668a5cb
Merge: 0f0886c54 b98d2230d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 19 09:39:08 2019 -0400
Merge branch 'sdc_diffusion' of ssh://github.com/AMReX-Astro/Castro into sdc_diffusion
commit 7b3639ecf71a0478fe1c7a56b5e73ba1ce404381
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 22:01:07 2019 -0400
switch to dimension agnostic
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/reacting_bubble/Prob_nd.F90
Exec/reacting_tests/reacting_bubble/Problem_Derive.H
Exec/reacting_tests/reacting_bubble/Problem_Derive.cpp
Exec/reacting_tests/reacting_bubble/Problem_Derive_F.H
Exec/reacting_tests/reacting_bubble/problem_derive_nd.F90
commit b98d2230d7f27c632e98d196380851ec0c759661
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 18:39:49 2019 -0400
add model file
Exec/science/flame/flame_4096_sdc4_plt2100952.slice
commit e49a51c755a0a7196ec21f93f66907de292d0e7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 18:36:25 2019 -0400
add some more mapping tests
Exec/science/flame/extract.sh
Exec/science/flame/inputs.1d.sdc.map.avg
Exec/science/flame/probin.sdc.map
Exec/science/flame/probin.sdc.map.avg
Exec/science/flame/test_conv.sh
commit 2bf2f0afb2755cac86f7aa81c885bf92a109f2b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 18:28:03 2019 -0400
implement the avg_to_center for same resolution
Util/conservative_interpolate/conservative_map.F90
commit 905115ed6bf6d6a598d2fad001862c693a5f03ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 18 14:42:21 2019 -0700
Set up Detonation problem on the GPU
Exec/science/Detonation/GNUmakefile
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Exec/science/Detonation/probdata.F90
commit 7f7daec2f96960334dae693df3881557d439f9b3
Merge: d8b63f0c5 cc73c471c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 13:00:17 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit d8b63f0c586a45677a9129ca02301fac590fdbb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 13:00:01 2019 -0400
deal with the model edges
Util/conservative_interpolate/conservative_map.F90
commit cc73c471caac78ba61e8b31dddca48f169198c87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 09:28:43 2019 -0700
sync up with the latest Cori runs
explicitly add a small_x used in the normalization
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
commit 576ceca7fbad7c1c796a961b89543785a7d32d94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 12:13:01 2019 -0400
rename smallx to smallx_init
Exec/science/flame/Prob_nd.F90
Exec/science/flame/inputs.1d.sdc.map
Exec/science/flame/probdata.F90
Exec/science/flame/probin.sdc
Exec/science/flame/probin.sdc.map
commit e28d0e31c727e161f38624c1da01fdf64550b9de
Merge: dcd720fcb 264ec9475
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 18 10:11:14 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 264ec9475027d0fae09b926326f04464168af5cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 18 07:09:57 2019 -0700
Tagging (#611)
The tagging routines have been reformulated so that they run on the GPU. Since the tags_and_untags routine in AMReX is not GPU-accelerated, we opt to directly fill in the TagBoxArray in the tagging routines. Since these are based on char data, which doesn't seem to work well with PGI CUDA Fortran, we pass the TagBox to Fortran as an int8_t.
Castro_prob_err_list.H and other related files have been deleted as they were not actually used anywhere.
Castro_error.cpp is now removed and there is no further support for writing custom tagging routines. The set of variables that we check for tagging is hard-coded in Castro and can be expanded as needed. Problem-specific tagging should be done through the set_problem_tags functionality.
CHANGES
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Exec/science/convective_flame/problem_tagging_nd.F90
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/probdata.F90
Exec/science/flame_wave/problem_tagging_nd.F90
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/xrb_mixed/problem_tagging_nd.F90
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_error.cpp
Source/driver/Castro_error_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/Tagging_nd.F90
Source/driver/prob_params.F90
Source/problems/Castro_prob_err.cpp
Source/problems/Castro_prob_err_F.H
Source/problems/Castro_prob_err_list.H
Source/problems/Make.package
Source/problems/problem_tagging_1d.f90
Source/problems/problem_tagging_2d.f90
Source/problems/problem_tagging_3d.f90
Source/problems/problem_tagging_nd.F90
commit dcd720fcbd2d69670b2c31775897dc9645df0e47
Merge: 886a07fa2 9cbc901fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 17 14:24:58 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 9cbc901fc44b9e1726c10e82980232587a4b1384
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 17 14:20:04 2019 -0400
fix the z BCs
Exec/science/flame_wave/inputs.boost_10_10.3d
commit 886a07fa26d821d3a4cb38f7e9b2c44fc9c95885
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 17 14:06:21 2019 -0400
add an interpolation from averages to centers
Util/conservative_interpolate/conservative_map.F90
commit c11a176a00085d1158362c1bd204bd6844dea15e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 17 14:05:23 2019 -0400
first pass at new interpolation
Exec/science/flame/Prob_nd.F90
Exec/science/flame/probdata.F90
Exec/science/flame/probin.sdc.map
commit 911b456818337eafa43d51a3ca0544a95fa72197
Merge: b2f483bcb 2c2e6e44c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 17 11:54:18 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit b2f483bcbe5ff33dbe102a096b58617d60e855b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 17 11:54:01 2019 -0400
move interpolate_conservative into the conservative_map module
Exec/science/flame/Prob_nd.F90
Source/driver/interpolate.F90
Util/conservative_interpolate/conservative_map.F90
commit 2c2e6e44c2f8ff1f944efe121bf41fd8c2307d3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 16 19:13:49 2019 -0400
fix fuel/ash keys
Exec/science/flame/Prob_nd.F90
commit d5a3561cc2332dc3717e50158a95509fe99e879b
Merge: e1a99a151 cd949a3b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 16 16:45:04 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit e1a99a151410e1bbba8c1eebb93c493004dd2550
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 16 16:44:36 2019 -0400
add tight_layout()
Exec/science/flame/analysis/flame_speed.py
commit cd949a3b0ba49943adfa9dcc4c2dbd9af175bcb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 16 07:58:32 2019 -0700
update for Cori
Exec/reacting_tests/reacting_convergence/job_scripts/cori.reacting_convergence.slurm
Exec/reacting_tests/reacting_convergence/job_scripts/edison.MPI.slurm
commit 33277e35cdeac5b26157462ef057f5a44e7282e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 15 20:57:40 2019 -0400
add a smallx
Exec/science/flame/Prob_nd.F90
Exec/science/flame/probdata.F90
Exec/science/flame/probin.sdc
commit 17609fa2b7ace87e8c324c5d3ebc8ab143f7a679
Merge: b29cd2ae5 a398f9db6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 14 10:59:59 2019 -0700
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit b29cd2ae544d4ed92ca5ba2e1d0f56b569a3985a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 14 10:59:40 2019 -0700
this uses less metadata to get the checkpoint file
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc4.slurm
commit a398f9db67bf4598648ccaf1c42de6432e28fddc
Merge: 0830fada3 5cad30853
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 14 11:38:28 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 0f0886c547bd7dc313bbfe1e928a45b841f20d11
Merge: 5b0203533 0830fada3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 13 16:41:55 2019 -0400
Merge branch 'sdc_diffusion' of ssh://github.com/AMReX-Astro/Castro into sdc_diffusion
commit 5cad3085321f737894bc54030c44c43ec24628e7
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Jun 13 15:39:41 2019 -0400
Set the gravity type integer for PrescribedGrav in meth_params.F90
Source/driver/meth_params.F90
commit 4931745076b3920097d062198246b219363433fc
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Jun 13 15:37:43 2019 -0400
more files for the code comparison problem
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/Problem_Derive.H
Exec/gravity_tests/code_comp/Problem_Derive.cpp
Exec/gravity_tests/code_comp/Problem_Derive_F.H
Exec/gravity_tests/code_comp/Problem_Derives.H
Exec/gravity_tests/code_comp/ext_src_nd.F90
Exec/gravity_tests/code_comp/hcore.dat
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/model_parser.F90
Exec/gravity_tests/code_comp/prescribe_grav_nd.f90
Exec/gravity_tests/code_comp/probdata.F90
Exec/gravity_tests/code_comp/probin
Exec/gravity_tests/code_comp/problem_derive_nd.F90
Exec/gravity_tests/code_comp/simple.net
Source/driver/meth_params.F90
Source/gravity/prescribe_grav_nd.f90
commit 52575c2e4bed90d400d26c0b6f80e465db64d6b8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Jun 13 10:46:17 2019 -0400
code comparison problem
Exec/gravity_tests/code_comp/GNUmakefile
Exec/gravity_tests/code_comp/Make.package
Exec/gravity_tests/code_comp/Prob_nd.F90
Exec/gravity_tests/code_comp/inputs_3d
Exec/gravity_tests/code_comp/probdata.F90
Exec/gravity_tests/code_comp/probin
commit a344ac93dbfefc8df904be9c9a3230b5b080bd51
Merge: 03544d9a2 0830fada3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 9 15:12:32 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 3896261dc503f27c327c2a198de3d6b1a6857308
Author: Chris DeGrendele <35853499+ChrisDeGrendele@users.noreply.github.com>
Date: Sun Jun 9 11:12:25 2019 -0700
Exec/hydro_tests/RT_particles/ won't compile without this (#618)
Source/driver/Castro.cpp
commit da2fe4a482e963c48a29dcac719971f3faf8a6c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 8 17:51:22 2019 -0400
Redefine tagging
Exec/science/wdmerger/probin
commit 56ae52932b46c68be007e84d3bd83d74a8170ec6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 7 17:45:05 2019 -0700
minor update of documentation
sphinx_docs/source/faq.rst
commit 0830fada3353fddd457281311055ec6bc9709fdb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 7 06:28:02 2019 -0400
set defaults _before_ we read the namelist
Exec/science/flame/Prob_nd.F90
commit 49da72deba821d13760101b577327562f75221c7
Merge: 83e9d8441 8c6a69426
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 6 20:06:39 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 8c6a69426a403c14b78dd6482135fd9ff511c1a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 6 16:24:47 2019 -0400
fix some math
sphinx_docs/source/gravity.rst
commit 2b530aa5fd834779d7ea07f797fa1ee526266ca4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 18:06:52 2019 -0400
fix the initialization of the total energy density
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/planet/Prob_3d.f90
commit b2d0e2845c30665de29961cb74d41018f48c581b
Author: taehoryu <30508125+taehoryu@users.noreply.github.com>
Date: Wed Jun 5 17:58:10 2019 -0400
update (#617)
some updates to the planet problem with radiation
Exec/science/planet/GNUmakefile
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/planet/Prob_3d.f90
Exec/science/planet/bc_ext_fill_1d.F90
Exec/science/planet/bc_ext_fill_2d.F90
Exec/science/planet/bc_ext_fill_3d.F90
Exec/science/planet/bc_fill_1d.F90
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/bc_fill_3d.F90
Exec/science/planet/ext_src_3d.f90
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/planet/probdata.f90
Exec/science/planet/probin
commit 03544d9a20927fced7e4f2e0cf84ffad8ef00a59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 14:47:45 2019 -0400
a flame model for mapping tests -- this has machine precision output
Exec/science/flame/flame_4096_sdc4_plt323427.slice
commit 83e9d844104b2d8c0dab44b6464445fd1c5014e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 12:41:26 2019 -0400
a script for some test runs
Exec/science/flame/mapping_tests/setup_runs.sh
commit b69866ccadcb646ea9ba21567b2635b699060eeb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 10:53:25 2019 -0400
convergence for SDC-4 with non-constant conductivity
Exec/unit_tests/diffusion_test/convergence_powerlaw_sdc4.txt
commit 8cd1d5c3a7a0d5c58b2e254a8ac10825f3ae497c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 10:35:03 2019 -0400
demonstration of second-order convergence with non-constant conductivityy
Exec/unit_tests/diffusion_test/convergence_powerlaw.txt
commit 458c247cc2a33c832e69b7022243f17b500e9cf2
Merge: 10b011ca5 ae180d2a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 10:11:32 2019 -0400
Merge branch 'development' into sdc_diffusion
commit ae180d2a35b9b6e4f759d70840947233146c5b2e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 10:11:13 2019 -0400
add a powerlaw conductivity
Microphysics/conductivity/powerlaw/Make.package
Microphysics/conductivity/powerlaw/_parameters
Microphysics/conductivity/powerlaw/powerlaw_conductivity.F90
commit 2fb9cda1e1ce1ac264cdf244739a10780e8b7507
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 10:10:40 2019 -0400
get the conductivity from the main interface instead of assuming constant
Exec/unit_tests/diffusion_test/Prob_nd.F90
commit 10b011ca5fd5fffd211db98e81135a0c90cd28c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 09:13:16 2019 -0400
summary of the convergence for SDC-4
Exec/unit_tests/diffusion_test/convergence_sdc4.txt
commit eb1781b2413b9901560ea0e50ab802694879471b
Merge: 322f47298 0b00041d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 09:05:25 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 0b00041d921cd3e9f89cd37b7bad1133f7da0339
Merge: 2b592749c b2cb6e074
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 09:03:55 2019 -0400
Merge branch 'development' into sdc_diffusion
commit b2cb6e0746616ca3795348452696a325370159dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 09:03:12 2019 -0400
probdata.f90 -> probdata.F90
Exec/gravity_tests/DustCollapse/Make.package
Exec/gravity_tests/DustCollapse/probdata.F90
Exec/gravity_tests/StarGrav/Make.package
Exec/gravity_tests/StarGrav/probdata.F90
Exec/gravity_tests/evrard_collapse/Make.package
Exec/gravity_tests/evrard_collapse/probdata.F90
Exec/gravity_tests/hydrostatic_adjust/Make.package
Exec/gravity_tests/hydrostatic_adjust/probdata.F90
Exec/gravity_tests/uniform_cube_sphere/Make.package
Exec/gravity_tests/uniform_cube_sphere/probdata.F90
Exec/scf_tests/single_star/Make.package
Exec/scf_tests/single_star/probdata.F90
Exec/unit_tests/particles_test/Make.package
Exec/unit_tests/particles_test/probdata.F90
Exec/unit_tests/reactions_driver_test/Make.package
Exec/unit_tests/reactions_driver_test/probdata.F90
commit 81003abb301fa9b67dbcaf0dbb7537a267270859
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 08:59:35 2019 -0400
rename probdata.f90 -> probdata.F90
Exec/reacting_tests/reacting_bubble/Make.package
Exec/reacting_tests/reacting_bubble/probdata.F90
Exec/reacting_tests/reacting_convergence/Make.package
Exec/reacting_tests/reacting_convergence/probdata.F90
Exec/reacting_tests/toy_flame/Make.package
Exec/reacting_tests/toy_flame/probdata.F90
commit 63e02dbf4a1e9a927a6733e0df0c35094fe52bcf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 08:57:46 2019 -0400
rename probdata.f90 -> probdata.F90
Exec/science/convective_flame/Make.package
Exec/science/convective_flame/probdata.F90
Exec/science/flame/Make.package
Exec/science/flame/probdata.F90
Exec/science/nova/Make.package
Exec/science/nova/probdata.F90
Exec/science/rotating_star/Make.package
Exec/science/rotating_star/probdata.F90
Exec/science/subchandra/Make.package
Exec/science/subchandra/probdata.F90
Exec/science/xrb_mixed/Make.package
Exec/science/xrb_mixed/probdata.F90
commit 636db79c78f97dd5574e28ba2e27e19491126aaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 08:55:57 2019 -0400
remove unneeded file
Exec/science/convective_flame/exploration/probdata.f90
commit cb0f9005105b90cae5cd27d2738bd1b7df5819db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 5 08:49:47 2019 -0400
rename probdata.f90 -> probdata.F90
Exec/hydro_tests/HCBubble/Make.package
Exec/hydro_tests/HCBubble/probdata.F90
Exec/hydro_tests/KH/Make.package
Exec/hydro_tests/KH/probdata.F90
Exec/hydro_tests/RT/Make.package
Exec/hydro_tests/RT/probdata.F90
Exec/hydro_tests/RT_particles/Make.package
Exec/hydro_tests/RT_particles/probdata.F90
Exec/hydro_tests/Sod/Make.package
Exec/hydro_tests/Sod/probdata.F90
Exec/hydro_tests/Sod_stellar/Make.package
Exec/hydro_tests/Sod_stellar/probdata.F90
Exec/hydro_tests/acoustic_pulse/Make.package
Exec/hydro_tests/acoustic_pulse/probdata.F90
Exec/hydro_tests/acoustic_pulse_general/Make.package
Exec/hydro_tests/acoustic_pulse_general/probdata.F90
Exec/hydro_tests/double_bubble/Make.package
Exec/hydro_tests/double_bubble/probdata.F90
Exec/hydro_tests/double_mach_reflection/Make.package
Exec/hydro_tests/double_mach_reflection/probdata.F90
Exec/hydro_tests/gamma_law_bubble/Make.package
Exec/hydro_tests/gamma_law_bubble/probdata.F90
Exec/hydro_tests/gresho_vortex/Make.package
Exec/hydro_tests/gresho_vortex/probdata.F90
Exec/hydro_tests/oddeven/Make.package
Exec/hydro_tests/oddeven/probdata.F90
Exec/hydro_tests/riemann_test_zone/Make.package
Exec/hydro_tests/riemann_test_zone/probdata.F90
Exec/hydro_tests/rotating_torus/Make.package
Exec/hydro_tests/rotating_torus/probdata.F90
Exec/hydro_tests/symmetry/Make.package
Exec/hydro_tests/symmetry/probdata.F90
Exec/hydro_tests/test_convect/Make.package
Exec/hydro_tests/test_convect/probdata.F90
Exec/hydro_tests/toy_convect/Make.package
Exec/hydro_tests/toy_convect/probdata.F90
commit a691d76b7c8103c47e71268bed7e2055ce0d18fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 4 18:35:46 2019 -0400
make tis dimension agnostic
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/Make.package
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_nd.F90
Exec/hydro_tests/Vortices_LWAcoustics/probdata.F90
commit 322f47298a60ff5a5dfca6429eda61f32f36fa48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 4 12:25:59 2019 -0400
we still need the flame parameters for the BCs
Exec/science/flame/probin.sdc.map
commit 2b592749c72009e1039bf21f6d6ac959056feb26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 4 09:39:40 2019 -0400
we always need to create pradial, not just for non-Cartesian
Source/hydro/Castro_mol_hydro.cpp
commit 9781b1cc99e5ee158cc6877b9516990b33189f25
Merge: 44bcc6cb8 63f4d95af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 4 08:22:02 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 44bcc6cb81a46cd722f3231f36a214ed4d77a729
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 18:19:09 2019 -0400
sync up the SDC papers with what was run on Cori
turn on initialization_is_cell_average for the mapping case
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.map
commit cfe5b9aa00c820fb2ec55d5d3e7f48ea56282d22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 15:54:27 2019 -0400
be careful with roundoff when comparing to 0
Source/driver/interpolate.F90
commit d8e8dc24c77e55579b5f966ca2e039e0498dfc3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 15:53:27 2019 -0400
new inputs for conservative mapping
Exec/science/flame/inputs.1d.sdc.map
Exec/science/flame/probin.sdc.map
commit 9c9d5898cf8fad41834c3b7f57f26c5be1b20b88
Merge: 04403a99c ef0663041
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 15:45:15 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 04403a99c63894741d49464aa8df61dc2d8f57ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 15:35:58 2019 -0400
remove the old rprox setup
Exec/science/flame/inputs.1d.rprox
Exec/science/flame/probin.rprox
commit ef066304145a0a5fbfd0e22e31ea719843bf2e8c
Merge: c261ff99c 28000f86c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 12:32:33 2019 -0700
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit c261ff99cc593325738cf5f421baf12cc524fc76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 12:32:20 2019 -0700
latest parameters
Exec/science/flame/inputs.1d.sdc
commit 28000f86cea396d50ec6ef4959ce552e8d82bb9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 15:06:03 2019 -0400
update the initialization to allow conservative model mapping
Exec/science/flame/Prob_nd.F90
Exec/science/flame/probdata.f90
commit c21312d3aae1fa1cbda758366c0f943522ba0158
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 14:19:25 2019 -0400
hook in the new conservative interpolator
Exec/Make.Castro
commit da6fbb38956907a149ab71841bafa568fbe98165
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 14:15:18 2019 -0400
a new model parser that expects conservative data
Util/conservative_interpolate/Make.package
Util/conservative_interpolate/conservative_map.F90
Util/model_parser/GPackage.mak
commit 1c1583fbe469b1a70a5d651d3c114c342b7ed91e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 13:23:41 2019 -0400
switch to dimension agnostic
Exec/hydro_tests/double_mach_reflection/GNUmakefile
Exec/hydro_tests/double_mach_reflection/Prob_2d.f90
Exec/hydro_tests/double_mach_reflection/Prob_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_ext_fill_nd.F90
Exec/hydro_tests/double_mach_reflection/bc_fill_2d.F90
commit 541821f1e6d05c820c3cc3dfcf6c1c805d464977
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 12:36:31 2019 -0400
add test file and fix spelling of castro for riemann solver choice
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/inputs.2d.test
commit 45492367cc121cf0934d1874994bf18d0db630eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 12:35:34 2019 -0400
turn on amr verbosity
Exec/hydro_tests/double_mach_reflection/inputs.2d
commit c5b758c619d64a7b89212e1b9a329e3ea611e35c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 12:31:16 2019 -0400
make dimension agnostic
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/riemann_test_zone/Prob_nd.F90
commit 5b020353335a2e8ab36fc22b42f820c1237e59c1
Merge: 5589e348e 63f4d95af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 10:35:41 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 63f4d95af9b61b4cb46ee006376f9cabf03bb29e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 22:11:58 2019 -0400
we are not using this custom BC
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
commit b1e6db78e5d47500e1be0ca8d31d030c0c25ef6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 22:07:27 2019 -0400
switch to dimension agnostic.
Also note that the probin sponge namelist was invalid
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/Prob_nd.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/test_convect/ext_src_nd.F90
Exec/hydro_tests/test_convect/probin
commit 6826b0dc8da8d0ed87d4003a079f9a8d0dbf1f8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 21:08:36 2019 -0400
switch to the centralized HSE BC
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/test_convect/probdata.f90
commit 654ee49bfd398f77ca911535693504475bf67b86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 20:57:49 2019 -0400
switch to the centralized "interp" BCs. They are mostly identical, aside from
the diode condition on normal velocity
Exec/reacting_tests/reacting_bubble/bc_fill_2d.F90
Exec/reacting_tests/reacting_bubble/bc_fill_3d.F90
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
commit d5b9df08d6601024d4a407a168645d3491394b3c
Merge: 28d4d1d41 2c0046b48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 20:22:49 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 28d4d1d41c80a96331731ca300415ea7ac6588eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 20:22:24 2019 -0400
switch this over to the centralized HSE BC. This gives diffs O(1.e-12)
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/inputs_2d
commit 2c0046b482959e2f4b16db33d73e29ac1f8a8fe4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 19:18:45 2019 -0400
fix center
Exec/hydro_tests/double_bubble/Prob_nd.F90
commit c6b7c30e1c376e0f82640034a261dd641a2de7ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 19:14:59 2019 -0400
make this dimension agnostic
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_bubble/Prob_nd.F90
Exec/hydro_tests/double_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/double_bubble/bc_fill_2d.F90
Exec/hydro_tests/double_bubble/probdata.f90
Exec/hydro_tests/double_bubble/probin
Exec/hydro_tests/double_bubble/probin.single
Exec/hydro_tests/double_bubble/probin.single.equal
commit fcf88f29fcf710fcfa276a6b1701017c1665b971
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 17:35:21 2019 -0400
make this dimension agnostic
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/Make.package
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/Prob_nd.F90
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.H
Exec/hydro_tests/gamma_law_bubble/Problem_Derive.cpp
Exec/hydro_tests/gamma_law_bubble/Problem_Derive_F.H
Exec/hydro_tests/gamma_law_bubble/bc_ext_fill_nd.F90
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
Exec/hydro_tests/gamma_law_bubble/problem_derive_nd.F90
commit 10ed1d8dac8013800c5c5937ea099fbde4b9d4ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 15:18:39 2019 -0400
remove USE_OLDPLOTPER -- it does not exist in the code anywhere
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/science/nova/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/reactions_driver_test/GNUmakefile
commit a169875338a0d388405679b72c01976287b477eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 14:10:12 2019 -0400
add an inputs for a non-Maestro run
Exec/hydro_tests/gamma_law_bubble/inputs_2d.test
Exec/hydro_tests/gamma_law_bubble/probin
commit 41771413f2ef85a6524b23f5a470e4e04adfe2b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 2 14:06:48 2019 -0400
add testsuite version
Exec/hydro_tests/double_bubble/inputs_2d.test
commit 5589e348eb7de1fa867f1a0345cd479ba64c7ffd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 1 22:02:11 2019 -0400
implement initialization_is_cell_average functionality
Source/driver/Castro.cpp
commit 055d1aebfc9493cfa7c3524b705f8b90c4d8f4c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 1 21:50:11 2019 -0400
add initialization_is_cell_average
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 3f9046f1c62c8821c50e86fc618ca670a4d9d4fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 1 20:48:20 2019 -0400
fix an error condition
Source/driver/interpolate.F90
commit 49c90f9af7086f686cebbdbc5a4185d776808d9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 1 20:29:51 2019 -0400
add a conservative interpolation routine that works with model_parser
Source/driver/interpolate.F90
commit 9326483b542ab95a5e6410a2d47bc0aef378c2f5
Merge: 64111dff5 223c72c99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 1 19:00:10 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 223c72c993343ba5df84613d058ffb0767c2a7c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 1 18:59:24 2019 -0400
update changes
CHANGES
commit 64111dff5bc05fa426976b93929b8aa3bfedbdb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 31 18:16:29 2019 -0400
add a script to make a flame speed convergence plot
Exec/science/flame/analysis/flame_speed.py
Exec/science/flame/analysis/flame_speed_convergence.py
commit c87e05e835858a4b9aefa5c6883b8c5fe1564a1d
Merge: 46d2ce5a5 306d8165e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 31 10:48:09 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 306d8165ed85d8abc8b0f4d4d96297db984220a1
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed May 29 12:06:50 2019 -0400
added submission scripts and inputs files
Util/scaling/sedov/summit_201905/CPU_runs/inputs.3d.sph
Util/scaling/sedov/summit_201905/CPU_runs/inputs.3d.sph_1level
Util/scaling/sedov/summit_201905/CPU_runs/probin.3d.sph
Util/scaling/sedov/summit_201905/CPU_runs/summit_16node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_32node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_4node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_64node_nogpu.sh
Util/scaling/sedov/summit_201905/CPU_runs/summit_8node_nogpu.sh
Util/scaling/sedov/summit_201905/GPU_runs/inputs.3d.sph
Util/scaling/sedov/summit_201905/GPU_runs/inputs.3d.sph_1level
Util/scaling/sedov/summit_201905/GPU_runs/probin.3d.sph
Util/scaling/sedov/summit_201905/GPU_runs/summit_16nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_32nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_4nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_64nodes.sh
Util/scaling/sedov/summit_201905/GPU_runs/summit_8nodes.sh
commit 237b7e8e72c583b3ccedfa4042f5777a92454452
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Tue May 28 14:31:52 2019 -0400
added scaling sedov txt file, and script I used for the plot.
Will add the inputs, and submission scripts once summit is operational
again
Util/scaling/sedov/summit_201905/plot_scaling.py
Util/scaling/sedov/summit_201905/summit_scaling_may19.txt
commit 1063c3fd9607bbf2966afd689987d6590da9448b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 26 10:42:35 2019 -0400
Add deprecation notices
CHANGES
commit 5c1b7099968a319519db3f81a7d880ba059a28ee
Merge: 461bfb580 8658597a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 25 20:10:31 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 461bfb580bf9e45ff7f10a314961d51a809b5be3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 25 19:43:13 2019 -0400
siwtch to dimension agnostic
Exec/science/bwp-rad/GNUmakefile
Exec/science/bwp-rad/Make.package
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/bwp-rad/Prob_nd.F90
Exec/science/bwp-rad/probdata.F90
commit 46d2ce5a57a66cd5a3d57e2055b0f2863479d8d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 25 14:55:14 2019 -0700
add more restart
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc4.slurm
commit 8658597a006f332239bbf2ed7bc80d374110d623
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 25 17:21:05 2019 -0400
fix compilation
Exec/radiation_tests/RadBreakout/Make.package
commit 42a97ed5ad4a972ad5cf970f40d89142d8b4eee3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 20:47:53 2019 -0400
switch to dimension agnostic
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/Rad2Tshock/Make.package
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_nd.F90
Exec/radiation_tests/Rad2Tshock/bc_ext_fill_nd.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_1d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/Rad2Tshock/probdata.F90
commit 52f7ef733461a396a866874b2d0294763cc57bff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 18:47:33 2019 -0400
make this dimension agnostic
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadFront/Prob_1d.f90
Exec/radiation_tests/RadFront/Prob_2d.f90
Exec/radiation_tests/RadFront/Prob_nd.F90
commit 82e83268bc3731f7102aa30a5d4b9b3563f0b65d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 18:28:34 2019 -0400
rename probdata.f90 -> probdata.F90
Exec/radiation_tests/Rad2Tshock/Make.package
Exec/radiation_tests/Rad2Tshock/probdata.F90
Exec/radiation_tests/RadBreakout/Make.package
Exec/radiation_tests/RadBreakout/probdata.F90
Exec/radiation_tests/RadFront/Make.package
Exec/radiation_tests/RadFront/probdata.F90
Exec/radiation_tests/RadShestakovBolstad/Make.package
Exec/radiation_tests/RadShestakovBolstad/probdata.F90
Exec/radiation_tests/RadSlope/Make.package
Exec/radiation_tests/RadSlope/probdata.F90
Exec/radiation_tests/RadSourceTest/Make.package
Exec/radiation_tests/RadSourceTest/probdata.F90
Exec/radiation_tests/RadSphere/Make.package
Exec/radiation_tests/RadSphere/probdata.F90
Exec/radiation_tests/RadSuOlson/Make.package
Exec/radiation_tests/RadSuOlson/probdata.F90
Exec/radiation_tests/RadSuOlsonMG/Make.package
Exec/radiation_tests/RadSuOlsonMG/probdata.F90
Exec/radiation_tests/RadThermalWave/Make.package
Exec/radiation_tests/RadThermalWave/probdata.F90
commit bbdb897f24349acdd2cc5bf74c40418ed9b0d01d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 17:50:57 2019 -0400
switch to dimension agnostic
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSourceTest/Make.package
Exec/radiation_tests/RadSourceTest/Prob_1d.f90
Exec/radiation_tests/RadSourceTest/Prob_nd.F90
commit d0d0c84b61befd4d51cddf06e8d7b69b0d8fd6fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 11:18:14 2019 -0400
make this dimension agnostic
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/Make.package
Exec/radiation_tests/RadShestakovBolstad/Prob_1d.f90
Exec/radiation_tests/RadShestakovBolstad/Prob_nd.F90
commit 2eca50086fa7598f7f6ca8f78fc2d523120185cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 10:58:09 2019 -0400
make this dimension agnostic
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadBreakout/Make.package
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadBreakout/Prob_nd.F90
commit e243b5c9c2df1454e15875b9be40ddd0165eb81b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 10:27:33 2019 -0400
switch to dimension agnostic
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSlope/Make.package
Exec/radiation_tests/RadSlope/Prob_1d.f90
Exec/radiation_tests/RadSlope/Prob_nd.F90
commit 40834647ca6000dc8b2354b832649612d0b29a8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 10:14:40 2019 -0400
switch to dimension agnostic
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/Make.package
Exec/radiation_tests/RadSuOlsonMG/Prob_1d.f90
Exec/radiation_tests/RadSuOlsonMG/Prob_nd.F90
commit 2507737801097454bffa901cc0d6a679e94f96ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 09:46:53 2019 -0400
update to dimension agnostic
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlson/Make.package
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
Exec/radiation_tests/RadSuOlson/Prob_nd.F90
commit 7d9579f8f776dd47adbd6f7dfe790f12340de84e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 24 06:49:13 2019 -0400
switch to dimension agnostic
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSphere/Make.package
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/radiation_tests/RadSphere/Prob_nd.F90
commit 8f9e9a5e59b538a417a1f053fd364d42fb3f1eb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 23 20:09:11 2019 -0400
make dimension agnostic
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/reacting_tests/toy_flame/Prob_nd.F90
commit 02aff00c5760233db7b10a7a77248026df6e67ea
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Wed May 22 17:44:56 2019 -0700
Prepare Castro for upcoming changes in AMReX (#614)
There are some upcoming changes in AMReX's Geometry class. This pull-request makes Castro work with the current AMReX development branch and the future version. I have tested this in CCSE's regression test suite.
Source/diffusion/Diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/radiation/HypreABec.cpp
Source/radiation/RadSolve.cpp
Source/radiation/energy_diagnostics.cpp
Util/ConvertCheckpoint/Embiggen.cpp
Util/ConvertCheckpoint/Make.package
commit 36e0e62028bed7116e73515715520c143f95fecc
Merge: c1fb20b64 01cb624f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 21 10:43:02 2019 -0400
Merge branch 'development' into sdc_diffusion
commit c1fb20b64394aad33cac61da67a28eedb2b4fed6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 20 12:54:16 2019 -0700
fix MPI stuff
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc2.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc4.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.strang.slurm
commit 01cb624f4a557258f85fd4f943c094dfa1f3a97a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 17 16:21:51 2019 -0400
fix crashy
Exec/hydro_tests/Sod/testsuite_analysis/sod.py
commit e0e5c993bbba17d71e5b363aa7079ab14504cd2c
Merge: 327bab501 6c13caff4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 17 16:17:17 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 327bab501fed06ce8f0aea9575e1c5d772768f5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 17 16:14:47 2019 -0400
add an analysis script for the test suite
Exec/hydro_tests/Sod/testsuite_analysis/sod.py
commit 6c13caff4e04b03b15fe925477ba5dbbbe0a0af4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 16 22:28:02 2019 -0400
backport the dimensional agnostification from sdc_diffusion
Exec/science/flame/GNUmakefile
Exec/science/flame/Prob_nd.F90
Exec/science/flame/bc_fill_nd.F90
Exec/science/flame/probdata.f90
commit a5d83c804acb49d8e5f0a8e0235cd815ed717cfe
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu May 16 17:36:24 2019 -0400
updated with git hashes
Exec/science/flame_wave/scaling/scaling.txt
commit ed919c6c403ae6051f55f25f08eb5fa5bdd1bab3
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu May 16 17:35:33 2019 -0400
scaling measurements for flame_wave
Exec/science/flame_wave/scaling/avg_time.sh
Exec/science/flame_wave/scaling/scaling.txt
commit 8ea11a4a426755758859df3622aa97e09f57e5dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 16 13:20:53 2019 -0400
fix the BC flags
Exec/science/flame_wave/scaling/inputs.scaling.3d
commit ba64ce3573ea2874c4b82fcc1bcf0189cd298c4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 15 18:52:14 2019 -0400
remove a print
Exec/science/flame_wave/Prob_nd.F90
commit c4af8e588532833e78ba9fe98014310efac8f255
Merge: f202d43b7 5a840ebaf
Author: Alice Harpole <harpolea@login5.summit.olcf.ornl.gov>
Date: Wed May 15 15:36:10 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit f202d43b75a8f6ad38619eed0ea325f452c3e9e7
Author: Alice Harpole <harpolea@login5.summit.olcf.ornl.gov>
Date: Wed May 15 15:35:54 2019 -0400
flame_wave scaling inputs file
Exec/science/flame_wave/scaling/inputs.scaling.3d
commit 5a840ebafa575d6f45bcc47f25c84f1e73e92474
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 15 15:14:01 2019 -0400
fix bug in dimensioning in calc_pdivu (#612)
calc_pdivu works on the Godunov states, so the input state vectors were dimensioned incorrectly.
Source/hydro/advection_util_nd.F90
commit 1b4eb8b4e67cca36bfa982badd319607ee5f9b68
Merge: 38c63e515 90bfbe830
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 14 16:46:13 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 38c63e515d051e804dbbf1f1b25cd333e2bccfd5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 14 16:46:00 2019 -0400
turn on plot_per_is_exact
Exec/science/flame/inputs.1d.sdc
commit 90bfbe830a64e41168e2ecbc579551afaffc76bc
Merge: 97829d53e 3fbba0b38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 14 13:42:31 2019 -0700
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 97829d53e2a870a0d0e0da089059f6ca3a96c8dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 14 13:42:18 2019 -0700
updated job scripts
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc2.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.sdc4.slurm
Exec/science/flame/job_scripts/cori_haswell.MPI.strang.slurm
Exec/science/flame/job_scripts/edison.MPI.slurm
commit 3fbba0b38b299e41c8b49f8d32170434af226de1
Merge: 6f417f1f0 e5e5ad3ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 14 16:36:28 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 6f417f1f04a8220d96c2940b7d0905d572441d08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 14 16:36:13 2019 -0400
bump density up even more -- this flame gets going much faster
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
Exec/science/flame/test_sdc4.sh
commit e5e5ad3cac0bf2e08975313dfd69a631acd17308
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 11:44:13 2019 -0700
add a Cori job script
Exec/science/flame/job_scripts/cori_haswell.MPI.slurm
commit ac1c544d24c40f6ea067b03378877fdd7b11fef5
Merge: 5f9c3f9d2 d6eaf4c65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 11:04:52 2019 -0400
Merge branch 'sdc_diffusion' of ssh://github.com/AMReX-Astro/Castro into sdc_diffusion
commit d6eaf4c6554267b83506482167aff01f302884cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 11:04:19 2019 -0400
add xmin
Exec/science/flame/analysis/profiles.py
commit 5f9c3f9d26ced43fd74bf2e784e9dd2730e3119e
Merge: b0c9a0266 df9cf5d83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 11:03:07 2019 -0400
Merge branch 'sdc_diffusion' of ssh://github.com/AMReX-Astro/Castro into sdc_diffusion
commit df9cf5d8338303113a933112f6953ae4ec3a60fb
Merge: 84c7abce5 247e99bd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 11:02:49 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit b0c9a02665ab976aa86b031da67222bb9fcd4cd3
Merge: 247e99bd7 84c7abce5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 11:01:57 2019 -0400
Merge branch 'sdc_multinewton' into sdc_diffusion
commit 84c7abce5bd3ced983670747e58662436e1198b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 11 10:52:19 2019 -0400
this is the version for the paper
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
Exec/science/flame/test_sdc4.sh
commit 247e99bd72cde09e791826d208247d18f9f048c6
Merge: ae304043e ddad5cbbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 10 10:04:55 2019 -0400
Merge branch 'development' into sdc_diffusion
commit ae304043e20361a239a39aa66034b1d20bf270de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 9 21:57:39 2019 -0400
make the domain smaller still + higher CFL
also switch to pure Newton -- this runs fine
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
Exec/science/flame/test_sdc4.sh
commit ddad5cbbba96a199aa1ca518d98608dbb4815ace
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Thu May 9 12:16:06 2019 -0700
Include ghost zones in enforce min density for type 1 and 2. (#608)
This uses the ghost zones as well to enforce the minimum density.
This sets Type 2 to also use s_lo and s_hi in the same way as Type 1.
Source/hydro/advection_util_nd.F90
commit 6b8c20e3e5bcd41dca3ef5f9ad479b8c799e893d
Merge: 4d1ff6daf f5d65a0be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 9 09:55:58 2019 -0400
Merge branch 'development' into sdc_multinewton
commit 4d1ff6dafa39d4471c65c85e48c80f5783d92629
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 9 09:52:53 2019 -0400
shrink the domain more
Exec/science/flame/inputs.1d.sdc
commit c033d5d3f75c0dc3acfbfc793b55d145d2aa8f18
Merge: 5132dee40 a082cd204
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 9 09:33:36 2019 -0400
Merge branch 'sdc_multinewton' of github.com:AMReX-Astro/Castro into sdc_multinewton
commit 5132dee40fa45947859f9189c9a9bcb7ade70fcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 9 09:33:18 2019 -0400
use a 4th order conservative intepolant to find flame speed
Exec/science/flame/analysis/flame_speed.py
commit a082cd20413ce8a18e0e70da14ec9e05dfe1f74f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 16:55:37 2019 -0700
update for the new flame problem
Exec/science/flame/job_scripts/edison.MPI.slurm
commit fed84facd84e4bbb11d83318a1e632daf40978b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 19:51:23 2019 -0400
new stop time
Exec/science/flame/inputs.1d.sdc
commit 9018b0c686f9ee9cd50ef29a9856348dd38cd935
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 18:22:04 2019 -0400
make the domain smaller yet -- these flames don't move much
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
commit 2084b4089851a0515b8fe32781efc789a125a86b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 13:01:00 2019 -0400
keep mass flux constant across the flame initially
Exec/science/flame/Prob_nd.F90
Exec/science/flame/probdata.f90
commit 606ed973eeade983beefcabd55b5eb6d0ff124bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 12:43:33 2019 -0400
add KE to UEDEN _not_ UEINT
Exec/science/flame/Prob_nd.F90
Exec/science/flame/probin.sdc
commit 119793e79709c550847287c14c2a94d4356f5339
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 12:22:36 2019 -0400
new SDC flame inputs -- this is a lower density flame
it is really a flame this time, not a detonation
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
Exec/science/flame/test_sdc4.sh
commit c3996d856bd0818fd4e76576d587ad94306f903f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 10:34:28 2019 -0400
add a scipt to show profiles in multiple variables
Exec/science/flame/analysis/profile_start_finish.py
commit 4c87b8aefe394d432abefb57d11823f203cf86cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 10:12:45 2019 -0400
put back in the old BC behavior if we do not set an inflow vel
Exec/science/flame/bc_fill_nd.F90
commit 031517540e5d7384d523e0c2c545a0fda6aded95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 8 09:58:20 2019 -0400
add the ability to have an inflow velocity
Exec/science/flame/Prob_nd.F90
Exec/science/flame/bc_fill_nd.F90
Exec/science/flame/probdata.f90
commit ca150ce98000b7055edbe8bc27ab8ef04818d78d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 7 19:12:05 2019 -0400
restore atol back to 1.e-10 -- this now works
Exec/science/flame/test_sdc4.sh
commit 4252865c06c29e4a75f386f8f95f6e399e0aad6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 7 19:04:56 2019 -0400
atol was not being enforced on the species, making the solve harder than it should be
Source/driver/sdc_util.F90
commit 9140ea64b7e2e64b86122c94bb068725638b1ef3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 7 15:08:04 2019 -0400
switch to solver 3 and loosen atol -- this runs successfully!
Exec/science/flame/test_sdc4.sh
commit 30d57c0f78b4764a0339d097a8fc091d208fb227
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 7 15:07:18 2019 -0400
split the sub-Newton into its own routine and add normalization
Source/driver/sdc_util.F90
commit bc0772c0a804548088eb3f0f714b7d0d4b4f2d95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 6 20:04:45 2019 -0400
add Newton subcycling to the hybrid solve
Source/driver/sdc_util.F90
commit 0d16e0402dc0b90c4f4efe2337a36d77231b5ca9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 6 19:36:37 2019 -0400
remove the eta stuff
Source/driver/sdc_util.F90
commit 5a240cc5d1ea53d3ffb2bf96b3f29670acf4da12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 6 19:04:47 2019 -0400
split the Newton solve into many pieces if we fail to converge
Source/driver/sdc_util.F90
commit 050f094418734f55467049fadbb14720b5ffee8b
Merge: 7c3cbd1fc e7a2a143c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 6 15:53:09 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 7c3cbd1fc65f0e158d3487b39a394d4b825d7a9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 6 15:52:33 2019 -0400
do a clean_state on the updated time node
this requires copying to S_new, clean_state, then copying back
Source/driver/Castro_advance_sdc.cpp
commit e7a2a143cad4f37343240fbd12aca9f7008f9c2d
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Sun May 5 17:06:36 2019 -0700
Add notebook to plot the ratio of delta rho/sum(delta rho*X)
Exec/science/flame/analysis/Density-Delta-Ratio.ipynb
commit b5b58d0ed3f5b73804fd77c016bc2b52189ce108
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 5 17:08:00 2019 -0400
switch to using a more VODE-like error check for convergence with Newton
add a "learning rate" like feature to the Newton to only use part of the update
if we sense it will make species negative
Source/driver/sdc_util.F90
commit f5d65a0be6001054b5e734051f5dbd5598450f74
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 4 16:43:01 2019 -0700
Use relative temperature gradient as the refinement criterion (#607)
Exec/radiation_tests/Rad2Tshock/Castro_error.cpp
Exec/radiation_tests/Rad2Tshock/probin.M2
Exec/radiation_tests/Rad2Tshock/probin.M5
commit 9b6b4d2bc224b03518b28c8ddbb54e200d475a0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 4 17:25:02 2019 -0400
Fix CUDA issues with enforce_min_density
Source/driver/Castro.cpp
Source/hydro/advection_util_nd.F90
commit 5cf526e6cd95620ae73bb802c514f7a7a6afb6ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 4 07:41:22 2019 -0700
fix restart file issue
Exec/science/flame/job_scripts/edison.MPI.slurm
commit 53fcd3b5f370cdf959c9ae96e7bb1eb5322b075a
Merge: 39d168ed0 d53c5c55f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 3 08:52:41 2019 -0700
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 39d168ed04d318a489f870733ecc3c35c98f5d06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 3 08:52:24 2019 -0700
this version has restart
Exec/science/flame/job_scripts/edison.MPI.slurm
commit d53c5c55f2e77a4d2242202a99c7a7e570765f25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 19:57:30 2019 -0400
clean up to make more readable
Exec/science/flame/test_sdc2.sh
commit 7859a15dd9e58edb1cf31f96182b733e521d0258
Merge: 72dd9181a ed0da2b2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 19:53:38 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 72dd9181ae84a69c6960b7a32c10dde19b8e9ebf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 19:48:42 2019 -0400
update the SDC4 test -- this works and gives a reasonable looking flame
(but generates a floating point exception if run with amrex.fpe_trap_invalid=1)
Exec/science/flame/test_sdc4.sh
commit ed0da2b2d7f0b4ea5ce82da424fd422897876644
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 12:23:17 2019 -0700
a script that runs a suite of SDC flame jobs
Exec/science/flame/job_scripts/edison.MPI.slurm
commit ec3ba03dd1f2e4bc0796ced2053b19ca02dc0f06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 15:07:49 2019 -0400
skip the Newton after VODE
Source/driver/sdc_util.F90
commit 56c72f04d5bdf79cc317a93bedcf18e31d631ef5
Merge: 96f5da5a6 b7cfdb744
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 15:07:33 2019 -0400
Merge branch 'sdc_diffusion' of github.com:AMReX-Astro/Castro into sdc_diffusion
commit 96f5da5a62e3347328b6d05bd0ab647182f6ad0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 15:07:23 2019 -0400
better ash composition
Exec/science/flame/probin.sdc
commit b7cfdb74477771a7f43fefded417efc126752110
Merge: d56541b56 c77b165c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 11:24:29 2019 -0700
Merge branch 'development' into sdc_diffusion
commit c77b165c0af3b04ce0d22044fa6026523883e20c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 11:23:54 2019 -0700
update runtime parameters
Exec/reacting_tests/reacting_convergence/job_scripts/edison.MPI.slurm
commit d56541b56878836b22f0acfff2549005778f44c2
Merge: ac08e0bbf d746553d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 2 11:22:47 2019 -0700
Merge branch 'development' into sdc_diffusion
commit d746553d4972b75cf28e05517acc977165343d42
Merge: 033b9299a d23770e07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 12:53:43 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 033b9299a29df86555210bf78dfa2d72d93591ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 12:53:33 2019 -0400
add sponge docs
sphinx_docs/Makefile
sphinx_docs/source/sponge.rst
commit d23770e07683fa700b5ba3350835a1164524b380
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 1 09:22:53 2019 -0700
Need to use the GPU-safe min reduction
Source/hydro/advection_util_nd.F90
commit 31dfc4d73207515dd52491d66df0551b4df5169e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 1 09:17:07 2019 -0700
Do enforce_min_density on the GPU
Source/driver/Castro.cpp
Source/hydro/advection_util_nd.F90
commit ed5b0cb2dba4eb04c44289e798d5f3ff8ced49d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 11:50:40 2019 -0400
some sponge docs
sphinx_docs/source/sponge.rst
commit e50f1f0395c335d6b5254d1e0ac1b2d0829d7d5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 1 11:18:26 2019 -0400
Limit Riemann speed to 0.1c
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit ac08e0bbfd550baf5b00c5a0f671b8fa95c7481c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 09:03:57 2019 -0400
remove outdated comment
Source/driver/sdc_util.F90
commit 39249c177da403651803da7604653609e12e66d2
Merge: b05b14b4f 0c4c56fbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 09:01:56 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 0c4c56fbbf5c657ea59e62ae09404eadfd3c711a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 08:47:02 2019 -0400
update version
CHANGES
commit b05b14b4f7f544ff45afe0d5fdb9190d1e94829a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 30 21:14:35 2019 -0400
decrease chk frequency
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/inputs.1d.sdc
commit 14a10a2132d05ccbbefb7a066d13573ed7017243
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 30 13:55:46 2019 -0400
clean up the scripts for easier diffing
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
Exec/science/flame/convergence_strang.sh
commit ae869d1962a5d9a69e0bd863f8925d5d33d6eddc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 22:37:50 2019 -0400
change the right BC to use fuel state
Exec/science/flame/Prob_nd.F90
Exec/science/flame/bc_fill_nd.F90
Exec/science/flame/probdata.f90
Exec/science/flame/test_sdc2.sh
commit ce809cc5574b5801385c9fee65e395bc26e3ab67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 20:54:43 2019 -0400
Make this problem dimension agnostic
use a reflecting BC on the left
Exec/science/flame/GNUmakefile
Exec/science/flame/Prob_nd.F90
Exec/science/flame/inputs.1d.sdc
commit 2dcba147662efe46e23573b374c131aae8aa6b36
Merge: 522fc4fc9 e46c1c4f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 18:12:42 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 522fc4fc93437a2a47c2ffb8a3b89023a7b05c48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 14:28:45 2019 -0400
add an xmax arugment and scale the range of enuc shown
Exec/science/flame/analysis/profiles.py
commit 6d5085e45bb4b5b107bc72d84f36add851426aec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 11:59:24 2019 -0400
add sdc_extra for iterations beyond the formal order
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 3ec2acabe7521d73e4e020808c44267b9d8bbce9
Merge: ce04a3084 11e79944c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 11:46:07 2019 -0400
Merge branch 'sdc_vodefix' into sdc_diffusion
commit e46c1c4f9905fafb0cbb9eb71725fa31b6746446
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 29 11:13:16 2019 -0400
Don't use fab.format=NATIVE_32
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit f5d8b874b7f032ff75f312e5acff4542bd6e6073
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 29 10:24:01 2019 -0400
Fix another missing statement
Exec/science/wdmerger/initial_model.F90
commit ce866ec122f2b82ad66a387e82e2c03a91a50def
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 29 10:22:27 2019 -0400
Fix a missing statement in wdmerger initial model construction
Exec/science/wdmerger/initial_model.F90
commit 9873ceb81fe56b0734ad1cd9f1e2f00ebf80e0ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 10:04:56 2019 -0400
fix compilation
Exec/science/flame_wave/Prob_nd.F90
commit 2baf2b52eb4bccb1d08a8d1caa03cbcd8e42a798
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 28 21:01:50 2019 -0700
Add box information to most of the kernels
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_io.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_hydro.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit d56ca119526b22278edd2487206cbfe3ae0d8b87
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 28 17:04:24 2019 -0700
Use different format for passing box to pragma
Exec/science/wdmerger/Prob.cpp
Source/driver/sum_utils.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_ctu_hydro.cpp
commit 8087bebd0bced646be565b67220316ab150fe702
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 28 16:30:43 2019 -0700
Use new shared memory reduction functions
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/wdmerger_util.F90
commit 23f497e846e1a215bf698a35be0cb0e6f2dd873b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 28 16:22:01 2019 -0700
Use new shared memory reduction functions
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
Source/gravity/Gravity.cpp
Source/gravity/Gravity_nd.F90
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_ctu_nd.F90
commit 11e79944c416428d7195abb3ac5bb2d69fcc2ab8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 28 16:08:33 2019 -0400
these are the current testing scripts
for SDC-2 we seem to run out for a while without issue
for SDC-4, we make it to ~2700 steps (with aprox13)
Exec/science/flame/test_sdc2.sh
Exec/science/flame/test_sdc4.sh
commit 034f7b55558ae8a6c77b2e8d6577a8d0f5ee4c55
Merge: 3b92f9ec4 5000bd1ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 28 15:40:56 2019 -0400
Merge branch 'development' into sdc_vodefix
commit ce04a3084ba69211979d57c3edc9c8e754c92a96
Merge: dd246c2a9 5000bd1ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 28 15:40:39 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 3b92f9ec49abcec8f480fc922a8e6255384267fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 28 15:04:30 2019 -0400
fix compilation
Source/driver/sdc_util.F90
commit 5000bd1ee77f76463a070bd733779363c29bf2b2
Merge: 1dd3fb7fc dda07cd31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 28 09:15:55 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 1dd3fb7fc823a34785ed305f0c5bb0363d1b8414
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 28 09:15:21 2019 -0400
add a check on small_dens vs. low_density_cutoff
(we are fine for the current inputs, but this will remind us in the future)
Exec/science/flame_wave/Prob_nd.F90
commit dda07cd311c7470049a342f0f9505bf0e299cdd8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 22:16:35 2019 -0700
Do ca_ext_src on the GPU
CHANGES
Exec/gravity_tests/hydrostatic_adjust/ext_src_nd.F90
Exec/science/wdmerger/ext_src_nd.F90
Source/driver/Castro_F.H
Source/sources/Castro_external.cpp
Source/sources/ext_src_nd.F90
commit 60b6b032d16b9c82d7d627c41995fd8ed81708ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 21:44:24 2019 -0700
Do wdmerger initialization on the GPU
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/Prob_nd.F90
commit 36f420da19321530561ec04d66727f8e32ef4b28
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 21:34:44 2019 -0700
Allocate directly, not through interface
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/wdmerger_util.F90
commit 6dc1580a2901e93de28edfae18e7303fc351c7c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 21:51:24 2019 -0400
Fix another function interface issue
Exec/science/wdmerger/Prob_nd.F90
commit bfc082352adf0019886b10e5f96b502b835c37b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 21:38:36 2019 -0400
Move copies of rho, T, xn, r to probdata module
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/initial_model.F90
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/wdmerger_util.F90
commit 21527c4334dce8f61d71795088a2935ef0583ab6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 19:48:56 2019 -0400
Fix location of allocate statement
Exec/science/wdmerger/wdmerger_util.F90
commit f596de9acdff4cc704229a9ee51f0707e98bf155
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 19:33:04 2019 -0400
Merge initialization into one big loop
Exec/science/wdmerger/Prob_nd.F90
commit 94c8635c96700ed16b4b708eb535062f5461b4f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 19:27:56 2019 -0400
Avoid statements that will be problematic on the device
Exec/science/wdmerger/Prob_nd.F90
commit 5d261de8fc4748e40a991f5b2d71e50b4d1e8bea
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 19:16:56 2019 -0400
Clean up module use statements
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/wdmerger_util.F90
commit 2fa0b366100c9538a61e12caebca7e6ac8822866
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 19:00:05 2019 -0400
Define namelist in correct place
Exec/science/wdmerger/wdmerger_util.F90
commit 5808c8d8b284183a9a8aa43b2dc6161427b2d6d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 18:57:22 2019 -0400
Initial model interpolation on the device
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/initial_model.F90
commit ec06ab5c4ac00d2515a148e7c3ba53a645973f56
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 18:21:03 2019 -0400
Make wdmerger probdata allocatable and managed
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/wdmerger_util.F90
commit 6f6c5d94a83205628d8a2651bf48e75591e0fa3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 27 17:33:52 2019 -0400
double precision -> real(rt)
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.F90
commit 454934b376f3756cca8081563f7d435e48ed0fb0
Merge: 3bf73f856 726df58ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 09:14:28 2019 -0400
Merge branch 'development' into sdc_vodefix
commit 3bf73f856394439208c12c395ae0964790603791
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 08:38:39 2019 -0400
preserve the temperature from the VODE prediction going into Newton
Source/driver/sdc_util.F90
commit 726df58ab788fe0faf96d32954c6b429a63bd543
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 22:52:51 2019 -0700
Only do a single atomicAdd
Exec/science/wdmerger/wdmerger_util.F90
commit c52025f089b9f4e71ce80b79e16eebf32e331454
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 22:19:46 2019 -0700
Do remainder of sum_utils on the GPU
Source/driver/Castro_F.H
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
commit 787232be3d3ff56f7433a401b5730c07fe018a9c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 20:50:22 2019 -0700
Hybrid source terms on the GPU
Source/driver/Castro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/hybrid_advection_nd.F90
commit f1a29cb937ff8adabc73de9e143cdc14318bf829
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 20:17:58 2019 -0700
Do some of wdmerger's post_timestep on the GPU
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/wdmerger_util.F90
commit 137786b17977d42ae9b602100ecaf7f46133eb42
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 15:32:07 2019 -0700
Do wdmerger derives on the device
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Problem_Derive.H
Exec/science/wdmerger/Problem_Derive.cpp
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/probdata.F90
Exec/science/wdmerger/problem_derive_nd.F90
Exec/science/wdmerger/wdmerger_util.F90
Source/problems/Problem_Derive.cpp
commit bc5a41913b4d49cc73d4752943aabd66fdcbdacb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 14:53:50 2019 -0700
Add Problem_Derive.cpp
Source/problems/Make.package
Source/problems/Problem_Derive.cpp
commit 78db8bcb122058e78c6f75844ccd945a25279364
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 13:30:20 2019 -0700
Change problem_derive_nd to F90 file
CHANGES
Exec/reacting_tests/reacting_bubble/problem_derive_nd.F90
Exec/science/wdmerger/problem_derive_nd.F90
Source/problems/Make.package
Source/problems/problem_derive_nd.F90
commit 538366e45f8b64f25141a36cc9000d0c2b12f55e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 26 12:45:33 2019 -0700
Enable multipole BCs for Poisson gravity on GPUs
Aside from normal markup, the main extra work here was to avoid
creating local dynamically allocated arrays of size lnum, since
those require a lot of local memory and were not known at
compile time. So the Legendre polynomial arrays and other related
data are now calculated using a running recursion relation rather
than being explicitly calculated in arrays.
Source/gravity/Gravity.cpp
Source/gravity/Gravity_nd.F90
commit 5424c117d048ceefa7fa7e933941dc6a98acbfec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 26 13:17:10 2019 -0400
more jacobian fixes
Source/reactions/react_util.F90
commit ac24f3e5218fbccc8d2ae380ceee31d923e6e96f
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Fri Apr 26 11:20:53 2019 -0400
update subchandra inputs
update sub_chandra inputs
Exec/science/subchandra/inputs_2d
commit 00bda92884c55206b55c58dd7ae4b3a5b7464367
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 24 21:48:05 2019 -0400
add a hybrid solve
Source/driver/sdc_util.F90
commit d9f8f4c06ea884f77bc11ad109c6f3b3e53c97fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 24 19:02:46 2019 -0400
change how we do the numerical Jac for the Newton solve
now we use the factored Jac, computing the conservative var transformation
analytically and using the Microphysics numerical_jac_module for the
reactive part. This is much more robust and the new code with VODE
preconditioning seems to run now
Source/driver/sdc_util.F90
Source/reactions/react_util.F90
commit d54455cd12a3f9e5d20314b23888f979eae49ad9
Merge: 8a8296181 dd246c2a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 24 16:31:18 2019 -0400
Merge branch 'sdc_diffusion' into sdc_vodefix
commit dd246c2a950715353e5d5bac505626d5e68b9e47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 24 16:29:33 2019 -0400
fix the relax_factor stuff -- make it easier not harder on early iters
Source/driver/sdc_util.F90
commit 8a8296181762b606811816ed837e0af4ba50bfe6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 24 16:28:35 2019 -0400
print tols on error too
Source/driver/sdc_util.F90
commit 23ae756815a9140442b60a7d1f5e7c2b2611c88f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 24 16:01:44 2019 -0400
split the solver into Newton and VODE parts and attempt to use VODE as a preconditioner
plus lots of numerical Jacobian fixes
Source/driver/sdc_util.F90
commit 2d9086d8ed3cf9987e6e544179c5ea65ce58cb6d
Merge: 56faaf30a d372bf017
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 23 20:22:11 2019 -0400
Merge branch 'sdc_diffusion' into sdc_vodefix
commit d372bf017b4912952eea12627e6bc85e86e61df6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 23 20:21:50 2019 -0400
fix compilation
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/hydro/Castro_fourth_order.F90
commit 56faaf30ac9e9aaa8b1b56460e9b6daa0c09fdee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 23 20:19:29 2019 -0400
fix compilation
Source/driver/sdc_util.F90
commit de0335384dccfad874a01461906303ec0319346f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 23 20:02:42 2019 -0400
split the solve routine into Newton and VODE parts
this will let us use VODE as a guess to the Newton
Source/driver/sdc_util.F90
commit e6c705c7306f202b81d84e55fd123ed849994758
Merge: 13bba0329 c9478a1d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 23 19:04:03 2019 -0400
Merge branch 'development' into sdc_diffusion
commit c9478a1d8ed661fc5862bec80cff63d2f68cfe73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 15:59:22 2019 -0400
roll back verisons -- sphinxfortran doesn't like Sphinx 2.0
requirements.txt
commit 7d55e6d0abc90cab76fc97329c17e8fd5d32c536
Merge: 6831eaf9d e602be308
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 15:53:12 2019 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 6831eaf9dd1bb1b53fc047b1c5ab7d720052a058
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 15:52:57 2019 -0400
relax sphinx version restriction
requirements.txt
commit e602be308e7c91a856a1b1d7f58b14762a48b691
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 15:41:53 2019 -0400
start of a section on the sponge
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/index.rst
sphinx_docs/source/sponge.rst
commit 9dd1b9e723d33679c26870688946f6a4fd9b2798
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 15:30:36 2019 -0400
fix files names
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc.sh
commit 8962d66f21c2561e3a64b0c9d38f69d6364dcc2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 15:29:30 2019 -0400
fix convergence check times
Exec/hydro_tests/acoustic_pulse_general/convergence_rk4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc.sh
commit 56fbaeb1aea1a61010b1d3044bf3ea38957c2483
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 14:42:08 2019 -0400
fix runs
Exec/hydro_tests/acoustic_pulse_general/convergence_rk4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse_general/helmeos_runs.sh
commit 59770024e133adbaa0f0386fc7117e19fef7814e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 14:21:00 2019 -0400
update style
Exec/hydro_tests/acoustic_pulse_general/convergence_1d_sdc4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_rk4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc4.sh
commit 47a0614d2876cf99cbfa5a87445dc718aeb04a9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 13:59:05 2019 -0400
rename
Exec/hydro_tests/acoustic_pulse_general/convergence_rk4.sh
commit f0aa9dab0f63515ac3ece69b9b072842bb95edf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 13:55:03 2019 -0400
fix convergence check
Exec/hydro_tests/acoustic_pulse/convergence_sdc4.sh
commit 589c4e15aa46b2b881b714eb2a3857d9d4fade05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 10:04:08 2019 -0400
update the script style
Exec/hydro_tests/acoustic_pulse/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse/gamma_law_runs.sh
commit 1abca1f414f2192cfb2f2960d0d3985d38578bd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 09:52:44 2019 -0400
rename and update the rk4 convergence
Exec/hydro_tests/acoustic_pulse/convergence.sh
Exec/hydro_tests/acoustic_pulse/convergence_rk4.sh
commit 13bba032989a028f2cc6d738873bf039a193d5fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 22 09:43:39 2019 -0400
ifdef out some diffusion stuff
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_hydro.cpp
commit fda9d57c02293a94cece975f48ee3e1c89ceb02e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 21 18:35:34 2019 -0700
Use vector instead of dynamic array to avoid PGI complaint
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit 26001f682f4fbbd3cf5e2b40f6f823d4d6b2af50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 21 19:46:55 2019 -0400
a little more about diffusion
Source/hydro/Castro_fourth_order.F90
commit 36282a06eeb6b44a6db86157d362366b615485c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 21 18:48:51 2019 -0400
more work on multidimensional 4th order diffusion
Source/hydro/Castro_fourth_order.F90
commit 9a37753dd1a8a954b55f520f2c0b04d362f30396
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 21 12:07:57 2019 -0700
Prep work for accelerating multipole BCs
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.F90
Source/gravity/Make.package
commit a74c5ca5d3737e9e7824a17be5e3ccc0fa471f15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 21 10:15:29 2019 -0400
fix memory leak
Source/hydro/Castro_fourth_order.F90
commit 13ca75430cbd94e96e2337eac8b8838e3fabc570
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 21 10:05:37 2019 -0400
block off some flux stuff for do_hydro == 0
Source/hydro/Castro_fourth_order.F90
commit ac0cbdcbe47272fdcd7386c5409ad79c8d3203de
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 20 20:07:34 2019 -0700
Fix typo in profiling tag
Source/gravity/Gravity.cpp
commit 37cbe686dd0b4557cb9326912db7d33ca3cf8f7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 19:14:34 2019 -0400
sync up the the 2nd order sdc version
Exec/science/flame/convergence_sdc4.sh
commit 6817fe7dc41e6207e9275da8b339a7a3a5200fdb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 18:57:25 2019 -0400
eliminate init_shrink
Exec/unit_tests/diffusion_test/inputs.1d
commit c89549a39f44e8492a921dbe375e5ca9b22b79dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 18:37:36 2019 -0400
for 4th order tests, compute the norm against cell averages
Exec/unit_tests/diffusion_test/Prob.cpp
commit 45479a0790aee1d6d43a7d39b9203a1ae690c690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 15:09:10 2019 -0400
the 4th order diffusion works, but still need to understand convergence
Source/hydro/Castro_fourth_order.F90
commit eec52dc6ed1647a330c6de2724523f6d3ef923ed
Merge: c3744b6dd e0316bd19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 14:59:13 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit c3744b6ddba9b96ede284cfa37131f1a3c07e6fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 14:58:13 2019 -0400
remove outdated comment
Source/hydro/Castro_fourth_order.F90
commit fff500f40eff9dbc9819d88127d41fcdc3bd7cd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 14:43:44 2019 -0400
still do cons_to_prim even if do_hydro = 0, since we will want that for diffusing
Source/driver/Castro_advance_sdc.cpp
commit e0316bd1933cf2c320fa5accec12a897ef9d1ce5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 20 12:19:05 2019 -0400
Mark up a few hybrid routines for the GPU
Source/hydro/hybrid_advection_nd.F90
commit caa7ad27963aac0f3959e40910d6c567e77d6800
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 20 12:18:48 2019 -0400
Fix macro
Source/hydro/Castro_hydro.cpp
commit 08ed52230d2e1ebc9bbdbb95a60a8d9deae4acf9
Merge: 674743170 8fdd2ee70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 11:46:26 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 8fdd2ee7097bef8df15b3f955ae34de5a5f61f89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 11:43:58 2019 -0400
fixes the potential negative dens/rhoe from converting averages -> centers (#601)
Source/driver/Castro.cpp
Source/hydro/Castro_hydro.cpp
commit 674743170c249cef6a5e4be00246d6e34aa70f80
Merge: a06e47942 1c5884b66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 11:38:09 2019 -0400
Merge branch 'development' into sdc_diffusion
commit 1c5884b66911bea33c82986b9d51d7db6dd149e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 11:37:27 2019 -0400
Sdc hybird (#596)
- Add a hybrid solver for the nonlinear SDC solve, that tries Newton first and then VODE if that fails
- Uses a better initial guess for T in all the solves
- Adjust the flame problem setup and add a enuc limiter
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/inputs.1d.sdc
Source/driver/sdc_util.F90
commit 0f42e36a6488d02596358959614e3dc69c1c624e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 10:43:12 2019 -0400
add note about riemann_speed_limit
sphinx_docs/source/Hydrodynamics.rst
commit e698d4fc25d82f733a8997f8de27d35c9c624454
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 20 07:37:09 2019 -0700
Riemann solver can not generate interface velocities > c (#603)
Castro is a Newtonian hydrodynamics code and has no knowledge of special
relativity. This means that spuriously large, unphysical velocities can
be generated. This commonly occurs in the wdmerger problem at poorly
resolved density gradients near the edge of the stars. Although a proper
solution to this problem involves adding SR to the code, a simple approach
to improving the situation is to enforce a speed limit in the Riemann solve.
By default this speed limit is c, but the user can lower it (for example,
to a value like 0.1c which is still in the relativistic regime where Castro
results should be distrusted) if they know the range of realistic values
taken by the velocity for their problem.
CHANGES
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/riemann_nd.F90
commit a17df2995c92280578364fabd46737d5db105e04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 20 09:27:14 2019 -0400
update changes
CHANGES
commit 1689a9dcb5f5aa25874f166c4ba1d91173bb7816
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 19 23:00:47 2019 -0700
Fix bug in post-reflux position-dependent source terms (#599)
The algorithm for recalculating source terms after an AMR reflux did not set some data needed to correctly calculate positions on the fine levels, so position-dependent source terms (rotation, hybrid momentum) were being calculated incorrectly. This caused some strange effects in AMR simulations
with rotation, such as binary star orbits getting wider with time and drifting relative to the system center of mass. This has now been fixed.
The issue is that the position() function implicitly needs to know what AMR level we're on to use the correct dx spacing for that level, so we need to call ca_set_amr_info() whenever we're looping over levels.
CHANGES
Source/driver/Castro.cpp
commit a06e479426ae21cfddcf304c7240b1bfeab0ad58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 17 18:46:04 2019 -0400
fix a pradial bug + add a first attempt at 1-d 4th order diffusion
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_hydro.cpp
commit c4ff8bf945f2e9fccc635e19e1cdbc251a8cad7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 16 15:26:43 2019 -0400
implement second order diffusion as a flux -- this seems to work
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
commit fc891f69b68ac7efb9baa165c396c7300152f40c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 16 13:36:53 2019 -0400
disable the diffusion source for MOL/SDC -- we'll do it in the MOL itself
Source/sources/Castro_sources.cpp
commit 7dd9e1c614c9f9be38779ed8c32a54bdf1513433
Merge: 6cc24be9f 418c7ca67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 16 10:26:00 2019 -0400
Merge branch 'development' into sdc_hybird
commit 35b994515164caf99fb80581b3f8cd164d689627
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 15 15:10:14 2019 -0400
Fix bug for state_in_rotating_frame = 0
Source/hydro/advection_util_nd.F90
commit 418c7ca67eb2d78668e6d908cc5abde9becd5a56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 15 09:57:37 2019 -0400
this is a version of the plotting script that crops the horizontal size
Exec/science/flame_wave/analysis/slice_multi_crop.py
commit 6cc24be9f031ff0dccaa590b97c4cc6cd2af9f1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 14 18:24:05 2019 -0400
tighten tol on ener
Exec/science/flame/convergence_sdc.sh
commit e432fc25cdcea6880d18fab34f83d97ecbe7f536
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 14 18:23:07 2019 -0400
for the hybrid solve, cap the number of initial Newton iterations
Source/driver/sdc_util.F90
commit 8c3f75a3b0775d7a7698c70ab6d973f94bd304a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 14 18:22:45 2019 -0400
add a dtnuc_e limiter
Exec/science/flame/inputs.1d.sdc
commit eabc833a4a06b33adf41bc5cb65b30decc3851f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 17:59:10 2019 -0400
Rename wdmerger problem 5 (TDE) as problem 2
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/tde/probin.test
Exec/science/wdmerger/wdmerger_util.f90
commit 8314c3a406e7242c7e33c821ca409edd459ade91
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 17:55:00 2019 -0400
Fold wdmerger problem 4 into problem 0
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/wdmerger_util.f90
commit 15c69e113b82cb73217e8a8b03e282ee1ce82cbd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 17:00:41 2019 -0400
Fold wdmerger problem 2 into problem 1
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/wdmerger_util.f90
commit 4844a92ed303a1ceca616cbbd8b2d47d7d358667
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 16:49:11 2019 -0400
Keep Coriolis terms on even when relaxing
Exec/science/wdmerger/wdmerger_util.f90
commit 88ba124e4846fb57494ab0498736048718ff85aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 16:47:10 2019 -0400
Fold wdmerger problem 3 into problem 2
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/wdmerger_util.f90
commit dc00d1894b6d55cf459cc7506d077a8ddc447234
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 16:24:10 2019 -0400
Fold wdmerger problem 6 into problem 3
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/wdmerger_util.f90
commit dc45d6dcc405c2fe4458452d36c01b37384c79a3
Merge: 0c4ea48b2 de792ec79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 14 14:26:12 2019 -0400
Merge branch 'development' into sdc_hybird
commit 0c4ea48b2dcf1cc1006185a271a470dcb9019106
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 14 14:24:05 2019 -0400
drop CFL a smidge -- ignition is hard
Exec/science/flame/inputs.1d.sdc
commit de792ec79b46fc635bc2ecc2cfa461988a808b33
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 13:30:45 2019 -0400
Skip explicit construction of time-centered phirot
Source/driver/Castro_F.H
Source/rotation/Castro_rotation.cpp
Source/rotation/rotation_sources_nd.F90
commit 966b683c6b864973fa1ebab5619fd506e2e67439
Merge: d83c0af8b 13072a0ae
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sun Apr 14 08:29:50 2019 -0700
Merge pull request #600 from AMReX-Astro/gravity_opt
Skip old-time gravity solve for uniform grid runs
commit 13072a0ae4b3c0d158f52185baf8cbfe1b50c9b9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 10:59:42 2019 -0400
Skip old-time gravity solve for uniform grid runs
Source/gravity/Castro_gravity.cpp
commit d83c0af8b39d0ae8c3c136e0e4f44ea842c7b2d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 14 01:27:34 2019 -0400
Add problem 6 that relaxes for a set period of time
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/wdmerger_util.f90
commit d5c21bba6dab8f08aab0c003cd9b291c77c9022b
Merge: 0421d350b 6f0fc4920
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 21:28:54 2019 -0400
Merge branch 'development' into sdc_hybird
commit 0421d350b2df19f6a5f320dd41346f89643492b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 21:24:23 2019 -0400
turn back on lower res
Exec/science/flame/convergence_sdc.sh
commit 6f0fc4920a7c59902e9153cdb0084276063a3256
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 21:11:35 2019 -0400
switch to a smooth transition from fuel to ash (tanh)
this allows for convergence
Exec/science/flame/Prob_1d.f90
Exec/science/flame/probin.sdc
commit 55e0a66843f9d125fe914975fe2e8a120b3c5cac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 12:43:20 2019 -0400
reduce duration
Exec/science/flame/inputs.1d.sdc
commit c941b643bef5942acbd8bb498dd54f3849072b59
Merge: 7b4aaf0f6 68ee4f8bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 09:45:21 2019 -0400
Merge branch 'development' into sdc_hybird
commit 68ee4f8bb468b801a99f57316b18efbab3c34207
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 09:06:48 2019 -0400
make the transition region isobaric
Exec/science/flame/Prob_1d.f90
commit 7b4aaf0f6ebbaa4429f760a463c9e9d81baccbc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 09:00:29 2019 -0400
catch singular matrix for hybrid
Source/driver/sdc_util.F90
commit 7c4b594becc13aaf0dcae48faa99015d4e1f7ba1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 08:59:55 2019 -0400
update tolerances
Exec/science/flame/convergence_sdc.sh
commit 115b442614e372d1a2a69120fd2a95197d0a1838
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 13 02:29:53 2019 -0400
SDC tols (#593)
This splits the tolerance that the nonlinear solve for SDC reactions uses to have separate values for density, species, and energy.
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_util.F90
commit 0b540d51fb4e634f839f35c159be99ba8e39c5f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 12 20:06:46 2019 -0400
Update flattening for CTU hydro using CUDA
Source/hydro/Castro_ctu_hydro.cpp
commit dacb435d748169130639ca97ba16766a7ebf5c69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 19:16:39 2019 -0400
increase max_grid_size
Exec/science/flame/inputs.1d.sdc
commit 627334ae3026cbdaef20164f159272f8ed600ae4
Merge: 328ba92ad 1fb709eef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 18:36:31 2019 -0400
Merge branch 'sdc_hybird' of github.com:AMReX-Astro/Castro into sdc_hybird
commit 328ba92adcaa05054144d710f5f58d651e174e2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 18:34:29 2019 -0400
update comments
Source/driver/sdc_util.F90
commit 1fb709eef16b302a6dd99051bdbfae8c6fa62d4a
Merge: a2f2bf6b1 5b9c4b2e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 11:53:13 2019 -0400
Merge branch 'sdc_temp' into sdc_hybird
commit 5b9c4b2e02501f106b3c7bb40b2801cff83ee623
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 11:50:49 2019 -0400
update the temperature guess as we burn
Source/driver/sdc_util.F90
commit b2bdf99ec29be1a04bf72d862c3400dbce7cc120
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 10:30:03 2019 -0400
use a more sensible EOS guess
Source/driver/sdc_util.F90
commit 5516a820e2ee02932868bc9e38e8641841d4c4ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 12 09:16:11 2019 -0400
update changes
CHANGES
commit 6a2ddd974b34d783c846105164df2e655071bec2
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Apr 11 22:25:08 2019 -0400
Fix sign error in hybrid_hydro (#594)
This addresses issue #462. After this change, the wdmerger problem works with hybrid momentum.
During commmit 0f09693, a change in signs was introduced in add_hybrid_momentum_sources, which should be analogous to linear_to_hybrid
Source/hydro/hybrid_advection_nd.F90
commit a2f2bf6b1b861b83ae84906ba620aab273b69f3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 11 15:59:35 2019 -0400
continue -> cycle
Source/driver/sdc_util.F90
commit 15592e07dc61c199c7f0194d402893db1de7da63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 11 15:22:33 2019 -0400
fix compilation
Source/driver/sdc_util.F90
commit 10ec2bbf5f28ce87ae4e2be7074aea13427b1ccb
Merge: 88edaed73 f5a748a1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 11 13:52:14 2019 -0400
Merge branch 'development' into sdc_hybird
commit 88edaed732de2b5bf3ffa7f9eb0a051193b41809
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 11 13:51:59 2019 -0400
start of logic for hybrid / retry solve
Source/driver/sdc_util.F90
commit 2375d38ceb1de9735aae86374dfb01ce7c853d9b
Merge: 1fce2f358 f5a748a1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 11 13:51:36 2019 -0400
Merge branch 'development' into sdc_tols
commit f5a748a1f76fbfd9d6d3ad9e765acb1b3a5f1b09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 11 13:49:55 2019 -0400
a bunch of optimizations: (#585)
* SDC optimizations:
* we no longer recreate the sources for m = 0 on the later iterations
* we no longer do the final source computation except for the last iteration
* we use Sborder for the initial burn instead of filling Sburn -- this changes
answers since we do a clean state on Sborder and were not doing one on
Sburn
Source/driver/Castro_advance_sdc.cpp
Source/hydro/fourth_order.F90
commit b340694651cff710aea09e840c644eceb3b56049
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 11 10:59:53 2019 -0400
Update overridden Fortran make rules
Exec/Make.cuda_rules
commit 1fce2f3582ebdb8654d80421fc9fb905f8b0e881
Merge: c75d24a21 6005a4938
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 17:32:06 2019 -0400
Merge branch 'sdc_tols' of github.com:AMReX-Astro/Castro into sdc_tols
commit c75d24a2120fff39b0859ccbbb9adedfaad0d52a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 17:31:50 2019 -0400
flame doesn't like the analytic Jacobian
Exec/science/flame/convergence_sdc.sh
commit 6005a49389090537d55c86f68ee042a0eafd36da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 14:15:32 2019 -0400
use atol in Newton solve
Source/driver/sdc_util.F90
commit 3c840b02fcd3ab4e4bc754f67c4ddf3f52b16a55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 12:22:19 2019 -0400
remove lower res run
Exec/science/flame/convergence_sdc.sh
commit 3e5b786328312788870a3fcc34b7f5f79ef83a73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 12:22:04 2019 -0400
use analytic Jacobian
Exec/science/flame/convergence_sdc.sh
commit 24efd22e77d9947547f75c5747237e5aa29e6bd6
Merge: a42fd4ec9 f4ff32f54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 12:12:53 2019 -0400
Merge branch 'sdc4-opt' into sdc_tols
commit f4ff32f540434f5bb25ba693d5e78e69daacb101
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 10 11:10:51 2019 -0400
remove maxval checks -- they don't change performance
Source/hydro/fourth_order.F90
commit b55773f219f08a639c610a8e7781072a1ba218eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 10 00:24:13 2019 -0400
Cancel force correctly for 2D axisymmetric
Exec/science/wdmerger/wdmerger_util.f90
commit a23e53e635620c5c87c7cf7b708d843c1efdec0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 10 00:16:21 2019 -0400
Revert "Unroll a loop to catch axisymmetric case"
This reverts commit bb2c471e4b88beea500d3b6ce4df3a64caf7dd33.
Exec/science/wdmerger/Problem.f90
commit bb2c471e4b88beea500d3b6ce4df3a64caf7dd33
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 10 00:10:11 2019 -0400
Unroll a loop to catch axisymmetric case
Exec/science/wdmerger/Problem.f90
commit a5863216339d436cce82285ba9616fe13705075e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 10 00:09:51 2019 -0400
Fix a dimension-agnostic interface
Exec/science/wdmerger/Prob.cpp
commit 9a82f6ae4ba3857209db5a5c8e25b19a0fc1dde7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 9 21:56:13 2019 -0400
revert zero check in make_cell_center
Source/hydro/fourth_order.F90
commit 92e5330083e67cf35db95a5daeb7d7b817e186c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 15:29:30 2019 -0400
sync up params + add slower rotating model
Exec/science/flame_wave/inputs.boost_10_10
Exec/science/flame_wave/inputs.boost_10_10_slow
Exec/science/flame_wave/inputs.boost_5_5
Exec/science/flame_wave/probin.boost_10_10_slow
Exec/science/flame_wave/probin.boost_5_5
commit 77b9628a693a4d1ce587291af99d558d7f9f0dbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 15:17:37 2019 -0400
move into old
Exec/science/flame_wave/old/inputs.boost_25_4
Exec/science/flame_wave/old/probin.boost_25_4
commit a42fd4ec9885b25b37813a9b8f753b383b21e45c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 12:33:02 2019 -0400
update tolerance parameters to new names
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
commit 51efa3511aafe732881231165a112cc45a9bb929
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 12:21:09 2019 -0400
add an absolute tolerance for the SDC nonlinear solve
this works on species
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_util.F90
commit f9ec11d3fb12d2262e6c78c0f7da64ae1fa20cd8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 8 11:49:35 2019 -0400
Cannot capture static class members in device lambdas
Source/hydro/Castro_mol_hydro.cpp
commit a84f61716b04e89d3dd0d22f20e82afe24677893
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 11:41:39 2019 -0400
implement different sdc tolerances on species, density, and energy
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_util.F90
commit e3266fd0d1e589509b4d5479522592407f45156d
Merge: f08e64eb4 bc9409e62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 10:44:48 2019 -0400
Merge branch 'development' into sdc4-opt
commit bc9409e6295e802552a6a71002687c2f154e71a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 10:44:32 2019 -0400
add runs
Exec/science/flame/convergence_sdc.sh
commit 638fae1afc84ff65ef157732e851437b494a0201
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 8 09:59:42 2019 -0400
remove comment
Source/driver/sdc_util.F90
commit 3da3ea51f89a4bec5cdcd1efbdaee94a8f25d23d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 8 01:29:32 2019 -0400
Reorder GPU pragma statement
Source/sources/sponge_nd.F90
commit fbe03031d674dac89a513acaf178f6a1eaab0cf7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 8 01:03:18 2019 -0400
Zero out rotation source terms before loop so variables are initialized
Source/rotation/rotation_sources_nd.F90
commit 5b2e0724a7a329868dd8925f084c9f461313d0ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 8 00:59:01 2019 -0400
Fix hybrid hydro source term for sponge and rotation
These were being done incorrectly because the source term was being
added on every loop iteration instead of being reset.
Source/rotation/rotation_sources_nd.F90
Source/sources/sponge_nd.F90
commit f08e64eb44f9c2ccf61a3e2acba0ca142f4fa255
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 21:04:31 2019 -0400
fix compilation
Source/driver/Castro_advance_sdc.cpp
commit 8d66bc13376cd5b1abc23fe2458b472d91de3b3a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 7 20:49:20 2019 -0400
Fix typo in hybrid momentum source terms
This bug has apparently been around for a while and resulted in non-conservation
of angular momentum in the presence of source terms when using hybrid_hydro.
This now matches my dissertation, Equation 9.
Source/hydro/hybrid_advection_nd.F90
commit cad196db0236330433a614419a231990fae4fa7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 20:39:21 2019 -0400
fix duplicate do_old_sources
Source/driver/Castro_advance_sdc.cpp
commit 3dcb84b45500e5bbbdd3eb376fe191ac7dc202c4
Merge: f6081296d cc87c9e67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 20:14:20 2019 -0400
Merge branch 'development' into sdc4-opt
commit cc87c9e670cb4d276b0bc53e1adb4e86057b4e32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 20:05:17 2019 -0400
sdc do_hydro (#588)
Implement castro.do_hydro for MOL/SDC solvers.
Source/driver/Castro_advance_sdc.cpp
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_hydro.cpp
commit c0c538c67d3504cd9eb377868325aa25c543c5e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 13:58:42 2019 -0400
lint
Exec/science/flame/analysis/profiles.py
commit 648b32600e344a7f9d104df40ba865d43e4f3378
Merge: 00e3d5e73 de1cf6688
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 09:03:22 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 00e3d5e733aed80ad06b74554bfb01f0bfb530e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 09:03:05 2019 -0400
fix the output for the 16384 run
Exec/science/flame/convergence_strang.sh
commit 553bd0b4b2796e7d9ae2a67c911b5a55cbe4447a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 7 09:02:43 2019 -0400
make the perturb fraction smaller -- this will change the test suite
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/probin.sdc
commit de1cf6688516f352d547867a7a1546b987ba9bc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 7 06:05:21 2019 -0400
Add data log
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
commit 3d77c6c7ff062f0f5f0f48c234da845403e182b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 7 05:31:40 2019 -0400
Improve ambient rotation velocity in inertial frame
The inertial frame setup for wdmerger forced the ambient material to
be stationary. This was done because rotating the ambient material at
the rigid body rotation rate would lead to unbounded velocities at
large distances from the center, which could cause undesired effects
such as limiting the hydrodynamic timestep. However, it also caused the
effect of the stars plowing through the stationary ambient material in
the inertial frame, which also can lead to small timesteps, especially
at low resolution.
A compromise is found between these two effects by applying the rigid
rotation rate in the region near the stars, but capping the rotation
rate as the edge of the domain is approached.
Exec/science/wdmerger/Prob_nd.F90
commit 0a07c2b68710c26958fbc8330064c9bec34e0bd4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 6 18:30:19 2019 -0700
State when diffusion is the timestep limiter (#592)
Closes #586
Source/driver/Castro.cpp
commit 8f10b280b974d0cac761e3e491be6e723d60a877
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 6 20:34:16 2019 -0400
we don't need hydro_source for MOL or SDC integration (#591)
This gets rid of the hydro_source MF in MOL and SDC integration -- it is not used.
Closes #584
Source/driver/Castro_advance.cpp
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
commit 05f541241ec9597ec4497aee813ae923fb40abaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 6 19:34:37 2019 -0400
update problem sizes
Exec/science/flame/convergence_strang.sh
commit 5efb40fd4b6aa8235619eb25620be5c37a90d4fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 6 19:33:16 2019 -0400
double domain size
Exec/science/flame/inputs.1d.sdc
commit 91672d76b81f9702b4ef5cab6a9352b56262716a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 6 16:51:57 2019 -0400
fix filenames + add strang version
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
Exec/science/flame/convergence_strang.sh
commit f6081296de8cc72bdb92bdd3502bba9c9aa4d39d
Merge: fa6e592a6 e14769c99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 6 15:49:38 2019 -0400
Merge branch 'development' into sdc4-opt
commit e14769c99cfa7542cc613aade372ffc71665411f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 6 15:14:32 2019 -0400
Mol cuda (#562)
This rewrites the CPU second-order (PLM/PPM) MOL hydro to be GPU friendly, and eliminates the need for a separate code path for the CUDA MOL.
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit fad2de1fcf40c99691f0fb05efd70a67a95e4c62
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 6 15:12:16 2019 -0400
Disable CUDA implementation of MOL due to known bug
Source/driver/Castro.cpp
commit 1b7d75a0f6cdd078f823bfb86e2303e7835d996f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 5 21:12:59 2019 -0400
add a note about saxpy and setVal
sphinx_docs/source/gpu_porting.rst
commit fa6e592a683df23478bbe51175616626b96b0982
Merge: 7b17773e3 25ac3d33d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 3 08:31:37 2019 -0400
Merge branch 'development' into sdc4-opt
commit 25ac3d33d738a9a04ad337ae78d01a9907bfceef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 20:44:16 2019 -0400
add a docstring
Source/hydro/Castro_mol_nd.F90
commit de29e88460f75b693943f364928a6e995bca5a22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 13:45:31 2019 -0400
update convergence test
Exec/science/flame/convergence_sdc.sh
Exec/science/flame/convergence_sdc4.sh
commit 0c684766b8e02a279292018eb146ac2d8ce9e509
Merge: 47754dfd9 4420d76bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 11:06:21 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 47754dfd98179a55f9c5f971fc96209fd3117953
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 11:06:07 2019 -0400
add a convergence test
Exec/science/flame/convergence_sdc4.sh
Exec/science/flame/inputs.1d.sdc
commit db19802ffb0dd5370576f1a9d7e7d6e541a6ff28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 10:58:55 2019 -0400
reduce stop time
Exec/science/flame/inputs.1d.sdc
commit 4420d76bd3d8cfe6d147907a2458f117a3f22be1
Merge: e2f60d325 9d72e2f56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 09:13:31 2019 -0400
Merge branch 'master' into development
commit 9d72e2f56287112e1e43f6146ddfb82fffd157cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 2 09:13:14 2019 -0400
add to the checklist
.github/PULL_REQUEST_TEMPLATE.md
commit e2f60d325a6ffeff11bde688a56a0d017d6fdf03
Merge: 07e5b29eb 41005e58d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Apr 1 18:53:30 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 07e5b29ebaba4f42d938556c75acfd6e5b8edd6a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Apr 1 18:53:19 2019 -0400
added in missing brackets
Diagnostics/Radiation/rad_sphere.cpp
commit 41005e58d4ce7ca6c19bee05ae783f1e9282e21b
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Mon Apr 1 18:45:28 2019 -0400
Added scripts for measuring flame speed (#583)
Exec/science/flame_wave/analysis/flame_speed.py
Exec/science/flame_wave/analysis/front_tracker.py
Exec/science/flame_wave/probin.boost_25_4
commit aa4c634afc707e386959d948091f4cd9d6a66b03
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Apr 1 18:28:23 2019 -0400
actually fixed(?) indexing in rad_sphere diagnostic
Diagnostics/Radiation/rad_sphere.cpp
commit f7b180257550d5a1c175b3cad1bbda94c1b785a4
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Apr 1 17:17:24 2019 -0400
fixed(?) indexing in rad_sphere diagnostic
Diagnostics/Radiation/rad_sphere.cpp
commit f23c5f8e6c3f36e25d797a0d1a4566a8e3077237
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 1 10:15:55 2019 -0700
Require clean_state to directly work on a state MultiFab (#538)
This change removes the indirect clean_state interface that took is_new as an argument, and now clean_state must be directly handed the MultiFab that it will operate on.
This change also removes the interface to clean_state that passes in an old state for comparison. This was not necessary but it is nicer to only have a single interface, and the logic there was a little complicated. This choice necessitated a change in how we do enforce_minimum_density, with two downstream consequences. First, density_reset_method == 3 no longer exists -- since we don't have the old state to compare to, we cannot reset to it. (No test problems are actually using that method.) Second, because we don't have the old state, we have to change the logic for the retry method based on negative densities. Now we look at the change from the negative density to what it is reset to, rather than the density it originally came from. This will change the outcome of that method a bit, but qualitatively it does the same thing, since the hope is that the density we reset to is at least in the same ballpark as the density from the beginning of the step (we reset to a density similar to the density in adjacent zones). This change also closes #353.
Finally, clean_state has been removed from expand_state for clarity. In places where we requested a clean_state call indirectly through expand_state, these have been replaced by an explicit clean_state call after the expand_state call.
CHANGES
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_sdc.cpp
Source/driver/_cpp_parameters
Source/hydro/Castro_hybrid.cpp
Source/hydro/advection_util_nd.F90
Source/radiation/Castro_radiation.cpp
Source/radiation/MGFLD.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.cpp
commit 64585505ffa959652ef713dfe88e496361c6563f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 1 13:11:03 2019 -0400
increment version #
CHANGES
commit a03075b7d0e3c9e0b33d0483d6b6502186eb4126
Merge: 281b24d4c e0cab45f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 1 13:10:45 2019 -0400
Merge branch 'development'
commit e0cab45f189c56d519e6cd07dc25925465bc54e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 20:34:35 2019 -0400
fix the plot
Exec/radiation_tests/RadSphere/testsuite_analysis/radsphere.py
commit 0dd593b4da18bba2e2cf53a211dcdd4414c2c0f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 20:09:31 2019 -0400
more work on getting this plot to work
the data still does not show
Exec/radiation_tests/RadSphere/testsuite_analysis/radsphere.py
commit b1e6ddb31c8dd971a0fd962479f2c434c490b4cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 19:59:08 2019 -0400
close the file
Diagnostics/Radiation/rad_sphere.cpp
commit 567b515dc9861003b13a941653183edbf95635eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 19:56:17 2019 -0400
output to a file
Diagnostics/Radiation/rad_sphere.cpp
commit def298b2e7e5729734dd6585bc675ce04c28efde
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 19:43:04 2019 -0400
fix variable name
Diagnostics/Radiation/GNUmakefile
commit 7fa6cc8ceaec065933560f5e816943fe5ba72627
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 19:35:12 2019 -0400
update help
Diagnostics/Radiation/README.md
commit 1f4c501a56a3cc4b0fb498e3a6d720fc63f88cf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 19:33:31 2019 -0400
fix the build so we can specify the target and it works
Diagnostics/Radiation/GNUmakefile
Diagnostics/Radiation/Make.package
Diagnostics/Radiation/rad_sphere.cpp
commit 7b17773e3dd94643f0d8bbee860f91dfdebb5a57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 17:18:58 2019 -0400
a bunch of optimizations:
* we no longer recreate the sources for m = 0 on the later iterations
* we skip center <-> average conversions if the state is 0
* we no longer do the final source computation except for the last iteration
* we use Sborder for the initial burn instead of filling Sburn -- this changes
answers since we do a clean state on Sborder and were not doing one on
Sburn
Still need to test convergence with all of this
Source/driver/Castro_advance_sdc.cpp
Source/hydro/fourth_order.F90
commit a1cf1c5c81fe2c4497e5eb1028a60a01d0826590
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 13:18:09 2019 -0400
update 2-d scripts to work with new tools
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_2d_cyl_in_cart.py
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
commit 1c2c6150927c1d8b7fd8be75708f56122c57c809
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 13:03:04 2019 -0400
update the 3-d script to work with the C++ tool
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_3d_sph.py
commit a48bb826d0006c1595f67c49b43fab4b53ed8320
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 13:01:44 2019 -0400
comment the header for np.loadtxt reads it
Diagnostics/Sedov/main.cpp
commit e7cc8136f257fc8754d7aa642b05f6ba5840486a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 12:56:42 2019 -0400
need --sphr for 3-d too
Diagnostics/Sedov/main.cpp
commit 818366d6dacba3bd427b3f703fe289d587aff952
Merge: 57caf0546 dbf857020
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 12:53:57 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 57caf0546cb2fefd84e412c7597a47b97f47be52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 12:53:50 2019 -0400
fix compilation
Diagnostics/Sedov/main.cpp
commit dbf8570205f90a19424f16a79c6987ca5789191f
Merge: 6726fba1d 47dc340b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 30 23:08:33 2019 -0400
Merge branch 'sdc-initialguess' into development
commit 6726fba1df268dbf7c8be20c802b41f802de7264
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 30 19:33:56 2019 -0700
Avoid merge statements so XL can compile CUDA Fortran (#579)
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 47dc340b7b526164f419daddd4f97463a4bc5cd2
Merge: 97b28eec2 d9438b62e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 30 19:04:27 2019 -0400
Merge branch 'development' into sdc-initialguess
commit 97b28eec2c540cf9ed4754eba4d65259755c5235
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 30 13:10:45 2019 -0700
fix the file names in convergence check and move it to analysis
Exec/reacting_tests/reacting_convergence/analysis/check_convergence.sh
commit d9438b62eb196c84b00d5f8a4e244df55c361673
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 30 15:55:50 2019 -0400
add no top level use
sphinx_docs/source/coding_conventions.rst
commit ee39115e704e52c5ae8a2beb240d4cec7b75c38a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 30 11:49:43 2019 -0700
Avoid stop in CUDA Fortran code
Microphysics/EOS/eos_type.F90
commit 473542b77aab038e62db5d12d20b4f244c23022d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 30 14:47:18 2019 -0400
clearer logic for testing if sources are zero before tracing
Source/hydro/Castro_ctu_nd.F90
commit 17ad0a0c0f41fea28c8261641abc810a54efaa92
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 30 11:29:50 2019 -0700
Generalize register capping to support xlf
Exec/Make.cuda_rules
commit 982dd2280e18e6b1cf77ae57884dac8608e3493e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 30 10:15:43 2019 -0700
Remove unrestricted private statements
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_ext_fill_nd.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.F90
commit 6f46034b49198255dad4c1db7b72cfdfd0d06bcb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 30 09:51:51 2019 -0700
Move attributes(managed) statement to please the XL gods
Util/model_parser/model_parser.F90
commit fe0a6e878f676997474e2c284e6595a202584a8e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 30 09:44:39 2019 -0700
Fix C++ make rules
Exec/Make.cuda_rules
commit 08205f6c4ecc4b73f3da6e881e0d6fbf7578525e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 29 17:02:39 2019 -0400
create initial guess for 4th order nonlinear solve
Source/driver/Castro_sdc.cpp
Source/driver/sdc_util.F90
Source/hydro/Castro_hydro_F.H
commit cdfc97a3e54c2f71632b3ec1199729c20b48dd76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 29 15:07:35 2019 -0400
some work on the initial guess for the 4th order stuff
Source/driver/Castro_sdc.cpp
Source/driver/sdc_util.F90
commit 51bc4fc2c2e3b6b672aecfadb4f0d5d90c69d862
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Mar 29 09:27:04 2019 +0100
specify Sphinx < 2.0 in requirements file as breathe is incompatible with it
requirements.txt
commit 8591d3e15bdb8c01205b86847e8f8bcfb714e232
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 28 21:52:44 2019 -0700
Only cap registers if needed
Exec/Make.cuda_rules
commit 7e8dde02d6e91d1e85e8af33943b3ff262eaee32
Merge: 4394175b9 8775099b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 28 19:59:30 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 4394175b9969a16bedd62412141fd1701f781416
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 28 19:59:10 2019 -0400
fix the quadrature for 4th order with reactions -- we were doing 2x too much
Source/driver/sdc_util.F90
commit 8775099b2071d438c91e6db9ee459bab7566430c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 28 15:59:51 2019 -0400
a plot script for visualizing the runs
Exec/reacting_tests/reacting_convergence/analysis/convergence_plots.py
commit 23b8573a0ed656e588ef239c2e4b370f7d74ee53
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Thu Mar 28 10:40:40 2019 -0700
Tuple -> Array (#575)
Tuple in AMReX is a class that was born before C++ standard introduced array and tuple. Unfortunately, amrex::Tuple is basically std::array and it's completely different from std::tuple. In this pull-request, all amrex::Tuple are replaced by amrex::Array.
Source/radiation/HypreABec.H
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/RadPlotvar.cpp
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGRadSolver.cpp
commit 3fd48566f9a07cc1fcb66ddce804d7d393af3c5a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 28 07:04:29 2019 -0700
post processing convergence script
Exec/reacting_tests/reacting_convergence/job_scripts/check_convergence.sh
commit 6595ee5accf71e3cda8dc9f16973e347f7ae27fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 27 17:19:12 2019 -0700
update to the latest params
Exec/reacting_tests/reacting_convergence/job_scripts/edison.MPI.slurm
commit e85b84cc5996379fb60f0e5180e5a57aa049a48b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 27 17:05:23 2019 -0700
these are the params used for the flame_wave_boost_10_10_new run
this tweaks the initial model a bit, resulting in a 30% speedup
Exec/science/flame_wave/inputs.boost_10_10
Exec/science/flame_wave/probin.boost_10_10
commit 82ca2047ace184417f729a11a0259ac8c2aa0c73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 27 16:35:57 2019 -0400
switch the convergence tests to the Newton solver with 1.e-10 tol
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
commit 42ef1178524bf17399b7106d21dbcdf9b425b881
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 27 16:33:33 2019 -0400
add sdc_solver_relax_factor parameter to reduce tolerance for early iterations
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_util.F90
commit 9a550a6a1a81c5d6a18ba6d521181722c198f3d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 27 00:04:53 2019 -0700
derdiffterm on GPU
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit 25e0d6ef8b835f697e26d737618bf6a337747945
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 26 23:25:41 2019 -0700
derdiffcoeff and dercond on GPU
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit d5ba6a75a9051e5c94706bf8061e9b699c4bd8c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 26 22:41:27 2019 -0700
Fix HSE BCs for 3D flame_wave
Exec/science/flame_wave/inputs.noboost.3d
commit 5334588d9f80ccb436170ad3f1a5701c6b07b38e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 26 22:30:22 2019 -0700
Use new AMReX prefetching functions
Source/driver/Castro_io.cpp
commit 18c497f39714806722c6c213e757b60b3643959f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 26 21:34:30 2019 -0400
Implement HSE BC fill on GPUs
This required splitting out the HSE fill from the main hypfill/denfill
routines, because the HSE fill calls the EOS, which has not been
register-capped, so it needs to be done in a separate kernel launch.
The HSE fill is implemented without requiring any synchronizations:
a single thread does the whole column. So there is no need to require
a specific number of threads in the block, the same way we do with
the normal BC fill.
Exec/Make.cuda_rules
Source/driver/Castro_generic_fill.H
Source/driver/Castro_generic_fill.cpp
Source/problems/Castro_bc_ext_fill_nd.H
Source/problems/Castro_bc_ext_fill_nd.cpp
Source/problems/Castro_bc_ext_fill_nd_F.H
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Make.package
Source/problems/bc_ext_fill_nd.F90
Source/problems/bc_fill_nd.F90
commit af4c846fb448700600dd2f3bfbe8fdb5ce0ac0c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 26 16:54:16 2019 -0700
various 4th order SDC fixes (#574)
* eliminate the ghost cell fills after the old_source call for MOL and SDC
Note: some of this is still only single-level safe closes #553
* for second-order SDC, use PLM reconstruction
* fix the conversion of R at centers to <R> for 4th order
* don't need a ghost fill for recomputing R_old
* convert the react term to a proper cell-average
* fix some doc strings + remove unused function
* fix dt used in the 4th order react path
this now gets 4th order convergence for reacting hydro
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_sdc.cpp
Source/driver/sdc_util.F90
Source/hydro/fourth_order.F90
commit 4027f66fd16ff277b038820a69a3d25bdac01483
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 25 00:10:39 2019 -0700
GPU compatible diffusion_test
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/diffusion_test/prob_util.F90
Exec/unit_tests/diffusion_test/probdata.F90
commit 241593675185842a42f9004135664ce4e79a5929
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 23:32:33 2019 -0700
blocking_factor = 8
Exec/unit_tests/diffusion_test/inputs.1d
Exec/unit_tests/diffusion_test/inputs.1d.sph
Exec/unit_tests/diffusion_test/inputs.2d
Exec/unit_tests/diffusion_test/inputs.2d.sph
Exec/unit_tests/diffusion_test/inputs.3d
commit 10016990fa3d25d633257ea6bf96f8837365025c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 23:24:49 2019 -0700
Only define in linpack bits if we're using VODE
Source/driver/sdc_util.F90
commit 6db239cc6d75578a5c6b1927058cdbef0950ae15
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 20:18:01 2019 -0700
Disable GPU tiling for some loops
Source/reactions/Castro_react.cpp
Source/sources/Castro_sponge.cpp
commit 5360ebf9b1cd25b7ccb7a35db5dd5ba4323d515b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 18:07:31 2019 -0700
GPU_COMPATIBLE_INITIALIZATION -> GPU_COMPATIBLE_PROBLEM
Exec/Make.Castro
Exec/hydro_tests/Sedov/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
commit 3c56acaa94384b16c2dbc634ea69f0471ff72b04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 20:51:20 2019 -0400
tanh causes problems on gnu too
clamp the value when abs(z) > 4
Exec/science/flame_wave/initial_model.F90
commit ef01705764ae397964a651966e82c17024f7ce45
Merge: 68368ca76 29d48d051
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 20:40:42 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 68368ca761ce9d70ecbe070df848b7092c21bfe3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 20:40:34 2019 -0400
update scripts
Exec/hydro_tests/acoustic_pulse_general/convergence_1d_sdc4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc4.sh
commit 29d48d0517d069aad9b08f00b1869360bed34908
Merge: 1b8eabc60 2d82f9e01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 20:02:51 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2d82f9e0140ea5cbc655d1d101684cd96d3613b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 13:52:19 2019 -0700
Fix errors in assigning total zone energy at initialization
Also rewrite some other problems along these lines that aren't wrong
but have code that is liable to be misused in the future.
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/convective_flame/Prob_nd.F90
Exec/science/flame_wave/Prob_nd.F90
Exec/science/rotating_star/Prob_nd.F90
Exec/science/subchandra/Prob_nd.F90
Exec/science/xrb_mixed/Prob_nd.F90
commit b7f5a21dcf4dd77d98d12f306cb6bfe5f1814b05
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 13:16:37 2019 -0700
Remove fix_mass_flux (#572)
This parameter is not well documented (not clear what the use case is) and isn't used in any of the test problems, so we don't have test suite coverage.
CHANGES
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
sphinx_docs/source/Hydrodynamics.rst
commit 9ef8006d5b71811f8f3894268bad861a638df3e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 13:15:52 2019 -0700
Decrease the amount of work done in the source_nonzero check (#571)
We only need to check the local tile, not the whole box. With this insight,
we can also now do this check on the GPU too, since the GPU will only be doing
the work of its current index +/- 2 zones, which gives a decent speedup there,
compared to doing the PPM reconstruction if the sources really are zero.
Source/hydro/Castro_ctu_nd.F90
commit 1b8eabc600a9919a036b679efa6e987c3227efa1
Merge: 6f507cdbb 4bb2118d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 14:04:38 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 6f507cdbbc968127a16b860e6ff7f1c969305812
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 14:04:30 2019 -0400
update comment
Source/driver/_cpp_parameters
commit 4bb2118d4f0e74aaa3a06f1c51a4f950d84fecdb
Merge: 0459ec17a 164405a97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:30:46 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 0459ec17ac25fffe7981f29801858222dd929fea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:30:33 2019 -0400
add a 4th order inputs for the test suite
Exec/reacting_tests/reacting_convergence/inputs.128.testsuite
commit 164405a973edef3fae349ceeeb39612f86928f27
Merge: baff9f4bd b8b792031
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:18:53 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit baff9f4bdc17a6feb61e2257f48cebb71adf626f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:18:30 2019 -0400
sync up the scripts and make them more flexible.
They now all work for 1 or 2-d
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Exec/reacting_tests/reacting_convergence/convergence_strang.sh
commit b8b792031ce07f45126089e5cd56eaa27525051b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:05:17 2019 -0400
fix probin
Exec/science/flame_wave/inputs.noboost.3d
commit c7f735cdb966284f560a9905445bb1ed4852767b
Merge: 90a8f1522 d48aaee96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:03:27 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 90a8f1522f4fd51fd910f496e7204594151168af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 13:03:19 2019 -0400
add the noboost probin
Exec/science/flame_wave/probin.noboost
commit d48aaee9680177f7b03fdbd549d1f265380db2e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 09:35:07 2019 -0700
Fix compile issue
Exec/science/flame_wave/problem_tagging_nd.F90
commit cf77c27c53674d6010c65842a836a633388b0bd9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 09:21:22 2019 -0700
Fix a race condition in CTU hydro for 2D non-Cartesian
The Elixir for pradial was scoped inside the conditional that tested
on whether we're Cartesian, so the memory was eligible to be reclaimed
immediately. This then will cause an issue when there are multiple
boxes or multiple tiles. Now the Elixir is scoped at the MFIter level,
so the race condition is avoided.
Fixes #570
Source/hydro/Castro_ctu_hydro.cpp
commit 60653a7d38cfb68b386b9dcafa7a05692deda5fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 12:15:47 2019 -0400
make the convergence script more flexible
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
commit c7c43ac6290d552b8993d3deb3387a58c7e75614
Merge: e55923aaf 9eac2ab53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 12:00:51 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 9eac2ab5300419573d2e91f3acea7ccd1ebd05d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 11:32:27 2019 -0400
add no-boost versions
Exec/science/flame_wave/inputs.noboost
Exec/science/flame_wave/inputs.noboost.3d
commit c905ef3fcde5955a742be02294b927bfc11dfe74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 11:30:36 2019 -0400
get x_refine_distance working in 3-d
it now is based off of center(1)
Exec/science/flame_wave/problem_tagging_nd.F90
commit 410b91847d1f3a833d20397d2a21de060c47d68e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 11:26:48 2019 -0400
define the problem center
for 2-d axisymmetric, the center will be at x=0
for 3-d, it will be the geometric center of the domain
Exec/science/flame_wave/Prob_nd.F90
commit 006b0da65bf0cfe45bba73e4fdef19582bc606ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 22:22:47 2019 -0700
Use arena to avoid explicit cudaMalloc/cudaFree
Source/driver/Castro_generic_fill.H
commit 0a9f8a06d2445c02e66087e0fea711eb51141c05
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 22:08:16 2019 -0700
Fix two BL_PROFILE issues
Source/driver/Castro.cpp
Source/hydro/Castro_ctu_hydro.cpp
commit ce004f82eb240e54e86a49a988386d506b722dd5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 21:47:21 2019 -0700
GPU-compatible initialization for flame_wave
Exec/science/flame_wave/GNUmakefile
Exec/science/flame_wave/Make.package
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/initial_model.F90
Exec/science/flame_wave/probdata.F90
Source/driver/interpolate.F90
commit ecf892c496eb2d9b636f9eee276159bf2cad1124
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 20:13:52 2019 -0700
Add capability for GPU-compatible problem initialization (#567)
When we're running a problem on GPUs, we're typically only running 1 MPI rank per
GPU. On a system like Summit, this means 6 MPI ranks per node, each with a fairly
large box size (typically we'll want something like 128^3). But this single CPU
core isn't enough to do CPU-side operations quickly, so problem initialization
becomes a bottleneck (especially given that we don't currently have OpenMP support
when we're using CUDA, so we can't currently thread the initialization). This
commit adds the option for a problem to opt-in to a version of ca_initdata that
is GPU friendly. The interface is slightly different, and supports the GPU pragma.
The user has the responsibility to ensure that all of the variables accessed in
ca_initdata are GPU friendly, so this will not necessarily make sense for every problem.
This also fixes a bug introduced in commit ea93ddb in August 2015, where we were
giving incorrect bounds to ca_initdata after a restart for grown problems. Thus
this fixes #566.
CHANGES
Exec/Make.Castro
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sedov/Make.package
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sedov/probdata.F90
Exec/hydro_tests/Sedov/probdata.f90
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_util.F90
commit 0e41a4ff059ef0d143e373b24dcce57045f2a045
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 19:09:06 2019 -0700
Specify number of ghost cells for reset_internal_energy (#568)
This makes the operation consistent with the other things done in
clean_state, and partially addresses #423.
Source/driver/Castro.H
Source/driver/Castro.cpp
commit e55923aaf0832b65745390d7d9fd0aaebc405a6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 23 21:50:37 2019 -0400
code style fix
Source/hydro/hybrid_advection_nd.F90
commit 14cc85b16f6463333ae5f37816de372d9f966f85
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 18:40:12 2019 -0700
Calculate offsets relative to problo, not xlo, in derives
This resolves an issue on the GPU: calculating offsets with respect to the
lo end of the box is not going to work, since we have lo == hi that matches
the thread index. Rather than try to get clever, we just calculate the grid
position using the index and the lo end of the domain using problo.
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit 256e3df78d23c3baf52b186d86cb5ab5e28a7680
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 16:12:10 2019 -0700
Do not zero out state boundary when using radiation (#569)
It may make sense to zero out the Rad_Type BCs in initialize_do_advance,
but it does not make sense to do so for State_Type: this data should be
valid as a result of FillPatching, and zeroing it makes it invalid.
Source/driver/Castro_advance.cpp
commit 6838bbf8427c3e9d0032d36580c4ded133afdc9c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 13:00:42 2019 -0400
Remove custom Rotation_frequency.F90, it doesn't do anything
Exec/science/wdmerger/Rotation_frequency.F90
commit 271b1c80ada4be63b7cb7e0475775dd1f9f7cf67
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 12:45:28 2019 -0400
Undo changes to archived inputs
Exec/hydro_tests/Sod/Figure3/inputs-test3-1d
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test4-helm
commit 6f763b4fa2e007a921ef4d7ebd1adcc627247da7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 12:41:55 2019 -0400
Update domain size to be consistent with new blocking_factor
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm.gammae
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
commit 9055c31d60059431015862469a48e22a23c39973
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 04:14:27 2019 -0700
Add some prefetching to avoid page faults
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
commit 259d7693af058dfa8e3b702d7cb6dad044e30e70
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 23 03:43:09 2019 -0700
Minimum blocking factor of 8 across the board
Exec/hydro_tests/HCBubble/inputs-sod-x
Exec/hydro_tests/HCBubble/inputs.L0
Exec/hydro_tests/KH/inputs.2d
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/inputs.3d
Exec/hydro_tests/RT/inputs.dungeon
Exec/hydro_tests/RT/inputs_2d
Exec/hydro_tests/RT/inputs_3d
Exec/hydro_tests/RT_particles/inputs_2d
Exec/hydro_tests/Sedov/inputs.1d.cyl
Exec/hydro_tests/Sedov/inputs.1d.sph
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/inputs.3d.sph
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sod/Figure3/inputs-test3-1d
Exec/hydro_tests/Sod/inputs-double-rarefaction
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test1-helm
Exec/hydro_tests/Sod/inputs-test2-helm
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-helm
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm.gammae
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test4-helm
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse/inputs.2d.128
Exec/hydro_tests/acoustic_pulse/inputs.2d.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.512
Exec/hydro_tests/acoustic_pulse/inputs.2d.64
Exec/hydro_tests/acoustic_pulse_general/inputs.128
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.256
Exec/hydro_tests/acoustic_pulse_general/inputs.512
Exec/hydro_tests/acoustic_pulse_general/inputs.64
Exec/hydro_tests/gresho_vortex/inputs.2d
Exec/hydro_tests/oddeven/inputs.2d
Exec/hydro_tests/oddeven/inputs.3d
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
Exec/hydro_tests/symmetry/inputs.1d
Exec/hydro_tests/symmetry/inputs.2d
Exec/hydro_tests/symmetry/inputs.3d
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/toy_convect/inputs_2d
commit 11601e8f6a3d055f64c19f76f9efbd93ea05b067
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 19:02:58 2019 -0700
eliminate castro.fourth_order. (#557)
This eliminates the castro.fourth_order runtime parameter, instead inferring whether we need
fourth order spatial reconstruction from the integrator's order for both MOL and SDC
This closes #556
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_sdc.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/Castro_mol_hydro.cpp
commit f2106208ce0fec57f0bbd509de6ee98e317ac004
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 22 18:58:18 2019 -0700
Improve logic for setting threadblock minimum in CUDA for BCs
The previous logic failed for pure outflow BCs in some cases; the new
logic is more robust, but requires a blocking factor that is a multiple
of 8.
Source/driver/Castro.cpp
Source/driver/Castro_setup.cpp
commit 5213418484c610b35d31f1ae205af073bd67d9e1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 22 18:24:23 2019 -0700
Fix CUDA logic for mixed BC types
Source/driver/Castro_setup.cpp
commit f0a7d125829f64d7539348c31eca4f20d72ebf37
Merge: 57e08c008 46060d16f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 19:58:15 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 46060d16fa9f68caf49bd0b186d1ec3a4c29726c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 22 16:57:35 2019 -0700
Update nx_model to dx_model
Exec/science/flame_wave/probin.testsuite
commit 57e08c008659a9294f08f0a034a52673525ca499
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 19:55:47 2019 -0400
fix name
Exec/science/flame_wave/probin.testsuite
commit d959128f474563cb79b689fea9e2c40a71a8e1fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 22 19:48:15 2019 -0400
source_flag = false if not diffusing temperature
Source/sources/Castro_sources.cpp
commit d100b5cec04e7ea9ee06f62992cab945b50d85b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 19:18:32 2019 -0400
abort the build if we are compiling with CUDA without VODE90
Exec/Make.Castro
commit 6b29778f9c2bb99d455be0a9e9d4da2a822c772e
Merge: 8f475d6ac 79fc82535
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 19:14:17 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8f475d6ac80b58bf6c24d8a4baf4bb62f20606c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 19:13:51 2019 -0400
remove some backwards compatibility hacks for old spelling of microphysics dirs
Exec/Make.Castro
commit 79fc82535b2ee2fd2402f5360f29aafdeef2c58b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Fri Mar 22 19:13:09 2019 -0400
Add comment explaining use of exponential form of tanh, endorsed by our Dear Leader Max.
Exec/science/flame_wave/initial_model.f90
commit 31341fa24bfb4d808ee18b99134277ba14a79959
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Fri Mar 22 19:06:57 2019 -0400
Use exponential form of tanh in initial model.
Exec/science/flame_wave/initial_model.f90
commit 4be85e533e0bf190d298e838a1d9a99955739694
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 18:59:36 2019 -0400
switch to specifying the dx of the model instead of the number of points
dx_model replaces nx_model
some of the initial model resolutions change here, because they were not
in sync with the finest resolution grid.
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost_10_10
Exec/science/flame_wave/probin.boost_25_4
Exec/science/flame_wave/probin.boost_5_5
Exec/science/flame_wave/probin.testsuite
commit 7b655aad03e77ed006dccbf167f679c819dde8c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 17:37:27 2019 -0400
switch these over to their own probin
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/probin.testsuite
commit 2528842cf11eb595cfcfaa22841fc5d219cdc11c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 17:36:05 2019 -0400
this file is not used
Exec/science/flame_wave/inputs_2d.boost.sdc_test
commit f7ccb49bd8515826ac9250b3545472147077a639
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 13:42:42 2019 -0400
add a 3d version
Exec/science/flame_wave/inputs.boost_10_10.3d
commit 0ddab0ba9c072ca0aedf06422fb97ede305da810
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 22 02:08:03 2019 -0400
ifdef out SDC if using CUDA
Source/driver/Castro.H
Source/driver/Castro_advance_sdc.cpp
Source/driver/Make.package
Source/hydro/Castro_hydro_F.H
commit 1640b2ff6830464faaab79f32d75f62d92110a91
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 21 13:29:42 2019 -0700
[WIP] Add self-consistent field initialization (#530)
* Check in SCF files from wdmerger
* [WIP] Get SCF compiling
* Check in a problem setup for testing SCF
* [WIP] Continue updating single star SCF method
* Point B should be on the z-axis
* Only print out info on ioproc
* Clean up the omega-squared calculation
* Fix the inputs
* Cleanup
* Require stricter convergence criterion
* Read max (rho, T) from grid rather than hardcoding them
* Use L-infinity norm, not L2 norm
* Add verbosity
* Print out rotation period in exponential form
* Handle the zero-rotation case gracefully
* Check in solution to non-rotating R=1e9 WD
* Rename parameters for easier interpretation
* Add sanity check: gravity and rotation required
* Set maximum density and temperature as input parameters
* Convert to loop over box indices
* Create subroutine for trilinear interpolation
* Do trilinear interpolation on demand
* Test on distance
* Simplify expression
* Simplify further
* Inline the trilinear interpolation
* Cleanup
* Generalize
* Add comment
* Find enthalpy maximum in separate step
* Split off diagnostics check into a separate call
* Move convergence check up to C++
* Explicitly construct psi in a separate step
* Get omega from rotation module
* Construct rotational psi in the rotation module
* Fix trilinear interp
* Use phi_rot from rotation module
* Use different initial guess
* Loosen tolerance
* Simplify logic for enthalpy_min
* Construct target h_max based on domain temp/composition
* Indentation
* Remove obsolete parameter
* Clean
* Start SCF docs
* Rename references to zreferences to be alphabetically last
https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/8
* Document single star SCF algorithm
* Add more SCF references
* Fix compilation
* Fix compile issues
* [WIP] Add AMR support
* Fix shadowing
* Fix diagnostics calculation
* Only do update if rho > 0
* Make number of SCF iterations a runtime parameter
* Use new density, not eos_state value
* Remove some unused variables
* Pass radii to Fortran
* Pass maximum density to Fortran
* Allow for dynamic AMR as SCF converges
* Disallow low density zones from being tested in SCF convergence
* Add a not terrible rotating model
* Break off Hachisu SCF solve into its own function
* Update the call to RegridOnly
* switch comment to sphinx-fortran style
Exec/Make.Castro
Exec/scf_tests/single_star/GNUmakefile
Exec/scf_tests/single_star/Make.package
Exec/scf_tests/single_star/Prob_nd.F90
Exec/scf_tests/single_star/inputs_helm_nonrotating
Exec/scf_tests/single_star/inputs_helm_rotating
Exec/scf_tests/single_star/probdata.f90
Exec/scf_tests/single_star/probin_helm_nonrotating
Exec/scf_tests/single_star/probin_helm_rotating
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.F90
Source/scf/Make.package
Source/scf/scf_relax.cpp
Source/scf/scf_relax_F.H
Source/scf/scf_relaxation.F90
sphinx_docs/source/index.rst
sphinx_docs/source/refs.bib
sphinx_docs/source/self_consistent_field.rst
commit fd1f8d08dd19373b75fac7188f850f597dc9f2d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 20 20:16:36 2019 -0400
cycle over variables that are not reconstructed in doing lateral fixes
Source/hydro/Castro_fourth_order.F90
commit bc0e53ab8a1374b270d3c2d95310c95b618e2f89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 20 19:07:14 2019 -0400
shrink the loops for some terms to avoid operating on invalid data
no results should change
Source/hydro/fourth_order.F90
commit e718ad42b66d09099aa5e247e316779a857bb5d2
Merge: d24edafc4 2c52adce5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 20 18:48:03 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d24edafc48719d1e0be6b68a2117dacff115efcd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 20 18:47:49 2019 -0400
remove obsolete comment
Source/hydro/Castro_fourth_order.F90
commit 2c52adce5d195be17779f54a24c399a25ccfefdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 20 15:37:43 2019 -0700
after transyz, we should do cmpflx on the same box (#560)
Source/hydro/Castro_ctu_hydro.cpp
commit b6219441972cf84bf51fd4894548db303d9d31b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 20 16:38:04 2019 -0400
fix parameter name
sphinx_docs/source/debugging.rst
commit 5830523dafe5225e35631192f3656e59eb605578
Merge: 463d433f8 4266e327c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 19 19:32:13 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 463d433f8d27184ce7b12199e3bc101b2302420d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 19 19:31:58 2019 -0400
add test suite inputs that use 4th order SDC
Exec/hydro_tests/acoustic_pulse/inputs.128.sdc4.testsuite
Exec/hydro_tests/acoustic_pulse_general/inputs.128.sdc4.testsuite
commit 4266e327cf900d0ecd25546666a396a83971e086
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 19 10:21:12 2019 -0700
fix SDC4 options
Exec/reacting_tests/reacting_convergence/job_scripts/edison.MPI.slurm
commit bc8b96bd72d0a7538e29e6a727f679cc86148dfd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 18 01:37:53 2019 -0400
Fix a CUDA synchronization problem in the symmetry/reflect BCs
For normal foextrap BCs, we fill the state from domlo(1) - NUM_GROW ... domlo(1) - 1
based on the state at domlo. Then we fill the domlo(2) - NUM_GROW ... domlo(2) - 1 values,
and the values in the corner require this to be done in order, which is why we synchronize
between the x, y, and z dimensions. This means that we need at least 5 zones per threadblock
in each dimension (5x5x5 = 125 in 3D) -- the 4 ghost zones and the first interior zone.
However for reflecting BCs, each ghost zone is based on its interior zone opposite to the
boundary at equal distance from the boundary. So the zone at -4 is based on zone 3, meaning
we need at least 8 zones per dimension. 8x8x8 = 512 threads per block, which is legal, and
should work since we cap registers for this kernel. But we were not enforcing this requirement -
the threadblock minimum size was assuming only enough threads to cover the `foextrap` case.
This has now been fixed: `hoextrap` and `reflect_even`/`reflect_odd` are now represented.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_generic_fill.H
Source/driver/Castro_setup.cpp
commit cfafbebf2b64802bb90a4d5d443e47b011cbeb72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 17 19:44:50 2019 -0400
fix PLM MOL interface state in 3-d
Source/hydro/Castro_mol_nd.F90
commit 35a629af82c0bdcb801c67b5ab1655f90506d222
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 15 12:35:30 2019 -0700
remove the FillPatch from do_old_sources (#554)
turns out a lot of times we don't need to FillPatch in do_old_sources. When we do, we can simply do so after the call. This increases the flexibility of things.
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
Source/sources/Castro_sources.cpp
commit b313387505624255a85fb8062ab6f40a86a98cba
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Mar 15 08:05:55 2019 -0400
uncomment lines in sdc_util.F90 so build is not broken, add a hack to preprocess_files.py to delete lines that sphinx-fortran does not like
Source/driver/sdc_util.F90
sphinx_docs/preprocess_files.py
commit 9a67de8d0dce9d5ad8fcf651d9f635d9cc090f72
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Mar 14 20:59:44 2019 -0400
Use sphinx-fortran to generate fortran documentation rather than doxygen (#552)
This changes the way the API for Fortran files is generated to use sphinx-fortran instead of Doxygen/breathe. This allows the Fortran docstrings to be cleaner and generates less-buggy documentation.
The main things this PR does (other than re-format the Fortran docstrings) is:
* add the sphinx-fortran extensions & options to conf.py
* adds fortran_apidoc to make_api.py, which goes through the Fortran files and creates the
.. f:automodule:: module boilerplate (as sphinx-apidoc does for python packages).
.gitignore
Source/diffusion/Diffusion_nd.F90
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/Tagging_nd.F90
Source/driver/amrinfo.F90
Source/driver/generic_fill.F90
Source/driver/interpolate.F90
Source/driver/math.F90
Source/driver/meth_params.F90
Source/driver/prob_params.F90
Source/driver/sdc_util.F90
Source/driver/timestep.F90
Source/gravity/Gravity_nd.f90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/trace_ppm.F90
Source/problems/Prob_nd.F90
Source/problems/Problem.f90
Source/problems/bc_ext_fill_nd.F90
Source/problems/problem_tagging_nd.F90
Source/rotation/Rotation_nd.F90
Source/rotation/rotation_sources_nd.F90
Source/sources/ext_src_1d.f90
Source/sources/ext_src_2d.f90
Source/sources/ext_src_3d.f90
Source/sources/ext_src_nd.F90
Source/sources/thermo_nd.F90
Source/sources/update_sponge_params.f90
requirements.txt
sphinx_docs/Doxyfile
sphinx_docs/Makefile
sphinx_docs/make_api.py
sphinx_docs/preprocess_files.py
sphinx_docs/source/coding_conventions.rst
sphinx_docs/source/conf.py
sphinx_docs/source/index.rst
commit 281b24d4c6aebccee9bb7f0c497204f872979132
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 14 16:12:39 2019 -0400
add a note about docstrings
.github/PULL_REQUEST_TEMPLATE.md
commit 864d12d713167cab10356725d4f9fe7129e26de4
Merge: 18462c3b0 1b24f10b6
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Mar 14 15:47:16 2019 -0400
Merge pull request #551 from ChrisDeGrendele/development
Rad2TShock support to run 3d length wise in x y or z.
commit 1b549b72d9e381aa375119d52573994e7b1a5a27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 14 15:40:07 2019 -0400
add a pull request template
.github/PULL_REQUEST_TEMPLATE.md
commit 1b24f10b69ab19bc8f189c463eac42e19b55c142
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Thu Mar 14 15:20:26 2019 -0400
removed second decleration of idir
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
commit 187c8d62caa282b9ee7eb8946ed2071c6c8b2d90
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Thu Mar 14 14:07:01 2019 -0400
added amrex error module
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
commit 18462c3b0a1dca47c06ba27e22e3a5884d1f9b3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 14 02:27:55 2019 -0400
Allow rotating_torus to be defined without rotation
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/probdata.f90
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
commit d433dcde4891ebe66a79677151c3c66cd0167ad7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 14 01:42:34 2019 -0400
Point mass update on GPU
Source/gravity/Castro_pointmass.cpp
Source/gravity/pointmass_nd.F90
commit 2bc1fc2066f0198c6acf7f54943b4c82ebaff690
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 14 01:42:21 2019 -0400
DustCollapse BCs on GPU
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
commit c928c1f0020dfe97850b203f5db078abf00ca1fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 14 00:46:21 2019 -0400
Update DustCollapse pointmass problem
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/DustCollapse/probin.pointmass
commit e6c2028f2b0b3a591a8072c383a9dc1b1c6eff1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 14 00:46:00 2019 -0400
Make point_mass work across restarts
CHANGES
Source/driver/Castro_io.cpp
commit cabd5285c580e891aaa6ce8bb33e360dae2a827f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 20:11:36 2019 -0400
make the source terms in SDC 4th order + fix a bug in the MOL version
closes #544
Source/driver/Castro_advance_mol.cpp
Source/driver/Castro_advance_sdc.cpp
commit 6d64ef6b1dc195a2351aa335f74520d4aaa22997
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Wed Mar 13 17:40:49 2019 -0400
changed idir back to 1
Exec/radiation_tests/Rad2Tshock/probin.M5
commit 66324b7ae306b37808c0f96d2ad88cafec6113bb
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Wed Mar 13 17:39:34 2019 -0400
addressed all commented issues
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/probin.M5
commit fb7255d122afa6debe43acda493fa2d7e8f080fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 15:52:47 2019 -0400
Make nsub a runtime parameter
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/probdata.f90
Exec/gravity_tests/DustCollapse/probin.pointmass
commit b680a1ea2ae9f85a028d505e3d6d235a02927d29
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 15:51:00 2019 -0400
Allow DustCollapse to have a non-zero offset where the mass starts
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/probdata.f90
Exec/gravity_tests/DustCollapse/probin.pointmass
commit 07d576e05ced24dc06be8445a9af239c460ecd2f
Merge: ba52fd57d fa2551142
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 11:53:10 2019 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ba52fd57dbc2493d3f04ed248464752d5713a1b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 11:48:15 2019 -0700
add an uber script to run all of the convergence tests in sequence at NERSC
Exec/reacting_tests/reacting_convergence/job_scripts/edison.MPI.slurm
commit fa255114296146649df09b434b0265c1af6ae82c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 14:39:48 2019 -0400
reorder some tasks
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
commit 87929568a16278d063cbc115a5587e6e503b818d
Merge: dbc1d3eae 3a9baeb7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 14:30:40 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit dbc1d3eaece09d5e7bdd42a10a422069a9025720
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 14:30:31 2019 -0400
turn off checkpointing
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
commit 3a9baeb7c59946ad7d5ef6ff3e605543897f9e8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 13 12:45:38 2019 -0400
add note about diagnostics
CHANGES
commit 0ea3994590714e9c81bd77ab46b98aa8e252b209
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Mar 13 12:35:14 2019 -0400
Cpp diagnostics (#515)
Converts the Fortran versions of the Diagnostics tests fsedov, fdustcollapse, and radiation to C++
See the individual README.md files for usage.
Diagnostics/DustCollapse/DustCollapse_F.H
Diagnostics/DustCollapse/GNUmakefile
Diagnostics/DustCollapse/Make.package
Diagnostics/DustCollapse/README
Diagnostics/DustCollapse/README.md
Diagnostics/DustCollapse/convert_backtrace.py
Diagnostics/DustCollapse/dustcollapse_util.F90
Diagnostics/DustCollapse/fdustcollapse1d.f90
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Diagnostics/DustCollapse/main.cpp
Diagnostics/Radiation/GNUmakefile
Diagnostics/Radiation/Make.package
Diagnostics/Radiation/README.md
Diagnostics/Radiation/Radiation_F.H
Diagnostics/Radiation/Radiation_utils.H
Diagnostics/Radiation/fgaussianpulse.f90
Diagnostics/Radiation/flgt_frnt1d.f90
Diagnostics/Radiation/fradshock.f90
Diagnostics/Radiation/fradsource.f90
Diagnostics/Radiation/fradsphere.f90
Diagnostics/Radiation/frhdshocktube.f90
Diagnostics/Radiation/gaussian_pulse.cpp
Diagnostics/Radiation/lgt_frnt1d.cpp
Diagnostics/Radiation/main.cpp
Diagnostics/Radiation/rad_shock.cpp
Diagnostics/Radiation/rad_source.cpp
Diagnostics/Radiation/rad_sphere.cpp
Diagnostics/Radiation/radiation_util.F90
Diagnostics/Radiation/rhd_shocktube.cpp
Diagnostics/Sedov/GNUmakefile
Diagnostics/Sedov/Make.package
Diagnostics/Sedov/README.md
Diagnostics/Sedov/Sedov_F.H
Diagnostics/Sedov/fsedov1d.f90
Diagnostics/Sedov/fsedov2d_cart.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cartcoords.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cylcoords.f90
Diagnostics/Sedov/fsedov2d_sph_in_cylcoords.f90
Diagnostics/Sedov/fsedov3d_cyl.f90
Diagnostics/Sedov/fsedov3d_sph.f90
Diagnostics/Sedov/main.cpp
Diagnostics/Sedov/sedov_util.f90
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSourceTest/GNUmakefile
Exec/radiation_tests/RadSourceTest/Make.package
Exec/radiation_tests/RadSourceTest/Prob_1d.f90
Exec/radiation_tests/RadSourceTest/README
Exec/radiation_tests/RadSourceTest/Verification/radsource.gp
Exec/radiation_tests/RadSourceTest/Verification/thermal_relax.ps
Exec/radiation_tests/RadSourceTest/Verification/verification.txt
Exec/radiation_tests/RadSourceTest/analytic.f90
Exec/radiation_tests/RadSourceTest/inputs-cooling
Exec/radiation_tests/RadSourceTest/inputs-heating
Exec/radiation_tests/RadSourceTest/inputs-heating-mg
Exec/radiation_tests/RadSourceTest/planck.f90
Exec/radiation_tests/RadSourceTest/probdata.f90
Exec/radiation_tests/RadSourceTest/probin-cooling
Exec/radiation_tests/RadSourceTest/probin-heating
Exec/radiation_tests/RadSphere/GNUmakefile
commit 191d6528fb761297191c411701d45ecbc5c01ae5
Merge: 96c030399 9b5063332
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Wed Mar 13 11:25:30 2019 -0400
Merge branch 'development' of https://github.com/AMReX-Astro/Castro into development
commit 9b50633327db2072a8ad1fe4fc7d17ead5998f9c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 09:58:16 2019 -0400
Update CHANGES
CHANGES
commit 9b3d16763f1949e86473cb1949d8d3b801142a17
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 04:36:27 2019 -0400
Add first cut at DustCollapse pointmass test
Exec/gravity_tests/DustCollapse/inputs_pointmass
Exec/gravity_tests/DustCollapse/probin.pointmass
commit 9cc744365ccebd4defebc6173530d76946c99cac
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 04:34:17 2019 -0400
Fix pointmass update in 1D/2D
Source/gravity/pointmass_nd.F90
commit 22bfb70c0ecefbc0457c24e803f71fe63ff90245
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 04:33:58 2019 -0400
If verbose > 1, print out pointmass change
Source/gravity/Castro_pointmass.cpp
commit e8aa07ed04c0b04c6c7da9370f9818167361b5b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 02:54:31 2019 -0400
Clean up DustCollapse problem
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/DustCollapse/probdata.f90
commit 9207122ba4310be739f905eeee433762c318e8ca
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 02:10:32 2019 -0400
Always compile in pointmass if USE_GRAV=TRUE
Exec/Make.Castro
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_nd.F90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Make.package
commit e4fdcc3d78593e6410c45a330c2211e6fae74401
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 01:02:38 2019 -0400
Move pointmass gravity to GPU
Source/driver/Castro_F.H
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/Make.package
Source/gravity/pointmass_nd.F90
Source/gravity/pointmass_nd.f90
commit 21cc4589afbcdcef3b85ec45145abc8acc57bf41
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 13 00:11:14 2019 -0400
Add note about adding Fortran files
sphinx_docs/source/coding_conventions.rst
commit 6e1517b33733c4eede3aa8482cf9590706f51b0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 22:26:12 2019 -0400
Remove outdated references to dual_energy_update_E_from_e
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc4.sh
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
sphinx_docs/source/Hydrodynamics.rst
commit 43742bf5078e1b4c0639a6ff4406ec1236b6c47d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 12 17:23:54 2019 -0700
fix thermo_src for MOL and SDC integration (#545)
This adds thermo_src (-pdivu U for rho e evolution) to source_flag() fucntion, to ensure that
we apply sources when using MOL and SDC integration. It also ensures that CTU and the
simplified-SDC do not use this thermo source, since they discretize it directly in the conservative
update.
This also fixes a sign error on the source term itself, makes it work for non-Cartesian geom, and
disables update_sources_after_reflux for MOL and SDC integration.
CHANGES
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/hydro/advection_util_nd.F90
Source/sources/Castro_sources.cpp
Source/sources/Castro_thermo.cpp
Source/sources/thermo_nd.F90
commit fa5bd0bc7e6bfabc96541415cd15a3e6d4838b69
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 19:43:34 2019 -0400
Add an error buffer
Exec/science/rotating_star/inputs_2d
commit 0f6a403d3e87331451523b1224b186a506089c96
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 19:28:48 2019 -0400
Disallow n_error_buf = 0 if doing hydro
Source/driver/Castro.cpp
commit 799b69425b35e86469c2a59a95c3b88764a6cae0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 12 19:21:21 2019 -0400
add comment about why n_error_buf = 0 0 0 0
Exec/gravity_tests/uniform_cube_sphere/inputs
commit ed0c195a175c00dddefb84a0e7a4a14b0ef16f8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 12 19:11:55 2019 -0400
apply an error buffer
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/StarGrav/inputs_3d
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
commit ca50236ee8e87545415d5349cd72b0f06019f730
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 12 19:03:48 2019 -0400
add an error buffer to prevent artifacts at jumps in refinement
Exec/science/subchandra/inputs_2d
commit 96c0303992763188709fa57f9e266740342cf316
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Tue Mar 12 16:38:36 2019 -0400
defaults
Exec/radiation_tests/Rad2Tshock/inputs.M5
commit 1aa6d561377464a22ddc67709e5459041f12dc6d
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Tue Mar 12 16:32:31 2019 -0400
Changed settings back to default
Exec/radiation_tests/Rad2Tshock/GNUmakefile
commit e571dce4791828a27c037ecef4adeebf462c5b43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 12 15:53:02 2019 -0400
store center in job_info
Source/driver/Castro_io.cpp
Source/driver/Castro_util.F90
commit a07516db0820d3ef1b237dcfb89f8ca5d9df3dc9
Author: Christopher Degrendele <cdegrendele@alcyone.iacs.stonybrook.edu>
Date: Tue Mar 12 15:50:34 2019 -0400
Added support for Rad2Tshock 3d to run lengthwise in x y or z
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs_y.M5
Exec/radiation_tests/Rad2Tshock/inputs_z.M5
Exec/radiation_tests/Rad2Tshock/probdata.f90
Exec/radiation_tests/Rad2Tshock/probin.M2
Exec/radiation_tests/Rad2Tshock/probin.M5
Exec/radiation_tests/Rad2Tshock/python/Analytical-Test.py
Exec/radiation_tests/Rad2Tshock/python/RadShock.py
commit 9ebfbe6c2383d44156a038813d27ddcb815a4628
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 07:43:08 2019 -0700
Offload gravity source terms onto the GPU (#548)
Source/driver/Castro_F.H
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/gravity/Castro_gravity.cpp
Source/gravity/gravity_sources_nd.F90
commit c19b6f9f592cd25e273294dca7449bfac8453585
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 06:28:50 2019 -0700
Overhaul dimension agnostic BCs for GPU compatibility (#546)
This PR includes quite a few changes centered around making physical boundary conditions compatible for running on GPUs. Summary:
The dimension agnostic ca_*fill interfaces have been moved up to C++, leaving the actual routines that do the work (*fill) in Fortran.
The Fortran routines now take (lo, hi) as their first two arguments. They also now accept time by value rather than by reference.
The declarations have been split into separate headers (some in driver/, some in problems/).
We no longer do CUDA profiling on the initialization.
For CUDA, the number of registers when running on the GPU is capped to 128 when doing BCs. This is because amrex_filccn needs to call syncthreads() as it works to ensure synchronization, and because of the way it is designed, can need as many as 8 threads per dimension == 512 total, which is too many registers required if 255 registers per thread are allowed. This requires some custom GNU Make rules in Make.cuda_rules
CHANGES
Exec/Make.Castro
Exec/Make.cuda_rules
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
Exec/gravity_tests/hydrostatic_adjust/ext_src_1d.f90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_generic_fill.H
Source/driver/Castro_generic_fill.cpp
Source/driver/Castro_generic_fill_F.H
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/generic_fill.F90
Source/problems/Castro_bc_fill.H
Source/problems/Castro_bc_fill.cpp
Source/problems/Castro_bc_fill_F.H
Source/problems/Castro_bc_fill_nd.H
Source/problems/Castro_bc_fill_nd.cpp
Source/problems/Castro_bc_fill_nd_F.H
Source/problems/Make.package
Source/problems/bc_fill_nd.F90
commit 4114e6a79de2d41667ce4399a51b4b35a88d1e09
Merge: b2ca68f79 f98de98fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 11 21:48:23 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b2ca68f79cd9052e0cf8a347691f33bce78eff53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 11 21:48:10 2019 -0400
don't plot empty sets
Exec/science/Detonation/nse_runs/make_plots.py
commit f98de98fb472bdd7752fb51243989320ec235197
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 11 10:08:59 2019 -0400
updated coding_conventions.rst
sphinx_docs/source/coding_conventions.rst
commit ce1c0cfaba8c44bf5e56fad967e598df8579287b
Merge: 31fe490fe 88fa814c9
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 11 10:02:55 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 88fa814c9f9458ae5b26b4823aa25bd1fdf829b9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 11 07:53:27 2019 -0400
Define CUDA
Exec/Make.Castro
commit 2b542f6357f30ea8ab2c8eb0bbde7a6134abc96c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 11 00:56:21 2019 -0400
Avoid assuming double precision
Source/driver/Derive_nd.F90
Source/driver/main.cpp
Source/hydro/fourth_order.F90
commit 1e9c3fd79cc2cc759cc7c76bef90fa9fa60428ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 10 18:41:49 2019 -0700
Profiling tags
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_error.cpp
Source/driver/Castro_sdc.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_sources.cpp
commit 80ac04d5474c521a6d3e390669c3cdda5eb58832
Merge: ec1392d4e fcc4d335b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 10 10:10:17 2019 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ec1392d4e3e8d5d04a175528aacaa5e3c93fb274
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 10 10:10:02 2019 -0400
update construction of plot vs cfl
Exec/science/Detonation/nse_runs/make_plots.py
commit fcc4d335b247a1b0b558b24c1e3274ba1480ecf7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 16:55:44 2019 -0800
Refactor diffusion for GPU compatibility (#541)
This PR refactors the Fortran code for diffusion to be GPU compatible. To do so, the call to calculate the cell-centered conductivity term was split into a separate call from the routine that averages the cell-centered value to edges.
The MGutils files were made dimension agnostic and also set up for GPUing.
The diffusion_test problem was made compatible with running in 1D and 3D. This allows us to do performance testing with the latter.
Exec/unit_tests/diffusion_test/Make.package
Exec/unit_tests/diffusion_test/Prob_nd.F90
Exec/unit_tests/diffusion_test/Problem_Derive_F.H
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_nd.F90
Exec/unit_tests/diffusion_test/inputs.1d
Exec/unit_tests/diffusion_test/inputs.1d.sph
Exec/unit_tests/diffusion_test/inputs.3d
Exec/unit_tests/diffusion_test/prob_util.F90
Exec/unit_tests/diffusion_test/prob_util.f90
Exec/unit_tests/diffusion_test/probdata.F90
Exec/unit_tests/diffusion_test/probin.1d
Exec/unit_tests/diffusion_test/probin.3d
Microphysics/conductivity/conductivity.F90
Microphysics/conductivity/constant/Make.package
Microphysics/conductivity/constant/constant_conductivity.F90
Microphysics/conductivity/constant_opacity/Make.package
Microphysics/conductivity/constant_opacity/constant_conductive_opacity.F90
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/Diffusion_nd.F90
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Make.package
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Derive_nd.F90
Source/driver/MGutils_1d.F90
Source/driver/MGutils_nd.F90
Source/driver/Make.package
Source/driver/timestep.F90
Source/gravity/Gravity.cpp
commit 816408ab2e2341532fb5d63e8149ce923cfeb628
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 17:34:19 2019 -0500
update run params for resolved dets
Exec/science/Detonation/nse_runs/setup_runs.py
commit 8689835627f3f4e7c77afbeea3120a0c1bfbca5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 17:33:57 2019 -0500
automate some of the plotting
Exec/science/Detonation/nse_runs/make_plots.py
commit 9075d221af1008cd8dfebd340581fd7faa5c15e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 17:32:16 2019 -0500
turn on castro.plot_per_is_exact, and set the VODE tolerances to 1.e-10 for all
Exec/science/Detonation/nse_runs/inputs.template.sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
Exec/science/Detonation/nse_runs/probin.nse_test.strang
commit cc886577ab2f398e72ba99c7538396b898b234e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 16:15:26 2019 -0500
separate out the runs with the dtnuc_e limiting
Exec/science/Detonation/nse_runs/make_plots.py
commit 77d0427f4fd5b6265ada20f8b99669c45b708fd7
Merge: 5e805a134 7af9e9ace
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 16:13:53 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 5e805a134c809b915900c8e94ba4c44a0cf520c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 16:13:37 2019 -0500
add the number of steps
Exec/science/Detonation/nse_runs/show_status.py
commit 7af9e9aceb42a526220ef044f266dce2d5384430
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 10:32:05 2019 -0800
Remove clean_state from apply_source_to_state (#537)
Remove clean_state from apply_source_to_state
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/sources/Castro_sources.cpp
commit 8b93db641c260a0470773f045983348f7b03b53f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 13:28:40 2019 -0500
Hydro methods need to be public for device lambdas to work
Source/driver/Castro.H
commit 60734c234b317d4840d407eb378f1da11e21bc02
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 11:12:43 2019 -0500
Uncomment k_stage for CUDA
Source/hydro/Castro_mol_hydro.cpp
commit d5c5b06113ec3b01c74568a5938e87cc8fc71fda
Merge: 8534e4ad0 d2f26d4e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 10:26:04 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8534e4ad07cf558d4b0c8d2bc2ed400d4cde48ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 10:20:50 2019 -0500
add support for dtnuc_e
Exec/science/Detonation/nse_runs/setup_runs.py
commit 7beacb9a3520fe1cc7cf9e3ba1b526497304df6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 10:20:22 2019 -0500
rename the smallscale parameter study inputs and sync with the options from larger
Exec/science/Detonation/nse_runs/inputs.template.sdc
Exec/science/Detonation/nse_runs/inputs.template.strang
commit 7aef10e830c922b688bcdd2d1f9da91da6dc7de5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 10:19:21 2019 -0500
smaller domain fraction for initial pert
Exec/science/Detonation/nse_runs/probin.nse_test.sdc
Exec/science/Detonation/nse_runs/probin.nse_test.strang
commit 97d44e2c578c7ee919401741756ec27b4545fe7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 9 10:19:06 2019 -0500
more steps allowed
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.big.template.strang
commit d2f26d4e184f15bd3920410530544cd4927bcd04
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 05:02:12 2019 -0500
Fix syntax issue when defining with CUDA
Source/driver/Castro_advance.cpp
commit ac50f0cfa8e84539b437f1eb5ff1f6431a26c00f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 04:56:38 2019 -0500
Make Castro_hydro_F.H a standalone header file
Source/driver/Castro_F.H
Source/driver/Castro_sdc.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
commit 2ab228cdef5df362881926906034c7e111233fe9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 02:41:46 2019 -0500
MGutils formatting
Source/driver/MGutils_1d.F90
Source/driver/MGutils_2d.F90
commit 9506507f90a0216018116d58e754334474bf06e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 9 02:22:45 2019 -0500
Remove dead diffusion code
Source/diffusion/Diffusion.cpp
commit 7114b04e35af9fad37a2da999921453b7803f310
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 8 23:09:09 2019 -0800
remove species, enthalpy, and velocity diffusion (#534)
CHANGES
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Enthalpy_nd.f90
Source/diffusion/Make.package
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/timestep.F90
commit c05af9827a114b89a2b226b172b2c333304059fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 7 21:14:45 2019 -0500
Fix error in diagnostics I/O in plotfiles
Source/driver/Castro_io.cpp
commit 31fe490fe97c3acbd41d4fb4f8dc3c400b7fcb64
Merge: b1183a521 fb70341d5
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Mar 7 16:55:20 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit fb70341d56302eb9c6388e8998083f5cd8d9f936
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Mar 7 16:40:03 2019 -0500
Radiation groups check (#540)
check not using a single group solver for a radiation problem with more than one group
Source/radiation/Radiation.cpp
commit b1183a5215a065e72bf633828b65c3c623d5c6b1
Merge: 042772519 151d7ad9f
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Mar 7 15:38:25 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 151d7ad9f50216ab1aa4bc1928f4d9af7488085f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 7 15:15:50 2019 -0500
for a run directory, print out the velocity history
Exec/science/Detonation/nse_runs/vel_history.py
commit 3a477549d6521ff517f1cd53f9520ff9986aa804
Merge: 78ba31157 26db2cb7d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 7 15:04:09 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 78ba31157cf01d6ac89c405b8c17ab898ed51feb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 7 15:03:39 2019 -0500
a script to print the current status of the runs
Exec/science/Detonation/nse_runs/show_status.py
commit 26db2cb7de053158d21cab48c318584692f16a88
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 6 21:21:14 2019 -0500
Add comment explaining reasoning
Source/driver/Castro_advance_ctu.cpp
commit 9fc539269a7376043af70fd801fd6161fd77d5a7
Merge: b8786c540 0e89dfe0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 6 20:30:25 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b8786c540328ac23a46a9a0a404d8dc66057e39a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 6 20:29:51 2019 -0500
make the domain bigger so the detonation doesn't run off then end
also change dtnuc_e to 0.5:
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.big.template.strang
Exec/science/Detonation/nse_runs/make_plots.py
Exec/science/Detonation/nse_runs/setup_runs.py
commit 0e89dfe0f61a8f1beae200c6ddfec7b58ca34f22
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 6 11:33:02 2019 -0800
Clean up some C++-to-F interfaces
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_util.f90
commit 42d45bdfc18dd1bcdc8e1fd7f82e46eb76ccc63a
Merge: 89392b70d 875da12d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 6 13:18:11 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 89392b70d32e9e3d8588dfa34178180961a9b80d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 6 13:17:43 2019 -0500
the parameter clamp_subcycles was removed a long time ago
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 875da12d25893b6c7cea399a7ce302a7285a15de
Merge: 0b3553eef faf39a423
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 6 13:02:58 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 0b3553eefd7b9026520d6812ddb8531514a06b18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 6 13:02:23 2019 -0500
add some runs with dtnuc_e and store stdout
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.big.template.strang
Exec/science/Detonation/nse_runs/make_plots.py
Exec/science/Detonation/nse_runs/probin.nse_test.strang
Exec/science/Detonation/nse_runs/setup_runs.py
commit faf39a42350026c0867d358475dfdb3201c0151e
Merge: defb58588 e5745d045
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 5 14:56:15 2019 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit defb5858862c6534ab942702680daba9c81d3832
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 5 14:53:14 2019 -0500
describe the drivers better + time_integration_method
sphinx_docs/source/FlowChart.rst
commit e5745d045636dad85f4e9cec7e9d362f6005b07b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 5 11:14:17 2019 -0500
separate inputs/probin for Strang vs SDC
Exec/science/Detonation/nse_runs/inputs.big.template.sdc
Exec/science/Detonation/nse_runs/inputs.big.template.strang
Exec/science/Detonation/nse_runs/probin.nse_test.sdc
Exec/science/Detonation/nse_runs/probin.nse_test.strang
Exec/science/Detonation/nse_runs/setup_runs.py
commit 7846b067f1ffa7355f7c317ba5db455f6225271b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 3 17:29:02 2019 -0800
Only apply sources on valid domain, then fill S_new ghost zones (#535)
The non-reacting source terms (including the hydro) are only calculated on the valid domain. The source terms are then FillPatched so that there is meaningful data in the ghost zones. So, it is fine to do apply_source_to_state and then do it on all of the State_Type ghost zones. However, the hydro_source has no ghost zones (and there is no meaning of a FillPatch, as this is a MultiFab which is locally defined on each level. So, we have to do a call to expand_state after we apply the hydro source. If this is going to be required anyway, then we should skip adding the (non-hydro) source terms to the State_Type ghost zones, and then defer all of the ghost-zone updates until after the corrector source terms have been applied.
Note that we still need to do the FillPatch in do_old_sources and do_new_sources, so that there's valid data in those ghost zones for interpolation on fine levels, and so that the FillPatchAdd to sources_for_hydro in CTU has data on the ghost zones.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance_ctu.cpp
Source/sources/Castro_sources.cpp
commit f5afc3479c7eb7f31c75ba756e45996391960475
Merge: 79d816d96 3aebeb115
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 3 17:43:11 2019 -0500
Merge branch 'master' into development
commit 79d816d962acaa68c4ca9c511a8d6ffe6572f034
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 3 12:52:43 2019 -0800
remove the code to extrapolate diffusion terms to ghost cells (#532)
This is not needed because we do a ghost zone fill on the source term data before it gets added to the state.
CHANGES
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion_nd.f90
commit d530903d9ebc95b13a1854eea0e78a4169782d60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 3 14:45:13 2019 -0500
some more fixes
sphinx_docs/source/Verification.rst
commit 8a848fb936e52dd18bcbaa79610dfd01d621ae7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 3 14:40:39 2019 -0500
Fix formatting on Castro_sponge.cpp
Source/sources/Castro_sponge.cpp
commit 7a5668dc7d64bbde74287378ee8e119ce9766143
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 3 08:14:53 2019 -0800
Fix some formatting issues
sphinx_docs/source/EOSNetwork.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/MAESTRO_restart.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/creating_a_problem.rst
sphinx_docs/source/inputs.rst
commit bff36ea65b8985dd5cdae632f7e138bd1e4636d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 3 07:54:31 2019 -0800
Add GR references
sphinx_docs/source/refs.bib
commit b730f894836d84317fbaf1f52fb71afb0edbfd02
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 3 07:46:46 2019 -0800
Update a couple references to fix build
sphinx_docs/source/refs.bib
commit 5ecacc2516d98dccdf8db0ad00d36d5c61278eba
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 3 06:44:12 2019 -0800
Allow optional disabling of Doxygen
sphinx_docs/Makefile
commit 766acba935747320fb7cdc360621d3179cce2fdf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 3 09:34:20 2019 -0500
fix some references
sphinx_docs/source/Verification.rst
sphinx_docs/source/refs.bib
commit 4ecb3796ee0932ef8a23252a6cb3ff32ac8e72c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 2 22:54:09 2019 -0500
this compiles again
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
commit e91ee6ee79e57039bfb83792318ebf6d4d0e81b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 2 17:03:13 2019 -0800
Rename references to zreferences to be alphabetically last
https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/8
sphinx_docs/source/index.rst
sphinx_docs/source/zreferences.rst
commit 99d98cc55b29c244ad8ebb5daa0fb68ff474712c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 2 16:47:36 2019 -0500
some more information stored during runs
Exec/science/Detonation/nse_runs/inputs.big.template
Exec/science/Detonation/nse_runs/probin-det-x.SDC
Exec/science/Detonation/nse_runs/setup_runs.py
commit 28c2542ae6ce731ed12ae1f9e2b9596dfbb11946
Merge: 29417f41f 4fbba3259
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 1 10:48:25 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 29417f41f8cc48a7f22bfb99feb4f54ddc7a3358
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 1 10:48:17 2019 -0500
more plots
Exec/science/Detonation/nse_runs/make_plots.py
commit 547285cebdb48ca98c7232b17534a901fd402c7d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 1 08:53:24 2019 -0500
some updates to the plotting
Exec/science/Detonation/nse_runs/.gitignore
Exec/science/Detonation/nse_runs/inputs.template
Exec/science/Detonation/nse_runs/make_plots.py
commit 3aebeb1157c95625aad23b6db374112df92f1fc6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 1 08:41:09 2019 -0500
at tag
CHANGES
commit 4fbba3259ae7fdf4d7e7a2dd59e740cfeabd55e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 28 19:13:57 2019 -0500
some notes about changes
CHANGES
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
commit 9dd7e1dddc920a5d8f336db37bc0d50b56dd006a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 28 16:13:48 2019 -0500
Update CHANGES
CHANGES
commit 75416ad4cbab6d7eb42a61a6b6b3bd5c16da97e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 28 16:01:44 2019 -0500
Fix number of components in FillPatch
Source/sources/Castro_sources.cpp
commit b094d50c66132c4e60327575cd6be2149e4b811a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 28 10:18:44 2019 -0800
create a new reacting_tests Exec subdirectory (#527)
Move tests with reactions from hydro_tests to reacting_tests
CHANGES
Exec/reacting_tests/nse_test/GNUmakefile
Exec/reacting_tests/nse_test/Make.package
Exec/reacting_tests/nse_test/Prob_nd.F90
Exec/reacting_tests/nse_test/README
Exec/reacting_tests/nse_test/inputs
Exec/reacting_tests/nse_test/probdata.F90
Exec/reacting_tests/nse_test/probin
Exec/reacting_tests/reacting_bubble/GNUmakefile
Exec/reacting_tests/reacting_bubble/Make.package
Exec/reacting_tests/reacting_bubble/Prob_2d.f90
Exec/reacting_tests/reacting_bubble/Prob_3d.f90
Exec/reacting_tests/reacting_bubble/Problem_Derive_F.H
Exec/reacting_tests/reacting_bubble/Problem_Derives.H
Exec/reacting_tests/reacting_bubble/bc_fill_2d.F90
Exec/reacting_tests/reacting_bubble/bc_fill_3d.F90
Exec/reacting_tests/reacting_bubble/initdata_others.f90
Exec/reacting_tests/reacting_bubble/inputs_2d
Exec/reacting_tests/reacting_bubble/inputs_2d_noentropy
Exec/reacting_tests/reacting_bubble/inputs_2d_test
Exec/reacting_tests/reacting_bubble/inputs_2d_zoom
Exec/reacting_tests/reacting_bubble/inputs_3d_test
Exec/reacting_tests/reacting_bubble/model.hse.cool.coulomb
Exec/reacting_tests/reacting_bubble/model.hse.cool.coulomb.6400
Exec/reacting_tests/reacting_bubble/probdata.f90
Exec/reacting_tests/reacting_bubble/probin
Exec/reacting_tests/reacting_bubble/probin.zoom
Exec/reacting_tests/reacting_bubble/problem_derive_nd.f90
Exec/reacting_tests/reacting_convergence/GNUmakefile
Exec/reacting_tests/reacting_convergence/Make.package
Exec/reacting_tests/reacting_convergence/Prob_nd.F90
Exec/reacting_tests/reacting_convergence/README
Exec/reacting_tests/reacting_convergence/convergence_sdc.sh
Exec/reacting_tests/reacting_convergence/convergence_sdc4.sh
Exec/reacting_tests/reacting_convergence/convergence_strang.sh
Exec/reacting_tests/reacting_convergence/helmeos_runs.sh
Exec/reacting_tests/reacting_convergence/inputs.128
Exec/reacting_tests/reacting_convergence/inputs.256
Exec/reacting_tests/reacting_convergence/inputs.512
Exec/reacting_tests/reacting_convergence/inputs.64
Exec/reacting_tests/reacting_convergence/probdata.f90
Exec/reacting_tests/reacting_convergence/probin
Exec/reacting_tests/toy_flame/GNUmakefile
Exec/reacting_tests/toy_flame/Make.package
Exec/reacting_tests/toy_flame/Prob.cpp
Exec/reacting_tests/toy_flame/Prob_1d.f90
Exec/reacting_tests/toy_flame/Problem.H
Exec/reacting_tests/toy_flame/Problem.f90
Exec/reacting_tests/toy_flame/Problem_F.H
Exec/reacting_tests/toy_flame/README
Exec/reacting_tests/toy_flame/exploration/flamefront.py
Exec/reacting_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/reacting_tests/toy_flame/exploration/probin_temp
Exec/reacting_tests/toy_flame/exploration/process.py
Exec/reacting_tests/toy_flame/exploration/setup_explore.py
Exec/reacting_tests/toy_flame/inputs.1d
Exec/reacting_tests/toy_flame/inputs.1d.testsuite
Exec/reacting_tests/toy_flame/probdata.f90
Exec/reacting_tests/toy_flame/probin
Exec/reacting_tests/toy_flame/sum_integrated_quantities.cpp
commit d4067238ab3536b12da5157e32a21c309c00d94f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 27 19:02:00 2019 -0500
rewrite t obe dimension agnostic
Exec/science/xrb_mixed/GNUmakefile
Exec/science/xrb_mixed/Prob_2d.f90
Exec/science/xrb_mixed/Prob_nd.F90
Exec/science/xrb_mixed/problem_tagging_2d.f90
Exec/science/xrb_mixed/problem_tagging_nd.F90
commit f03a97aae6c6c814e94eea8304bc680bd9c837ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 27 17:23:33 2019 -0500
add a new nse test
Exec/hydro_tests/nse_test/GNUmakefile
Exec/hydro_tests/nse_test/Make.package
Exec/hydro_tests/nse_test/Prob_nd.F90
Exec/hydro_tests/nse_test/README
Exec/hydro_tests/nse_test/inputs
Exec/hydro_tests/nse_test/probdata.F90
Exec/hydro_tests/nse_test/probin
commit b9b01021fa9bb48c55cb37a0354bfa9ebae7bcc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 27 11:48:00 2019 -0500
this seems to work now
Exec/science/Detonation/nse_runs/inputs.template
Exec/science/Detonation/nse_runs/setup_runs.py
commit 8733d4d0ca05ad7c956f475f5a1eee342e9439ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 27 11:23:43 2019 -0500
this sets up the suite of runs for the det paper
Exec/science/Detonation/nse_runs/probin-det-x.SDC
Exec/science/Detonation/nse_runs/setup_runs.py
commit 98754c156366ccd9006507f06733f4426f2a2897
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 26 18:46:46 2019 -0500
start of some automating
Exec/science/Detonation/nse_runs/inputs.template
Exec/science/Detonation/nse_runs/nse_plot.py
Exec/science/Detonation/nse_runs/setup_runs.py
commit d65b18e91c3486c9ee064e38b6b9f0c29444675f
Merge: 811e58e8a b573dd5ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 26 10:44:20 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 811e58e8ae86afd855b56616adf4e86da0e288b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 26 10:43:35 2019 -0500
add the suggestions from #524 to coding conventions
sphinx_docs/source/coding_conventions.rst
commit b573dd5eab8c1b3a9db56f866713ed3e34bfd553
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 26 09:43:02 2019 -0500
Fix sanity check for Strang reactions
Source/reactions/Castro_react.cpp
commit d1b2513c98369112408c6c1add02887c860cb334
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 25 14:06:56 2019 -0500
these now live in actual_test_files
Util/regression_testing/Castro-SBU-amrex-tests-pgi.ini
Util/regression_testing/Castro-SBU-amrex-tests.ini
commit 180d6ea4922982877ddaca5bacc5779f841ad905
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 13:53:54 2019 -0500
Avoid using D_DECL in Fortran calls
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
commit 4b764ec50166cd5ad0b1b9ab8ecdfd3e33d6f0f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:30:11 2019 -0500
Allow cons_to_prim_fourth to be defined with CUDA
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
commit c25e8f62a4ae297c26883abc3a9575e5d57fe678
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:19:29 2019 -0500
Fix calls to cons_to_prim
Source/sources/Castro_sources.cpp
commit eb237102baf84656ae42e09ba27b28a8a9474e9b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:14:05 2019 -0500
Fix header for get_react_source_prim
Source/driver/Castro.H
commit 5ba806355a6efc4e63cd590ae6fbdd680c1da086
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 03:08:46 2019 -0500
Move second cons_to_prim interface to Castro_hydro.cpp
Source/driver/Castro.cpp
Source/hydro/Castro_hydro.cpp
commit 9170dac15147dcb84c2fd31d2606ad9a49b26ed9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 03:07:24 2019 -0500
Fix SDC cons_to_prim call when radiation is enabled
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.H
Source/sources/Castro_sources.cpp
commit a01ed7e2c1751574e7b07890ed7219d5e4ce6177
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 01:43:29 2019 -0500
Split CTU and MOL advances into separate files
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_ctu.cpp
Source/driver/Castro_advance_mol.cpp
Source/driver/Make.package
commit 0cd4192f778a64c4b38c4af798d0d8279bf3b548
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 01:14:32 2019 -0500
Move hydro functions to separate C++ files and headers
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_ctu_hydro.cpp
Source/hydro/Castro_hydro.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_hydro_F.H
Source/hydro/Castro_mol_hydro.cpp
Source/hydro/Make.package
commit a366babf246c214b285e0699d8e59afffd4234ae
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 24 20:24:33 2019 -0500
Create SimplifiedSpectralDeferredCorrections as a time_integration_method option
USE_SDC=TRUE is still required for using simplified SDC (the "old" SDC method).
And when building with USE_SDC=TRUE, we still don't support other integration methods.
CHANGES
Exec/science/Detonation/inputs-det-x.simplified_sdc
Exec/science/Detonation/probin-det-x.simplified_sdc
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/hydro/Castro_hydro.cpp
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
Source/sources/Castro_sources.cpp
commit 0f8e4d1644e6cdd49c7bbd80d62b647840671bec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 24 18:37:06 2019 -0500
SDC infrastructure (#310)
This adds a framework for a new spectral deferred corrections method. This will allow for higher-order time integration. The 4th order hydro was extended to support general equations of state (it is still single level only). Artificial viscosity was also added.
CHANGES
Exec/Make.Castro
Exec/science/Detonation/inputs-det-x.sdc
Exec/science/Detonation/inputs-det-x.sdc.test
Exec/science/flame/inputs.1d.sdc
Exec/science/flame/inputs.1d.sdc.test
Exec/science/flame/probin.sdc
Exec/science/flame_wave/inputs_2d.boost.sdc_test
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_advance_sdc.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_sdc.cpp
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/_cpp_parameters
Source/driver/_variables
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/sdc_plan.txt
Source/driver/sdc_util.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/radiation/Castro_radiation.cpp
Source/radiation/MGFLD.cpp
Source/reactions/Make.package
Source/reactions/react_util.F90
sphinx_docs/source/gpu_porting.rst
commit d9e6a3c7e916f4551ba0b598dbbce90df9e5d09b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 23 23:31:51 2019 -0500
Update CHANGES
CHANGES
commit 293aff16b8ec089f49e3b1ec529f8792561d373c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 23 23:30:34 2019 -0500
set self_heat (#521)
Bug fix: we were not setting `self_heat` in estdt_burning.
Source/driver/timestep.F90
commit 04277251993443819f53f0415e956f7878ca325a
Merge: aa2832458 8ad4f2a46
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 22 09:02:28 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8ad4f2a4621e437ab214491864de5d2a607c3f06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 21 15:03:48 2019 -0500
switch over to model_parser_init
Exec/science/flame_wave/Prob_nd.F90
commit 4e77ea3d0af00a1bc61973783777dcb54b2a478d
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Feb 21 14:47:17 2019 -0500
model_parser_init function (#520)
This addresses #403, and creates a model_parser_init function which allocates and initializes the module information for problems that don't read this information in from a file.
Util/model_parser/model_parser.F90
commit aa2832458d69e94118be21d1cae371c897c91f29
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Feb 21 14:19:26 2019 -0500
model_parser_init function
Util/model_parser/model_parser.F90
commit a90847d7d78393396d33ca24f99fef5af945aabb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 20 11:38:05 2019 -0500
get rid of species sources by default (#519)
This change eliminates species sources by requiring us to set the parameter `PRIM_SPECIES_HAVE_SOURCES`. To support this the `set_variables.py` script was updated to now allow the "adds-to" field to have an optional if-def requirement.
This change also fixes 2 bugs. In `srctoprim`, we were converting the velocity sources twice. And in the radiation tracing, we were not adding species sources.
This closes #350
CHANGES
Exec/Make.Castro
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_variables
Source/driver/set_variables.py
Source/hydro/advection_util_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 4c39f1aa732ba7d49581b221be81ffa58cd641bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 20 11:16:28 2019 -0500
rename QVAR -> NQSRC (#517)
also fix a number of places where NQ should have been used instead of QVAR
CHANGES
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_variables
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_job_info_tests.H
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
Source/radiation/trace_ppm_rad_nd.F90
Source/sources/Castro_sources.cpp
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/software.rst
commit b6d6362f658133b1516f3263ac935900fb229e5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 20 09:19:17 2019 -0500
forgot to commit this
Exec/science/nova/Prob_nd.F90
commit 6218d39296390928959d75d9bc264fe1b35ac9c0
Merge: da7464992 aec32c368
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Feb 19 15:30:56 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit da7464992dcf30e2da680fba0943ec5778190c25
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Feb 19 15:30:46 2019 -0500
fix eos_type_module import in radiation_tests/RadFront/Prob_1d.f90
Exec/radiation_tests/RadFront/Prob_1d.f90
commit aec32c3688df93272c44a08a3370f031ac4820f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 19 09:13:12 2019 -0500
sync with sdc
Exec/hydro_tests/Sod_stellar/compare_sdc.py
commit 6b07f87787cbe284d93af719fd8db9e6b45ee0d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 19 09:11:55 2019 -0500
sync with sdc
Exec/hydro_tests/Sod_stellar/compare_methods.sh
commit d10aa28e6a08d4c6fbea5db9e814531a08a7dca7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 19 09:09:50 2019 -0500
fix location
Exec/Make.Castro
commit 743b70dfe0cb74e26cd01290c60024f641aa0e96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 19 09:05:31 2019 -0500
add extra thermo hook
Exec/Make.Castro
commit 01487f0f57f3df5c83d806bbbf37a2805bef9c38
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 23:16:05 2019 -0800
ca_check_timestep on the GPU
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/timestep.F90
commit 2de6f730bf95b7a0432251032aef00cf70a31a1a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 23:05:08 2019 -0800
Add some checks to protect against incorrect MOL usage
Source/driver/Castro.cpp
commit cbc7d9cd09cd6d0383ee9cbefd32906f44b12d4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 15:45:01 2019 -0800
Actually enable (large) tiles for the GPU
Source/driver/Castro.cpp
commit c7ea90d051747b0f904e5cfde9f731fbeec24ac0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 15:21:04 2019 -0800
Revert "Enable (large) tiles for the GPU"
This reverts commit 52062cd73338d60166425b7d3af386a14a356259.
Source/driver/Castro.cpp
commit 52062cd73338d60166425b7d3af386a14a356259
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 15:09:03 2019 -0800
Enable (large) tiles for the GPU
Source/driver/Castro.cpp
commit f7d9432170977756c3b0217348c18ef1c19f3cfe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 18 15:35:46 2019 -0500
CTU plm ppm split (#514)
Split the call to ctu_normal_states into separate routines for PPM and PLM. Also, loop over dimensions in PLM/PPM to decrease the memory footprint.
Source/driver/Castro_F.H
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 8d470dea9990c0c559b49ba4bafa0b9d15a068e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 13:08:04 2019 -0500
Fix the box used in MOL CUDA
Source/hydro/Castro_hydro.cpp
commit 19c79d0f826f9bc2f52606678f176270f8f20d51
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 18 12:57:27 2019 -0500
Remove a stray device synchronize
Source/hydro/Castro_hydro.cpp
commit 172aa1d7879ee9d22ea358219e5d18ad5399cc8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 18 10:19:30 2019 -0500
update CHANGES
CHANGES
commit e383e7dcadb8f0282ba77f8be393285c8a881875
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 17 19:52:32 2019 -0500
Add a setup for regression testing
Exec/science/wdmerger/tests/tde/inputs.test
Exec/science/wdmerger/tests/tde/probin.test
commit bcb5907d7b21beec35e856080d8cc3cc650cae28
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 17 16:06:05 2019 -0800
Write grid losses to plotfile if they're tracked
Source/driver/Castro_io.cpp
commit 998acbc78d128e0f254511f85a655420f476ed66
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 17 08:17:18 2019 -0800
Move ca_track_grid_losses to the device
Source/driver/Castro_F.H
Source/driver/Castro_util.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
commit 945d2692aa6b880bb1a4eb6d91f4fd5f43047d19
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 17 06:15:26 2019 -0800
Move clean_fluxes up to C++ (#513)
Source/driver/Castro_F.H
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit 304b91c99ce9eb4215783ebc8c0a942749c0364b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 16 15:29:17 2019 -0800
Merge MOL CUDA into a single MFIter loop
Source/hydro/Castro_hydro.cpp
commit d8a1546bb8760486576a9cd401e400fddcfb9ee8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 16 15:01:45 2019 -0800
Move CUDA MOL up to C++
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit 9510d2ed26af976e014f1c2225c5e4850f6e874f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 16 14:34:24 2019 -0800
Move store_pradial to C++ (#511)
.gitignore
Exec/Make.Castro
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_variables
Source/driver/set_variables.py
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit f07b5ac754abf8281c5df25de98351eb5f07f8cf
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri Feb 15 15:13:55 2019 -0500
fixing typo
Source/hydro/riemann_nd.F90
commit a20b52281a5675b85804c1c2d585e8ebf42150f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 15 09:27:53 2019 -0800
Enable CTU advance on GPUs (#510)
this marks up the CTU hydro routines to work on GPUs.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
commit c008ae59ffc844ebf92055dd6f0206b0a6617ca9
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri Feb 15 09:33:46 2019 -0500
Added T_guess parameter (#509)
closes #321
Exec/unit_tests/particles_test/Prob_nd.F90
Exec/unit_tests/particles_test/inputs.2d
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/riemann_nd.F90
Source/hydro/trans.F90
sphinx_docs/source/EOSNetwork.rst
commit 58770dcc15e0965ca1b23638be1e71296542e7cf
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 13 16:50:20 2019 -0500
added deleted files
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.aprox13
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.cool
commit 3b3820fafba4234c80b5bdc12c8a53e14a2584ee
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 13 16:47:15 2019 -0500
added deleted file
Exec/science/flame_wave/old/inputs/inputs_2d
commit f2b8ecb4fa2cb7940fb7dc43d09e13920733f7b0
Merge: beb7e5c07 ee411a98a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 13 16:40:42 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into particle_unit_test
commit beb7e5c07bdcab8d7b51a62fce1f03da4830b0d4
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 13 16:40:24 2019 -0500
change BCs to outflow
Exec/unit_tests/particles_test/Prob.cpp
Exec/unit_tests/particles_test/inputs.2d
commit 57ad142cad51a4173861dd0c9f4221f9ad7d2c66
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 13 16:22:00 2019 -0500
Prob.cpp reads in particle_file and calculates change in position - assumes that the particles should have returned to their original positions
Exec/unit_tests/particles_test/GNUmakefile
Exec/unit_tests/particles_test/Prob.cpp
Exec/unit_tests/particles_test/Prob_nd.F90
Exec/unit_tests/particles_test/inputs.2d
Exec/unit_tests/particles_test/make_particles_file.py
Exec/unit_tests/particles_test/particle_file
Exec/unit_tests/particles_test/probin.2d
commit ee411a98af861ca68efa1cf30921974ee4d31964
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 13 10:19:38 2019 -0800
fix format of high density burning cutoff
for the 5/5 boost, use the flame limiter
Exec/science/flame_wave/inputs.boost_10_10
Exec/science/flame_wave/inputs.boost_5_5
commit d77f33c30366fa3a3b8fc43fe90839e0cc47da25
Merge: d604f6492 23f300fd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 13 09:17:11 2019 -0800
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d604f6492fb966b5768e90e32bb16efc5fc8a5e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 13 09:16:46 2019 -0800
update script to work with new esslurm module
Util/job_scripts/edison/edison.xfer.slurm
commit 2156e5c4435fbe17887279a54af63b0881085834
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 13 11:55:44 2019 -0500
started writeing particles unit test
Exec/science/flame_wave/analysis/schlieren.py
Exec/science/flame_wave/old/inputs/inputs_2d
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.aprox13
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.cool
Exec/unit_tests/particles_test/GNUmakefile
Exec/unit_tests/particles_test/Make.package
Exec/unit_tests/particles_test/Prob_nd.F90
Exec/unit_tests/particles_test/inputs.2d
Exec/unit_tests/particles_test/make_particles_file.py
Exec/unit_tests/particles_test/particle_file
Exec/unit_tests/particles_test/probdata.f90
Exec/unit_tests/particles_test/probin.2d
commit 23f300fd40f2ef5fd85de9f7636e68c46fd23a6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 12 23:40:25 2019 -0800
Fix Elixir identification
Source/hydro/Castro_hydro.cpp
commit b3e4b907d06891d7f9a4cd68ddbd8c5c79e7f125
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 12 23:21:50 2019 -0800
Remove unused variable
Source/driver/Castro_advance.cpp
commit 85b06e3f622d1e766749c7fcb682467321d3fbc6
Merge: 94eccd785 588a86ac1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 20:59:57 2019 -0500
Merge branch 'master' into development
commit 588a86ac1e57a4949c46b9e4864bffbf33296ea3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 20:57:14 2019 -0500
update travis badge: travis-ci.org -> travis-ci.com
README.md
commit 94eccd7855a0e53d99c1aab51db97264735b15ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 20:57:14 2019 -0500
update travis badge: travis-ci.org -> travis-ci.com
README.md
commit dcd2fff8ec3e818c29e247a5700f1eabc1486ed9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 20:38:36 2019 -0500
update changes
CHANGES
commit 0e30ab85550a3d0f00732ae217cc3db80ffb4b05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 20:35:44 2019 -0500
C++ version of the CTU driver (#498)
All the CTU kernels are now called from C++.
Exec/science/rotating_star/probin
Source/driver/Castro_F.H
Source/driver/check_for_nan.f90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
commit 5419b84035c4f1904e651cb7860f5bdc599ae336
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Tue Feb 12 20:22:56 2019 -0500
Added inputs/probin files for 25-4 flame wave run (#507)
Exec/science/flame_wave/inputs.boost_25_4
Exec/science/flame_wave/probin.boost_25_4
commit 0447b9d3269f1b96eb63f51350adfdc766a890af
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Tue Feb 12 17:37:49 2019 -0500
New ihe4 variable in Probably_nd.f90 conflicts with aprox13 (#505)
The ihe4 variable was conflicting with a variable in aprox13's actual network file so I gave the variable in this file an underscore to resolve the conflict.
I checked and make succeeds when compiling the subchandra model using the aprox13 network.
Exec/science/subchandra/Prob_nd.F90
commit f45c638e6f3da159dd4e366e17d90d85701b2df0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 13:17:38 2019 -0800
smaller boost
Exec/science/flame_wave/inputs.boost_5_5
Exec/science/flame_wave/probin.boost_5_5
commit 372c65c8d8faa27f255dc1da3602a44173b43284
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 12 10:54:51 2019 -0800
rename to be clear about the boosting
Exec/science/flame_wave/inputs.boost_10_10
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/old/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/probin.boost_10_10
commit 9a703b828afbc2c83bb3cd479c10e282650bd1ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 11 21:33:55 2019 -0500
change the mass fraction threshold for refinement to prevent excess grids from
being created beneath the fuel layer.
Exec/science/flame_wave/probin.boost.aprox13
commit daa6c38c6026c050dfc55856cdf76b90cfec1105
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 11 18:31:50 2019 -0500
added schlieren.py plotting script
Exec/science/flame_wave/analysis/schlieren.py
commit 03f21fef023aab4d26a373529efa17667073a6fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 11 17:56:44 2019 -0500
index_base_from_temp is not used
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/job_scripts/aprox13/probin.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/probin.boost.aprox13
Exec/science/flame_wave/old/inputs/probin.boost.base
Exec/science/flame_wave/old/probin
Exec/science/flame_wave/old/probin.boost
Exec/science/flame_wave/old/probin.boost.hires
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost.aprox13
commit 2fc089a9ee562e4c2520534655a8a9faaaeeeb89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 11 15:48:43 2019 -0500
add a new tagging parameter -- now we can keep the finest level
to only a small portion of the horizontal extent of the domain
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost.aprox13
Exec/science/flame_wave/problem_tagging_nd.F90
commit 2820eee8385c97c9c9ae680d31925ccd5b45165e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 11 15:09:25 2019 -0500
fix the perturbation location and multiply by X(He4)
Exec/science/subchandra/Prob_nd.F90
Exec/science/subchandra/probin
commit dd6d22c8a6be3e96f257de0f64221f09c4719728
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 17:49:25 2019 -0500
bl_warning -> print
Source/hydro/advection_util_nd.F90
commit a5ef240162425091020d82c740a7871d68a454ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 17:35:35 2019 -0500
fix my previous changelog entry
CHANGES
commit a6ae7f65365064c8d2ab5e09b09e9713de099a48
Merge: 2ee6afed1 c6351c155
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 10 14:10:56 2019 -0800
Rename do_ctu (#503)
This renames castro.do_ctu to castro.time_integration_method.
This will allow for more integration methods to be added, and makes the code more readable.
commit c6351c155cd70c87acab56a863ca0be008371fc9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 10 17:10:30 2019 -0500
Update CHANGES
CHANGES
commit a63dc311a529971a916f66cf19308918e9c1ca28
Merge: f0afe43ab 2ee6afed1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 16:55:51 2019 -0500
Merge branch 'development' into rename_do_ctu
commit 2ee6afed141a2d71a2911ffe545f7d2a2f1f7a98
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 16:45:17 2019 -0500
implement PLM reconstruction for MOL integration
backported from sdc
Source/hydro/Castro_mol_nd.F90
commit bc9643d47c90f278f8605e11a2a31e10f62bd763
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 15:33:48 2019 -0500
fix indentation
Source/hydro/fourth_order.F90
commit bb7870e75e1ba9dc7f7dd9740a50f9cd0e5bf4c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 15:28:31 2019 -0500
sync up some 4th order limiting changes (from sdc)
no production code uses these
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/fourth_order.F90
commit f0afe43aba16b5ce42b35cb195398e3d62885569
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 14:58:03 2019 -0500
fix logic for source term predictor
Source/driver/Castro_advance.cpp
commit 484d0107c1b5092af0d00db10125684c54842ebc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 13:48:30 2019 -0500
rename do_ctu to time_integration_method
this allows for more options, like SDC. This is a port from the sdc branch
Exec/hydro_tests/Sedov/inputs.starlord
Exec/hydro_tests/Sedov/inputs.starlord.gpu_test
Exec/unit_tests/reactions_driver_test/inputs.ignition.16
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/timestep.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
Source/sources/Castro_thermo.cpp
commit 316e3a8354286f97c26fd02ed08925646e61b788
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 13:11:49 2019 -0500
this doesn't use reactions
Exec/hydro_tests/toy_convect/GNUmakefile
commit 417dfd31f41a6117574d3a0517a9ce6235d886b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 13:05:04 2019 -0500
port the proper 4th order artificial viscosity over from sdc
this doesn't affect anything other than the fourth order solver
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit 03e4bb42d8449216c0ee1e7a65cd7d8e8d54fe6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 10:14:22 2019 -0500
this problem doesn't use reactions
Exec/science/bwp-rad/GNUmakefile
commit 95ff40a7a3777e8fbfda82e8c5a3abc2122fb931
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 10 10:07:44 2019 -0500
port some setups from the sdc branch
these are used to assess convergence
Exec/hydro_tests/Sod/compare_methods.sh
Exec/hydro_tests/Sod/compare_sdc.py
Exec/hydro_tests/Sod_stellar/compare_methods.sh
Exec/hydro_tests/Sod_stellar/compare_sdc.py
Exec/hydro_tests/acoustic_pulse/convergence.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse/gamma_law_runs.sh
Exec/hydro_tests/acoustic_pulse/inputs.2d.128
Exec/hydro_tests/acoustic_pulse/inputs.2d.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.512
Exec/hydro_tests/acoustic_pulse/inputs.2d.64
Exec/hydro_tests/acoustic_pulse_general/GNUmakefile
Exec/hydro_tests/acoustic_pulse_general/Make.package
Exec/hydro_tests/acoustic_pulse_general/Prob_nd.F90
Exec/hydro_tests/acoustic_pulse_general/README
Exec/hydro_tests/acoustic_pulse_general/convergence.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_1d_sdc4.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc.sh
Exec/hydro_tests/acoustic_pulse_general/convergence_sdc4.sh
Exec/hydro_tests/acoustic_pulse_general/helmeos_runs.sh
Exec/hydro_tests/acoustic_pulse_general/inputs.128
Exec/hydro_tests/acoustic_pulse_general/inputs.256
Exec/hydro_tests/acoustic_pulse_general/inputs.512
Exec/hydro_tests/acoustic_pulse_general/inputs.64
Exec/hydro_tests/acoustic_pulse_general/probdata.f90
Exec/hydro_tests/acoustic_pulse_general/probin
Exec/hydro_tests/reacting_convergence/GNUmakefile
Exec/hydro_tests/reacting_convergence/Make.package
Exec/hydro_tests/reacting_convergence/Prob_nd.F90
Exec/hydro_tests/reacting_convergence/README
Exec/hydro_tests/reacting_convergence/convergence_sdc.sh
Exec/hydro_tests/reacting_convergence/convergence_sdc4.sh
Exec/hydro_tests/reacting_convergence/convergence_strang.sh
Exec/hydro_tests/reacting_convergence/helmeos_runs.sh
Exec/hydro_tests/reacting_convergence/inputs.128
Exec/hydro_tests/reacting_convergence/inputs.256
Exec/hydro_tests/reacting_convergence/inputs.512
Exec/hydro_tests/reacting_convergence/inputs.64
Exec/hydro_tests/reacting_convergence/probdata.f90
Exec/hydro_tests/reacting_convergence/probin
commit 60459f581fafeca7951f34a70146358b7853093c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 9 22:36:30 2019 -0500
start of the rotating star setup
Exec/science/rotating_star/GNUmakefile
Exec/science/rotating_star/Make.package
Exec/science/rotating_star/Prob_nd.F90
Exec/science/rotating_star/inputs_2d
Exec/science/rotating_star/probdata.f90
Exec/science/rotating_star/probin
commit 14cb02c7f6c67e3405aa8d4854ffe562e8400267
Merge: 6703f4dd6 233292246
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 9 21:31:30 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 6703f4dd6a2e530253045dbeb790e63a1009f9df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 9 21:31:17 2019 -0500
switch this to dimension agnostic
Exec/science/subchandra/GNUmakefile
Exec/science/subchandra/Prob_2d.f90
Exec/science/subchandra/Prob_nd.F90
commit 2332922467b864eae89649b8b488ec5e606a6dba
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 9 18:30:10 2019 -0500
Be more careful with floating point logic
Source/driver/Castro.cpp
commit 62ec128938b1bc5d54690bcb16bfa05849d820f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 9 17:35:11 2019 -0500
Rearrange and add comment to clarify reasoning
Source/driver/Castro.cpp
commit 4aa698a843249b7f327ff81ec458c2fa5af6fa10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 9 17:24:32 2019 -0500
have cmpflx call riemann_state to reduce duplicate code (#501)
closes #479
Source/hydro/riemann_nd.F90
commit 70ca9fc9bc69b6091d40350e79d37be630186052
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 9 17:12:02 2019 -0500
Avoid incorrect check on writing final smallplot
Source/driver/main.cpp
commit aa491834d600fb7f124311574ca5ba844c70c68f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 9 16:01:20 2019 -0500
Use Real, not float
Source/driver/Castro.cpp
commit c883cd07f5660f8934ee23dd0873b3521d8a7140
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 9 16:00:38 2019 -0500
Use machine epsilon in stop_time calculation
Source/driver/Castro.cpp
commit d31123d1ee1801a9598c65345c40f92f8c3bb020
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 9 13:06:56 2019 -0500
add url to main page
sphinx_docs/source/index.rst
commit 43b86bf67db400bccdb0c260fc4aa78958cb273f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 9 09:54:06 2019 -0500
remove ppm_trace_sources -- that is no longer an option (and is on by default)
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame_wave/inputs_2d.boost.aprox13
Exec/science/flame_wave/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
commit e4649de2aa163c354490d68ee6d12b3b3887397f
Merge: 91d19b7f8 f71a31719
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 8 22:58:11 2019 -0500
Merge branch 'master' into development
commit f71a31719bb8ed2a8e8fa3821a5b9204ba66a512
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Fri Feb 8 13:06:50 2019 -0500
Created a 1.1 Solar Mass model with inputs that allow it to run for a while. (#496)
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/probin
Exec/science/subchandra/sub_chandra.M_WD-1.10.M_He-0.050.hse.C.2560
commit 91d19b7f85d385e42259117b32d98eb83af3bbca
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 8 10:54:43 2019 -0500
velz should not be omp private
Exec/hydro_tests/KH/Prob_nd.F90
commit 727d4c5ee30636badf78c90a05f788d8fe4f7a96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 7 21:26:48 2019 -0500
set languages for code blocks
sphinx_docs/source/debugging.rst
commit ff75912db5050a99ec213373a07be2052d789816
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 7 21:07:23 2019 -0500
some more debugging
sphinx_docs/source/debugging.rst
commit a56c86c68c7a52b6573eb1fd6a55286050ba0256
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 7 14:57:16 2019 -0500
start of some notes on debugging
sphinx_docs/source/debugging.rst
sphinx_docs/source/index.rst
commit 667c955270afd69b8254018a36f3ae531b635278
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 6 20:19:14 2019 -0500
fix compilation problem that was only picked up with PGI in debug mode...
Exec/science/flame_wave/Prob_nd.F90
commit 205e06e6b3cc8ebcae38993fe2f8ec763514e264
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 6 11:20:41 2019 -0500
for 2-d axisymmetric, we should do the correct weighting when subsampling
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
commit 7f6112a68606fb1b691abdea7181ddfb97d24d9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 6 09:36:41 2019 -0500
fix compilation
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
commit 5df2b1a9ae27007fd010a49485ba9bb07deb5cb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 19:06:51 2019 -0500
fix dimensioning
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
commit e451b53e1ce6a9a580fa66be9c6ab1fa10e55353
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 19:06:23 2019 -0500
add intents
Source/sources/ext_src_nd.F90
commit 72c3697f5b4324602571b9aeb40ec65386d60768
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 19:04:26 2019 -0500
add a dimension agnostic version of the BCs
Exec/gravity_tests/DustCollapse/bc_fill_nd.F90
commit cb5808678308274a49318ca08f7626ecde663b66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 19:02:27 2019 -0500
fix dimension of bc(:,:,:)
Source/problems/bc_fill_nd.F90
commit 496401244a6eff6eba29d0a3d4cbfa15cc51c287
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 15:43:59 2019 -0500
make the source dimension agnostic
Exec/gravity_tests/hydrostatic_adjust/ext_src_nd.F90
commit 7fbf6102cc563e918475a3b3b1beae7185f7a90b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 15:02:37 2019 -0500
set some more variables
Exec/gravity_tests/DustCollapse/Prob_nd.F90
commit ec0c0ab028840a52ca15fe097c319fb0874358f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 14:55:15 2019 -0500
restore the custom BCs, now dimension-agnostic
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_nd.F90
commit dcf882c7aaebf5b57b615f7d6565460b9a1dd6f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 14:23:12 2019 -0500
we are not using the custom BC
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
commit 2ff1c586595f7b0897ce6138bf6bb785a96f89ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 5 13:49:59 2019 -0500
fix center for 1-d
Exec/gravity_tests/DustCollapse/Prob_nd.F90
commit a1f86e35daf0b160942a3797e38c06df43be31c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 4 17:49:45 2019 -0500
cutoff burning at a lower high density, 1.5e7 instead of 5.e7
this should reduce a lot of calls to the network
Exec/science/flame_wave/inputs_2d.boost.aprox13
commit bbae5581e95ffcd74bca97ceb983fddf039030d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 20:50:03 2019 -0500
fix coordinates
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
commit daba3e7be1342abe49dfc68f500c10a45f5ebd1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 18:08:54 2019 -0500
fix the link
sphinx_docs/Makefile
sphinx_docs/source/Hydrodynamics.rst
commit 3859fb3b6abcd46047802263862c18b539b5df6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 17:50:04 2019 -0500
fix up and reference the original ppm_temp_fix docs
change ref style
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/references.rst
commit 4921e104824dde63c30b3fc46375a729638cead5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 17:38:40 2019 -0500
document ppm_temp_fix
sphinx_docs/source/Hydrodynamics.rst
commit 5c6d235486224cba0bd9a2ad48150bc49e74b6df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 12:07:27 2019 -0500
remove dupe
CHANGES
commit 4420f979f46cdbc993d1442cabbbd3a8c3d88484
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 10:46:47 2019 -0500
update changes
CHANGES
commit b2b90550eae99a9333c896f4b6a86a4c19fd6285
Merge: d70f69581 ffefe9de7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 10:45:10 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d70f695817badcc467381cfbaeb8450d517d372e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 3 10:44:52 2019 -0500
fix ppm_type = 1 -- we were not reconstructing T
Source/hydro/Castro_ctu_nd.F90
Source/hydro/ppm_nd.F90
commit ffefe9de79008432e43839f80250b9f18310251e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 22:01:47 2019 -0500
switch to dimension agnostic
this also fixes a bug in the total energy when a perturbation is applied
Exec/science/nova/GNUmakefile
Exec/science/nova/Prob_2d.f90
commit c8e2650ea74cdcfe0971d4d9b6a659122ac8af10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 21:41:03 2019 -0500
add a small_temp
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.SDC
Exec/science/Detonation/inputs-det-x.regrid
Exec/science/Detonation/inputs-det-x.subch
commit f4d415729b6f92b28b843ac4903faf11c0064e04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 20:28:40 2019 -0500
add support for dimension agnostic radiation problems and convert RadThermalWave
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/radiation_tests/RadThermalWave/Make.package
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
Exec/radiation_tests/RadThermalWave/Prob_nd.F90
Source/driver/Castro.cpp
Source/driver/Castro_F.H
commit 1dc10d99976f1771157a9b27504b0623c76999a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 19:11:36 2019 -0500
Dimension agnostic Gresho vortex problem
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/gresho_vortex/Make.package
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/Prob_nd.F90
commit 1970e85591e41832d40ccbbadc9dd2e2655d5056
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:58:58 2019 -0500
fix a dimensioning
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
commit 743c1175f066edac04da855609fe1ebb7c50e2cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:58:43 2019 -0500
make diffusion_test dimension agnostic
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/diffusion_test/Prob_nd.F90
commit 52d58b0a6a7b130c4794baf794823d2345c64277
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:42:01 2019 -0500
add missing Prob_nd's
Exec/gravity_tests/DustCollapse/Prob_nd.F90
Exec/gravity_tests/StarGrav/Prob_nd.F90
Exec/gravity_tests/evrard_collapse/Prob_nd.F90
commit ed1f5bb1e54ca9f452f0766cd878a0a81b306e72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:41:13 2019 -0500
forgot to add Prob_nd.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_nd.F90
commit 9abe9e2a5d12213c25ca10a9a005d51911a0a270
Merge: 54a5edebd 2f5baadf1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:39:59 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 54a5edebdf6d09cfeb2482d6964f156f9fcd04ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:38:26 2019 -0500
update to be dimension agnostic
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
commit 2f5baadf1cb18482ecf0c015937fc871a98eaaa6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 18:29:14 2019 -0500
Dimension agnostic HCBubble problem
Also, fix a bug in UEDEN calculation. It didn't matter for the default setup.
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/HCBubble/Prob_nd.F90
commit 111b23139cbf46a2a537da41444f55ac77f80d26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 18:19:32 2019 -0500
make this dimension agnostic
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/Prob_nd.F90
Exec/gravity_tests/hydrostatic_adjust/probdata.f90
commit 274a3f127c7fb8023c18171cc277636f1594732b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 17:45:44 2019 -0500
make evrard_collapse dimension agnostic
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
commit cf10f9750ad93c32253800c684874acd4c91a875
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 17:25:00 2019 -0500
remove files that are no longer needed
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
commit 1d5d2d5ad090edc0bf57486df642bfcc291879cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 17:24:36 2019 -0500
make dustcollapse dimension agnostic
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/probdata.f90
commit d88a696b0f7edc8083aded73d002838020a1ab4a
Merge: b38660806 8b60fd902
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 16:59:59 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b38660806e88b8494718782a0b4538e915cbda83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 16:59:43 2019 -0500
make StarGrav dimension agnostic
Exec/gravity_tests/StarGrav/GNUmakefile
commit 8b60fd9027d8ee6ab1f552b6f018ddad3e149a94
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 16:53:06 2019 -0500
Dimension agnostic symmetry problem
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/symmetry/Prob_nd.F90
commit 287e3bc3cd9565aa3539a129015e458cdb3aea7f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 16:38:02 2019 -0500
Fix inputs file
Exec/hydro_tests/symmetry/inputs.3d
commit 449709ace4cfd766e56a01368089da85096739a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 16:32:08 2019 -0500
Dimension agnostic oddeven problem
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/oddeven/Prob_nd.F90
commit ce0176e8df848ad80efffc8493f1abdedf927599
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 16:14:15 2019 -0500
Dimension agnostic acoustic_pulse problem
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse/Prob_2d.f90
Exec/hydro_tests/acoustic_pulse/Prob_nd.F90
commit 06adbdbe938533997a2db0b90fe89de40abf3779
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 2 15:31:10 2019 -0500
Dimension agnostic RT problem
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT/Prob_nd.F90
commit 642efb92b24ceeaf0c35b9cbe5cee241f7498b15
Merge: 083365c6d 106b56d3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 12:31:12 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 083365c6d789e3309fc4f1531da86319ac6b0e38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 12:31:00 2019 -0500
small plotfiles have a derive list too
sphinx_docs/source/visualization.rst
commit 106b56d3c6257f9d3fe96adbec66c9db1461921f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 12:27:41 2019 -0500
setup small plotfiles
Exec/science/flame_wave/inputs_2d.boost.aprox13
commit f930f611b8133be1faa95537226bc2611b397ee2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 12:01:14 2019 -0500
remove old parameter
Exec/science/flame_wave/inputs_2d.boost.aprox13.hires
commit 50449727cd6406819e8cb7db32a0da1bbfd90206
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 08:58:58 2019 -0800
update to reflect what was run with the flame_wave_highres_ref simulation
Exec/science/flame_wave/inputs_2d.boost.aprox13
commit 30c31b213f988f4e2834fd889a531e80f481c5c3
Merge: 3c06c78f9 20b349ca8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 11:47:24 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 3c06c78f989a86ea26f7b66c6a1d7be58bff6584
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 2 11:46:51 2019 -0500
add more documentation about controlling plotfile output and variables
sphinx_docs/source/visualization.rst
commit 20b349ca868c03bf5b2aaf5bb78e1526f6d2688e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 1 09:16:37 2019 -0500
update version
CHANGES
commit 19d886c1ff230be2b30ba15c90059cfc11d6317f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 31 22:13:37 2019 -0800
Dimension agnostic Sod_stellar problem
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_nd.F90
commit 617f0838b98a577d12cbebef3245143869680c8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 31 22:05:03 2019 -0800
Dimension agnostic Sod problem
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_nd.F90
commit 1d2fe1aaf0bc499e5da216532defcb8e9581cebb
Author: Chris DeGrendele <35853499+ChrisDeGrendele@users.noreply.github.com>
Date: Wed Jan 30 14:27:35 2019 -0500
Analytical solution vs Plotfile for Rad2TShock python script (#492)
* Script to compare analytical solutions to a plot file for Rad2TShock
Exec/radiation_tests/Rad2Tshock/python/Analytical-Test.py
commit a471478ee4bdf3f8fb841f2de1c02c0a5d280716
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 30 11:47:19 2019 -0500
add zenodo DOI link
CITATION
commit 83f82b05dcab71b454e31cbb0c75ac42657deafb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 28 17:48:46 2019 -0500
clear some more bits out of consup (#491)
This removes some more bits out of consup to allow for GPU offloading
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit 6847fd0b51d626b85a87cab1909d40fd32ed8869
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 26 22:02:17 2019 -0500
add note about limit_fluxes_on_small_dens
CHANGES
commit f425b08aa2aaa43b794e17116d8915ae70eba373
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 26 12:58:03 2019 -0500
split some stuff out of consup (#488)
This splits some flux clean ups out of consup, and calls it on their proper lo:hi. This is prep for the GPUing. We can actually reuse this code for the other solvers too.
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit 23422ed2b431d527b7a860701aaf61bb22c3c427
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 26 12:44:32 2019 -0500
Save some more work
Source/hydro/advection_util_nd.F90
commit a5baf650fae1a08ba7a054eefc5ca13fbf33ce79
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 26 12:10:37 2019 -0500
Fix some dimensional notation
Source/hydro/advection_util_nd.F90
commit f992acb8f3b8a02bde22314f810f198f67d19ea0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 26 11:55:37 2019 -0500
Save some work in a temp variable
Source/hydro/advection_util_nd.F90
commit 761a4c1351e0dc4ecb709a1cd15616069855c8bb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 26 01:06:54 2019 -0500
Fix some issues in problem_tagging_*d
Source/driver/Castro_error_F.H
Source/problems/problem_tagging_1d.f90
Source/problems/problem_tagging_2d.f90
Source/problems/problem_tagging_3d.f90
Source/problems/problem_tagging_nd.F90
commit 96b85e64cb3713b2f1dd061ed79ab710d620f59b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 25 17:22:06 2019 -0800
Fix the hydro flux limiter for small densities (#493)
This limiter was not correctly applying the formulas from the source paper.
Now the code is much simpler and correctly implements the algorithm.
Source/hydro/advection_util_nd.F90
commit c6b533d7512384713b5cac928bf25e24bcd9a0d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 24 15:01:06 2019 -0500
add note about zenodo
README.md
commit 9147aa5be1dc1540423718f2fd0705e94cfe0b26
Merge: b50997e85 d83c151f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 24 13:16:10 2019 -0500
Merge branch 'master' into development
commit d83c151f0828c0587b056acb9a7d41b762f767cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 24 12:26:48 2019 -0500
formatting
README.md
commit 9349788e8b0f9fe032663878f8f81fb6cf45c4de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 24 12:26:01 2019 -0500
add Zenodo badge
README.md
commit e90f5fbe10e296d354a40368846912e1197cbb5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 24 12:02:51 2019 -0500
fix JSON
.zenodo.json
commit 7ea79ed258f889490bc04827481c4501b83927e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 24 11:56:35 2019 -0500
remove license -- this might give zenodo errors
.zenodo.json
commit b50997e85d6af03c2002c82d1083891ed82610be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 23 20:30:40 2019 -0500
create bindings for trans* and cmpflx_plus_godunov and reorganize calls in main driver (#487)
Source/driver/Castro_F.H
Source/hydro/Castro_ctu_nd.F90
Source/hydro/trans.F90
commit ec63c512094bdcb77f540e43a4c244521776eb37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 21 20:52:28 2019 -0500
fix radiation compilation
Source/hydro/riemann_nd.F90
commit d47fb5dbbcabba873bf059332f9ebe0626d6fce2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 21 11:56:25 2019 -0500
combine cmpflx and store_godunov_state (#486)
Source/hydro/Castro_ctu_nd.F90
Source/hydro/riemann_nd.F90
commit 5d60636d3018eded9697707a73a7f47433afa872
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 21 11:35:12 2019 -0500
more CTU reorg (#484)
This makes explicit the bounds of all of the arrays passed into the cmpflx and trans routines and also
moves all of the allocations into the main driver. This prepares us for the GPU offload now.
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trans.F90
commit 10e7947cc64134b372b1a7db97915444421bb5b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 19 13:18:27 2019 -0500
CTU reorg (#480)
This is the start of splitting the CTU functions into pieces that are grouped together by the same lo:hi, so we can offload to the GPU
Source/hydro/Castro_ctu_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit b73b50edb99c20071b23f57e28918a535c76335b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 18 19:32:34 2019 -0500
switch CUDA code to main cmpflx routine (#478)
This gets rid of the separate cmpflx_cuda code in the GPU MOL code path, and now offloads the
normal Riemann solver to GPUs
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/prob_params.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
commit 40f8dbefc002420f87525dd0afc375d40c7d9697
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 17 12:54:11 2019 -0500
initialize USHK
Source/hydro/riemann_util.F90
commit 39a78fe320c8c67fbaf184d7536693e331fab07d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 17 10:24:27 2019 -0500
zero out the temperature and shock fluxes
Source/hydro/riemann_util.F90
commit 2545007020ca92d5e3a9620e4f50be2059372310
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 15 20:17:19 2019 -0500
move lo/hi to the front for uslope and pslope
Source/hydro/Castro_ctu_nd.F90
Source/hydro/slope_nd.F90
commit c1f8cbead803deadff871504871b6f6bda4c276f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 15 20:06:49 2019 -0500
get rid of the multidimensional BDS limiter -- it is only 2d and never used
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Make.package
Source/hydro/multid_slope_2d.f90
commit 4f56e665d08e8c9b8f698a3c0b182ff5e56aafc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 15 17:24:52 2019 -0500
fix compilation
Source/hydro/Castro_ctu_nd.F90
commit 342d8a878eb70e31a9fe0caddea293deb5500e1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 15 15:17:23 2019 -0500
more *4 gpu changes (#458)
use apply_av in CTU, change trace* routines to explicitly pass in bounds we loop over
Source/hydro/Castro_ctu_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 2c73fa34a1200e2325d1cb01a606b97af47bdfb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 16:02:04 2019 -0500
rename store_godunov_state -> ca_store_godunov_state
and make a C binding
Source/driver/Castro_F.H
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/riemann_util.F90
commit f7dc55c1623052948b71627c82a902bd14750ce3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 15:33:47 2019 -0500
the C prototype for ca_shock
Source/driver/Castro_F.H
commit 7f44ae2026ea5fbdf9464fda0c143b6a3ad86d01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 15:33:16 2019 -0500
rename shock() -> ca_shock() and write a C prototype
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit 3bbc4b8632090644e5efacfb23e8e9b53ca089b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 15:13:15 2019 -0500
adjust the cmpflx interface to put lo/hi at the front
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/riemann_nd.F90
commit 8b80de926bb55d1ee1c8ca5071f66b0c7cd69548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 12:42:22 2019 -0500
add CUDA_LAUNCH_BLOCKING
sphinx_docs/source/gpu_porting.rst
commit 54891e988dbca8fd46fcf1894056fdfd886fdff0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 12:10:39 2019 -0500
update region disabling
sphinx_docs/source/gpu_porting.rst
commit eaa85c7a2f65609471f6c1f49e3d72ccc8d495f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 11:00:11 2019 -0500
another formatting fix
sphinx_docs/source/gpu_porting.rst
commit 7404afa076dcc0875d3ba3f99baafa3cb71c6efa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 10:56:54 2019 -0500
fix some formatting
sphinx_docs/source/gpu_porting.rst
commit a77dea53113aff737cc6b81e2280a55df503ab21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 14 10:02:12 2019 -0500
more more more GPU CTU changes (#456)
This makes explicit the range of cells looped over in the transverse routines.
CHANGES
Source/hydro/Castro_ctu_nd.F90
Source/hydro/trans.F90
commit 716827e5451a6b3afcd5a91f183d30934a7c9741
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 13 10:16:49 2019 -0500
update the diffusion docs
sphinx_docs/source/diffusion.rst
commit 2ea2ae15ab04ead1e2416762152364ad14f6a236
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 13 09:54:04 2019 -0500
add note about cutoffs
CHANGES
commit e2ba2ca0e1c73fe57effd309be108aa774e059f2
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Sun Jan 13 09:52:18 2019 -0500
Added option for linear dropoff of diffusion term (#476)
Added the diffuse_cutoff_density_hi parameter. The diffusion term will
now drop off linearly between diffuse_cutoff_density_hi and
diffuse_cutoff_density when former is set to be higher than the latter.
Source/diffusion/Diffusion_nd.f90
Source/driver/Derive_nd.F90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit dc104814eaaf84a50f885f6489348b3c9bd43c8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 12 19:47:33 2019 -0500
remove an unneeded bl_allocation for radiation
Source/hydro/riemann_nd.F90
commit a6c450b3f9ba21e1cb67daf2654457b27cfa1346
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 12 13:50:04 2019 -0500
update changes
CHANGES
commit d0bcfb8e5062daa0192538bfe4f616bd32db1082
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 12 13:23:05 2019 -0500
still more GPU changes (#455)
this eliminates all of the remaining bl_allocates downstream of the main hydro drivers.
CHANGES
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
commit 1946b343fbff2443975dc7eeeed1fda5e4096757
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 12 10:14:16 2019 -0500
update CHANGES
CHANGES
commit 4ba1073cfd6a78000fc38dbed309640192510926
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 12 01:34:17 2019 -0500
add enuc tagging (#473)
* add enuc tagging
closes #437
* move dxnuc to Fortran.
closes #364
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/inputs-det-x.regrid
Exec/science/Detonation/probin-collision
Exec/science/Detonation/probin-det-x.regrid
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/probin
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro_error.cpp
Source/driver/Castro_error_F.H
Source/driver/Castro_nd.F90
Source/driver/Tagging_nd.F90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 57e19e5db5765d21202ad2425f14c2ec1c8088dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 9 19:04:52 2019 -0500
remove the license -- it should respect what github gives it,
this may be the cause of the "unknown error" from zenodo
.zenodo.json
commit 4dc8f2994820fb6946365ba008bfdd837b4dc22d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 9 18:56:21 2019 -0500
info on zenodo fix
CHANGES
commit 48db0f7c18fc709d8f5656f6fd197182e3026d9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 9 18:55:42 2019 -0500
cherry pick from development
.zenodo.json
commit 984090c59f3125d8ee1211f7d553b34dc087006f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 9 16:18:25 2019 -0500
update zenodo to have "the Castro Development Team" listed first
also lint the json
.zenodo.json
commit 0b50fd6dbb325de197dd0751459ba1e6435b6764
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 8 13:48:27 2019 -0500
add Lupe's ORCiD
.zenodo.json
sphinx_docs/Makefile
commit 44ef62a284b374ba8710bb02b64f619ca1fe915e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 7 19:13:55 2019 -0500
add John's ORCiD
.zenodo.json
commit bd27ac3f3a82c9779cdf6cde2dc3959aa75356a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 7 18:55:17 2019 -0500
fix spelling, update Max's affiliation
.zenodo.json
commit 728102c05aa018055a217617c29659ce48eb3125
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 7 18:51:44 2019 -0500
add Weiqun's ORCiD, fix affiliation spelling, add Max's affiliation
.zenodo.json
commit ac8c73e71953adeadd624e16857fe30679e776dc
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Mon Jan 7 15:04:56 2019 -0800
Add ORCiDs for Ann and Max.
.zenodo.json
commit fe844c2da0db20aff7fc9c871bbf6758d3f034dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 7 17:54:18 2019 -0500
add Max's ORCiD
.zenodo.json
commit 60df79215cbdaebd2c509119fe9ce2b416076056
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 6 12:29:26 2019 -0500
document the build system
sphinx_docs/source/build_system.rst
commit cacdc9bebb9577da21981a94331e55ea10fe5e54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 5 11:06:12 2019 -0500
fix index separator
sphinx_docs/rp.py
commit 81e14e261f3fbb3682f7fd69769528a78f9e9138
Merge: 2ac76e50e 4f809540c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 5 10:07:28 2019 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2ac76e50e06692a1864019f002ebadb0469df898
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 5 10:07:15 2019 -0500
automagically add runtime parameters to the index
sphinx_docs/rp.py
commit 4f809540c07bb3b3fac99ec3cb7741437f8e986a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 4 19:24:15 2019 -0500
we can access gravity_type directly from Fortran so no need to hack it through ca_set_meth_params
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/meth_params.template
commit 2f0099017b1384365811b8a86fecefc2d0befb9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 4 18:45:33 2019 -0500
move castro.v and castro.dump_old into _cpp_parameters
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
commit 18499ed341f114c49cc67d87a3df9207387b7431
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 4 17:51:17 2019 -0500
we were querying sum_interval twice
Source/driver/Castro.cpp
commit 38182a6dd65ff494f3803f25d0a99b8a2d6c8853
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 4 17:25:39 2019 -0500
update changes
CHANGES
commit d00287fcab46b6aae0c7861b5c9c3a8c6e6f1302
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 4 16:31:01 2019 -0500
write out the state variables to the checkpoint and compare on restart
this makes sure we didn't do something funny, like swap networks
closes #390
Source/driver/Castro_io.cpp
commit 0ed13b3e73a3928a027cd2d39a0f2a79cf0aa41b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 4 12:02:46 2019 -0500
add some documentation about the role of center
sphinx_docs/source/creating_a_problem.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/rotation.rst
sphinx_docs/source/visualization.rst
commit 94a9e00934b33a9b8e333db9c20d382b56554f87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 3 19:25:57 2019 -0500
fix sphinx
sphinx_docs/source/build_system.rst
commit 6998c064c5adb6eaf7a748fc65639e2d2c7b30b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 3 19:13:38 2019 -0500
add some build system docs
sphinx_docs/source/build_system.rst
sphinx_docs/source/index.rst
commit a7166a465e2c831ed478152892a8e129916695a9
Merge: 0a89177db 43bb376ea
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed Jan 2 12:40:26 2019 -0500
Merge pull request #471 from AMReX-Astro/job_info
add domain info to job_info
commit 0a89177dbec785c2fce0ebf797a7c703b766934f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 12:39:49 2019 -0500
create derived field abar (#470)
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit cebc3261ed7408de34c508786443a46c9db468ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 11:46:26 2019 -0500
add a hack for CUDA to define EXTRA_THERMO until the Fortran device script respects ifdefs
Exec/Make.Castro
commit cef1caf921926b4f79ca471991e855bb08b8e84d
Merge: 566287988 96e393295
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 10:57:31 2019 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 56628798850eaf66e6310f8d9921b15ccc867078
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 10:57:20 2019 -0500
update changes
CHANGES
commit 96e393295252209418b1266a56e237d93b89426b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 10:42:12 2019 -0500
plotfile quantities for axisymmetric coords (#472)
* fix the vorticity in axisymmetric coords
closes #449
* make the divu plotfile variable work for other geometries
closes #448
* fix the thermal diffusion term
it was not scaled correctly and did not handle axisymmetric coords
closes #446
Source/driver/Derive_nd.F90
commit dcfc4b6a07831d0cf32dccbe2a6d54ced7ebc7ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 09:39:38 2019 -0500
update changes
CHANGES
commit 636eaf15c1820b434e9b0307d922b298c96997e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 1 09:23:27 2019 -0500
update changes
CHANGES
commit d78199f851d831505af0e0ea383ec7986a962e0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 31 19:03:16 2018 -0500
store job_info in checkpoints too
closes #450
Source/driver/Castro_io.cpp
commit 43bb376eadaafd3d607cf0aa10420497b6376565
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 31 09:08:58 2018 -0500
add domain info to job_info
closes #451
Source/driver/Castro_io.cpp
commit 7e59446b290f74a4c9315a7d90ddbc9a365bec1f
Merge: 47b3424b8 d35280a92
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 30 20:32:25 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d35280a92dba5f89e95891143c981e7f77c3d35d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 30 14:35:24 2018 -0500
make some vertical profiles through the domain
Exec/science/flame_wave/analysis/profiles.py
commit 47b3424b867418fed0598857e7ee40a52833aece
Merge: 8a6271531 60aca3144
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 28 19:17:40 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 60aca3144d674f4eb630af169640c3291b10b62e
Author: Alice Harpole <ah1e14@soton.ac.uk>
Date: Wed Dec 26 17:49:04 2018 -0500
Filled in more docstrings in Gravity.H
Source/gravity/Gravity.H
commit b9ae777b409653a3f4f3dbe773729b797b048015
Author: Alice Harpole <ah1e14@soton.ac.uk>
Date: Wed Dec 26 15:00:41 2018 -0500
Filled in some docstrings
Source/driver/Castro.H
Source/driver/Castro_util.F90
Source/hydro/hybrid_advection_nd.F90
Source/sources/Castro_sources.cpp
commit 0d8fdaf4bcbc9a4e2f712c7f83dd3f90a1361a93
Merge: ce9f38280 2ddf2a04f
Author: Alice Harpole <ah1e14@soton.ac.uk>
Date: Mon Dec 24 08:21:18 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8a6271531cd3d4e6c5754038f490d6b10646cf8f
Merge: 7f0e89fc7 2ddf2a04f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 19 19:38:22 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2ddf2a04f355d9b136abdf05f1d5cd2bc173109b
Merge: bd85585cc 2def85821
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 19 10:50:36 2018 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit bd85585cc6e1cd9ff27f5a159d3452dd5b3ed194
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 19 10:49:26 2018 -0500
these are historical scaling #s.
These used to live in Docs/ but were lost in the move to sphinx
Util/scaling/bwp/edison_20160609/scaling.txt
Util/scaling/sedov/titan_20171011/1level/avg_time.sh
Util/scaling/sedov/titan_20171011/1level/inputs.starlord
Util/scaling/sedov/titan_20171011/1level/probin.starlord
Util/scaling/sedov/titan_20171011/1level/titan-MPI1024-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP16-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI2048-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level/titan-MPI4096-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/avg_time.sh
Util/scaling/sedov/titan_20171011/1level_4x/inputs.starlord
Util/scaling/sedov/titan_20171011/1level_4x/probin.starlord
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/inputs.starlord
Util/scaling/sedov/titan_20171011/64_1024/probin.starlord
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI2-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/inputs.starlord
Util/scaling/sedov/titan_20171011/64_1536/probin.starlord
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI2-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/64_512/avg_time.sh
Util/scaling/sedov/titan_20171011/64_512/inputs.starlord
Util/scaling/sedov/titan_20171011/64_512/probin.starlord
Util/scaling/sedov/titan_20171011/64_512/titan-512-MPI-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-MPI2-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-OMP2-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-OMP4-PE16.run
Util/scaling/sedov/titan_20171011/64_512/titan-512-OMP8-PE16.run
Util/scaling/sedov/titan_20171011/castro-sedov-scaling.txt
Util/scaling/wdmerger/cori_201710/cori-nodes_128.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_16.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_32.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_64.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/cori-nodes_96.knl.MPI.OMP.slurm
Util/scaling/wdmerger/cori_201710/inputs_test_wdmerger_3D
Util/scaling/wdmerger/cori_201710/probin_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/inputs_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/probin_test_wdmerger_3D
Util/scaling/wdmerger/summitdev_201806/scaling.txt
Util/scaling/wdmerger/summitdev_201806/summitd-160MPI.run
Util/scaling/wdmerger/summitdev_201806/summitd-320MPI.run
Util/scaling/wdmerger/summitdev_201806/summitd-80MPI.run
Util/scaling/wdmerger/titan_041516/README
Util/scaling/wdmerger/titan_041516/one_level_omp4.txt
Util/scaling/wdmerger/titan_041516/three_level_omp4.txt
Util/scaling/wdmerger/titan_041516/three_level_omp8.txt
Util/scaling/wdmerger/titan_041516/two_level_omp4.txt
Util/scaling/wdmerger/titan_20171011/256_0amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/256_0amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_0amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI128-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI2-PE16.run
Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI64-PE16.run
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Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx4-OMP4-PE16.run
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Util/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx8-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/256_1amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_1amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI-PE16.run
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Util/scaling/wdmerger/titan_20171011/256_1amr/titan-MPI512-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/256_2amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_2amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPI-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPI2-OMP4-PE16.run
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Util/scaling/wdmerger/titan_20171011/512_0amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/512_0amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_0amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI1024-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI2048-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-PE16.run
Util/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI512-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/avg_time.sh
Util/scaling/wdmerger/titan_20171011/512_1amr/inputs_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_1amr/probin_test_wdmerger_3D
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI1024-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-OMP8-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-OMP2-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-OMP4-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-PE16.run
Util/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI512-PE16.run
Util/scaling/wdmerger/titan_20171011/avg_time.sh
Util/scaling/wdmerger/titan_20171011/castro-wdmerger-scaling.txt
commit 2def85821d0cf702dacd0c2265ad8b7793551c9c
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Dec 19 10:42:43 2018 -0500
Gpu porting (#466)
sphinx_docs/source/gpu_porting.rst
sphinx_docs/source/index.rst
commit ce9f38280f4cf58e5d11275b876a25120f8a079a
Merge: dd15c855a 66fc4602e
Author: Alice Harpole <ah1e14@soton.ac.uk>
Date: Tue Dec 18 13:23:15 2018 -0500
merge conflicts
commit 66fc4602ecb3306d534500d12ef910e97e806ccb
Author: Cy P Chan <cychan@lbl.gov>
Date: Tue Dec 18 09:30:01 2018 -0800
optimize domain containment check in gravity::sanity_check() (#464)
Source/gravity/Gravity.cpp
commit 7f0e89fc71c5e2a1c658e68bd279a8101e1a9881
Merge: 0decbb6fb 56eb9e10e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 19:35:33 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 56eb9e10e2bac0c299a229c2ad8182f8e9f4395d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 16:25:26 2018 -0500
remove rad
sphinx_docs/source/index.rst
commit 533f7241662a0bc64c600ed47b3731f4f64a4cc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 15:51:06 2018 -0500
try ubuntu 16.04
.travis.yml
commit 65c31789765f005c7c850c7abf1bd16a1af9ced6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 15:26:10 2018 -0500
try different stable version
.travis.yml
commit ce5b1f5b5b85b2fe99b903ae6e8a609714629981
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 15:20:20 2018 -0500
bump up the gcc version
.travis.yml
commit 7542baf9b3f01a0c5280325647630d8b4798aaf3
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Dec 17 15:02:51 2018 -0500
Doxygen docstrings (#461)
This reformats some of the function comments to be in the form that Doxygen expects.
Also added a python script that is run after breathe has been executed which organizes the API's filelist into a more helpful structure.
.gitignore
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Enthalpy_nd.f90
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/interpolate.F90
Source/driver/math.F90
Source/driver/timestep.F90
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_nd.f90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/problems/Prob_1d.f90
Source/problems/Prob_2d.f90
Source/problems/Prob_3d.f90
Source/problems/Prob_nd.F90
Source/problems/Problem.f90
Source/radiation/DumpModel1d.H
Source/radiation/HypreABec.H
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreMultiABec.H
Source/radiation/MGRadBndry.H
Source/radiation/NGBndry.H
Source/radiation/RadBndry.H
Source/radiation/RadSolve.H
Source/radiation/Rad_nd.f90
Source/radiation/Radiation.H
Source/rotation/Rotation_nd.F90
Source/sources/Castro_sources.cpp
Source/sources/ext_src_nd.F90
Source/sources/update_sponge_params.f90
sphinx_docs/Doxyfile
sphinx_docs/Makefile
sphinx_docs/add_doxy_headers.py
sphinx_docs/make_api.py
sphinx_docs/source/AMR.rst
sphinx_docs/source/conf.py
sphinx_docs/source/gravity.rst
sphinx_docs/source/index.rst
sphinx_docs/source/radiation.rst
sphinx_docs/source/rotation.rst
commit 06805c822a724eb3e02bafa660b753403562e7ab
Merge: 19a7e430a 3f50c0593
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 14:48:59 2018 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 19a7e430ae845ad29c9f1baa1861a7060ebb66c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 14:48:30 2018 -0500
initial hybrid_momentum docs
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/refs.bib
commit 3f50c059378e7238f0fad710765a44f961c3a465
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 14:26:59 2018 -0500
move some module variables to their local routine
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/wdmerger_util.f90
commit 9c3ded4c182802e81e5fad53bea465deea54fe4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 13:50:29 2018 -0500
add some figures for the hybrid momentum
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/rotating_torus_00000_density.png
sphinx_docs/source/rotating_torus_00200_density.png
sphinx_docs/source/rotating_torus_hybrid_00200_density.png
commit 0decbb6fb6bfa307faf88ba3c39d653a5956fd17
Merge: 85e1d44fd 53b013992
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 15 19:40:47 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 53b013992f4790d17b6448529b131dd600ed8bd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 15 18:30:45 2018 -0500
first crack at a Zenodo JSON -- lots of ORCiD's missing
.zenodo.json
commit ceeb6c85bcdbff1c0053b29e209b3dd623f6903d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 15 18:19:43 2018 -0500
more mailmap
.mailmap
commit 4121d5530dcedc22486abc32b4f500effd2ec64c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 14 13:17:40 2018 -0500
add pressure as a derived variable
Exec/hydro_tests/Sedov/inputs.starlord.gpu_test
commit f6997ff68a6249654a2d2accf6e5053336a966de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 12 10:23:29 2018 -0500
fix location of the User's Guide
README.md
commit e0a2cddf284c7c529948123d9cb5233fcc3e9986
Merge: 5e22e3363 661839b5a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 12 10:20:50 2018 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 5e22e3363131a486ba65353397d7e294baebbc87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 12 10:20:41 2018 -0500
add travis badge
README.md
commit 85e1d44fd5388df40653130b6732d8c8db5f94ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 19:58:52 2018 -0500
remove old notes
sphinx_docs/notes.txt
commit 661839b5a7736dd8a1d9202ec793d413ca42d806
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 19:42:20 2018 -0500
finish a pass through rotation
sphinx_docs/source/rotation.rst
commit a2d6434ec68a4d8bda99b18755c3bc3e216d0d4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 19:30:44 2018 -0500
some formatting fixes
sphinx_docs/source/rotation.rst
commit d728b72e7bc0192afb12937ac836f6a8dd92055c
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 15:57:28 2018 -0800
Add more_itertools to requirements.
requirements.txt
commit 96d05c597c8be26346c338a5b6ad1e8f70d18710
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 15:53:41 2018 -0800
Use python 3.7-dev.
.travis.yml
commit 70ce7fb0136c9fba9f3c83465159e5140a55c324
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 15:50:38 2018 -0800
Use unique_everseen
sphinx_docs/rp.py
commit f56aa8aba2ea8b1b8bdc44b14fd3cc8e89091d44
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 15:29:45 2018 -0800
add comment
sphinx_docs/rp.py
commit ac3182ce1b43ea7515b60021b6aebbf66bb292c1
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 15:25:07 2018 -0800
Use list_unique instead of list(set()) to make order deterministic.
sphinx_docs/rp.py
commit be46ce2a9c6ac7c7e3f1f509b96828f30165ca48
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 15:07:10 2018 -0800
clarify comment
deploy_docs.sh
commit 1b062a7c4fc74dbfbd8c7eedb09b72816481091b
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 14:24:18 2018 -0800
Use git diff --staged --quiet to check for changes.
deploy_docs.sh
commit a54966f9e1616cafe52718cdcbb06f3525a57597
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 17:18:36 2018 -0500
add index
sphinx_docs/source/index.rst
commit bf579b205db3517708983804ae3f9b2ad4c7c075
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 17:12:59 2018 -0500
rename
sphinx_docs/source/conf.py
sphinx_docs/source/index_docs.rst
commit 1b3931666b2f9fa79a73f01ab51d4d106f369681
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 17:04:06 2018 -0500
remove the diff-index check`
deploy_docs.sh
commit 3663af322ca4c671370ae1cbccda4238ef698992
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 13:51:59 2018 -0800
slight wording
sphinx_docs/source/Introduction.rst
commit d1f5c974b0f9aa3e959f149f3c33c34c02d4aec8
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 13:38:36 2018 -0800
add quiet
deploy_docs.sh
commit 899b2339c3af9747bea68fb20e4545a793fc4f68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 16:33:09 2018 -0500
look at return code
deploy_docs.sh
commit 08d846eef9a77661ac858493704dff70698236dd
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Tue Dec 11 13:28:30 2018 -0800
testing
deploy_docs.sh
commit dd15c855aeb4acf14659a3640fb947733ce9f2e3
Merge: 53850e8ba 3db9e81b6
Author: Alice Harpole <ah1e14@soton.ac.uk>
Date: Tue Dec 11 16:25:20 2018 -0500
merge conflicts
commit da496ff6f88803ee5d8729ee4efd46bae7e6e5f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 16:23:28 2018 -0500
some debugging
deploy_docs.sh
commit 3db9e81b6b484fee9032bfa4045770a57cdd73f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 16:15:58 2018 -0500
more verbose
deploy_docs.sh
commit 53850e8ba10daf5c991ddcdbd00ab8c665dfb020
Author: Alice Harpole <ah1e14@soton.ac.uk>
Date: Tue Dec 11 16:15:43 2018 -0500
create docs/sphinx if it's been deleted by make clean
sphinx_docs/Makefile
commit 306fda7a38678b8ba8bf84820b89c1816033e236
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 16:08:28 2018 -0500
remove more extensions
sphinx_docs/source/conf.py
commit 39c3afab6f6d9b9b4ed66dce60fb79563237cec9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 16:01:56 2018 -0500
add numpydoc
requirements.txt
commit fde39050a1e56c62eb3cf06e548dfab1adc5164f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:57:27 2018 -0500
remove nbsphinx
sphinx_docs/source/conf.py
commit 777b25d91c7d037d9b0726c0a0783aa112e7d66c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:54:21 2018 -0500
more ignores
.gitignore
commit d12ee1386a6be538e8c80b9ee12ffc1f0e5f2644
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:53:29 2018 -0500
add requirements
requirements.txt
commit 312a38f6346fcf62a447f8066b15c08cdb9007e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:53:16 2018 -0500
more ignores
.gitignore
commit 099bbbeb79b3e564273adc8cc8dc8882168d7e1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:49:50 2018 -0500
add the building of the docs
.travis.yml
commit 92257970624036b17f6cdacf3f454a8dc297cd36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:49:26 2018 -0500
add the deploy docs
deploy_docs.sh
commit 86dda1b8cdd76aebf87f43c0224269cf63b528de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:36:09 2018 -0500
remove the docs -- if all goes well, travis will do this for us shortly on gh-pages
docs/.nojekyll
docs/LICENSE.txt
docs/about.html
docs/css/font-awesome.min.css
docs/css/skel.css
docs/css/style-large.css
docs/css/style-medium.css
docs/css/style-small.css
docs/css/style-xlarge.css
docs/css/style-xsmall.css
docs/css/style.css
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docs/who.html
commit 72cdd0d4bf6e6a931d78128632eadfc1a969406f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 15:35:34 2018 -0500
add a encoded key for travis deployment
id_rsa_travis.enc
commit 756e06b4c394eb45059d5f023f385a2910a41509
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 14:53:18 2018 -0500
remove the copy
sphinx_docs/Makefile
commit 3e69e6dd890242e930d25cea12d3129cb98de896
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Tue Dec 11 13:48:09 2018 -0500
runtime parameter docs styled rst
Source/driver/_cpp_parameters
commit 3a489b62fbb655e0a5c7d72cac9253ff6f29405a
Author: Xinlong <42697364+sailoridy@users.noreply.github.com>
Date: Tue Dec 11 11:19:49 2018 -0500
modify getting_started.rst (#460)
sphinx_docs/source/getting_started.rst
commit c6e80d9d24f3dd4f3cc965701c765bc7ce6e50f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 11 11:06:05 2018 -0500
Move mention of gravity types to the very top
sphinx_docs/source/gravity.rst
commit 06a0d048a7b7a086924e72d213b4fb7d26a3b4d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 11 10:57:40 2018 -0500
make the sphinx/ subdirectory
sphinx_docs/Makefile
sphinx_docs/source/rotation.rst
commit 51bd74b3002c8a2187f080da84b99d957be9340e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 10 15:10:36 2018 -0500
runtime parameters are no longer latex
Source/driver/mk_params.sh
commit ce6b833333a44f979677c2982249d86a460c3fbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 10 10:14:19 2018 -0500
we remove ppm_type = 2, so switch these to ppm_type = 1
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/hydro_tests/HCBubble/inputs-sod-x
Exec/hydro_tests/HCBubble/inputs.L0
Exec/hydro_tests/Sod/Figure2/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Vortices_LWAcoustics/inputs.2d
Exec/hydro_tests/reacting_bubble/inputs_2d_zoom
commit ca9e3d71f14c0de06e27fa76102c4a994d232b97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 5 19:33:51 2018 -0500
the CUDA fix was already merged in the last merge-day
CHANGES
commit 0260278e8bef946689615ad8ed7b3ac80936d8a1
Merge: 1ac7bd77b 8f08cdab5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:05:57 2018 -0500
Merge branch 'master' into development
commit 1ac7bd77b009c47e7d09b3f5b1e19f89ff1eb55e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:05:51 2018 -0500
update changes
CHANGES
commit 8f08cdab5cbffc44fb8b4837630ffb5d92e83714
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:05:07 2018 -0500
update docs location
README.md
commit 0a9e4b849c50382a91828180bbb23802c8fefb9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:00:47 2018 -0500
add a nojekyll
docs/.nojekyll
commit 1f65c6e9c68d5032a38afc8a95058b00aa08d69e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 2 20:08:28 2018 -0500
more GPU changes (#442)
removed ppm_type = 2
made the conservative variable indices available in C++
switched to the CUDA version of the ppm reconstruction routines (threadsafe + no allocates)
some more deslabbing in the 4th order
the ppm reconstruction routines can not automatically set the interface states for MOL
merged the CUDA flattening and non-CUDA flattening
the Riemann routines can now take interface states for all directions in a single array
CHANGES
Exec/Make.Castro
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/_variables
Source/driver/set_variables.py
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_plm.F90
commit 917f6ef178b1e5a52ba364efa87f2372583df3ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 1 20:44:11 2018 -0500
update changes
CHANGES
commit 29a5b94a46b1ebe37901973cfb729af5b678c8fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 30 13:38:00 2018 -0500
address some compiler warnings (#444)
address some compiler warnings
mostly unused variables, some shadowing
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/initial_model.f90
Microphysics/EOS/eos_type.F90
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_util.F90
Source/driver/sum_integrated_quantities.cpp
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
Source/rotation/Rotation_frequency.F90
Source/sources/Castro_sources.cpp
commit 17040506abd37ad73d6041e815c320dc6b37dbc1
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Nov 29 13:32:57 2018 -0500
Got rid of allow_negative_energy option from input files
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/StarGrav/inputs_2d
Exec/gravity_tests/StarGrav/inputs_2d.test
Exec/gravity_tests/StarGrav/inputs_3d
Exec/gravity_tests/evrard_collapse/inputs
Exec/hydro_tests/HCBubble/inputs-sod-x
Exec/hydro_tests/HCBubble/inputs.L0
Exec/hydro_tests/KH/inputs.2d
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/inputs.3d
Exec/hydro_tests/Noh/inputs_3d
Exec/hydro_tests/RT/inputs.dungeon
Exec/hydro_tests/RT/inputs_2d
Exec/hydro_tests/RT/inputs_3d
Exec/hydro_tests/RT_particles/inputs_2d
Exec/hydro_tests/Sedov/inputs.1d.cyl
Exec/hydro_tests/Sedov/inputs.1d.sph
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/inputs.3d.sph
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
Exec/hydro_tests/Sedov/inputs.starlord
Exec/hydro_tests/Sedov/inputs.starlord.gpu_test
Exec/hydro_tests/Sod/Figure1/inputs-sod-1d
Exec/hydro_tests/Sod/Figure2/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-slowshock-x
Exec/hydro_tests/Sod/inputs-sod-rt1
Exec/hydro_tests/Sod/inputs-sod-rt2
Exec/hydro_tests/Sod/inputs-sod-rt3
Exec/hydro_tests/Sod/inputs-sod-x
Exec/hydro_tests/Sod/inputs-sod-y
Exec/hydro_tests/Sod/inputs-sod-z
Exec/hydro_tests/Sod/inputs-test1-helm
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/hydro_tests/Sod/inputs-test2-helm
Exec/hydro_tests/Sod/inputs-test2-x
Exec/hydro_tests/Sod/inputs-test2-y
Exec/hydro_tests/Sod/inputs-test2-z
Exec/hydro_tests/Sod/inputs-test3-helm
Exec/hydro_tests/Sod/inputs-test3-x
Exec/hydro_tests/Sod/inputs-test3-y
Exec/hydro_tests/Sod/inputs-test3-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/inputs-test1-helm.gammae
Exec/hydro_tests/Sod_stellar/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/CW/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test1-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test2-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test3-helm
Exec/hydro_tests/Sod_stellar/runs/MC/inputs-test4-helm
Exec/hydro_tests/Vortices_LWAcoustics/inputs.2d
Exec/hydro_tests/acoustic_pulse/inputs.2d.128
Exec/hydro_tests/acoustic_pulse/inputs.2d.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.512
Exec/hydro_tests/acoustic_pulse/inputs.2d.64
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
Exec/hydro_tests/gresho_vortex/inputs.2d
Exec/hydro_tests/reacting_bubble/inputs_2d
Exec/hydro_tests/reacting_bubble/inputs_2d_noentropy
Exec/hydro_tests/reacting_bubble/inputs_2d_test
Exec/hydro_tests/reacting_bubble/inputs_2d_zoom
Exec/hydro_tests/reacting_bubble/inputs_3d_test
Exec/hydro_tests/rotating_torus/inputs_3d
Exec/hydro_tests/rotating_torus/inputs_3d.test
Exec/hydro_tests/symmetry/inputs.1d
Exec/hydro_tests/symmetry/inputs.2d
Exec/hydro_tests/symmetry/inputs.3d
Exec/hydro_tests/test_convect/inputs_2d
Exec/hydro_tests/toy_convect/inputs_2d
Exec/hydro_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/hydro_tests/toy_flame/inputs.1d
Exec/hydro_tests/toy_flame/inputs.1d.testsuite
docs/sphinx/_sources/Hydrodynamics.rst.txt
commit 45005324b2e02b1df92e40c1e3c1e7c1ae7bb21a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 28 10:57:59 2018 -0500
update sphinx location
sphinx_docs/Makefile
commit 8585f0449f791fe0338d7ddd800d8f28c42238cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 27 13:49:38 2018 -0500
remove runtime_parameters.rst -- this is automagically generated
sphinx_docs/source/runtime_parameters.rst
commit 71bfb15346b5533905cab4774f00ecd397f81773
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 20:31:31 2018 -0500
merge the existing webpage and sphinx docs -- we no longer
rely on gh-pages
docs/LICENSE.txt
docs/about.html
docs/css/font-awesome.min.css
docs/css/skel.css
docs/css/style-large.css
docs/css/style-medium.css
docs/css/style-small.css
docs/css/style-xlarge.css
docs/css/style-xsmall.css
docs/css/style.css
docs/elements.html
docs/fonts/FontAwesome.otf
docs/fonts/fontawesome-webfont.eot
docs/fonts/fontawesome-webfont.svg
docs/fonts/fontawesome-webfont.ttf
docs/fonts/fontawesome-webfont.woff
docs/generic.html
docs/help.html
docs/images/bokeh_car_lights_bg.jpg
docs/images/dark_tint.png
docs/images/med_tint.png
docs/images/pic02.jpg
docs/images/pic03.jpg
docs/images/pic04.jpg
docs/images/pic07.jpg
docs/images/pic08.jpg
docs/images/profile_placeholder.gif
docs/index.html
docs/js/html5shiv.js
docs/js/init.js
docs/js/jquery.min.js
docs/js/skel-layers.min.js
docs/js/skel.min.js
docs/paper-parser/README
docs/paper-parser/castro-papers.txt
docs/paper-parser/papers.bib
docs/paper-parser/papers.template
docs/paper-parser/parser.py
docs/paper-parser/write_papers_html.py
docs/papers.html
docs/science-images/L2.3_ent_volrend_explosion.png
docs/science-images/fdp2_plt00550.png
docs/science-images/sedov_scaling.png
docs/science-images/slice_grid.png
docs/science-images/wdmerger_08030_new.png
docs/science-images/wdmerger_scaling.png
docs/science.html
docs/sphinx/AMR.html
docs/sphinx/ConvertCheckpoint.html
docs/sphinx/EOSNetwork.html
docs/sphinx/FlowChart.html
docs/sphinx/Hydrodynamics.html
docs/sphinx/Introduction.html
docs/sphinx/MAESTRO_restart.html
docs/sphinx/Particles.html
docs/sphinx/Preface.html
docs/sphinx/Verification.html
docs/sphinx/_images/LineQueryPlot_0_t_magvel.png
docs/sphinx/_images/OffAxisProjection_density.png
docs/sphinx/_images/Profile2D_1_Density_magvel_kineng.png
docs/sphinx/_images/RT_ppm_type.png
docs/sphinx/_images/Slice_z_pressure.png
docs/sphinx/_images/center.png
docs/sphinx/_images/corner.png
docs/sphinx/_images/domain-tile.png
docs/sphinx/_images/fluid_motion.png
docs/sphinx/_images/index_grid2.png
docs/sphinx/_images/isocontours.png
docs/sphinx/_images/radiating_source.png
docs/sphinx/_images/radiating_sphere.png
docs/sphinx/_images/sedov_cyl.png
docs/sphinx/_images/sedov_sph.png
docs/sphinx/_images/sod_3d.png
docs/sphinx/_images/sod_3d_ppm0.png
docs/sphinx/_images/test2_3d.png
docs/sphinx/_images/test3_3d.png
docs/sphinx/_images/tframes.png
docs/sphinx/_images/tracer_trajectory.png
docs/sphinx/_images/volume.png
docs/sphinx/_sources/AMR.rst.txt
docs/sphinx/_sources/ConvertCheckpoint.rst.txt
docs/sphinx/_sources/EOSNetwork.rst.txt
docs/sphinx/_sources/FlowChart.rst.txt
docs/sphinx/_sources/Hydrodynamics.rst.txt
docs/sphinx/_sources/Introduction.rst.txt
docs/sphinx/_sources/MAESTRO_restart.rst.txt
docs/sphinx/_sources/Particles.rst.txt
docs/sphinx/_sources/Preface.rst.txt
docs/sphinx/_sources/Verification.rst.txt
docs/sphinx/_sources/castrosymbols.rst.txt
docs/sphinx/_sources/class/classAuxVar.rst.txt
docs/sphinx/_sources/class/classAuxVarBox.rst.txt
docs/sphinx/_sources/class/classAuxVar_1_1Connex.rst.txt
docs/sphinx/_sources/class/classBndryAuxVar.rst.txt
docs/sphinx/_sources/class/classBndryAuxVarBase.rst.txt
docs/sphinx/_sources/class/classCastro.rst.txt
docs/sphinx/_sources/class/classCastroBld.rst.txt
docs/sphinx/_sources/class/classCrseBndryAuxVar.rst.txt
docs/sphinx/_sources/class/classDiffusion.rst.txt
docs/sphinx/_sources/class/classGradPhiPhysBCFunct.rst.txt
docs/sphinx/_sources/class/classGravity.rst.txt
docs/sphinx/_sources/class/classHypreABec.rst.txt
docs/sphinx/_sources/class/classHypreExtMultiABec.rst.txt
docs/sphinx/_sources/class/classHypreMultiABec.rst.txt
docs/sphinx/_sources/class/classMGRadBndry.rst.txt
docs/sphinx/_sources/class/classMGRadBndryBld.rst.txt
docs/sphinx/_sources/class/classNGBndry.rst.txt
docs/sphinx/_sources/class/classNGBndryBld.rst.txt
docs/sphinx/_sources/class/classProxyGeometry.rst.txt
docs/sphinx/_sources/class/classRadBndry.rst.txt
docs/sphinx/_sources/class/classRadBndryBld.rst.txt
docs/sphinx/_sources/class/classRadBndryData.rst.txt
docs/sphinx/_sources/class/classRadBoundCond.rst.txt
docs/sphinx/_sources/class/classRadInterpBndryData.rst.txt
docs/sphinx/_sources/class/classRadSolve.rst.txt
docs/sphinx/_sources/class/classRadTests.rst.txt
docs/sphinx/_sources/class/classRadiation.rst.txt
docs/sphinx/_sources/classlist.rst.txt
docs/sphinx/_sources/coding_conventions.rst.txt
docs/sphinx/_sources/creating_a_problem.rst.txt
docs/sphinx/_sources/diffusion.rst.txt
docs/sphinx/_sources/faq.rst.txt
docs/sphinx/_sources/file/CastroBld_8cpp.rst.txt
docs/sphinx/_sources/file/CastroParticles_8cpp.rst.txt
docs/sphinx/_sources/file/Castro_8H.rst.txt
docs/sphinx/_sources/file/Castro_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__F_8H.rst.txt
docs/sphinx/_sources/file/Castro__advance_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__diffusion_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__error_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__error__F_8H.rst.txt
docs/sphinx/_sources/file/Castro__external_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__gravity_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__hybrid_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__hydro_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__io_8H.rst.txt
docs/sphinx/_sources/file/Castro__io_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__pointmass_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__prob__err_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__prob__err__F_8H.rst.txt
docs/sphinx/_sources/file/Castro__prob__err__list_8H.rst.txt
docs/sphinx/_sources/file/Castro__radiation_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__react_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__rotation_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__setup_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__sources_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__sponge_8cpp.rst.txt
docs/sphinx/_sources/file/Castro__thermo_8cpp.rst.txt
docs/sphinx/_sources/file/Derive_8H.rst.txt
docs/sphinx/_sources/file/Derive_8cpp.rst.txt
docs/sphinx/_sources/file/Derive__F_8H.rst.txt
docs/sphinx/_sources/file/Diffusion_8H.rst.txt
docs/sphinx/_sources/file/Diffusion_8cpp.rst.txt
docs/sphinx/_sources/file/DumpModel1d_8H.rst.txt
docs/sphinx/_sources/file/DumpModel1d_8cpp.rst.txt
docs/sphinx/_sources/file/Gravity_8H.rst.txt
docs/sphinx/_sources/file/Gravity_8cpp.rst.txt
docs/sphinx/_sources/file/Gravity__F_8H.rst.txt
docs/sphinx/_sources/file/HABEC__F_8H.rst.txt
docs/sphinx/_sources/file/HypreABec_8H.rst.txt
docs/sphinx/_sources/file/HypreABec_8cpp.rst.txt
docs/sphinx/_sources/file/HypreExtMultiABec_8H.rst.txt
docs/sphinx/_sources/file/HypreExtMultiABec_8cpp.rst.txt
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docs/sphinx/_sources/file/HypreMultiABec_8cpp.rst.txt
docs/sphinx/_sources/file/MGFLDRadSolver_8cpp.rst.txt
docs/sphinx/_sources/file/MGFLD_8cpp.rst.txt
docs/sphinx/_sources/file/MGRadBndry_8H.rst.txt
docs/sphinx/_sources/file/MGRadBndry_8cpp.rst.txt
docs/sphinx/_sources/file/NGBndry_8H.rst.txt
docs/sphinx/_sources/file/Prob_8cpp.rst.txt
docs/sphinx/_sources/file/Problem_8H.rst.txt
docs/sphinx/_sources/file/Problem__Derive_8H.rst.txt
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docs/sphinx/_sources/file/Problem__F_8H.rst.txt
docs/sphinx/_sources/file/RADINTERPBNDRYDATA__F_8H.rst.txt
docs/sphinx/_sources/file/RAD__F_8H.rst.txt
docs/sphinx/_sources/file/RadBndryData_8H.rst.txt
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docs/sphinx/_sources/file/RadBoundCond_8H.rst.txt
docs/sphinx/_sources/file/RadInterpBndryData_8H.rst.txt
docs/sphinx/_sources/file/RadInterpBndryData_8cpp.rst.txt
docs/sphinx/_sources/file/RadMultiGroup_8cpp.rst.txt
docs/sphinx/_sources/file/RadPlotvar_8cpp.rst.txt
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docs/sphinx/_sources/file/RadSolve_8cpp.rst.txt
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docs/sphinx/_sources/file/RadTypes_8H.rst.txt
docs/sphinx/_sources/file/Radiation_8H.rst.txt
docs/sphinx/_sources/file/Radiation_8cpp.rst.txt
docs/sphinx/_sources/file/SGFLD_8cpp.rst.txt
docs/sphinx/_sources/file/SGRadSolver_8cpp.rst.txt
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docs/sphinx/_sources/file/diffusion__params_8H.rst.txt
docs/sphinx/_sources/file/diffusion__queries_8H.rst.txt
docs/sphinx/_sources/file/energy__diagnostics_8cpp.rst.txt
docs/sphinx/_sources/file/gravity__defaults_8H.rst.txt
docs/sphinx/_sources/file/gravity__job__info__tests_8H.rst.txt
docs/sphinx/_sources/file/gravity__params_8H.rst.txt
docs/sphinx/_sources/file/gravity__queries_8H.rst.txt
docs/sphinx/_sources/file/main_8cpp.rst.txt
docs/sphinx/_sources/file/particles__defaults_8H.rst.txt
docs/sphinx/_sources/file/particles__job__info__tests_8H.rst.txt
docs/sphinx/_sources/file/particles__params_8H.rst.txt
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docs/sphinx/_sources/file/sum__utils_8cpp.rst.txt
docs/sphinx/_sources/filelist.rst.txt
docs/sphinx/_sources/getting_started.rst.txt
docs/sphinx/_sources/gravity.rst.txt
docs/sphinx/_sources/index.rst.txt
docs/sphinx/_sources/index_docs.rst.txt
docs/sphinx/_sources/inputs.rst.txt
docs/sphinx/_sources/io.rst.txt
docs/sphinx/_sources/namespace/namespace_0D9.rst.txt
docs/sphinx/_sources/namespace/namespaceamrex.rst.txt
docs/sphinx/_sources/namespacelist.rst.txt
docs/sphinx/_sources/rad.rst.txt
docs/sphinx/_sources/radiation.rst.txt
docs/sphinx/_sources/references.rst.txt
docs/sphinx/_sources/rotation.rst.txt
docs/sphinx/_sources/rp_intro.rst.txt
docs/sphinx/_sources/runtime_parameters.rst.txt
docs/sphinx/_sources/software.rst.txt
docs/sphinx/_sources/vis_tools.rst.txt
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docs/sphinx/_static/jquery-3.1.0.js
docs/sphinx/_static/jquery-3.2.1.js
docs/sphinx/_static/jquery.js
docs/sphinx/_static/js/modernizr.min.js
docs/sphinx/_static/js/theme.js
docs/sphinx/_static/mathjax_conf.js
docs/sphinx/_static/minus.png
docs/sphinx/_static/plus.png
docs/sphinx/_static/pygments.css
docs/sphinx/_static/searchtools.js
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docs/sphinx/_static/websupport.js
docs/sphinx/castrosymbols.html
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docs/sphinx/class/classAuxVarBox.html
docs/sphinx/class/classAuxVar_1_1Connex.html
docs/sphinx/class/classBndryAuxVar.html
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docs/sphinx/class/classCastro.html
docs/sphinx/class/classCastroBld.html
docs/sphinx/class/classCrseBndryAuxVar.html
docs/sphinx/class/classDiffusion.html
docs/sphinx/class/classGradPhiPhysBCFunct.html
docs/sphinx/class/classGravity.html
docs/sphinx/class/classHypreABec.html
docs/sphinx/class/classHypreExtMultiABec.html
docs/sphinx/class/classHypreMultiABec.html
docs/sphinx/class/classMGRadBndry.html
docs/sphinx/class/classMGRadBndryBld.html
docs/sphinx/class/classNGBndry.html
docs/sphinx/class/classNGBndryBld.html
docs/sphinx/class/classProxyGeometry.html
docs/sphinx/class/classRadBndry.html
docs/sphinx/class/classRadBndryBld.html
docs/sphinx/class/classRadBndryData.html
docs/sphinx/class/classRadBoundCond.html
docs/sphinx/class/classRadInterpBndryData.html
docs/sphinx/class/classRadSolve.html
docs/sphinx/class/classRadTests.html
docs/sphinx/class/classRadiation.html
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docs/sphinx/coding_conventions.html
docs/sphinx/creating_a_problem.html
docs/sphinx/diffusion.html
docs/sphinx/faq.html
docs/sphinx/file/CastroBld_8cpp.html
docs/sphinx/file/CastroParticles_8cpp.html
docs/sphinx/file/Castro_8H.html
docs/sphinx/file/Castro_8cpp.html
docs/sphinx/file/Castro__F_8H.html
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docs/sphinx/file/Castro__hydro_8cpp.html
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docs/sphinx/file/Castro__io_8cpp.html
docs/sphinx/file/Castro__pointmass_8cpp.html
docs/sphinx/file/Castro__prob__err_8cpp.html
docs/sphinx/file/Castro__prob__err__F_8H.html
docs/sphinx/file/Castro__prob__err__list_8H.html
docs/sphinx/file/Castro__radiation_8cpp.html
docs/sphinx/file/Castro__react_8cpp.html
docs/sphinx/file/Castro__rotation_8cpp.html
docs/sphinx/file/Castro__setup_8cpp.html
docs/sphinx/file/Castro__sources_8cpp.html
docs/sphinx/file/Castro__sponge_8cpp.html
docs/sphinx/file/Castro__thermo_8cpp.html
docs/sphinx/file/Derive_8H.html
docs/sphinx/file/Derive_8cpp.html
docs/sphinx/file/Derive__F_8H.html
docs/sphinx/file/Diffusion_8H.html
docs/sphinx/file/Diffusion_8cpp.html
docs/sphinx/file/DumpModel1d_8H.html
docs/sphinx/file/DumpModel1d_8cpp.html
docs/sphinx/file/Gravity_8H.html
docs/sphinx/file/Gravity_8cpp.html
docs/sphinx/file/Gravity__F_8H.html
docs/sphinx/file/HABEC__F_8H.html
docs/sphinx/file/HypreABec_8H.html
docs/sphinx/file/HypreABec_8cpp.html
docs/sphinx/file/HypreExtMultiABec_8H.html
docs/sphinx/file/HypreExtMultiABec_8cpp.html
docs/sphinx/file/HypreMultiABec_8H.html
docs/sphinx/file/HypreMultiABec_8cpp.html
docs/sphinx/file/MGFLDRadSolver_8cpp.html
docs/sphinx/file/MGFLD_8cpp.html
docs/sphinx/file/MGRadBndry_8H.html
docs/sphinx/file/MGRadBndry_8cpp.html
docs/sphinx/file/NGBndry_8H.html
docs/sphinx/file/Prob_8cpp.html
docs/sphinx/file/Problem_8H.html
docs/sphinx/file/Problem__Derive_8H.html
docs/sphinx/file/Problem__Derive__F_8H.html
docs/sphinx/file/Problem__Derives_8H.html
docs/sphinx/file/Problem__F_8H.html
docs/sphinx/file/RADINTERPBNDRYDATA__F_8H.html
docs/sphinx/file/RAD__F_8H.html
docs/sphinx/file/RadBndryData_8H.html
docs/sphinx/file/RadBndryData_8cpp.html
docs/sphinx/file/RadBndry_8H.html
docs/sphinx/file/RadBndry_8cpp.html
docs/sphinx/file/RadBoundCond_8H.html
docs/sphinx/file/RadInterpBndryData_8H.html
docs/sphinx/file/RadInterpBndryData_8cpp.html
docs/sphinx/file/RadMultiGroup_8cpp.html
docs/sphinx/file/RadPlotvar_8cpp.html
docs/sphinx/file/RadSolve_8H.html
docs/sphinx/file/RadSolve_8cpp.html
docs/sphinx/file/RadTests_8H.html
docs/sphinx/file/RadTypes_8H.html
docs/sphinx/file/Radiation_8H.html
docs/sphinx/file/Radiation_8cpp.html
docs/sphinx/file/SGFLD_8cpp.html
docs/sphinx/file/SGRadSolver_8cpp.html
docs/sphinx/file/castro__defaults_8H.html
docs/sphinx/file/castro__job__info__tests_8H.html
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docs/sphinx/file/diffusion__defaults_8H.html
docs/sphinx/file/diffusion__job__info__tests_8H.html
docs/sphinx/file/diffusion__params_8H.html
docs/sphinx/file/diffusion__queries_8H.html
docs/sphinx/file/energy__diagnostics_8cpp.html
docs/sphinx/file/gravity__defaults_8H.html
docs/sphinx/file/gravity__job__info__tests_8H.html
docs/sphinx/file/gravity__params_8H.html
docs/sphinx/file/gravity__queries_8H.html
docs/sphinx/file/main_8cpp.html
docs/sphinx/file/particles__defaults_8H.html
docs/sphinx/file/particles__job__info__tests_8H.html
docs/sphinx/file/particles__params_8H.html
docs/sphinx/file/particles__queries_8H.html
docs/sphinx/file/sum__integrated__quantities_8cpp.html
docs/sphinx/file/sum__utils_8cpp.html
docs/sphinx/filelist.html
docs/sphinx/genindex.html
docs/sphinx/getting_started.html
docs/sphinx/gravity.html
docs/sphinx/index_docs.html
docs/sphinx/inputs.html
docs/sphinx/io.html
docs/sphinx/namespace/namespace_0D9.html
docs/sphinx/namespace/namespaceamrex.html
docs/sphinx/namespacelist.html
docs/sphinx/objects.inv
docs/sphinx/rad.html
docs/sphinx/radiation.html
docs/sphinx/references.html
docs/sphinx/rotation.html
docs/sphinx/rp_intro.html
docs/sphinx/runtime_parameters.html
docs/sphinx/search.html
docs/sphinx/searchindex.js
docs/sphinx/software.html
docs/sphinx/vis_tools.html
docs/sphinx/visualization.html
docs/who.html
commit f8c6966626a6083fa9de5a5c454d2ead046a3c86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 20:20:44 2018 -0500
make the main page index_docs.rst/html
docs/AMR.html
docs/ConvertCheckpoint.html
docs/EOSNetwork.html
docs/FlowChart.html
docs/Hydrodynamics.html
docs/Introduction.html
docs/MAESTRO_restart.html
docs/Particles.html
docs/Preface.html
docs/Verification.html
docs/_sources/index_docs.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/class/classAuxVar.html
docs/class/classAuxVarBox.html
docs/class/classAuxVar_1_1Connex.html
docs/class/classBndryAuxVar.html
docs/class/classBndryAuxVarBase.html
docs/class/classCastro.html
docs/class/classCastroBld.html
docs/class/classCrseBndryAuxVar.html
docs/class/classDiffusion.html
docs/class/classGradPhiPhysBCFunct.html
docs/class/classGravity.html
docs/class/classHypreABec.html
docs/class/classHypreExtMultiABec.html
docs/class/classHypreMultiABec.html
docs/class/classMGRadBndry.html
docs/class/classMGRadBndryBld.html
docs/class/classNGBndry.html
docs/class/classNGBndryBld.html
docs/class/classProxyGeometry.html
docs/class/classRadBndry.html
docs/class/classRadBndryBld.html
docs/class/classRadBndryData.html
docs/class/classRadBoundCond.html
docs/class/classRadInterpBndryData.html
docs/class/classRadSolve.html
docs/class/classRadTests.html
docs/class/classRadiation.html
docs/classlist.html
docs/coding_conventions.html
docs/creating_a_problem.html
docs/diffusion.html
docs/faq.html
docs/file/CastroBld_8cpp.html
docs/file/CastroParticles_8cpp.html
docs/file/Castro_8H.html
docs/file/Castro_8cpp.html
docs/file/Castro__F_8H.html
docs/file/Castro__advance_8cpp.html
docs/file/Castro__diffusion_8cpp.html
docs/file/Castro__error_8cpp.html
docs/file/Castro__error__F_8H.html
docs/file/Castro__external_8cpp.html
docs/file/Castro__gravity_8cpp.html
docs/file/Castro__hybrid_8cpp.html
docs/file/Castro__hydro_8cpp.html
docs/file/Castro__io_8H.html
docs/file/Castro__io_8cpp.html
docs/file/Castro__pointmass_8cpp.html
docs/file/Castro__prob__err_8cpp.html
docs/file/Castro__prob__err__F_8H.html
docs/file/Castro__prob__err__list_8H.html
docs/file/Castro__radiation_8cpp.html
docs/file/Castro__react_8cpp.html
docs/file/Castro__rotation_8cpp.html
docs/file/Castro__setup_8cpp.html
docs/file/Castro__sources_8cpp.html
docs/file/Castro__sponge_8cpp.html
docs/file/Castro__thermo_8cpp.html
docs/file/Derive_8H.html
docs/file/Derive_8cpp.html
docs/file/Derive__F_8H.html
docs/file/Diffusion_8H.html
docs/file/Diffusion_8cpp.html
docs/file/DumpModel1d_8H.html
docs/file/DumpModel1d_8cpp.html
docs/file/Gravity_8H.html
docs/file/Gravity_8cpp.html
docs/file/Gravity__F_8H.html
docs/file/HABEC__F_8H.html
docs/file/HypreABec_8H.html
docs/file/HypreABec_8cpp.html
docs/file/HypreExtMultiABec_8H.html
docs/file/HypreExtMultiABec_8cpp.html
docs/file/HypreMultiABec_8H.html
docs/file/HypreMultiABec_8cpp.html
docs/file/MGFLDRadSolver_8cpp.html
docs/file/MGFLD_8cpp.html
docs/file/MGRadBndry_8H.html
docs/file/MGRadBndry_8cpp.html
docs/file/NGBndry_8H.html
docs/file/Prob_8cpp.html
docs/file/Problem_8H.html
docs/file/Problem__Derive_8H.html
docs/file/Problem__Derive__F_8H.html
docs/file/Problem__Derives_8H.html
docs/file/Problem__F_8H.html
docs/file/RADINTERPBNDRYDATA__F_8H.html
docs/file/RAD__F_8H.html
docs/file/RadBndryData_8H.html
docs/file/RadBndryData_8cpp.html
docs/file/RadBndry_8H.html
docs/file/RadBndry_8cpp.html
docs/file/RadBoundCond_8H.html
docs/file/RadInterpBndryData_8H.html
docs/file/RadInterpBndryData_8cpp.html
docs/file/RadMultiGroup_8cpp.html
docs/file/RadPlotvar_8cpp.html
docs/file/RadSolve_8H.html
docs/file/RadSolve_8cpp.html
docs/file/RadTests_8H.html
docs/file/RadTypes_8H.html
docs/file/Radiation_8H.html
docs/file/Radiation_8cpp.html
docs/file/SGFLD_8cpp.html
docs/file/SGRadSolver_8cpp.html
docs/file/castro__defaults_8H.html
docs/file/castro__job__info__tests_8H.html
docs/file/castro__params_8H.html
docs/file/castro__queries_8H.html
docs/file/diffusion__defaults_8H.html
docs/file/diffusion__job__info__tests_8H.html
docs/file/diffusion__params_8H.html
docs/file/diffusion__queries_8H.html
docs/file/energy__diagnostics_8cpp.html
docs/file/gravity__defaults_8H.html
docs/file/gravity__job__info__tests_8H.html
docs/file/gravity__params_8H.html
docs/file/gravity__queries_8H.html
docs/file/main_8cpp.html
docs/file/particles__defaults_8H.html
docs/file/particles__job__info__tests_8H.html
docs/file/particles__params_8H.html
docs/file/particles__queries_8H.html
docs/file/sum__integrated__quantities_8cpp.html
docs/file/sum__utils_8cpp.html
docs/filelist.html
docs/genindex.html
docs/getting_started.html
docs/gravity.html
docs/index_docs.html
docs/inputs.html
docs/io.html
docs/namespace/namespace_0D9.html
docs/namespace/namespaceamrex.html
docs/namespacelist.html
docs/objects.inv
docs/rad.html
docs/radiation.html
docs/references.html
docs/rotation.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/search.html
docs/searchindex.js
docs/software.html
docs/vis_tools.html
docs/visualization.html
sphinx_docs/source/conf.py
sphinx_docs/source/index_docs.rst
sphinx_docs/source/runtime_parameters.rst
commit 904c05237ec070313e9576c87c753dc36c6ba3d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 14:59:47 2018 -0500
try to figure out where we are
.travis.yml
commit 1fc07e12df1ec874b45500325fa44d05b1490d5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 14:56:25 2018 -0500
force travis
.travis.yml
commit 6bb0da91e9eccf6cf75bbcc153de07b7ea3a9032
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 14:52:33 2018 -0500
some travis experiments
.travis.yml
commit f4988c4b96eeaa210b4c494d032fd335bc6b7ae2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 11:24:23 2018 -0500
add note about sphinx
CHANGES
commit 4d3ff75f7220184f446b2103a5d844045e4d3092
Merge: d3e4f8c36 147c78eab
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon Nov 26 10:53:31 2018 -0500
Merge pull request #435 from AMReX-Astro/sphinx
Sphinx conversion of docs
commit d3e4f8c3690be3807efe92027154bf7fe5eff2f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 26 10:44:56 2018 -0500
decrease frequency of output
Exec/science/flame_wave/inputs_2d.boost.aprox13.hires
commit 147c78eab62509fb66f0efefe3fe51a80130eb8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 25 10:00:00 2018 -0500
update docs
docs/AMR.html
docs/ConvertCheckpoint.html
docs/EOSNetwork.html
docs/FlowChart.html
docs/Hydrodynamics.html
docs/Introduction.html
docs/MAESTRO_restart.html
docs/Particles.html
docs/Preface.html
docs/Verification.html
docs/_sources/Preface.rst.txt
docs/_sources/references.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/_sources/visualization.rst.txt
docs/class/classAuxVar.html
docs/class/classAuxVarBox.html
docs/class/classAuxVar_1_1Connex.html
docs/class/classBndryAuxVar.html
docs/class/classBndryAuxVarBase.html
docs/class/classCastro.html
docs/class/classCastroBld.html
docs/class/classCrseBndryAuxVar.html
docs/class/classDiffusion.html
docs/class/classGradPhiPhysBCFunct.html
docs/class/classGravity.html
docs/class/classHypreABec.html
docs/class/classHypreExtMultiABec.html
docs/class/classHypreMultiABec.html
docs/class/classMGRadBndry.html
docs/class/classMGRadBndryBld.html
docs/class/classNGBndry.html
docs/class/classNGBndryBld.html
docs/class/classProxyGeometry.html
docs/class/classRadBndry.html
docs/class/classRadBndryBld.html
docs/class/classRadBndryData.html
docs/class/classRadBoundCond.html
docs/class/classRadInterpBndryData.html
docs/class/classRadSolve.html
docs/class/classRadTests.html
docs/class/classRadiation.html
docs/classlist.html
docs/coding_conventions.html
docs/creating_a_problem.html
docs/diffusion.html
docs/faq.html
docs/file/CastroBld_8cpp.html
docs/file/CastroParticles_8cpp.html
docs/file/Castro_8H.html
docs/file/Castro_8cpp.html
docs/file/Castro__F_8H.html
docs/file/Castro__advance_8cpp.html
docs/file/Castro__diffusion_8cpp.html
docs/file/Castro__error_8cpp.html
docs/file/Castro__error__F_8H.html
docs/file/Castro__external_8cpp.html
docs/file/Castro__gravity_8cpp.html
docs/file/Castro__hybrid_8cpp.html
docs/file/Castro__hydro_8cpp.html
docs/file/Castro__io_8H.html
docs/file/Castro__io_8cpp.html
docs/file/Castro__pointmass_8cpp.html
docs/file/Castro__prob__err_8cpp.html
docs/file/Castro__prob__err__F_8H.html
docs/file/Castro__prob__err__list_8H.html
docs/file/Castro__radiation_8cpp.html
docs/file/Castro__react_8cpp.html
docs/file/Castro__rotation_8cpp.html
docs/file/Castro__setup_8cpp.html
docs/file/Castro__sources_8cpp.html
docs/file/Castro__sponge_8cpp.html
docs/file/Castro__thermo_8cpp.html
docs/file/Derive_8H.html
docs/file/Derive_8cpp.html
docs/file/Derive__F_8H.html
docs/file/Diffusion_8H.html
docs/file/Diffusion_8cpp.html
docs/file/DumpModel1d_8H.html
docs/file/DumpModel1d_8cpp.html
docs/file/Gravity_8H.html
docs/file/Gravity_8cpp.html
docs/file/Gravity__F_8H.html
docs/file/HABEC__F_8H.html
docs/file/HypreABec_8H.html
docs/file/HypreABec_8cpp.html
docs/file/HypreExtMultiABec_8H.html
docs/file/HypreExtMultiABec_8cpp.html
docs/file/HypreMultiABec_8H.html
docs/file/HypreMultiABec_8cpp.html
docs/file/MGFLDRadSolver_8cpp.html
docs/file/MGFLD_8cpp.html
docs/file/MGRadBndry_8H.html
docs/file/MGRadBndry_8cpp.html
docs/file/NGBndry_8H.html
docs/file/Prob_8cpp.html
docs/file/Problem_8H.html
docs/file/Problem__Derive_8H.html
docs/file/Problem__Derive__F_8H.html
docs/file/Problem__Derives_8H.html
docs/file/Problem__F_8H.html
docs/file/RADINTERPBNDRYDATA__F_8H.html
docs/file/RAD__F_8H.html
docs/file/RadBndryData_8H.html
docs/file/RadBndryData_8cpp.html
docs/file/RadBndry_8H.html
docs/file/RadBndry_8cpp.html
docs/file/RadBoundCond_8H.html
docs/file/RadInterpBndryData_8H.html
docs/file/RadInterpBndryData_8cpp.html
docs/file/RadMultiGroup_8cpp.html
docs/file/RadPlotvar_8cpp.html
docs/file/RadSolve_8H.html
docs/file/RadSolve_8cpp.html
docs/file/RadTests_8H.html
docs/file/RadTypes_8H.html
docs/file/Radiation_8H.html
docs/file/Radiation_8cpp.html
docs/file/SGFLD_8cpp.html
docs/file/SGRadSolver_8cpp.html
docs/file/castro__defaults_8H.html
docs/file/castro__job__info__tests_8H.html
docs/file/castro__params_8H.html
docs/file/castro__queries_8H.html
docs/file/diffusion__defaults_8H.html
docs/file/diffusion__job__info__tests_8H.html
docs/file/diffusion__params_8H.html
docs/file/diffusion__queries_8H.html
docs/file/energy__diagnostics_8cpp.html
docs/file/gravity__defaults_8H.html
docs/file/gravity__job__info__tests_8H.html
docs/file/gravity__params_8H.html
docs/file/gravity__queries_8H.html
docs/file/main_8cpp.html
docs/file/particles__defaults_8H.html
docs/file/particles__job__info__tests_8H.html
docs/file/particles__params_8H.html
docs/file/particles__queries_8H.html
docs/file/sum__integrated__quantities_8cpp.html
docs/file/sum__utils_8cpp.html
docs/filelist.html
docs/getting_started.html
docs/gravity.html
docs/index.html
docs/inputs.html
docs/io.html
docs/namespace/namespace_0D9.html
docs/namespace/namespaceamrex.html
docs/namespacelist.html
docs/rad.html
docs/radiation.html
docs/references.html
docs/rotation.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/searchindex.js
docs/software.html
docs/vis_tools.html
docs/visualization.html
commit 86422dd6bac1432b6680afa7718cbb362699de11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 25 09:59:42 2018 -0500
update params
sphinx_docs/source/runtime_parameters.rst
commit 351b5577f9641e8e359409c643db2320806e40f8
Merge: 684b6fdc3 6f7b58533
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 25 09:58:42 2018 -0500
Merge branch 'development' into sphinx
commit 684b6fdc3578319a1d1183fbab09ace0b2331df8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 25 09:57:57 2018 -0500
a little fixing
sphinx_docs/source/Preface.rst
sphinx_docs/source/runtime_parameters.rst
commit 6f7b58533aeab6a69a6dfae6b4fa6207c02083fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 24 14:32:26 2018 -0500
max_step was too short
Exec/science/Detonation/inputs-collision
commit b7b1a680e57c896722d15f7dda6eca7e584907ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 20:48:50 2018 -0500
some more units
sphinx_docs/source/visualization.rst
commit d04b50a206fcce75c5006fc495e34eb4a297ff50
Merge: 877b52214 83404e1d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 19:03:27 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 877b522145b229f00702db83170f76c8c8cc3cfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 18:31:10 2018 -0500
remove interp_BC and zero_vels -- these were never used
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/planet/Prob_3d.f90
Exec/science/planet/probdata.f90
Exec/science/planet/probin
commit 0b9771699441ad708723a21fd240e2e7d1aefb37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 18:40:27 2018 -0500
interp_BC and zero vels don't have are not used here
Exec/science/nova/Prob_2d.f90
Exec/science/nova/probdata.f90
Exec/science/nova/probin
commit 03c25ec41d32e27e1dc81a3b1951d3c2f3875e62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 19:02:25 2018 -0500
update docs
docs/AMR.html
docs/ConvertCheckpoint.html
docs/EOSNetwork.html
docs/FlowChart.html
docs/Hydrodynamics.html
docs/Introduction.html
docs/MAESTRO_restart.html
docs/Particles.html
docs/Preface.html
docs/Verification.html
docs/_sources/AMR.rst.txt
docs/_sources/EOSNetwork.rst.txt
docs/_sources/FlowChart.rst.txt
docs/_sources/Hydrodynamics.rst.txt
docs/_sources/Verification.rst.txt
docs/_sources/getting_started.rst.txt
docs/_sources/gravity.rst.txt
docs/_sources/index.rst.txt
docs/_sources/inputs.rst.txt
docs/_sources/rotation.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/_sources/visualization.rst.txt
docs/class/classAuxVar.html
docs/class/classAuxVarBox.html
docs/class/classAuxVar_1_1Connex.html
docs/class/classBndryAuxVar.html
docs/class/classBndryAuxVarBase.html
docs/class/classCastro.html
docs/class/classCastroBld.html
docs/class/classCrseBndryAuxVar.html
docs/class/classDiffusion.html
docs/class/classGradPhiPhysBCFunct.html
docs/class/classGravity.html
docs/class/classHypreABec.html
docs/class/classHypreExtMultiABec.html
docs/class/classHypreMultiABec.html
docs/class/classMGRadBndry.html
docs/class/classMGRadBndryBld.html
docs/class/classNGBndry.html
docs/class/classNGBndryBld.html
docs/class/classProxyGeometry.html
docs/class/classRadBndry.html
docs/class/classRadBndryBld.html
docs/class/classRadBndryData.html
docs/class/classRadBoundCond.html
docs/class/classRadInterpBndryData.html
docs/class/classRadSolve.html
docs/class/classRadTests.html
docs/class/classRadiation.html
docs/classlist.html
docs/coding_conventions.html
docs/creating_a_problem.html
docs/diffusion.html
docs/faq.html
docs/file/CastroBld_8cpp.html
docs/file/CastroParticles_8cpp.html
docs/file/Castro_8H.html
docs/file/Castro_8cpp.html
docs/file/Castro__F_8H.html
docs/file/Castro__advance_8cpp.html
docs/file/Castro__diffusion_8cpp.html
docs/file/Castro__error_8cpp.html
docs/file/Castro__error__F_8H.html
docs/file/Castro__external_8cpp.html
docs/file/Castro__gravity_8cpp.html
docs/file/Castro__hybrid_8cpp.html
docs/file/Castro__hydro_8cpp.html
docs/file/Castro__io_8H.html
docs/file/Castro__io_8cpp.html
docs/file/Castro__pointmass_8cpp.html
docs/file/Castro__prob__err_8cpp.html
docs/file/Castro__prob__err__F_8H.html
docs/file/Castro__prob__err__list_8H.html
docs/file/Castro__radiation_8cpp.html
docs/file/Castro__react_8cpp.html
docs/file/Castro__rotation_8cpp.html
docs/file/Castro__setup_8cpp.html
docs/file/Castro__sources_8cpp.html
docs/file/Castro__sponge_8cpp.html
docs/file/Castro__thermo_8cpp.html
docs/file/Derive_8H.html
docs/file/Derive_8cpp.html
docs/file/Derive__F_8H.html
docs/file/Diffusion_8H.html
docs/file/Diffusion_8cpp.html
docs/file/DumpModel1d_8H.html
docs/file/DumpModel1d_8cpp.html
docs/file/Gravity_8H.html
docs/file/Gravity_8cpp.html
docs/file/Gravity__F_8H.html
docs/file/HABEC__F_8H.html
docs/file/HypreABec_8H.html
docs/file/HypreABec_8cpp.html
docs/file/HypreExtMultiABec_8H.html
docs/file/HypreExtMultiABec_8cpp.html
docs/file/HypreMultiABec_8H.html
docs/file/HypreMultiABec_8cpp.html
docs/file/MGFLDRadSolver_8cpp.html
docs/file/MGFLD_8cpp.html
docs/file/MGRadBndry_8H.html
docs/file/MGRadBndry_8cpp.html
docs/file/NGBndry_8H.html
docs/file/Prob_8cpp.html
docs/file/Problem_8H.html
docs/file/Problem__Derive_8H.html
docs/file/Problem__Derive__F_8H.html
docs/file/Problem__Derives_8H.html
docs/file/Problem__F_8H.html
docs/file/RADINTERPBNDRYDATA__F_8H.html
docs/file/RAD__F_8H.html
docs/file/RadBndryData_8H.html
docs/file/RadBndryData_8cpp.html
docs/file/RadBndry_8H.html
docs/file/RadBndry_8cpp.html
docs/file/RadBoundCond_8H.html
docs/file/RadInterpBndryData_8H.html
docs/file/RadInterpBndryData_8cpp.html
docs/file/RadMultiGroup_8cpp.html
docs/file/RadPlotvar_8cpp.html
docs/file/RadSolve_8H.html
docs/file/RadSolve_8cpp.html
docs/file/RadTests_8H.html
docs/file/RadTypes_8H.html
docs/file/Radiation_8H.html
docs/file/Radiation_8cpp.html
docs/file/SGFLD_8cpp.html
docs/file/SGRadSolver_8cpp.html
docs/file/castro__defaults_8H.html
docs/file/castro__job__info__tests_8H.html
docs/file/castro__params_8H.html
docs/file/castro__queries_8H.html
docs/file/diffusion__defaults_8H.html
docs/file/diffusion__job__info__tests_8H.html
docs/file/diffusion__params_8H.html
docs/file/diffusion__queries_8H.html
docs/file/energy__diagnostics_8cpp.html
docs/file/gravity__defaults_8H.html
docs/file/gravity__job__info__tests_8H.html
docs/file/gravity__params_8H.html
docs/file/gravity__queries_8H.html
docs/file/main_8cpp.html
docs/file/particles__defaults_8H.html
docs/file/particles__job__info__tests_8H.html
docs/file/particles__params_8H.html
docs/file/particles__queries_8H.html
docs/file/sum__integrated__quantities_8cpp.html
docs/file/sum__utils_8cpp.html
docs/filelist.html
docs/genindex.html
docs/getting_started.html
docs/gravity.html
docs/index.html
docs/inputs.html
docs/io.html
docs/namespace/namespace_0D9.html
docs/namespace/namespaceamrex.html
docs/namespacelist.html
docs/objects.inv
docs/rad.html
docs/radiation.html
docs/rotation.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/search.html
docs/searchindex.js
docs/software.html
docs/vis_tools.html
docs/visualization.html
commit d4b0d0cce71b200f3f57d6bb3370efb03a00f690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 18:40:27 2018 -0500
interp_BC and zero vels don't have are not used here
Exec/science/nova/Prob_2d.f90
Exec/science/nova/probdata.f90
Exec/science/nova/probin
commit 1a2827554db95590bca1a1c45972faeeb2cdfabe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 18:31:10 2018 -0500
remove interp_BC and zero_vels -- these were never used
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/planet/Prob_3d.f90
Exec/science/planet/probdata.f90
Exec/science/planet/probin
commit 83404e1d3f6803491177f2c07c7fe161a8928f77
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 23 17:31:50 2018 -0500
Angular momentum is now calculated wrt center
Source/driver/Derive_nd.F90
commit 4c16b00289f4bb7267fcf166249ac4dc64282193
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 16:55:13 2018 -0500
add references
sphinx_docs/source/AMR.rst
sphinx_docs/source/EOSNetwork.rst
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/getting_started.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/index.rst
sphinx_docs/source/inputs.rst
sphinx_docs/source/references.rst
sphinx_docs/source/refs.bib
sphinx_docs/source/rotation.rst
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/visualization.rst
commit 6ba9fd324668f39e21b830bf2a2c51baaeefbe97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 23 09:11:33 2018 -0500
more plotfile docs
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/visualization.rst
commit 8ce6be788a3c7eb736858195f0512d9822848163
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 21 21:15:21 2018 -0500
a little more
sphinx_docs/source/visualization.rst
commit 2377067f7bf463517de3d519b0f20da6d9af1e5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 21 20:07:47 2018 -0500
more docs on variables
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/visualization.rst
commit 8d09bbd52abb8f1f9f208003dbbd47defa2aa1df
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 21 16:39:36 2018 -0500
Revert back to auto subcycling
Exec/science/Detonation/inputs-collision
commit 813fcfc3e3192f45220224fdafc44c07e85c9891
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 21 15:04:33 2018 -0500
Update detonation collision test inputs
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/probin-collision
commit 35b003157c7f1daa8fafe04aa6651e3f83639fdd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 21 11:46:05 2018 -0500
some plotfile docs
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/visualization.rst
commit ccb62bda4e60c162ca51f8142f8603a13177bcb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 20 20:28:22 2018 -0500
more docs
docs/_sources/vis_tools.rst.txt
docs/vis_tools.html
sphinx_docs/source/vis_tools.rst
commit 2c4a029d2ff73b4d428a90e97b4e993d93f47405
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 20 20:27:50 2018 -0500
start of a table of plotfile variables
docs/AMR.html
docs/ConvertCheckpoint.html
docs/EOSNetwork.html
docs/FlowChart.html
docs/Hydrodynamics.html
docs/Introduction.html
docs/MAESTRO_restart.html
docs/Particles.html
docs/Preface.html
docs/Verification.html
docs/_sources/runtime_parameters.rst.txt
docs/_sources/visualization.rst.txt
docs/class/classAuxVar.html
docs/class/classAuxVarBox.html
docs/class/classAuxVar_1_1Connex.html
docs/class/classBndryAuxVar.html
docs/class/classBndryAuxVarBase.html
docs/class/classCastro.html
docs/class/classCastroBld.html
docs/class/classCrseBndryAuxVar.html
docs/class/classDiffusion.html
docs/class/classGradPhiPhysBCFunct.html
docs/class/classGravity.html
docs/class/classHypreABec.html
docs/class/classHypreExtMultiABec.html
docs/class/classHypreMultiABec.html
docs/class/classMGRadBndry.html
docs/class/classMGRadBndryBld.html
docs/class/classNGBndry.html
docs/class/classNGBndryBld.html
docs/class/classProxyGeometry.html
docs/class/classRadBndry.html
docs/class/classRadBndryBld.html
docs/class/classRadBndryData.html
docs/class/classRadBoundCond.html
docs/class/classRadInterpBndryData.html
docs/class/classRadSolve.html
docs/class/classRadTests.html
docs/class/classRadiation.html
docs/classlist.html
docs/coding_conventions.html
docs/creating_a_problem.html
docs/diffusion.html
docs/faq.html
docs/file/CastroBld_8cpp.html
docs/file/CastroParticles_8cpp.html
docs/file/Castro_8H.html
docs/file/Castro_8cpp.html
docs/file/Castro__F_8H.html
docs/file/Castro__advance_8cpp.html
docs/file/Castro__diffusion_8cpp.html
docs/file/Castro__error_8cpp.html
docs/file/Castro__error__F_8H.html
docs/file/Castro__external_8cpp.html
docs/file/Castro__gravity_8cpp.html
docs/file/Castro__hybrid_8cpp.html
docs/file/Castro__hydro_8cpp.html
docs/file/Castro__io_8H.html
docs/file/Castro__io_8cpp.html
docs/file/Castro__pointmass_8cpp.html
docs/file/Castro__prob__err_8cpp.html
docs/file/Castro__prob__err__F_8H.html
docs/file/Castro__prob__err__list_8H.html
docs/file/Castro__radiation_8cpp.html
docs/file/Castro__react_8cpp.html
docs/file/Castro__rotation_8cpp.html
docs/file/Castro__setup_8cpp.html
docs/file/Castro__sources_8cpp.html
docs/file/Castro__sponge_8cpp.html
docs/file/Castro__thermo_8cpp.html
docs/file/Derive_8H.html
docs/file/Derive_8cpp.html
docs/file/Derive__F_8H.html
docs/file/Diffusion_8H.html
docs/file/Diffusion_8cpp.html
docs/file/DumpModel1d_8H.html
docs/file/DumpModel1d_8cpp.html
docs/file/Gravity_8H.html
docs/file/Gravity_8cpp.html
docs/file/Gravity__F_8H.html
docs/file/HABEC__F_8H.html
docs/file/HypreABec_8H.html
docs/file/HypreABec_8cpp.html
docs/file/HypreExtMultiABec_8H.html
docs/file/HypreExtMultiABec_8cpp.html
docs/file/HypreMultiABec_8H.html
docs/file/HypreMultiABec_8cpp.html
docs/file/MGFLDRadSolver_8cpp.html
docs/file/MGFLD_8cpp.html
docs/file/MGRadBndry_8H.html
docs/file/MGRadBndry_8cpp.html
docs/file/NGBndry_8H.html
docs/file/Prob_8cpp.html
docs/file/Problem_8H.html
docs/file/Problem__Derive_8H.html
docs/file/Problem__Derive__F_8H.html
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commit d85110b9931536e553039b15fd1e707bfbbf1d92
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 19 16:14:53 2018 -0500
Avoid potential static destructor issues
Source/driver/main.cpp
commit 68d3a905b12fa1e76341c64938435644911d4e12
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 19 10:08:30 2018 -0500
Remove obsolete inputs
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/inputs.1d.test
Exec/science/Detonation/inputs-collision
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/inputs_3d
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/inputs.3d.test
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame/inputs.1d
Exec/science/flame/inputs.1d.aprox13
Exec/science/flame/inputs.1d.aprox13.boost
Exec/science/flame/inputs.1d.rprox
Exec/science/flame_wave/inputs_2d.boost.aprox13
Exec/science/flame_wave/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/inputs_3d.testsuite
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/old/inputs/inputs_2d
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
Exec/science/nova/inputs_2d
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/subchandra/inputs_2d
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/xrb_mixed/inputs_2d
commit d3ea0c2a9fcce25861801e5bf429eaf1e1898f1b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 18 20:18:46 2018 -0500
Enforce verbosity
Source/driver/Castro.cpp
commit 8dde104d96f80c32640d27fce88e20041ebd0516
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 18 12:36:25 2018 -0500
Enforce verbosity restrictions on prints
Source/driver/Castro.cpp
commit f5ef24695c98cf3840167e87c909c57d7bfdb1ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:53:19 2018 -0500
readd the docs
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docs/ConvertCheckpoint.html
docs/EOSNetwork.html
docs/Hydrodynamics.html
docs/Introduction.html
docs/MAESTRO_restart.html
docs/Particles.html
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commit 397b7ae60ecf5052363ca1384249327dbfb3a91b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:52:39 2018 -0500
lots of minor fixes
docs/FlowChart.html
docs/_sources/runtime_parameters.rst.txt
docs/runtime_parameters.html
docs/searchindex.js
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/software.rst
commit 2937a3cbc56b0d084fe9c46adb2ad7326b001274
Merge: fecb38ded 3b925369d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:17:46 2018 -0500
Merge branch 'sphinx' of github.com:AMReX-Astro/Castro into sphinx
commit fecb38dede44b395782992b6abc8a264e1221cc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:17:12 2018 -0500
update
sphinx_docs/source/runtime_parameters.rst
commit 3b925369dd22e8f2aa6ed97dd8019b9b4fabe593
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:16:32 2018 -0500
some fixes
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/getting_started.rst
sphinx_docs/source/inputs.rst
sphinx_docs/source/runtime_parameters.rst
commit 0dbaa6f264378dff2ee96d9b1eaf76db60370016
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:05:27 2018 -0500
new files
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docs/_sources/creating_a_problem.rst.txt
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commit 68c35383c9f10bc03fd7855dff8b74f1b2ee2a32
Merge: 15680f136 6630e6ed8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:04:59 2018 -0500
Merge branch 'sphinx' of ssh://github.com/AMReX-Astro/Castro into sphinx
commit 15680f136c06df2e4bc3ebacebbc33a29f662c95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 12:02:54 2018 -0500
update docs
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docs/file/temp_8f90.html
docs/file/thermo__nd_8F90.html
docs/file/timestep_8F90.html
docs/file/trace__nd_8F90.html
docs/file/trace__ppm__nd_8F90.html
docs/file/trace__ppm__rad__nd_8F90.html
docs/file/update__sponge__params_8f90.html
docs/filelist.html
docs/genindex.html
docs/getting_started.html
docs/gravity.html
docs/index.html
docs/inputs.html
docs/namespace/namespace_0D9.html
docs/namespace/namespaceadvection__util__module.html
docs/namespace/namespaceamrex.html
docs/namespace/namespaceamrex__constants__module.html
docs/namespace/namespaceamrex__error__module.html
docs/namespace/namespaceamrinfo__module.html
docs/namespace/namespacebc__ext__fill__module.html
docs/namespace/namespacebc__fill__module.html
docs/namespace/namespaceblackbody__module.html
docs/namespace/namespaceburn__type__module.html
docs/namespace/namespaceburner__module.html
docs/namespace/namespacecastro__sums__module.html
docs/namespace/namespacecastro__util__module.html
docs/namespace/namespaceconductivity__module.html
docs/namespace/namespacectu__advection__module.html
docs/namespace/namespacectu__module.html
docs/namespace/namespacederive__module.html
docs/namespace/namespacediffusion__module.html
docs/namespace/namespaceenthalpy__module.html
docs/namespace/namespaceeos__module.html
docs/namespace/namespaceeos__type__module.html
docs/namespace/namespacefilter__module.html
docs/namespace/namespaceflatten__module.html
docs/namespace/namespacefluxlimiter__module.html
docs/namespace/namespacefourth__order.html
docs/namespace/namespacegeneric__fill__module.html
docs/namespace/namespacegravity__1d__module.html
docs/namespace/namespacegravity__2d__module.html
docs/namespace/namespacegravity__3d__module.html
docs/namespace/namespacegravity__module.html
docs/namespace/namespacegravity__sources__module.html
docs/namespace/namespacehabec__module.html
docs/namespace/namespacehybrid__advection__module.html
docs/namespace/namespaceinterpolate__module.html
docs/namespace/namespaceio__module.html
docs/namespace/namespacemath__module.html
docs/namespace/namespacemeth__params__module.html
docs/namespace/namespacemgutils__1d__module.html
docs/namespace/namespacemgutils__2d__module.html
docs/namespace/namespacemodel__parser__module.html
docs/namespace/namespacemol__module__cuda.html
docs/namespace/namespacemultid__slope__module.html
docs/namespace/namespacenetwork.html
docs/namespace/namespaceppm__module.html
docs/namespace/namespaceprescribe__grav__module.html
docs/namespace/namespaceprescribe__phi__module.html
docs/namespace/namespaceprob__params__module.html
docs/namespace/namespaceproblem__tagging__module.html
docs/namespace/namespacerad__module.html
docs/namespace/namespacerad__params__module.html
docs/namespace/namespacerad__util__module.html
docs/namespace/namespaceradhydro__nd__module.html
docs/namespace/namespacereact__util__module.html
docs/namespace/namespacereactions__module.html
docs/namespace/namespaceriemann__module.html
docs/namespace/namespaceriemann__util__module.html
docs/namespace/namespacerotation__frequency__module.html
docs/namespace/namespacerotation__module.html
docs/namespace/namespacerotation__sources__module.html
docs/namespace/namespacerpar__sdc__module.html
docs/namespace/namespaceslope__module.html
docs/namespace/namespacesponge__module.html
docs/namespace/namespacestate__sizes__module.html
docs/namespace/namespacetagging__module.html
docs/namespace/namespacethermo__sources.html
docs/namespace/namespacetimestep__module.html
docs/namespace/namespacetrace__module.html
docs/namespace/namespacetrace__ppm__module.html
docs/namespace/namespacetrace__ppm__rad__module.html
docs/namespace/namespaceviscosity__module.html
docs/namespacelist.html
docs/objects.inv
docs/rad.html
docs/radiation.html
docs/rotation.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/search.html
docs/searchindex.js
docs/software.html
docs/visualization.html
commit 6630e6ed879df7420840ed1180d0176b9cd6a619
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 11:05:00 2018 -0500
add categories into the runtime parameter documentation
sphinx_docs/rp.py
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/runtime_parameters.rst
commit ae6c6608950f2da29010b0796e4a01d5d454b94d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 09:48:41 2018 -0500
fix runtime parameter parsing -- it now groups by namespace
sphinx_docs/rp.py
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/runtime_parameters.rst
commit b9cad7eb61c3a9ba29352926c9e6624310894415
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 09:26:28 2018 -0500
port old coding conventions document
sphinx_docs/source/coding_conventions.rst
commit 0c76abd46ea89d02a7396d088c10bb4d5c489244
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 17 09:03:53 2018 -0500
add coding standards
docs/AMR.html
docs/ConvertCheckpoint.html
docs/EOSNetwork.html
docs/FlowChart.html
docs/Hydrodynamics.html
docs/Introduction.html
docs/MAESTRO_restart.html
docs/Particles.html
docs/Preface.html
docs/Verification.html
docs/_sources/ConvertCheckpoint.rst.txt
docs/_sources/EOSNetwork.rst.txt
docs/_sources/Verification.rst.txt
docs/_sources/diffusion.rst.txt
docs/_sources/gravity.rst.txt
docs/_sources/index.rst.txt
docs/_sources/software.rst.txt
docs/_static/documentation_options.js
docs/class/classAuxVar.html
docs/class/classAuxVarBox.html
docs/class/classAuxVar_1_1Connex.html
docs/class/classBndryAuxVar.html
docs/class/classBndryAuxVarBase.html
docs/class/classCastro.html
docs/class/classCastroBld.html
docs/class/classCrseBndryAuxVar.html
docs/class/classDiffusion.html
docs/class/classGradPhiPhysBCFunct.html
docs/class/classGravity.html
docs/class/classHypreABec.html
docs/class/classHypreExtMultiABec.html
docs/class/classHypreMultiABec.html
docs/class/classMGRadBndry.html
docs/class/classMGRadBndryBld.html
docs/class/classNGBndry.html
docs/class/classNGBndryBld.html
docs/class/classProxyGeometry.html
docs/class/classRadBndry.html
docs/class/classRadBndryBld.html
docs/class/classRadBndryData.html
docs/class/classRadBoundCond.html
docs/class/classRadInterpBndryData.html
docs/class/classRadSolve.html
docs/class/classRadTests.html
docs/class/classRadiation.html
docs/classlist.html
docs/diffusion.html
docs/faq.html
docs/file/CastroBld_8cpp.html
docs/file/CastroParticles_8cpp.html
docs/file/Castro_8H.html
docs/file/Castro_8cpp.html
docs/file/Castro__F_8H.html
docs/file/Castro__advance_8cpp.html
docs/file/Castro__diffusion_8cpp.html
docs/file/Castro__error_8cpp.html
docs/file/Castro__error__F_8H.html
docs/file/Castro__external_8cpp.html
docs/file/Castro__gravity_8cpp.html
docs/file/Castro__hybrid_8cpp.html
docs/file/Castro__hydro_8cpp.html
docs/file/Castro__io_8H.html
docs/file/Castro__io_8cpp.html
docs/file/Castro__pointmass_8cpp.html
docs/file/Castro__prob__err_8cpp.html
docs/file/Castro__prob__err__F_8H.html
docs/file/Castro__prob__err__list_8H.html
docs/file/Castro__radiation_8cpp.html
docs/file/Castro__react_8cpp.html
docs/file/Castro__rotation_8cpp.html
docs/file/Castro__setup_8cpp.html
docs/file/Castro__sources_8cpp.html
docs/file/Castro__sponge_8cpp.html
docs/file/Castro__thermo_8cpp.html
docs/file/Derive_8H.html
docs/file/Derive_8cpp.html
docs/file/Derive__F_8H.html
docs/file/Diffusion_8H.html
docs/file/Diffusion_8cpp.html
docs/file/DumpModel1d_8H.html
docs/file/DumpModel1d_8cpp.html
docs/file/Gravity_8H.html
docs/file/Gravity_8cpp.html
docs/file/Gravity__F_8H.html
docs/file/HABEC__F_8H.html
docs/file/HypreABec_8H.html
docs/file/HypreABec_8cpp.html
docs/file/HypreExtMultiABec_8H.html
docs/file/HypreExtMultiABec_8cpp.html
docs/file/HypreMultiABec_8H.html
docs/file/HypreMultiABec_8cpp.html
docs/file/MGFLDRadSolver_8cpp.html
docs/file/MGFLD_8cpp.html
docs/file/MGRadBndry_8H.html
docs/file/MGRadBndry_8cpp.html
docs/file/NGBndry_8H.html
docs/file/Prob_8cpp.html
docs/file/Problem_8H.html
docs/file/Problem__Derive_8H.html
docs/file/Problem__Derive__F_8H.html
docs/file/Problem__Derives_8H.html
docs/file/Problem__F_8H.html
docs/file/RADINTERPBNDRYDATA__F_8H.html
docs/file/RAD__F_8H.html
docs/file/RadBndryData_8H.html
docs/file/RadBndryData_8cpp.html
docs/file/RadBndry_8H.html
docs/file/RadBndry_8cpp.html
docs/file/RadBoundCond_8H.html
docs/file/RadInterpBndryData_8H.html
docs/file/RadInterpBndryData_8cpp.html
docs/file/RadMultiGroup_8cpp.html
docs/file/RadPlotvar_8cpp.html
docs/file/RadSolve_8H.html
docs/file/RadSolve_8cpp.html
docs/file/RadTests_8H.html
docs/file/RadTypes_8H.html
docs/file/Radiation_8H.html
docs/file/Radiation_8cpp.html
docs/file/SGFLD_8cpp.html
docs/file/SGRadSolver_8cpp.html
docs/file/castro__defaults_8H.html
docs/file/castro__job__info__tests_8H.html
docs/file/castro__params_8H.html
docs/file/castro__queries_8H.html
docs/file/diffusion__defaults_8H.html
docs/file/diffusion__job__info__tests_8H.html
docs/file/diffusion__params_8H.html
docs/file/diffusion__queries_8H.html
docs/file/energy__diagnostics_8cpp.html
docs/file/gravity__defaults_8H.html
docs/file/gravity__job__info__tests_8H.html
docs/file/gravity__params_8H.html
docs/file/gravity__queries_8H.html
docs/file/main_8cpp.html
docs/file/particles__defaults_8H.html
docs/file/particles__job__info__tests_8H.html
docs/file/particles__params_8H.html
docs/file/particles__queries_8H.html
docs/file/sum__integrated__quantities_8cpp.html
docs/file/sum__utils_8cpp.html
docs/filelist.html
docs/genindex.html
docs/getting_started.html
docs/gravity.html
docs/index.html
docs/inputs.html
docs/namespace/namespace_0D9.html
docs/namespace/namespaceamrex.html
docs/namespacelist.html
docs/objects.inv
docs/rad.html
docs/radiation.html
docs/rotation.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/search.html
docs/searchindex.js
docs/software.html
docs/visualization.html
sphinx_docs/source/coding_conventions.rst
sphinx_docs/source/index.rst
commit ae1abba121fa1d6ac74903dddb62c400248d7941
Merge: 994df4966 7023089ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 16 18:42:28 2018 -0500
Merge branch 'development' into sphinx
commit 7023089ad5783e205da563deb93241b779d672e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 16 17:41:36 2018 -0500
more CTU GPUing (#432)
This set of changes merges the trans routines and moves the source terms in PLM into the trace routines instead of having them sprinkled into the trans routines.
CHANGES
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Make.package
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans.F90
Source/hydro/trans_2d.F90
commit 3dc72d5bb2055de0b268e0eded92088eca726193
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 15 19:42:41 2018 -0500
update style / python
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test1-helm.py
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test2-helm.py
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test3-helm.py
commit 994df496620e2d06a8becdc7d9c75394840a2886
Merge: 1245ead24 030cc75cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 15 17:36:05 2018 -0500
Merge branch 'development' into sphinx
commit 1245ead2452d70dc419f7e54dd75ab0d21d58a43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 14 13:51:07 2018 -0500
some more fixes
sphinx_docs/source/diffusion.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/index.rst
sphinx_docs/source/software.rst
commit 030cc75ccfbac2b01963f141853ab5e6ce0ab1ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 14 10:21:21 2018 -0500
fix latex build
Docs/FAQ/faq.tex
commit 046f60a7ba15d0bd4842f5c8ef62b874004d404f
Merge: 236b34cca 38ff04378
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 13 21:25:29 2018 -0500
Merge branch 'development' into sphinx
commit 38ff04378b50f2b4558e2446122b902668a473b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 13 21:06:00 2018 -0500
CTU noslab gpu (#428)
this merges the CTU driver routines.
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Make.package
Source/hydro/flatten_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/trace_ppm.F90
Source/hydro/trans_2d.F90
commit 3c4d2ccfd100311e7e0d51b829943b647b511d7e
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Tue Nov 13 11:25:15 2018 -0800
minor updates due to AMReX changes (#439)
Source/driver/Castro.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit 650d15362548fe07102166911a3cd99c58213d34
Author: Ying Tai Chen <30877545+yingtchen@users.noreply.github.com>
Date: Tue Nov 13 13:55:30 2018 -0500
changed refinement criteria (#438)
Exec/science/nova/probin
commit 236b34ccaefeafae241744de8ed0d95150ec14de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 13 12:18:13 2018 -0500
some fixes
sphinx_docs/source/creating_a_problem.rst
sphinx_docs/source/index.rst
sphinx_docs/source/io.rst
sphinx_docs/source/software.rst
commit 6b032940421464dba121afeedce57182387ed759
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 13 11:57:15 2018 -0500
split up a long section
sphinx_docs/source/creating_a_problem.rst
sphinx_docs/source/index.rst
sphinx_docs/source/index_grid2.png
sphinx_docs/source/software.rst
commit 5d8dabf2386fc88b4e2daa6e498320252d78643c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 21:39:00 2018 -0500
update gravity
sphinx_docs/source/gravity.rst
commit 2ffa9563a7cb97af75b1d03a0bf6af79e92a3e6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 19:43:03 2018 -0500
fix figures
sphinx_docs/source/ConvertCheckpoint.rst
commit e5dc832aa3392bfb804baa7c0f63e60f00fb0e51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 19:39:22 2018 -0500
fix the embiggener
sphinx_docs/source/ConvertCheckpoint.rst
sphinx_docs/source/center.png
sphinx_docs/source/corner.png
sphinx_docs/source/grown_center_2.png
sphinx_docs/source/grown_center_3.png
sphinx_docs/source/grown_corner_2.png
sphinx_docs/source/grown_corner_3.png
sphinx_docs/source/orig_center.png
sphinx_docs/source/orig_corner.png
commit dd849929dff8c4dbdb5373bc5ebf47acd6a4c270
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 16:55:34 2018 -0500
remove enskip
sphinx_docs/source/EOSNetwork.rst
sphinx_docs/source/Verification.rst
commit 2012cde947cd8528062bfef85cb830e54f138e09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 14:22:49 2018 -0500
automagically set the doc version from the last git tag
sphinx_docs/source/conf.py
commit b8af0d8c65125d1f7f1608f6c3c15102df6e5e80
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:59:23 2018 -0500
update docs
docs/_sources/faq.rst.txt
docs/faq.html
docs/objects.inv
docs/searchindex.js
commit 662d859516a9549bd0c5f3f7da6dee5e6775fc86
Merge: e114f10f4 cadeb5685
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:57:00 2018 -0500
Merge branch 'development' into sphinx
commit e114f10f4cf399dbcf342338dfde93d5da1aedd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:53:51 2018 -0500
add math symbols
sphinx_docs/source/mathsymbols.tex
commit c57c8e39c79b8a70ae05e0b80c5688dbe38fce79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:53:35 2018 -0500
add bibtex
sphinx_docs/source/conf.py
commit c2e2ec2632fe9cf46d7e56c1f2dcb9ad5ffb7dd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:22:06 2018 -0500
update sphinx docs
Docs/AMR/AMR.tex
Docs/CastroUserGuide.tex
Docs/Coding_Standards.md
Docs/ConvertCheckpoint/ConvertCheckpoint.tex
Docs/ConvertCheckpoint/grown_center_2.eps
Docs/ConvertCheckpoint/grown_center_3.eps
Docs/ConvertCheckpoint/grown_corner_2.eps
Docs/ConvertCheckpoint/grown_corner_3.eps
Docs/ConvertCheckpoint/orig_center.eps
Docs/ConvertCheckpoint/orig_corner.eps
Docs/Diffusion/CastroDiffusion.tex
Docs/EOSNetwork/EOSNetwork.tex
Docs/FAQ/faq.tex
Docs/FlowChart/FlowChart.tex
Docs/GNUmakefile
Docs/GettingStarted/CastroGettingStarted.tex
Docs/Gravity/CastroGravity.tex
Docs/Gravity/gr.bib
Docs/Hydrodynamics/Hydrodynamics.tex
Docs/Inputs/CastroInputs.tex
Docs/Introduction/Introduction.tex
Docs/MAESTRO_restart/MAESTRO_restart.tex
Docs/ManagingJobs/managingjobs.tex
Docs/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/avg_time.sh
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI1024-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP16-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/avg_time.sh
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/avg_time.sh
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docs/rotation.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/search.html
docs/searchindex.js
docs/software.html
docs/visualization.html
commit 2d5a4ef4ebe63e1fb3bd63574b277b5abaa82860
Merge: 3d2bc2d87 a4aabcce3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:17:20 2018 -0500
Merge branch 'sphinx' of ssh://github.com/AMReX-Astro/Castro into sphinx
commit a4aabcce3d992725b9cd37c095a39071ceed965e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:16:52 2018 -0500
automagically create the docs/ if it doesn't exist
sphinx_docs/Makefile
commit 3d2bc2d87bda771cfa37a83d6d05dcba5fe659a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:16:27 2018 -0500
update newcommands
sphinx_docs/create_newcommands.py
commit e643b14e5b58603ca6fe0d488ba841fd2ec2a6e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:16:10 2018 -0500
some updates on math
sphinx_docs/converting_docs.txt
sphinx_docs/create_newcommands.py
sphinx_docs/mathsymbols.tex
sphinx_docs/source/_static/mathjax_conf.js
sphinx_docs/source/_templates/layout.html
sphinx_docs/source/conf.py
commit 76c3554792e6c1c720ed30e96afa571340ee4f6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 12:41:24 2018 -0500
updated symbols
Docs/castrosymbols.tex
commit 1d78b5f158d68c88aabf8be78b8ea22c07078dc8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 11 21:55:40 2018 -0500
update style
sphinx_docs/source/FlowChart.rst
commit a04909442ea1df4fd6a3d1e98661f24cad855e2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 11 08:39:02 2018 -0500
some fixes to formatting
sphinx_docs/source/Hydrodynamics.rst
commit 89c7352d9717331f4e2bfe75db1aaeddc1054c79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 21:11:09 2018 -0500
some fixes
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/_static/mathjax_conf.js
commit cc8d4bc16922737443ad7c4cbfdb6483752fad4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 20:56:57 2018 -0500
not needed
sphinx_docs/source/castrosymbols.rst
commit 0b4ab89b29ea9e640742ad14da50438b447e0b5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 20:52:44 2018 -0500
fix macro
sphinx_docs/mathsymbols.tex
commit 6caac2252f96ad21dd17961d472ff27eaecb78fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 20:08:34 2018 -0500
this needs lots of updating
sphinx_docs/source/visualization.rst
commit fc02a4a95386cc76e217ccc027a4a43dd1ecaa17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 20:00:06 2018 -0500
some fixes to the conversion
sphinx_docs/source/Particles.rst
sphinx_docs/source/software.rst
commit d5625421800fd35d1c405bee405ca3a86bac2b58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 19:46:08 2018 -0500
these are auto-generated
sphinx_docs/source/classlist.rst
sphinx_docs/source/filelist.rst
sphinx_docs/source/namespacelist.rst
commit d530c89cc2b12a5330c11a49c8d62aaf62c4b577
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 19:45:36 2018 -0500
fix some figures
sphinx_docs/source/LineQueryPlot_0_t_magvel.png
sphinx_docs/source/OffAxisProjection_density.png
sphinx_docs/source/Profile2D_1_Density_magvel_kineng.png
sphinx_docs/source/RT_ppm_type.png
sphinx_docs/source/Slice_z_pressure.png
sphinx_docs/source/Verification.rst
sphinx_docs/source/domain-tile.png
sphinx_docs/source/fluid_motion.png
sphinx_docs/source/grown_center_2.png
sphinx_docs/source/grown_center_3.png
sphinx_docs/source/grown_corner_2.png
sphinx_docs/source/grown_corner_3.png
sphinx_docs/source/isocontours.png
sphinx_docs/source/orig_center.png
sphinx_docs/source/orig_corner.png
sphinx_docs/source/radiating_source.png
sphinx_docs/source/radiating_sphere.png
sphinx_docs/source/rotation.rst
sphinx_docs/source/sedov_cyl.png
sphinx_docs/source/sedov_sph.png
sphinx_docs/source/sod_3d.png
sphinx_docs/source/sod_3d_ppm0.png
sphinx_docs/source/test2_3d.png
sphinx_docs/source/test3_3d.png
sphinx_docs/source/test_suite_day.png
sphinx_docs/source/test_suite_main.png
sphinx_docs/source/tframes.png
sphinx_docs/source/tracer_trajectory.png
sphinx_docs/source/visualization.rst
sphinx_docs/source/volume.png
commit d224133061efddaffc52f7ea6f251d50772bab7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 19:33:30 2018 -0500
add a fix for table with
add in some missing sections:
sphinx_docs/source/CastroUserGuide.rst
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/_static/theme_overrides.css
sphinx_docs/source/index.rst
sphinx_docs/source/rotation.rst
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/software.rst
sphinx_docs/source/visualization.rst
commit 6036609753261c318bb420bf17101d95791067b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 19:10:17 2018 -0500
hook in the doxygen stuff
sphinx_docs/source/index.rst
commit a2f02f77089711137fabd802b3e6c76faf68b27c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 19:06:47 2018 -0500
update headings
sphinx_docs/source/AMR.rst
sphinx_docs/source/CastroInputs.rst
sphinx_docs/source/ConvertCheckpoint.rst
sphinx_docs/source/EOSNetwork.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/MAESTRO_restart.rst
sphinx_docs/source/Particles.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/classlist.rst
sphinx_docs/source/diffusion.rst
sphinx_docs/source/faq.rst
sphinx_docs/source/filelist.rst
sphinx_docs/source/gravity.rst
sphinx_docs/source/index.rst
sphinx_docs/source/inputs.rst
sphinx_docs/source/managingjobs.rst
sphinx_docs/source/namespacelist.rst
sphinx_docs/source/radiation.rst
sphinx_docs/source/rotation.rst
sphinx_docs/source/software.rst
sphinx_docs/source/visualization.rst
commit a6a2abb523538dba013303d5a27dce01806549ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 10 15:12:44 2018 -0500
more work on cleaning up the docs
sphinx_docs/source/CastroGettingStarted.rst
sphinx_docs/source/Introduction.rst
sphinx_docs/source/Preface.rst
sphinx_docs/source/getting_started.rst
sphinx_docs/source/index.rst
commit 84aee3c75c1ec63b1b80d951898afaeb8f523c1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 9 19:43:35 2018 -0500
update ignore
.gitignore
commit 4411db8b2cff72017fbb931a4480e222169c5630
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 9 19:38:08 2018 -0500
fix runtime parameters
sphinx_docs/rp.py
sphinx_docs/source/runtime_parameters.rst
commit 9b26049f13b4bd5aed1bdf87a70121b02605dbf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 9 19:17:45 2018 -0500
fix param file
sphinx_docs/rp.py
commit 4c7facb4b89b677acc488bea88f8b2803ccf6e9c
Merge: df9b25956 77b54c9a2
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Nov 9 16:06:37 2018 -0500
Doxyfile ignores fortran
commit df9b2595628b936b669d673b048bbb7d2167dbd3
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Nov 9 16:04:01 2018 -0500
Doxyfile ignores fortran
sphinx_docs/Doxyfile
sphinx_docs/Makefile
commit 77b54c9a20088a7e563dd0045d22e0633ac1270a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 9 14:06:18 2018 -0500
port over the stuff from the Microphysics build
sphinx_docs/converting_docs.txt
sphinx_docs/create_newcommands.py
sphinx_docs/mathsymbols.tex
sphinx_docs/source/AMR.rst
sphinx_docs/source/CastroDiffusion.rst
sphinx_docs/source/CastroGettingStarted.rst
sphinx_docs/source/CastroGravity.rst
sphinx_docs/source/CastroInputs.rst
sphinx_docs/source/CastroRadiation.rst
sphinx_docs/source/CastroRotation.rst
sphinx_docs/source/CastroSoftware.rst
sphinx_docs/source/CastroUserGuide.rst
sphinx_docs/source/CastroVisualization.rst
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/Introduction.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/_static/mathjax_conf.js
sphinx_docs/source/_temp.rst
sphinx_docs/source/_templates/layout.html
sphinx_docs/source/faq.rst
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/tiling.rst
commit 4abc03632bdce046fe420f04bdd110c8d473efe9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 9 13:50:57 2018 -0500
move
sphinx_docs/Doxyfile
sphinx_docs/Makefile
sphinx_docs/notes.txt
sphinx_docs/pandoc.sh
sphinx_docs/rp.py
sphinx_docs/source/AMR.rst
sphinx_docs/source/CastroDiffusion.rst
sphinx_docs/source/CastroGettingStarted.rst
sphinx_docs/source/CastroGravity.rst
sphinx_docs/source/CastroInputs.rst
sphinx_docs/source/CastroRadiation.rst
sphinx_docs/source/CastroRotation.rst
sphinx_docs/source/CastroSoftware.rst
sphinx_docs/source/CastroUserGuide.rst
sphinx_docs/source/CastroVisualization.rst
sphinx_docs/source/ConvertCheckpoint.rst
sphinx_docs/source/EOSNetwork.rst
sphinx_docs/source/FlowChart.rst
sphinx_docs/source/Hydrodynamics.rst
sphinx_docs/source/Introduction.rst
sphinx_docs/source/MAESTRO_restart.rst
sphinx_docs/source/Particles.rst
sphinx_docs/source/Preface.rst
sphinx_docs/source/Verification.rst
sphinx_docs/source/_temp.rst
sphinx_docs/source/castrosymbols.rst
sphinx_docs/source/conf.py
sphinx_docs/source/faq.rst
sphinx_docs/source/index.rst
sphinx_docs/source/managingjobs.rst
sphinx_docs/source/rad.rst
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/tiling.rst
commit df927bd67ade30775788c0db806ea47aa91c8013
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Nov 9 11:01:48 2018 -0500
Added Doxyfile and update conf.py & docs_new's Makefile so that sphinx will build an API using Doxygen
docs_new/Doxyfile
docs_new/Makefile
docs_new/source/conf.py
commit cadeb5685a4723860ed1952181eb1ec551ca3706
Author: Donald E. Willcox <dwillcox@users.noreply.github.com>
Date: Wed Nov 7 16:26:23 2018 -0800
Put conductivity into the eos type (#431)
* Put conductivity into the eos type consistent with the conductivity update in Microphysics.
* Make eos_state intent(inout) for constant conductivity.
* Make eos_state intent(inout) for constant_conductive_opacity.
CHANGES
Microphysics/EOS/eos_type.F90
Microphysics/conductivity/conductivity.F90
Microphysics/conductivity/constant/constant_conductivity.f90
Microphysics/conductivity/constant_opacity/constant_conductive_opacity.f90
Source/diffusion/Diffusion_nd.f90
Source/driver/Derive_nd.F90
Source/driver/timestep.F90
commit 16cb3a5c5ac2195b916050b0be51d6b1e33bf167
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 6 14:45:39 2018 -0500
bigger atm_delta -- needed to resolve the transition
Exec/science/convective_flame/probin
commit b7fcd24d9cec83190a0c1b2cec2b05e13a0529b2
Merge: fb9945c18 2c71f4c5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 5 14:46:35 2018 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit fb9945c182772bb7224f110bd9227b1db9e15aa9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 5 14:46:23 2018 -0500
add note about flux limiter
Docs/FAQ/faq.tex
commit 2c71f4c5b77b3643f2ba7b5c9d6b9f46d507cb99
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 4 22:20:59 2018 -0500
Enforce CFL constraint rigorously for old-time data
When the timestep check was originally written, we did not enforce violations
of the CFL timestep greater than 1 and less than 1 + 1 / CFL, because we found
that many small violations of the CFL criterion would pop up over a run, and
this caused many retries. But the retry_tolerance parameter was subsequently
added which allows for dealing with this more generally. Now, for safety, we
are re-asserting the full CFL constraint, and the user can override this with
a larger retry_tolerance parameter if they desire.
Also, we are now only applying the CFL constraint on the old-time data, not
the new-time data.
Source/driver/timestep.F90
Source/hydro/Castro_hydro.cpp
commit 214c30d8e415d305a27e9fa48db48bf3cf133ab0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 22:07:10 2018 -0400
Fix typo
Source/reactions/Castro_react.cpp
commit 8efd97c31121549ea95e08171ef2861d410e7456
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 22:00:11 2018 -0400
Make burning prints consistent and use amrex::Print()
Source/reactions/Castro_react.cpp
commit 0109c908f029ac1708748ee620d6ffc130274051
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 16:31:25 2018 -0400
Ensure that the custom knapsack weights are always valid
This fixes #382, which reported the issue that the weights were being
set to the minimum of 1 and the number of RHS calls, which meant that
the weights were usually uniformly 1, so the custom knapsack was not
doing what we wanted. Also, in certain cases this could result in all
of the weights being zero, which caused a numerical issue and segfault
in the knapsack generation routine.
CHANGES
Source/driver/Castro.cpp
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
commit 8d8916701b84cdc584bcf052f437cfb8dcdc6872
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 15:28:25 2018 -0400
Remove obsolete inputs parameters
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 982085e402454d5464d998e5bbb5c425360112f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 15:09:50 2018 -0400
Clean up various verbosity settings
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_hydro.cpp
Source/reactions/Castro_react.cpp
commit d1e9b681c4e090e64ed0d4e2fea669d2aca61258
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 14:53:11 2018 -0400
Change verbosity setting for update from the burn
Source/reactions/Castro_react.cpp
commit 91ef1f9a099621cd5f6c1ba42635834edb3bba14
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 14:36:55 2018 -0400
Add some profiling to the source term construction
Source/gravity/Gravity.cpp
Source/sources/Castro_sources.cpp
commit 73039bd1c686f14642ad909209ff1188db22048a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 14:28:33 2018 -0400
Add some profiling to the hydro
Source/hydro/Castro_hydro.cpp
commit 3ef7c37d767803fa355bff2e4dcc5b670c94d3f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 3 03:05:06 2018 -0400
Handle edge case: restarting but stopping criteria met
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
commit 5b92b7569c5c4b1f42f72e20bd5c88c747a3613b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 1 10:10:40 2018 -0400
update changes
CHANGES
commit 7b479e13389e4803403d235e6c27c8d587a2fa1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 31 22:28:20 2018 -0400
ctu noslab opt (#427)
This further optimizes and simplifies the noslab CTU by creating a single tracing routine regardless of dimension. With this change, each of the tracing routines is specific to an eigensystem.
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Make.package
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_plm.F90
Source/hydro/trace_ppm.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 5c8c5d3ca20700d2ed5c67352cd98781dc3dd437
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 26 16:37:41 2018 -0400
update according to AMReX changes
Source/hydro/Castro_hydro.cpp
commit f3d6e8dc4f4b1dd1f3183614fd1e1b5b0afc78b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 15:44:50 2018 -0400
switch to blended HSE + dimension agnostic
Exec/science/convective_flame/GNUmakefile
Exec/science/convective_flame/Make.package
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/Prob_nd.F90
Exec/science/convective_flame/bc_fill_2d.F90
Exec/science/convective_flame/bc_fill_3d.F90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/convective_flame/probdata.f90
Exec/science/convective_flame/probin
Exec/science/convective_flame/probin_good
Exec/science/convective_flame/problem_tagging_2d.f90
Exec/science/convective_flame/problem_tagging_nd.F90
commit c6d65698cd8cc57a9642fb77ddc9b0996af0d1b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 15:01:13 2018 -0400
remove unused variables
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/probdata.f90
commit 79fcf5ea274946fa9c2595abf2230eca1e53593a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 14:40:49 2018 -0400
remove unused variables
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/job_scripts/aprox13/probin.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/probin.boost.aprox13
Exec/science/flame_wave/old/inputs/probin.boost.base
Exec/science/flame_wave/old/probin
Exec/science/flame_wave/old/probin.boost
Exec/science/flame_wave/old/probin.boost.hires
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost.aprox13
commit 7fbbfb3afd4915a14a5e16bd294e79cc09acc7cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 14:35:50 2018 -0400
hot_ash is no longer used
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/job_scripts/aprox13/probin.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/probin.boost.aprox13
Exec/science/flame_wave/old/inputs/probin.boost.base
Exec/science/flame_wave/old/probin
Exec/science/flame_wave/old/probin.boost
Exec/science/flame_wave/old/probin.boost.hires
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost.aprox13
commit 960451fc42ac59a3c122807ccf0fc391b220d777
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 13:10:52 2018 -0400
fix 1-d bounds errors
Source/problems/bc_ext_fill_nd.F90
commit ba1a70e3381c7725e307f6e25e1260acdcfa6fa7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 20:21:01 2018 -0400
update changes
CHANGES
commit 4747501511624be384216c980f631307bb9fb69d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 20:05:55 2018 -0400
for reasons I don't understand, this fixes a StarGrav problem
Source/hydro/advection_util_nd.F90
commit 0613854b8b60bf0c0bef15b3c91df57c0fe7c660
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 14:15:40 2018 -0400
no slab version of CTU (#408)
Removes slabbed update from CTU that looped over the k index and for each k, did the entire 2D slice corresponding to that index. This approach was used for cache re-use benefits. This rewrite loses some of that benefit but makes the code more maintainable and better ready for a port to GPUs.
Exec/hydro_tests/Sedov/inputs.3d.sph
Source/driver/check_for_nan.f90
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/Make.package
Source/hydro/advection_util_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans.F90
Source/radiation/trace_ppm_rad_nd.F90
commit a61605a1a3b7ef8d023a07833a2a8af2eb58c015
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 20 19:49:06 2018 -0400
output the hydro_tile_size to the job_info
closes #422
Source/driver/Castro_io.cpp
commit 4e706a995168ce73a9378cc277b557f6a17c7885
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 16 13:31:54 2018 -0400
fix HSE boundary
looser burning tolerances
Exec/science/nova/inputs_2d
Exec/science/nova/probin
commit e4fa9f897fae88c53f7a66131694055d5f26c5d5
Merge: fd8c96c51 544eadc90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 15 14:10:15 2018 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit fd8c96c51cafefd6e87aa7af701ecc613cb92122
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 15 14:09:56 2018 -0400
fix compilation
Docs/ManagingJobs/managingjobs.tex
commit 544eadc9010ec8a96ddee6603111041dddb19758
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 15 10:23:33 2018 -0400
add missing eddington factor in transz
Source/hydro/Castro_ctu_3d.F90
commit 35ffce3ec3afd1b54c46999864dfcc38e72432eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 15 09:49:08 2018 -0400
add missing transverse correction for radiation
Source/hydro/Castro_ctu_3d.F90
commit 39da356d93b3da0f364a684d6d11a67660a55a6a
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 13 22:27:33 2018 -0400
Update burn type and DEFINES for sparse jacobian interface in Microphysics.
Exec/Make.Castro
Microphysics/networks/burn_type.F90
commit 690914753b35419bbb4088f41ca322f0a7543ecf
Merge: b95bb0bfa efba4704a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 11 12:56:30 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit b95bb0bfa121986b53bb3e5a4b27eac272453c4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 11 12:56:15 2018 -0400
move docs to workflow webpage
Docs/ManagingJobs/managingjobs.tex
commit efba4704afa91c4e52867eb7b06a580143fd431e
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed Oct 10 07:23:04 2018 -0700
removing extra "use amrex_fort_module, only : rt => amrex_real"
Source/hydro/Castro_ctu_3d.F90
commit ef67cfef3c589593008a84d1d92006bdcac0b62a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 9 12:01:09 2018 -0400
make dx = dy = dz
Exec/radiation_tests/Rad2Tshock/inputs.M5
commit 781816907580d13a8c6f3e5cfd575d3869dee7dd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Oct 6 22:16:43 2018 -0700
fix missing variable
Source/problems/bc_ext_fill_3d.F90
commit fe1bd993e3a094805f7dcfbb885d4e025b8e8617
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 5 20:02:27 2018 -0400
some more attempts
docs_new/notes.txt
docs_new/pandoc.sh
docs_new/source/AMR.rst
docs_new/source/CastroDiffusion.rst
docs_new/source/CastroGettingStarted.rst
docs_new/source/CastroRotation.rst
docs_new/source/CastroSoftware.rst
docs_new/source/CastroUserGuide.rst
docs_new/source/FlowChart.rst
docs_new/source/Hydrodynamics.rst
docs_new/source/Introduction.rst
docs_new/source/Verification.rst
docs_new/source/castrosymbols.rst
commit 154d2d2949e06dbcc6801f83b033ddf7b1f9e679
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 5 19:36:03 2018 -0400
move to symbols to make pandoc easier
Docs/CastroUserGuide.tex
Docs/castrosymbols.tex
commit 42e3bf3957d2b764044e3205c39879d97cf4c656
Merge: 6860c2a40 23ab95b54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 5 11:10:21 2018 -0400
Merge branch 'flame_wave_anyd' into development
commit ddc45739670ce9d5a21af7414cdc79d2b39fff4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 5 09:59:35 2018 -0400
updated conversion -- this gets the symbols correct
docs_new/pandoc.sh
docs_new/pandoc.txt
docs_new/source/AMR.rst
docs_new/source/CastroDiffusion.rst
docs_new/source/CastroGettingStarted.rst
docs_new/source/CastroGravity.rst
docs_new/source/CastroInputs.rst
docs_new/source/CastroRadiation.rst
docs_new/source/CastroRotation.rst
docs_new/source/CastroSoftware.rst
docs_new/source/CastroVisualization.rst
docs_new/source/ConvertCheckpoint.rst
docs_new/source/EOSNetwork.rst
docs_new/source/FlowChart.rst
docs_new/source/Hydrodynamics.rst
docs_new/source/Introduction.rst
docs_new/source/MAESTRO_restart.rst
docs_new/source/Preface.rst
docs_new/source/Verification.rst
docs_new/source/faq.rst
docs_new/source/managingjobs.rst
docs_new/source/rp_intro.rst
docs_new/source/runtime_parameters.rst
commit 23ab95b54c18db3e06b58e220a9eed1c51c75270
Merge: 7d4673f49 57a087ced
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 20:56:06 2018 -0400
Merge branch 'flame_wave_anyd' of github.com:AMReX-Astro/Castro into flame_wave_anyd
commit 6860c2a4006c229efb23818f6e4a1cf84f2560eb
Merge: 8759933b2 faf5bd005
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 20:32:54 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 8759933b2ee1ca5c1b3d0591e28562742a52652a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 20:32:43 2018 -0400
fix interpolation
Exec/science/flame_wave/Prob_3d.f90
commit 57a087ced4c21faa3ebe31423ab24a6891afa92a
Merge: 9393a776f faf5bd005
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 20:12:09 2018 -0400
Merge branch 'development' into flame_wave_anyd
commit 53715c99a1c63fd2a6007c2610f2ee37169b968d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 19:01:05 2018 -0400
first cut at a sphinx doc conversion
the main problem at the moment, is that castrosymbols is not being respected
we need to cat it onto the top of each .tex file via some script magic
docs_new/Makefile
docs_new/pandoc.txt
docs_new/source/AMR.rst
docs_new/source/CastroDiffusion.rst
docs_new/source/CastroGettingStarted.rst
docs_new/source/CastroGravity.rst
docs_new/source/CastroInputs.rst
docs_new/source/CastroRadiation.rst
docs_new/source/CastroRotation.rst
docs_new/source/CastroSoftware.rst
docs_new/source/CastroUserGuide.rst
docs_new/source/CastroVisualization.rst
docs_new/source/ConvertCheckpoint.rst
docs_new/source/EOSNetwork.rst
docs_new/source/FlowChart.rst
docs_new/source/Hydrodynamics.rst
docs_new/source/Introduction.rst
docs_new/source/MAESTRO_restart.rst
docs_new/source/Particles.rst
docs_new/source/Preface.rst
docs_new/source/Verification.rst
docs_new/source/castrosymbols.rst
docs_new/source/conf.py
docs_new/source/faq.rst
docs_new/source/index.rst
docs_new/source/managingjobs.rst
docs_new/source/rad.rst
docs_new/source/rp_intro.rst
docs_new/source/runtime_parameters.rst
commit faf5bd00518a497943ec21ddacb8df1ee16cdb88
Merge: 0f5044a67 a5253c62c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 18:58:26 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 0f5044a677b2a30f0cb970b54822dbe7b1e1aff4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 18:58:09 2018 -0400
some formatting fixes
Docs/CastroUserGuide.tex
Docs/ManagingJobs/managingjobs.tex
commit a5253c62cc594794cf77b6933f97340c3daacae2
Merge: be6b2541a 912ad5bf0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 17:24:23 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit be6b2541a1eddd6ed3c550197e32c2768e63031b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 17:24:08 2018 -0400
initial attempts at a subCh detonation
Exec/science/Detonation/inputs-det-x.subch
Exec/science/Detonation/probin-det-x.subch
commit 912ad5bf084efd6330d9e38f6bedbdcce2ffbda8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 14:45:27 2018 -0400
a notebook that loops over plotfiles showing the profiles
Exec/science/Detonation/analysis/detonation.ipynb
commit 5e21c7ea3e6e414d395c3d92c22e9c63420f5707
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 11:50:24 2018 -0400
use rate tables -- speeds things up by about 10%
Exec/science/flame_wave/probin.boost.aprox13
commit 4d4bdd337abc471d4543133b6f04d7ed66c5073a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Oct 2 12:15:58 2018 -0700
add USE_GPU_PRAGMA=TRUE when USE_CUDA is TRUE
Exec/Make.Castro
commit e1fa4f16e3334c622a6159692e64c79894a10d16
Merge: bdaa10378 57ce78bd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 13:37:33 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit bdaa10378600388e0a49934b948e689a39057a0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 13:36:45 2018 -0400
normalize the abundances on interpolation
Exec/science/nova/Prob_2d.f90
commit 57ce78bd35818c27e3474ec0d3fb2aed18103396
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 2 13:24:24 2018 -0400
Fix GPU reduction in sumproduct
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
commit 7e695cc2312f15eeadff9495c46025a4cec30666
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 1 12:53:39 2018 -0400
update changes
CHANGES
commit 2aa5b36609c31c0b2d02a09030b01369761fc60b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 21:24:58 2018 -0400
small optimization
Source/hydro/trace_ppm_nd.F90
commit 7d4673f49ddb1b4e2234bd66b2d4d6a9c220b215
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 18:34:30 2018 -0400
sync with the 2d version
Exec/science/flame_wave/Prob_nd.F90
commit 9393a776f8274fbd18ee4e30757f7a15acf67ce7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 18:01:41 2018 -0400
fix dimension
Source/problems/bc_ext_fill_nd.F90
commit 518297a6f47498713548c47c194d04ec47a51baf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 15:44:16 2018 -0400
some more BC fixing
Source/problems/bc_fill_nd.F90
commit fb24b01ccbd3cb05e3fa6904fe70c91bbea94828
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 11:57:18 2018 -0400
fix a bounds issue
Source/problems/bc_ext_fill_nd.F90
commit 2fad07e557e51de17f825eda031923c7db158843
Merge: a4d431eba 32f300634
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 11:34:53 2018 -0400
Merge branch 'development' into flame_wave_anyd
commit 32f30063485e7ff0156dfd30e54cfbc145e22efd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 08:18:12 2018 -0700
fix tagging
Exec/science/flame_wave/problem_tagging_3d.f90
commit ef141021edfcd4e60509fde4f45d26a66e0b5792
Merge: da35a08fa db577525a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 09:15:31 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit da35a08fad17a5d60740f756055451fa0b320dc6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 28 09:15:18 2018 -0400
remove allow_negative_energy
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
commit a4d431eba2b1cc43bb1212863c355e1f863d296a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:53:24 2018 -0400
fix the dimensions of bc(). This seems to work now for HSE bcs
Source/problems/bc_ext_fill_nd.F90
commit b13ed002402a8e91538cdd4f36936291bea67bae
Merge: 7de5b1382 db577525a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:39:10 2018 -0400
Merge branch 'development' into flame_wave_anyd
commit db577525a0456f6c38d494b8909d1ec3ef65a7f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:36:15 2018 -0400
remove extra call to filccn
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
commit 7de5b1382fa9074ff2fcc147697f2bdc428572dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:25:53 2018 -0400
fix call
Source/problems/bc_fill_nd.F90
commit 8bbae0ec7beb098b4cc2db005a159a117d7bc224
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:10:44 2018 -0400
not needed
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/problem_tagging_2d.f90
commit c806f3679ef7cf6e7a1ff16e6def91597297c778
Merge: f31f2bfe3 082158d89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:06:54 2018 -0400
Merge branch 'development' into flame_wave_anyd
commit 082158d8995284bfa88ffd9e8799362089f113b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 20:01:04 2018 -0400
remove allow_negative_energy
Exec/hydro_tests/reacting_bubble/problem_derive_nd.f90
commit 2eeafc06ccee56c6b36436096cb8c0a4bcf8adaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 19:23:01 2018 -0400
more optimization
Source/hydro/ppm_nd.F90
commit 19cdc6df0c97b51c30388afa1ab6329ea22a3dd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 19:00:12 2018 -0400
new refinement strategy
Exec/science/flame_wave/inputs_2d.boost.aprox13.hires
Exec/science/flame_wave/probin.boost.aprox13
commit 286d85f0d8b9282053bbbca322dcba73ccc512ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 18:52:48 2018 -0400
a few optimizations
Source/hydro/ppm_nd.F90
commit 642b17821a60888d7029aaa8071fc0682fbcbb6e
Merge: 4e6ea7649 2f5ae2fa7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 15:16:00 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 2f5ae2fa759b900671b35ba4a64119ee0866ed63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 13:12:32 2018 -0600
remove allow_negative_energy (#414)
This removes the allow_negative_energy option
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro_util.F90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
commit 4e6ea76492adc416d9eacba574d7aeee2cab9ea5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 15:00:01 2018 -0400
remove unneeded uses
Source/hydro/advection_util_nd.F90
commit 23ce5cf9730da27788f3776bb8c17434cf39e91d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 06:09:21 2018 -0400
fix NaNs
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
commit 8adb27c90468c560b6fbd336d318d3b1ca4d6f55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 27 06:01:54 2018 -0400
fix NaNs
Exec/hydro_tests/double_bubble/bc_fill_2d.F90
commit b073235dc3cd6f60cf9e2f16208ed6b83fb5a433
Merge: db1d33778 bfc85e2f5
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Wed Sep 26 11:49:32 2018 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit db1d33778b3fa40c16b0f4e5cbf8d8519b486a68
Author: Donald E. Willcox <dewillcox@lbl.gov>
Date: Wed Sep 26 11:49:30 2018 -0700
Updated mailmap.
.mailmap
commit bfc85e2f5ffaa63f015390e67eab77db65a3ba60
Merge: b1f57e972 70f443994
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 26 14:15:19 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit b1f57e9726b10036a1a24281e9bed0c13302102c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 26 14:14:57 2018 -0400
a script to plot multiple variables together
Exec/science/flame_wave/analysis/slice_multi.py
commit 70f443994e6669460a55386c9e126842004b296b
Merge: 454200b12 d80131e38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 25 15:36:50 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 454200b127c161623dd5b2d9dd56a81b0251743e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 25 15:35:36 2018 -0400
refine the refinement strategy
previously, we were always refining the atmosphere all the way to the
bottom (including the Nickel layer). Now we instead have 2 separate
critera that allow us to focus refinement on the burning layer
(the old method tried to do this, but had a bug, considering rhoX,
instead of X)
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/Prob_3d.f90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost.aprox13
Exec/science/flame_wave/problem_tagging_2d.f90
Exec/science/flame_wave/problem_tagging_3d.f90
commit d80131e383aa1de815a04c90662ee2d8f012ed1c
Merge: f3caf05b6 dccd3a0b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 25 11:53:48 2018 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit f3caf05b610052dc2f9131099326b30a583a1cd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 25 11:03:48 2018 -0700
get around Intel catastropic errors
Source/driver/extern_probin.template
Source/hydro/Castro_ctu_2d.F90
commit dccd3a0b9a42e360195c60475d0ce11563a98b55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 25 13:08:05 2018 -0400
intel 17, 18, and 19 can't compile Castro
Docs/ManagingJobs/managingjobs.tex
commit 31121a8b7556cc81ff9e83d113a21d4222dd8859
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 17:21:51 2018 -0400
add some changes
CHANGES
commit 1cdb11f0350abb7b293c0465a9a76330ab6ee4b2
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Mon Sep 24 17:08:45 2018 -0400
Coloring profiles.py (#411)
Fixes the labels in the profiles.py plot to correctly match the color of the lines
Exec/science/flame/analysis/profiles.py
commit e34f9984f911037f417e75c9e9f43f7f6434acf2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 15:49:22 2018 -0400
add 3d inputs
Exec/science/flame_wave/inputs_3d.testsuite
commit f31f2bfe325fe75be55982129cc6549fa478c11f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 15:48:59 2018 -0400
remove dimensional versions from merge
Exec/science/flame_wave/Prob_3d.f90
Exec/science/flame_wave/problem_tagging_3d.f90
commit d9cbab9ab966788c24661a7e320575b794e38ec5
Merge: 71806ce79 b910605bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 15:34:18 2018 -0400
Merge branch 'development' into flame_wave_anyd
commit b910605bfd636989cd7f39715aa18bdd2ea0e680
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 15:32:58 2018 -0400
add needed loop over components :)
Exec/hydro_tests/reacting_bubble/bc_fill_3d.F90
commit 4ef852a39aef283a504ac17a45b7f1ce03d82acf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 15:25:25 2018 -0400
sync and make the extrapolation for external BCs more robust
Source/problems/bc_fill_2d.F90
Source/problems/bc_fill_3d.F90
commit 880577f24d3f3f1f4117ac4e14f328c7d778be10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 14:30:31 2018 -0400
add loop
Source/problems/bc_fill_3d.F90
commit 6dce975d94288d8cc60d00f8b060ef149a134172
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 14:27:37 2018 -0400
handle external BCs vis FOEXTRAP
Source/problems/bc_fill_3d.F90
commit ead1ae1cecd839676cbf96540886f507806f73eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 14:06:13 2018 -0400
working 3d version
Exec/science/flame_wave/Prob_3d.f90
commit f4ae104319bad89392ed57eff24a85d6a9a582b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 13:49:42 2018 -0400
add 3d version
Exec/science/flame_wave/problem_tagging_3d.f90
commit 71806ce796f287b4645595735865727ef7eff086
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 13:42:05 2018 -0400
remove dimension-specific routine
Exec/science/flame_wave/problem_tagging_2d.f90
commit 5779cdeef78c83d3dce36a15c82178b7c0b3e046
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 13:41:37 2018 -0400
fix index
Source/problems/bc_ext_fill_nd.F90
commit 54cbab886834682513ee53c0f541211fcc39a63c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 12:55:02 2018 -0400
add a dimension-agnostic version of the external BCs
eventually we will cut out the 2- and 3-d implementations in
favor of this
Source/problems/Make.package
Source/problems/bc_ext_fill_nd.F90
Source/problems/bc_fill_nd.F90
commit dc734e0a381fb95b7acce3e0124fba86e55ff5ea
Merge: 8b33dc6d3 400863c90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 11:38:30 2018 -0400
Merge branch 'development' into flame_wave_anyd
commit 400863c90acd9a55cb0ea79657b075471c8eeb75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 24 09:36:27 2018 -0400
compilation fixes
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_3d.F90
commit 44f9faca8acc39902aa10bff80db781db4d564ff
Author: blaireness <blaireness@users.noreply.github.com>
Date: Sun Sep 23 21:41:14 2018 -0400
more flame automation scripts for exploring toy flames
* Created exploration directory with files necessary to create a test suite
* Added comments to flamefront code
* setup_explore.py now copies model files into folders
* setup_explore.py now copies executable into each folder
* Updated readme
* Added code to automatically run tests
* Added exploration directory in 1d toy flame directory
* Added script to run tests in parallel
* Updated flamefront.py
Exec/hydro_tests/toy_flame/exploration/flamefront.py
Exec/hydro_tests/toy_flame/exploration/inputs.1d.testsuite.temp
Exec/hydro_tests/toy_flame/exploration/probin_temp
Exec/hydro_tests/toy_flame/exploration/process.py
Exec/hydro_tests/toy_flame/exploration/setup_explore.py
Exec/science/convective_flame/exploration/README
Exec/science/convective_flame/exploration/flamefront.py
Exec/science/convective_flame/exploration/runtests.py
Exec/science/convective_flame/exploration/setup_explore.py
commit abb2efbdfd2516439d11910cbb72f1d27fed3c55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 21:11:00 2018 -0400
sync with 2d
Source/problems/bc_ext_fill_3d.F90
commit 87ac63c0699e128220a7ed9f43ebeea30ebfe0dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 21:10:33 2018 -0400
some protection for external BCs
Source/problems/bc_fill_nd.F90
commit e96cf6a25f244cddb296f0e8f4e72ff9b7a953a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 18:40:21 2018 -0400
some syncing of the extern stuff with 2d
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit 8bc230b0aae3884e2b709586207901c0318285ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 18:36:21 2018 -0400
fix error message
Source/problems/bc_ext_fill_2d.F90
commit e22e74d2ca959375be35a4d9df8675f6c20186d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 18:33:22 2018 -0400
fix error message
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit 8b33dc6d38b81df3dd97d5943eb5ff20b4b85c9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 18:33:22 2018 -0400
fix error message
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit fe2f2b9228d7b3d2e04ddc0492bbca7fd98bd046
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 16:51:30 2018 -0400
dimension agnostic version -- this crashes currently
Exec/science/flame_wave/GNUmakefile
Exec/science/flame_wave/Prob_nd.F90
Exec/science/flame_wave/problem_tagging_nd.F90
commit dd9f99aa92ea302eaf1d8de0bc073604b07411e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 16:48:25 2018 -0400
handle the external boundaries
Source/problems/bc_fill_3d.F90
commit b088bf426c3586369c5ad723ccc60eb69f05771f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 22 10:54:01 2018 -0400
Tagging_nd.f90 -> F90
Source/driver/Make.package
Source/driver/Tagging_nd.F90
commit 85bee058aecdc7636ea2d88bf1b2d4ea576a7d9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 21 19:30:41 2018 -0400
fix compilation
Source/hydro/advection_util_nd.F90
commit ec2b509c85d78f1a03b320ffe06bdbd22f3656bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 21 19:01:25 2018 -0400
fix the divu calls
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
commit aa96b9c0d58270561d4eec11f6f5c14126f5477b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 17:02:51 2018 -0400
Unify apply_av
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit c9d00f2260bf523543720993145b1657b31e06ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 16:52:28 2018 -0400
Unify scale_flux
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit 12adc0870631c5ef82a568d652c49ea4f4518db7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 21 16:21:24 2018 -0400
fix compilation
Source/hydro/advection_util_nd.F90
commit 92418d6818ba58ad31d18ba19e2ecd70c67c7a35
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 12:54:27 2018 -0400
Fix hydrostatic_adjust derives
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive_F.H
Exec/gravity_tests/hydrostatic_adjust/Problem_Derives.H
commit bd01b66d9d45338449704d109538c97b408cef42
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 12:27:44 2018 -0400
Unify divu
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit d6e4c5b7aa7a4c122c2d69f2803f736d2f2fcc01
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 12:07:20 2018 -0400
Clean up dxinv
Source/hydro/advection_util_nd.F90
commit 62157dddd66425b2df5db8091663fd5b9b1199ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 21 11:31:09 2018 -0400
also write cuda attributes
Source/driver/meth_params.F90
Source/driver/parse_castro_params.py
commit b20fa3422dc112fbe5696f6b0987be3064373e79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 21 11:04:18 2018 -0400
wrap acc creates
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
commit 7b0ed68592068dcb07457bcd44adce78932b642d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 10:37:14 2018 -0400
Avoid array reshaping
Source/hydro/advection_util_nd.F90
commit 0233a4e7dd81d16d88326cb6e380e022dcdb754b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 10:31:21 2018 -0400
Don't acc update parameters
Source/driver/Castro_nd.F90
commit 7c8a5e162056f50ed71586d062c38fb6161a7836
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 10:21:25 2018 -0400
Remove acc routine
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_override.F90
Microphysics/EOS/eos_type.F90
Microphysics/networks/burn_type.F90
Microphysics/networks/burner.F90
Microphysics/networks/general_null/actual_rhs.f90
commit 9afd12c37d4f5139ca609939843e62930a25a0fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 20 22:31:20 2018 -0400
fix bounds issue
Source/rotation/rotation_sources_nd.F90
commit fdddcc2ef038d4040c8876db9bcee2277461768d
Merge: 47736946e ef3723f3b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 17:46:10 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 47736946ee5e97fe1337c4fac2ffaed42dff21e9
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 17:45:22 2018 -0400
Be more flexible in problem setup, support initializing boxes
with a different number of zones than are present in the model file.
Exec/unit_tests/reactions_driver_test/Prob_nd.F90
commit ef3723f3b63dbb6c8fd780e31433f316cccbab2c
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Sep 20 16:50:40 2018 -0400
Rotation gpu (#407)
Offload the rotation onto GPUs
Source/driver/Castro_F.H
Source/driver/Castro_util.F90
Source/driver/Make.package
Source/driver/main.cpp
Source/driver/sum_integrated_quantities.cpp
Source/hydro/hybrid_advection_nd.F90
Source/rotation/Castro_rotation.cpp
Source/rotation/Make.package
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.F90
Source/rotation/rotation_sources_nd.F90
commit d67ad01bdd13967d0aa13ac0e86c1e3dd1385479
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 16:06:04 2018 -0400
Unify ctoprim
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit b20e4e60c5ec3d35600ec841c0a0fc85614d1d7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 15:55:48 2018 -0400
Put compute_cfl on the device
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit 99751fc5ca4862f1600cc5b4eeb5ad9d042178ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 15:38:32 2018 -0400
Clean up enforce_min_density
Source/driver/Castro.cpp
Source/hydro/advection_util_nd.F90
commit 794977594db0496a2e0527ef43861c9185e926cd
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 15:36:46 2018 -0400
Revert "Mark ca_enforce_minimum_density as !$gpu"
This reverts commit d777d0a76aeacf8f7a1a1774439a7d002470940b.
Source/hydro/advection_util_nd.F90
commit d777d0a76aeacf8f7a1a1774439a7d002470940b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 15:30:58 2018 -0400
Mark ca_enforce_minimum_density as !$gpu
Source/hydro/advection_util_nd.F90
commit 6982f6c496e388073827ecf9a0b5180ad060e0a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 20 15:27:23 2018 -0400
BL_SPACEDIM -> AMREX_SPACEDIM
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
commit baa64adfa4227dfcda41704a9e7dd70574840628
Merge: 676d998c4 a2e5a3093
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 14:40:44 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 676d998c45dde89f9323fd7716b388cc75dd419f
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 14:40:41 2018 -0400
Uncomment some code from testing.
Source/reactions/React_nd.F90
commit a2e5a30932872af5a25215b5f28063db6a399506
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 20 12:36:57 2018 -0600
merge consup to a non-dimensional routine (#399)
This makes a dimensionless version of consup
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Make.package
commit 56924df2c47331f8dee1766757bf66439011e87c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 14:34:02 2018 -0400
Unify enforce_minimum_density
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/hydro/advection_util_nd.F90
commit 6ec8a75bf6276ed7efc8343e72345f6a2ba64af1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 14:10:50 2018 -0400
Get CPU code compiling again
Source/hydro/advection_util_nd.F90
Source/hydro/ppm_nd.F90
commit 818ae5fa030dff23bac532adbe16376bdf2d4bf7
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 14:02:22 2018 -0400
Add readme to reactions_driver_test
Exec/unit_tests/reactions_driver_test/README.md
commit 32f327b5aeb796e8706b6c401d17ae32cbd109a2
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 13:55:19 2018 -0400
Fix logic for burn success.
Source/reactions/Castro_react.cpp
commit 22a4f807ef36d874f8b101c85df6646b6a4718c8
Merge: 588348fcd 9118ca3d6
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 13:52:22 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 588348fcd4e3f9e42d21001387aaa1549e799bbe
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 13:50:53 2018 -0400
Remove debugging prints
Exec/unit_tests/reactions_driver_test/Prob_nd.F90
commit 9118ca3d6cf06225b81a3696f8e25b84be827cb8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 13:36:30 2018 -0400
Unify CUDA/non-CUDA normalize_species_fluxes
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
commit feda430e28f5036cb587483733f58fd7b3dab4a2
Merge: 6f3ebcfba 8f5c9fec2
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 13:33:19 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 6f3ebcfbac87aceef843f34f41fadd3477f60423
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 13:33:17 2018 -0400
Add a reactions unit test that uses the Castro main driver.
Exec/unit_tests/reactions_driver_test/GNUmakefile
Exec/unit_tests/reactions_driver_test/Make.package
Exec/unit_tests/reactions_driver_test/Prob_nd.F90
Exec/unit_tests/reactions_driver_test/inputs.ignition.16
Exec/unit_tests/reactions_driver_test/make_react_model.py
Exec/unit_tests/reactions_driver_test/model.ignition_simple.16
Exec/unit_tests/reactions_driver_test/probdata.f90
Exec/unit_tests/reactions_driver_test/probin.ignition.16
Exec/unit_tests/reactions_driver_test/xin.ignition.16
commit 602c660bb4b752a3fbaed84b943b60fb7f62798c
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 13:29:08 2018 -0400
Update new react state line in the header.
Source/driver/Castro_F.H
commit 8f5c9fec272fe9bb3258bd95d2d00e28ad93db79
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 11:15:23 2018 -0400
Merge CUDA hydro routines into existing modules
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/Make.package
Source/hydro/advection_util_nd.F90
Source/hydro/cuda_Castro_mol_nd.F90
Source/hydro/cuda_advection_util_nd.F90
Source/hydro/cuda_flatten_nd.F90
Source/hydro/cuda_ppm_nd.F90
Source/hydro/cuda_riemann_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
commit aad086215575ca8e29072627984cbaab8172e174
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 09:54:53 2018 -0400
Define area with three dimensions always
Source/driver/Castro.H
Source/driver/Castro.cpp
commit 576a1beb4bc01e36d8730ffcf5d110744e4c483d
Merge: 7e7b89299 10ac9e386
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:46:55 2018 -0400
Merged remote branch development.
commit 7e7b892998ade50fe053e9985979e22b1d0d61a9
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:45:03 2018 -0400
Revert "add amrinfo.F90 to the build."
This reverts commit 7ce1e71ea0d44cb1c1f077f9c8a87eb747bc8404.
Source/driver/Make.package
commit 606d65b80bde0e4f62420177bd755df7a7512753
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:44:51 2018 -0400
Revert "make amr_level a CUDA managed variable"
This reverts commit 376d5d7449324c3294c15d5ab53006e19e5b65c8.
Source/driver/Castro_nd.F90
Source/driver/amrinfo.f90
commit 9d18cf6d19077dd43163a6c0dd1ded437773eb8e
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:37:24 2018 -0400
Get ca_sumproduct marked up for CUDA.
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
commit 4fee9f103a92b260425ebc7503ca6674dc094ad7
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:36:17 2018 -0400
Use success/failure flag that reduces properly on GPU.
Source/driver/prob_params.F90
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
commit 7ce1e71ea0d44cb1c1f077f9c8a87eb747bc8404
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:30:51 2018 -0400
add amrinfo.F90 to the build.
Source/driver/Make.package
commit 376d5d7449324c3294c15d5ab53006e19e5b65c8
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 20 09:30:16 2018 -0400
make amr_level a CUDA managed variable
Source/driver/Castro_nd.F90
Source/driver/amrinfo.F90
commit 2f7a6b4f72b94e23db91c1772eeb4bc369907e32
Author: Donald E. Willcox <dwillcox@groot.astro.sunysb.edu>
Date: Thu Sep 20 09:25:47 2018 -0400
Update Castro burner for CUDA reactions.
Microphysics/networks/burner.F90
commit 10ac9e386d379325ca437627e1c8bcd0aa2a9ae8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 09:22:36 2018 -0400
Fix lo boundary condition for Sedov
Exec/hydro_tests/Sedov/inputs.1d.cyl
commit c72c09a5838b4f011239c44201a3b983b50e368f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 20 09:12:56 2018 -0400
Fix another ghost cell issue
Source/hydro/cuda_advection_util_nd.F90
commit 0de1494488f00292bfefd68cdefcf61154405393
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 19 20:32:41 2018 -0400
generalize to arbitary number of species
closes #401
Exec/hydro_tests/reacting_bubble/Prob_3d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/bc_fill_3d.F90
commit 767324ba856dd2ff377149ac9dd043c23ea7c34b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 19:03:28 2018 -0400
Do some safeguarding for CUDA hydro for 1D/2D
Source/hydro/cuda_advection_util_nd.F90
commit 299664efe9c51563826cda2ed939da6249870e52
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 18:12:45 2018 -0400
Make CUDA hydro friendly to <3D
Source/hydro/Castro_hydro.cpp
commit 9e70be03513229ebec7bd6a70ea3fa990199d577
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 14:08:20 2018 -0400
Initialize velocities inside the initdata loop
Exec/science/flame_wave/Prob_2d.f90
commit 25249b1d63c2e0497e00897c3797695782b25046
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 12:56:54 2018 -0400
Use amrex_error, not stop
Source/driver/extern_probin.template
commit 4a91a4adca49b614162cc0e02274fb7492316cf2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 12:41:40 2018 -0400
Remove unused variable
Source/driver/Castro.cpp
commit d99b7694a77ba140f814c045d05ef5475c5aefa2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 12:28:46 2018 -0400
Restore bc_ext_fill when CUDA is on
Source/problems/Make.package
commit 864e1524050c9bf2a205038a127161d3afc0682e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 12:12:17 2018 -0400
Don't ifdef out derenuctimescale
Source/driver/Derive_nd.F90
commit 4d89b24946783bbaa86ebc78a46b548a5278f88d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 11:55:17 2018 -0400
Move amrinfo, etc. to the GPU
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/amrinfo.F90
Source/driver/amrinfo.f90
Source/driver/prob_params.F90
commit 53d44ab689289cd7808dc9b1849759da88a084e3
Merge: 9c81aa2c2 cc5501df1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 19 10:59:39 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 9c81aa2c2a88a70ee7dee15006096a9947131329
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 19 10:59:31 2018 -0400
fix an allocate
Exec/science/flame_wave/Prob_2d.f90
commit cc5501df179736a0d9587e5872c8addc32fc5ff3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 10:53:15 2018 -0400
Don't add rho*phi if not using PoissonGrav
Source/driver/sum_integrated_quantities.cpp
commit a5469076fcb494a35477fb8be85d32be05875a01
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 19 10:41:02 2018 -0400
Move derives to the GPU
Source/driver/Castro_setup.cpp
Source/driver/Derive.H
Source/driver/Derive.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
Source/driver/Make.package
Source/driver/math.F90
Source/problems/Make.package
Source/problems/Problem_Derive.H
commit 6ef1eec75195221d33346fbfd9c62fbd2b98c644
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 16:06:42 2018 -0400
style
Exec/hydro_tests/reacting_bubble/bc_fill_3d.F90
commit 850346149527ccc180d3bff26f9f8ef4697e1562
Merge: 2bf7b2ab0 bede5ce4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 15:58:07 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 2bf7b2ab0b9c1af854acdbfa7d58f04a7c51761a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 15:57:52 2018 -0400
some BC protection
Exec/hydro_tests/reacting_bubble/bc_fill_3d.F90
Exec/hydro_tests/reacting_bubble/inputs_3d_test
commit bede5ce4ec0f06737d92c2d4b45efec3fead3122
Merge: 1de25097c 363affd0e
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 18 19:51:07 2018 +0000
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 1de25097c9682ec420e2f02a9b00a2ac2baa8f85
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 18 19:51:00 2018 +0000
Update interfaces for CUDA StarKiller.
Microphysics/EOS/eos_type.F90
Microphysics/networks/burn_type.F90
commit 363affd0e956cf4ae95d7055e183efabd898dfe4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 15:34:53 2018 -0400
some tweaks -- this does not seem to work yet
Exec/hydro_tests/reacting_bubble/bc_fill_3d.F90
commit c7244eae8c81704f3a85ac21c861014f6a3595f6
Merge: ad1e8f256 566b6df9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 15:19:10 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ad1e8f256a7f8a58656b721c2d1afaeb5942d492
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 15:19:01 2018 -0400
more work on 3-d
Exec/hydro_tests/reacting_bubble/Prob_3d.f90
commit f809889d31b97f5e315b1fa3e8b34502e4cdf631
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 15:18:17 2018 -0400
fix the fix to the function
Source/sources/sponge_nd.F90
commit 566b6df9fc3bc37a20073fce0c749f1cebf9f67e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 18 12:05:31 2018 -0700
Remove unused variables
Source/driver/Castro.cpp
commit 2687fb940b9843e84a121e50a7e54fb69ad23e3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 18 14:19:47 2018 -0400
fix compilation error
Source/sources/sponge_nd.F90
commit e83d0462626b131f8e8117d0eea30941fcd27a89
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 18 12:51:11 2018 -0400
Have an explicit result for update_factor
Source/sources/sponge_nd.F90
commit 7b94ab2864a3d8e63bf140d3d06ead706e0a76c0
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Tue Sep 18 09:25:24 2018 -0700
change due to StateData change in amrex (#394)
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
commit 8f1f443db4b6d728a204b905d0f48898c4b4ca85
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 18 11:25:28 2018 -0400
Need to pass domlo/domhi to GPU correctly
Source/hydro/Castro_hydro.cpp
commit e6507239bd891940f6fa6cc6c412ed206e54180f
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Sep 18 10:49:20 2018 -0400
Offload the sponge onto GPUs (#396)
The sponge can now execute on the GPU
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/sources/Castro_sponge.cpp
Source/sources/sponge_nd.F90
commit fa43333d125f09cf16e0d3be1c89a2ecc6da34de
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon Sep 17 17:02:07 2018 -0400
check that running with gpu is with do_ctu=0
Source/driver/Castro.cpp
commit 444b64755dc6e088d10207d11925c56f5e49a5f6
Merge: 4a6ed5834 b6f1f8189
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 12 16:18:16 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 4a6ed58342ae263868abd512c554b2951ab189d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 12 16:18:06 2018 -0400
add an rprox flame
Exec/science/flame/inputs.1d.rprox
Exec/science/flame/probin.rprox
commit b6f1f81890e354a411796998389e4eb5bf84b7c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 12 12:35:59 2018 -0400
AMREX prefix on ifdefs
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Microphysics/networks/general_null/network.template
Microphysics/networks/network.F90
Util/model_parser/model_parser.F90
commit f464a30a84cc6e158194c8f21b866fd2a8a67532
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 12 11:10:39 2018 -0400
fix ash
Exec/science/flame/Prob_1d.f90
commit 13d38943beb4071993e3ae051f05de12ae6b27e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 12 10:53:56 2018 -0400
generalize to allow for different fuel mixtures
Exec/science/flame/Prob_1d.f90
Exec/science/flame/probdata.f90
commit 2651e0a7cc1fad8a28cda34f41bd2d1a8a83a3dc
Merge: 58cce468f 6506bde21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 11 13:35:09 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 58cce468f29527644f5a65710367c0fb05353cbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 11 13:34:56 2018 -0400
better gravity
Exec/science/nova/inputs_2d
commit 6506bde2175295dfb7ab9a576109f5f11a602b9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 7 21:00:06 2018 -0400
use the new nova network
Exec/science/nova/GNUmakefile
commit bc6196768ffa996ca63c47e07cde620dc0449e0d
Merge: 2b8d82363 3970af0da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 4 13:40:41 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 2b8d82363ec865587b150b3468eca9edf0edcabd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 4 13:40:33 2018 -0400
start of a nova problem
Exec/science/nova/GNUmakefile
Exec/science/nova/Make.package
Exec/science/nova/Prob_2d.f90
Exec/science/nova/glasner_T5_Gconst_Snone.hse
Exec/science/nova/inputs_2d
Exec/science/nova/probdata.f90
Exec/science/nova/probin
commit 3970af0da3a3d5e6dc2859cc0e603f8c55c82d9c
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Tue Sep 4 12:41:05 2018 -0400
Added Abar derived field to plot generator script (#393)
Exec/science/flame_wave/analysis/plot_generator.py
commit 96f45b5b0ffe1be4a660bbe9ff38ce5216760ff4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 3 12:36:58 2018 -0400
update changes
CHANGES
commit d9a35a82ba0ae0c8a8e4742a432126c7a0133568
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 2 23:33:20 2018 -0400
Use the new NUMADV interface
Exec/hydro_tests/KH/GNUmakefile
commit a2737ef095235d8b08943acfa673f5ad6c6814ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 26 19:53:41 2018 -0400
Remove empty file
Exec/science/wdmerger/Castro_prob_err_list.H
commit 26607af70533324131fd49d8996f11b6dc3b0e51
Merge: ac6010143 9786ea273
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 26 17:18:58 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ac6010143c8b1d65e51d8c8257779beb14bb7602
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 26 17:18:31 2018 -0400
for the SDC case (this is the "old" SDC), the analytic Jacobian is wrong,
so switch to the numerical one
Exec/science/Detonation/inputs-det-x.SDC
Exec/science/Detonation/probin-det-x.SDC
commit 9786ea273551ea6e41ac28010351e76588ec1a14
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 26 08:44:14 2018 -0700
Add hooks to return the maximum tagging levels
Source/driver/Tagging_nd.f90
commit e147892d540fddfe2a8e8000c1c099bc45461192
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 26 08:09:22 2018 -0700
max_dxnuc_lev to -1 by default
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 7ada7798ae86ac9a2a30aa6ce18e71028b642488
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 26 08:00:01 2018 -0700
hires version
Exec/science/flame_wave/inputs_2d.boost.aprox13.hires
commit 4788b503eabb83da7c9c8c4caa8c67ad9aa3fbb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 26 10:59:22 2018 -0400
move the triple-alpha inputs to old
make the test suite use aprox13
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/old/inputs_2d.boost.hires
Exec/science/flame_wave/old/inputs_2d.boost.wide
Exec/science/flame_wave/old/probin
Exec/science/flame_wave/old/probin.boost
Exec/science/flame_wave/old/probin.boost.hires
commit 54def86b7dbac6bb6120e3b22de6cf3f7c400008
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 26 07:45:15 2018 -0700
max_denerr_lev to -1 for consistency
Source/driver/Castro_nd.F90
commit 086f71a8aabb70bc6ab659e04b9d4bbffc4580e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 26 07:37:41 2018 -0700
Sync up with StarLord: only tag on dengrad_rel
Exec/hydro_tests/Sedov/inputs.starlord.gpu_test
Exec/hydro_tests/Sedov/probin.starlord
commit ff949f0b406289e8499cafe9bac20e45fcc3e371
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 25 15:18:17 2018 -0700
Move some reals to AMREX_REAL_ANYD
Source/driver/sum_utils.cpp
Source/hydro/Castro_hydro.cpp
Source/sources/Castro_thermo.cpp
commit 417cbe40dec9dca1d8186a49ee2e7c28ed861ee0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 25 14:24:03 2018 -0700
Switch to eint-based Sedov initialization to avoid EOS calls
Exec/hydro_tests/Sedov/Prob_nd.F90
Exec/hydro_tests/Sedov/probdata.f90
commit 41ab63a2024ea32a46aaa398730728887c29dc37
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 25 14:13:39 2018 -0700
Add clean_state call after initialization
Source/driver/Castro.cpp
commit dd6cb0f287c3fedf197a62fd50a0aefe7955ce23
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 25 14:04:38 2018 -0700
Take initial species check off the GPU
Source/driver/Castro.cpp
Source/driver/Castro_util.F90
commit a78047a86f027e17a25369ead128a4c6d797d718
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 23 11:40:54 2018 -0400
make aprox13 the default
Exec/science/flame_wave/GNUmakefile
commit ece0e73e681db8f1899ab790990cd630bb67dea5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 19 17:59:42 2018 -0400
Use the correct volume weightings for Sedov
Exec/hydro_tests/Sedov/Prob_nd.F90
commit 58572ce592c52a511e7a76d310bec76b9671ae4b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 19 13:29:10 2018 -0400
Generate managed by default (for realsies this time)
Exec/Make.Castro
commit baed2b4dc5ac985343820d83efbd4774b20bb4a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 19 10:51:41 2018 -0400
wrap --managed in USE_CUDA
Exec/Make.Castro
commit dad081d1150e833bad14d62b7e50f90617df18d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 23:46:48 2018 -0400
Clean up the inputs
Exec/hydro_tests/Sedov/inputs.starlord
commit b5ac2a953e2394b09543c4a2cd1578c71fda482d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 23:16:33 2018 -0400
ZFILL -> AMREX_REAL_ANYD
Source/driver/Castro.cpp
commit 5c7aedd69349d68c9a77515604d2029d16874fe0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 23:12:07 2018 -0400
Remove BC operations from the device
Source/driver/filcc_nd.F90
Source/driver/generic_fill.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_1d.F90
Source/problems/bc_fill_2d.F90
Source/problems/bc_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit b304548c50cd48bb1b4ae608b1b3f0793d7b7002
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 22:39:44 2018 -0400
Remove unused file
Source/driver/Make.package
Source/driver/castro_c_interfaces_nd.F90
commit 6e6d0752cff2dd1015c2e2b0f002b5fbf5274ee9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 18:51:22 2018 -0400
Move Sedov to dimension agnostic setup
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_nd.F90
commit 7a9027eb0abf65dcdcfbe24337d1bdd903f097fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 18:21:22 2018 -0400
Sync up 1D and 2D with 3D
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
commit a8a302211bcd0dbecd7b83774ab22ae14b45cb3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 18:16:49 2018 -0400
Fill in initial Sedov temperature in 3D
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
commit 17648d89b2a4b564611cb4da0d5292d78ce29af1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 18:16:04 2018 -0400
Always add managed flag to extern
Exec/Make.Castro
commit 1a89978e33a4753d650b16b48f7f18da07ffd6ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 17:00:23 2018 -0400
Use a dt reduction that is GPU-aware
Source/driver/timestep.F90
commit a614a207e44d499fae9b249a17236da8e86f9bb3
Merge: 7756a2be6 6dcddcec1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 16:23:20 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 6dcddcec1f5d92ffb2af28231fe689646106fd86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 18 15:44:38 2018 -0400
use the names of the state component indices when setting up the BCs (#386)
this makes sure we are not dependent on the ordering.
Closes #379
Source/driver/Castro_setup.cpp
commit 7756a2be66558588e5b7c40b7cb3d8236f7bd46a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 05:38:39 2018 -0400
3D -> ANYD
Source/driver/sum_utils.cpp
commit 3e1f27bd6655d49e0d607a49f6d15f3e31525ed3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 05:37:59 2018 -0400
amrex_arlim_arg -> amrex_int_anyd
Source/driver/Castro.cpp
Source/driver/sum_utils.cpp
Source/hydro/Castro_hydro.cpp
Source/sources/Castro_thermo.cpp
commit 2973e4a6556d6dc95dea6207f7c1b05b581bace0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 18 05:17:48 2018 -0400
3D -> ANYD
Exec/hydro_tests/toy_flame/Prob.cpp
Exec/science/Detonation/Prob.cpp
Exec/science/flame/Prob.cpp
Exec/science/wdmerger/Prob.cpp
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/sum_utils.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/radiation/MGFLD.cpp
Source/reactions/Castro_react.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Castro_thermo.cpp
commit b53c2464fd88cd7da3e3d8cc90e1e12f12681e4f
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Tue Aug 14 12:11:58 2018 -0400
Removed extraneous redirection operator from test script (#385)
The convergence.sh script for the acoustic pulse test problem would previously crash due to an extra '>'
Exec/hydro_tests/acoustic_pulse/convergence.sh
commit d3c890e01b634d604a13c21bdb4e3866a1897882
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 13 15:58:43 2018 -0400
Source tracing (#381)
* mask out source tracing -- if the sources are zero, we don't trace
CHANGES
Exec/hydro_tests/Sedov/Prob_1d.f90
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
commit 401db309f9450f34a312652099ab275c9378baf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 13 13:08:35 2018 -0400
remove tag
CHANGES
commit 9bbb1cb457c5a4b9f800e64a500eeefd38ff07bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 10:07:40 2018 -0700
Update T for consistency when resetting small e (#384)
* Update T for consistency when resetting small e
Source/driver/Castro_util.F90
commit a1df385c64984bb20dc4b186902fdff0b17df1c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 13 12:33:34 2018 -0400
redirect output
Exec/hydro_tests/acoustic_pulse/convergence.sh
commit cf937e6e4bc49954485b8b584eead49551ca5a5a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 12 20:31:51 2018 -0400
Update CHANGES
CHANGES
commit 2c71deb27e9dc07b2ed2e2b7c7e8513ac4dc6059
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 12 20:26:15 2018 -0400
remove dual_energy_update_E_from_e -- it is never a good idea (#368)
override eos_input_is_constant from StarKiller to be true by default
Docs/runtime_parameters/runtime_parameters.tex
Microphysics/EOS/_parameters
Source/driver/Castro_util.F90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit f655bebbec0aab17b226d0b030ec54f6e9f65c63
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 12 06:21:00 2018 -0400
Update to the new burn retry strategy
Exec/science/wdmerger/probin
commit ec520a6061e3937af60766c060da0b6716f4fbdb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 12 03:42:07 2018 -0400
Fix a size comparison
Exec/science/wdmerger/wdmerger_util.f90
commit f4fa44d2f1d2bb243f93cf58bb3d5f7e84bee91c
Merge: 83353658c 44924867d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 11 20:16:33 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 83353658ce37491882f0226b7f67fada006b30f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 11 20:16:14 2018 -0400
position="append" is the F95 standard way to append to a file
Source/driver/extern_probin.template
commit 44924867d40045806977983db5cbf66f275fd403
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 11 13:44:02 2018 -0400
Make the stopping logic more robust
Exec/science/wdmerger/Prob.cpp
commit 1574ce2bec1b3f1ab49b6f6e92166a48bf41e42e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 9 20:27:35 2018 -0400
add the extern runtime parameters to the job_info (#380)
this includes showing if the default was overridden
closes #367
Source/driver/Castro_F.H
Source/driver/Castro_io.cpp
Source/driver/extern_probin.template
commit ae27f1135c8dd7b7c6f645f593ea1696dd7c9d3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 9 16:24:28 2018 -0400
Handle the case where the lower boundary is symmetryic
Exec/science/wdmerger/problem_tagging_nd.F90
commit 29f37fa7ab41b0836ca1de663cdae65f3f13748f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 8 02:11:22 2018 -0400
Fix calculation of extrema for AMR simulations
Exec/science/wdmerger/Prob.cpp
commit 685c7d3c8ad7d71355f2e15ed91fa32013b23f58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 7 08:22:48 2018 -0400
restore
Microphysics/EOS/_parameters
commit a3c1eaf24e6972b659ef872075e58f4384fd2f5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 7 08:17:47 2018 -0400
add PR
CHANGES
Microphysics/EOS/_parameters
commit af4668d7173bffc180125dc07d6840dfd63436fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 7 05:14:57 2018 -0700
Check whether there are any zones to burn before entering react_state() (#376)
* Check whether there are any zones to burn before entering react_state().
If the user has set react_{rho,T}_{min,max} then we can save some time
before the burning has started in the simulation by checking to see if
any of the zones meet the minimum or maximum criteria for burning. If none
do, we can skip the call to react_state(). This ends up saving some cycles.
Source/driver/Castro.H
Source/reactions/Castro_react.cpp
commit 5350ca76e479c37e90298b7d0be40c981f8698f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 6 17:35:16 2018 -0700
Skip the initial EOS call prior to starting the burn (#377)
* Skip the initial EOS call prior to starting the burn
Since we always call clean_state after updating the state, T should already
be consistent with e, so this EOS call is unnecessary. This requires the
deletion of the dual_energy_eta3 parameter.
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/reactions/React_nd.F90
commit 6ad5a6509818ea7732ab3e63ca1bffa63765d2bb
Merge: e94f080cb ce81a66f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 6 18:51:00 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ce81a66f3cd0bda9d1dd67061645aca09f0c6b67
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 5 21:27:54 2018 -0400
Differentiate the overloaded clean_state profiler tags
Source/driver/Castro.cpp
commit 8f4a4e25508c53b607c963dcdc49f569d160a6eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 5 20:33:18 2018 -0400
Add some profiler tags
Source/driver/Castro.cpp
commit 888d63f70fd2210bda3a274aa27a0353cbde7076
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 5 03:34:17 2018 -0400
Restore the gravity.max_solve_level parameter
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_job_info_tests.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit a6eb0e9d594c916e0da88520bad8809bf052da3a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 5 01:53:35 2018 -0400
Be more conservative with error checks
Exec/science/wdmerger/wdmerger_util.f90
commit 1b3a9d0ec8664cc4cf3c825971914301bf88210a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 5 01:14:46 2018 -0400
Fix some error checks for the 2D half-domain case
Exec/science/wdmerger/wdmerger_util.f90
commit ae2e65d92c79b482dea874e16447abd4b1d00496
Merge: 10a4caa43 547f673bf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 5 00:23:27 2018 -0400
Merge branch 'development' into wdmerger_half_domain
commit 547f673bfd390bbbc974452e72bafc0b61eb082c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Fri Aug 3 06:51:38 2018 -0700
Replace hypre_CTAlloc with FArrayBox::resize. This fixes the issue due to Hypre API change. (#373)
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.cpp
commit d59413c517e8088901c40ea1485b024d5677b29c
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Fri Aug 3 09:31:41 2018 -0400
Added stack feature to image_animator script (#374)
Added a feature to the image_animator script in the flame_wave/analysis directory, which allows for several animations to be played simultaneously on separate subplots.
Exec/science/flame_wave/analysis/image_animator.py
commit e94f080cba9b5a8ded32c8187570931b04c19b49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 1 08:55:56 2018 -0400
update list of changes
CHANGES
commit 35a38e6ade9b7d1ea29e00810bb7f21728a0a452
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 29 06:21:25 2018 -0400
Initialize variables on level creation
Source/driver/Castro.cpp
commit 8149658dd3522a2c69147af687b224786539c369
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 28 13:39:19 2018 -0400
Add denerr/dengrad_rel to the collision probin
Exec/science/Detonation/probin-collision
commit 600b61f09e96de765cfe9162d1e90345e8be17aa
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Thu Jul 26 14:08:12 2018 -0400
Updates to flame_wave visualization scripts (#371)
* Updates to flame_wave visualization scripts
* Turned off additional colorbar by default
The --flame_wave option to plot_generator.py no longer turns on a colorbar
If a colorbar is not requested the script will not supply it to annotate_streamlines, which avoids an error if yt's streamline callback lacks the additional setting
Exec/science/flame_wave/analysis/image_animator.py
Exec/science/flame_wave/analysis/multirays.py
Exec/science/flame_wave/analysis/plot_generator.py
commit e7a03e4c6261648b6895b068fa3e005263d10de1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 20 12:13:27 2018 -0400
remove the old use_mlmg_solver parameters -- these are no longer used anywhere
Docs/runtime_parameters/runtime_parameters.tex
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame_wave/inputs_2d.boost.aprox13
Exec/science/flame_wave/inputs_2d.boost.hires
Exec/science/flame_wave/inputs_2d.boost.wide
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
Exec/unit_tests/diffusion_test/inputs.2d.sph
Source/driver/_cpp_parameters
Source/driver/param_includes/diffusion_defaults.H
Source/driver/param_includes/diffusion_job_info_tests.H
Source/driver/param_includes/diffusion_params.H
Source/driver/param_includes/diffusion_queries.H
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_job_info_tests.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
commit f3b2feb11193a39699090dde135a2b5cc5b15d74
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 16 13:29:16 2018 -0400
lo, hi -> const
Exec/science/Detonation/Problem_F.H
commit 8cca68e42d0c5eb9fbb5baa86968c5408f7ccd2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 12 12:57:42 2018 -0400
update and make in markdown
Exec/hydro_tests/Sedov/Verification/README.md
Exec/hydro_tests/Sedov/Verification/Readme
commit 9575128feec82a242032cc01f380ac7ffa3a99a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 14 12:27:41 2018 -0400
this problem doesn't need reactions
Exec/gravity_tests/StarGrav/GNUmakefile
commit e250868a23aa37d745edde46c99366788936eedb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 14 03:10:31 2018 -0400
Add new files
Exec/science/Detonation/Problem.f90
Exec/science/Detonation/Problem_F.H
commit 97761ff8c206db3f5bfbe49a529aca4ab66534f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 14 02:47:25 2018 -0400
Add radial velocity requirement to stopping criterion
Exec/science/Detonation/Prob.cpp
commit 0f992f61055985a3270daadb1da0d9d7faf6f534
Merge: 89bc2e87c 84a92fc68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 12 10:33:24 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 89bc2e87ccd24ae0e1f8292c7dc20729f94b1115
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 12 10:33:15 2018 -0400
change network
Exec/science/flame/GNUmakefile
commit 84a92fc685ec1a25b3d102ae10ed29ef794ab797
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 21:10:18 2018 -0400
update authors
Docs/Preface/Preface.tex
commit 5eccca59dc80d2b711c5fc3d92e76ba6006274d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 18:00:18 2018 -0400
reset to more sane values
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
commit d1e1a6cb9fefdc77bd35507662fb14a8c6d8308f
Merge: 8eeb3d17a 4d7772d1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 17:52:56 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 4d7772d1f65325956e22a0213f324d5837684757
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 10 17:39:58 2018 -0400
Initialize success in state_in not state_out
Source/reactions/React_nd.F90
commit 8eeb3d17ad6c688d9ba7990d43ba1b173ec66662
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 16:58:59 2018 -0400
test files
Exec/science/flame_wave/job_scripts/aprox13_test/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13_test/probin.boost.aprox13
commit 2bf2e0a30bfdbf9adc8d380ee3ad1a1ae663c46b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 13:52:37 2018 -0700
new inputs files
Exec/science/flame_wave/job_scripts/aprox13/inputs_2d.boost.aprox13
Exec/science/flame_wave/job_scripts/aprox13/probin.boost.aprox13
commit 77d605981e254c778919f8ab63de3ed9f37836d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 10 12:28:56 2018 -0400
Up max_subcycles to 1000
Exec/science/Detonation/inputs-collision
commit 1620ab37d0cfad18f64b49b17b4c5179c5074ea2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 10 02:42:48 2018 -0400
Enforce the max_subcycles parameter again
Source/driver/Castro_advance.cpp
commit cde112deb2bf5287288010cfcc828d5d31317593
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 10 01:21:03 2018 -0400
Ensure that both C and O are >= smallx
Exec/science/Detonation/Prob_nd.F90
commit 71520f6fc6d63353f7f1fd14b17c05d941f62728
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 9 00:30:04 2018 -0400
Specify even C/O mixture for collision
Exec/science/Detonation/probin-collision
commit 5eb6f602f404850d16a5830eb18a5f14bbbd268e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 9 00:29:42 2018 -0400
Allow the Detonation setup to contain oxygen
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/probdata.F90
commit d50e8ba9dd2d628ab8cd56f729d5238d694b81a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 8 22:26:00 2018 -0400
Apply use_post_step_regrid to all tagging criteria
CHANGES
Source/driver/Castro.cpp
commit c4702c48af20bbf3461b33bc87f340480c1da592
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 8 15:51:25 2018 -0400
Add max_dxnuc_lev to control burning tagging
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Tagging_nd.f90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 053cc0f5904049114c3de42ccb9fbcc0b3dc0773
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 8 15:47:57 2018 -0400
ref_ratio -> 2
Exec/science/Detonation/inputs-collision
commit 43b57ffb43fb556d8fb6418efec02ea2092b34cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 8 15:43:01 2018 -0400
Update collision probin
Exec/science/Detonation/probin-collision
commit f460eb8e3f75672f4123dcd4ac1045593dd4f7d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 7 12:46:57 2018 -0400
Also remove Castro_error.cpp
Exec/radiation_tests/RadThermalWave/Castro_error.cpp
commit 2ae551fc8d192538ce310e724dd8ff283e427c46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 7 11:56:54 2018 -0400
remove the custom tagging -- it was doing a relative error. The new
relative gradient functionality gets us this. probin was modified to
use the default relative error measure and we agree with the old
results
Exec/radiation_tests/RadThermalWave/Tagging_nd.f90
Exec/radiation_tests/RadThermalWave/probin.1d
Exec/radiation_tests/RadThermalWave/probin.2d
Exec/radiation_tests/RadThermalWave/probin.3d
commit fe5089dd8cad1b42bfc4c46de37907e4dcb57816
Merge: d83a11cac 0ae98064c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 7 11:02:59 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit d83a11cac94d271097df91f36b79bf279bf94595
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 7 11:02:45 2018 -0400
az*82 -> az**2
Exec/radiation_tests/RadThermalWave/Tagging_nd.f90
commit 0ae98064cfbf657f94c4e7f3aa175fdf7c316e08
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 7 00:50:04 2018 -0400
MAX_LEV 15 -> 30
Source/gravity/Gravity.cpp
commit 105f7f35102141d1f77e0f86f359b741cf080376
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 6 15:23:05 2018 -0400
Revert recently updated Detonation inputs
Exec/science/Detonation/inputs-collision
commit 85a1bcb0606a435095c65c538c65c970c4f9d73c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 6 13:36:46 2018 -0400
Disable new dt on regrid to avoid hang
Exec/science/Detonation/inputs-collision
commit 5eee6e4cecdc6f7563cc54b9f5eed63e1e4a6aac
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 6 02:38:03 2018 -0400
Update local copy of Tagging_nd.f90
Exec/radiation_tests/RadThermalWave/Tagging_nd.f90
commit 1433acf21ccf616d7116d9e37e221d5bb055f226
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 6 01:22:40 2018 -0400
Update collision inputs
Exec/science/Detonation/inputs-collision
commit e69aeb28c3d41b0b9b369ed13ff63d0a1fcd40af
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 5 18:46:38 2018 -0700
Fix incorrect flux register logic when using retries (#361)
* Zero out the fluxes when doing a retry
This ensures that the reflux will be correct after a retry.
Fixes #357
CHANGES
Source/driver/Castro_advance.cpp
commit 1746a6c13e807eef262928a537680d039b9ce3e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 5 18:44:00 2018 -0700
Restart from the beginning of the step on a retry (#360)
This fixes the inconsistency that we were copying back in the state
from the beginning of the step, but only resetting the time level
to the beginning of the last subcycle.
Fixes #358
CHANGES
Source/driver/Castro_advance.cpp
commit 1f7e579d09c93ee747e3132992d88a3110080205
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 5 14:27:05 2018 -0400
Disable subcycling
Exec/science/Detonation/inputs-collision
commit 9c77da3c5c5faeafbfdcbd2089961e8ee98a4528
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 5 14:25:40 2018 -0400
Add temperature tagging
Exec/science/Detonation/probin-collision
commit f26450b43c3218431be064c634e1cbaec6c9c48d
Merge: ede8bbee8 2dba11ab3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 5 14:03:43 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit ede8bbee826c32fe7a726a02a469b6666db5d1d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 5 14:03:38 2018 -0400
add missing implicit nones
Source/driver/Castro_nd.F90
commit 2dba11ab37bcc35fa6ab3eb7f6f219e4f04d95f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 5 10:59:40 2018 -0700
Add tagging criteria for relative gradients (#355)
Tagging can now be done on relative gradients, in addition
to the existing capability for absolute gradients.
For example, tempgrad_rel is a relative gradient criterion
that will tag a zone with temperature T if any adjacent zone
has a temperature that is different by more than tempgrad_rel * T.
The tagging is enabled up to a given level with the parameter
max_tempgrad_rel_lev. The corresponding new tagging criteria
for other fields are named similarly.
Closes #354
CHANGES
Source/driver/Castro_nd.F90
Source/driver/Tagging_nd.f90
commit 89cefd11447b1ef8eee73f167a6b3463d0ab23dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 5 03:18:56 2018 -0400
Add new build-time files to .gitignore
.gitignore
commit efc7a8e0bb1a9a401dc9539bfa1071d7058db414
Merge: 0a8141350 15de32878
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 4 12:27:19 2018 -0400
Merge branch 'docs' into development
commit 0a81413507098a2ec0bbd3d69b721ca7bf1923db
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 2 23:49:34 2018 -0400
n_error_buf -> 4
Exec/science/Detonation/inputs-collision
commit d284fd06e6c8da9465647db1098fed9fa9f9cce8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 2 23:48:30 2018 -0400
Correct comment
Exec/science/Detonation/inputs-collision
commit c863f5a38579a0cf90626b2bd964a4ca11c53e37
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 2 14:56:05 2018 -0700
Implement dynamic retry capability (#344)
Retries can now be done in a dynamic fashion. An advance is itself a subcycled advance always, and we keep subcycling until we are done with the step. By default we still do only a single timestep, but this helps in cases where we have to reject the timestep for (say) a CFL violation, and then during the retry the CFL criterion is violated again. In the past, we would simply have to abort the run if this happened. Now we can cut the timestep again and keep going.
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Exec/science/Detonation/probin-collision
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/reactions/Castro_react.cpp
Source/reactions/React_nd.F90
commit f833c726820e6ab534a763532896316901dbf781
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 2 14:03:29 2018 -0400
add FAQ about plotfile precision
Docs/FAQ/faq.tex
commit f23935a21bb62f4460b75dcae60c71f5327c3985
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 2 09:31:32 2018 -0400
update version
CHANGES
commit 5b3ff63f5f590a9ca4a26ece50e4ad865cc11017
Merge: 198769f5f 21dbd70be
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 2 01:44:51 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 198769f5f170eb30199a6dbb8b51e197f15f80db
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 2 01:44:46 2018 -0400
Update n_error_buf
Exec/science/Detonation/inputs-collision
commit 21dbd70be4d15f716de8b267cae8c251c3eada50
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 1 17:47:36 2018 -0400
Switch the path on the Python interpreter
Source/driver/set_variables.py
commit 6774eff84024ed7815a88750e9bcf3546d3a708a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 1 17:46:38 2018 -0400
Fix the application of the Detonation ambient BCs
Exec/science/Detonation/bc_fill_nd.F90
commit d92afe107412c20ce23fce155b4cf3e339781c1d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 1 15:09:13 2018 -0400
Update dual energy options
Exec/science/Detonation/inputs-collision
commit ade646097ebc3fc2d4353653148b444f2f3bf5c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 1 14:00:51 2018 -0400
Add custom ambient BCs to Detonation
Exec/science/Detonation/Make.package
Exec/science/Detonation/Prob_nd.F90
Exec/science/Detonation/bc_fill_nd.F90
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/probdata.F90
Exec/science/Detonation/probdata.f90
Exec/science/Detonation/probin-collision
commit d4fa13319235db5c3327cbd969315f8a483d500e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 1 13:06:52 2018 -0400
Move Detonation to dimension agnostic setup
Exec/science/Detonation/GNUmakefile
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_nd.F90
commit f7ab2d932805e90f9ca6fc376382f3e1eb2b0136
Author: blaireness <blaireness@users.noreply.github.com>
Date: Sat Jun 30 11:33:19 2018 -0400
Created exploration directory with test suite codes (#330)
* Created exploration directory with files necessary to create a test suite
* Added comments to flamefront code
Exec/science/convective_flame/exploration/README
Exec/science/convective_flame/exploration/flamefront.py
Exec/science/convective_flame/exploration/index_temp.html
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/exploration/probdata.f90
Exec/science/convective_flame/exploration/probin_temp
Exec/science/convective_flame/exploration/process.py
Exec/science/convective_flame/exploration/setup_explore.py
Exec/science/convective_flame/setup_explore.py
commit 3f7541753ef3bf8b68085098773cdaeba6584787
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 30 09:42:15 2018 -0400
Clean state (#336)
* create a clean_state that works on StateData directly
This converts most of them (and in fact, all of the ones that would
need converting for 4th order)
* switch up expand_state to be State_Type aware
* now clean_state (and dependencies) requires the number of ghost cells
this allows us to do an clean_state in expand_state _before_ the ghost fill
Some small answer differences
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/radiation/Castro_radiation.cpp
Source/radiation/MGFLD.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.cpp
commit b79b97f6fe6a30979fce733c5eda899df0bcb371
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 29 17:59:39 2018 -0400
make the state vector sizes known at compile time (#346)
Note, as part of this change, we now need to specify the number of radiation groups
at compile time, via NGROUPS. Analogous compile-time parameters exist for
the neutrino information (see Make.Castro).
Also, now it is possible to specify the number of advected quantities (that are not
species or thermodynamic auxillary variables) at compile time via NUMADV
CHANGES
Exec/Make.Castro
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/set_conserved.H
Source/driver/set_indices.F90
Source/driver/set_variables.py
Source/radiation/Radiation.cpp
Source/radiation/rad_params.f90
commit 08e2700aeda951324e9df9009a6b242359fe2c8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 27 12:58:13 2018 -0400
add an eos_finalize call to free up any allocated tables
Microphysics/EOS/eos.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
commit 803480112be868908d94269c51faf1766f68494f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 27 11:43:07 2018 -0400
Exact riemann port to C++ build system (#348)
Exec/Make.Castro
Util/exact_riemann/GNUmakefile
Util/exact_riemann/GPackage.mak
Util/exact_riemann/Make.package
Util/exact_riemann/dummy.probin.template
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/main.cpp
Util/exact_riemann/riemann_F.H
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit 8ab71a7cd0dbcc5d47a0d6818c0ae6ddf17b7898
Merge: 19aca5b41 01f00fa07
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 26 03:08:57 2018 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 19aca5b4158b61dd0d9c8dee265970e8e5e02a36
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 26 03:08:52 2018 -0700
Let device script handle host version of EOS call
Microphysics/EOS/eos.F90
commit 01f00fa07e326ffd3c2f0f8d7d1cc4ea1efe8f67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 25 09:55:30 2018 -0400
keep track of what we've processed
Exec/science/flame_wave/analysis/parallel
commit 5c72c6bf374fec61bf900da7e1000fea554aef39
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 25 00:50:03 2018 -0700
AMREX_DEVICE -> !$gpu
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_override.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Microphysics/networks/burn_type.F90
Source/driver/Castro_util.F90
Source/driver/interpolate.F90
Source/driver/sums_nd.F90
Source/driver/timestep.F90
Source/hydro/cuda_Castro_mol_nd.F90
Source/hydro/cuda_advection_util_nd.F90
Source/hydro/cuda_flatten_nd.F90
Source/hydro/cuda_ppm_nd.F90
Source/hydro/cuda_riemann_nd.F90
Source/sources/thermo_nd.F90
commit 35c1ce7af066b270143743517f1b1e6a9c4dbc40
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 23 20:41:24 2018 -0700
Update GPU defines
Source/driver/extern_probin.template
Source/driver/filcc_nd.F90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
Source/driver/prob_params.F90
Source/hydro/cuda_advection_util_nd.F90
Source/hydro/cuda_ppm_nd.F90
Source/reactions/React_nd.F90
commit fd9b28268add02fc114147a8aaca4191e34d0643
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 23 14:46:34 2018 -0700
Use new CUDA reduction macros
Source/driver/Castro.cpp
Source/driver/sum_utils.cpp
commit c65d77652c15de2b8bd4936bbfc1a093c990c126
Merge: a80ae60d7 165829bf9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 23 14:47:23 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit a80ae60d7fc0d1e5da4317f512fc7bcab2be2fa8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 23 14:47:15 2018 -0400
turn on outputting:
Exec/hydro_tests/Sedov/inputs.starlord.gpu_test
commit 165829bf982758eca761f8da59f280f56bcac67a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 23 10:52:37 2018 -0400
fix cuda compilation
Source/hydro/cuda_advection_util_nd.F90
Source/hydro/cuda_flatten_nd.F90
Source/hydro/cuda_ppm_nd.F90
Source/hydro/cuda_riemann_nd.F90
commit 44aa1a7f3b62e356971fd3660646f7698c244f32
Merge: 953c196f2 8708d465c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 23 09:43:57 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 953c196f2c91225d04e9187053232ebb1cc85ad1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 23 09:43:47 2018 -0400
get these compiling again
Diagnostics/Radiation/GNUmakefile
Diagnostics/Sedov/fsedov1d.f90
Diagnostics/Sedov/fsedov2d_cart.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cartcoords.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cylcoords.f90
Diagnostics/Sedov/fsedov2d_sph_in_cylcoords.f90
Diagnostics/Sedov/fsedov3d_cyl.f90
Diagnostics/Sedov/fsedov3d_sph.f90
commit 8708d465c4515d2e779b0fd2de09e01cc65b3a82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 21:43:44 2018 -0400
bl_constants_module -> amrex_constants_module
Exec/science/flame/Problem.f90
commit e3ca245197a0612fb3147488453108b9b940b9b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 21:42:54 2018 -0400
bl_error -> amrex_error
Exec/Make.Castro
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/flame/Prob_1d.f90
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/initial_model.f90
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/planet/Prob_3d.f90
Exec/science/planet/bc_ext_fill_1d.F90
Exec/science/planet/bc_ext_fill_2d.F90
Exec/science/planet/bc_ext_fill_3d.F90
Exec/science/planet/bc_fill_1d.F90
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/bc_fill_3d.F90
Exec/science/subchandra/Prob_2d.f90
Exec/science/xrb_mixed/Prob_2d.f90
commit 3591ba6fc3544e31dca95709bc767ea5b1af5877
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 19:49:08 2018 -0400
temporarily reenable F_BoxLib
Exec/Make.Castro
commit 9d7f46c78084292a682d695cbca0bc97bd8d14ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 19:14:48 2018 -0400
remove remaining dependencies on F_BaseLib
Exec/Make.Castro
Source/driver/extern_probin.template
commit 425893f8e4ed2aeed79d3a8bf5d5b67a8eaa1cfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 19:14:39 2018 -0400
fix compilation
Microphysics/networks/burn_type.F90
commit bddf559f01551c081e437389b2eea7be8a9a23a0
Merge: 57d4f6f7f cffb785c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 18:46:35 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit cffb785c040f96bfe71413e4099d1fdf35651e8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 18:46:02 2018 -0400
a version for the test suite
Exec/hydro_tests/Sedov/inputs.starlord.gpu_test
commit 57d4f6f7fe307dd5e7e93c426300fdd1c47c3026
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 22 18:02:13 2018 -0400
more changes
CHANGES
commit e930fa3a548c8f48ae285015cc1efbfcbde91207
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 21 13:45:36 2018 -0400
for CUDA, we still get q and qaux from cons_to_prim
Source/hydro/Castro_hydro.cpp
Source/hydro/cuda_riemann_nd.F90
commit cb3352780c0cc79e2d1ef27a517b33313a3501de
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 21 09:25:18 2018 -0700
Do reductions on the host when not offloading
Exec/hydro_tests/Sedov/inputs.starlord
Source/driver/Castro.cpp
Source/driver/sum_utils.cpp
commit 50ebced2407e510aa35397e040c017d5482771d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 21 12:11:25 2018 -0400
fix compile string
Docs/ManagingJobs/managingjobs.tex
commit d26d24efe90e2b687137c1a29c67c95df2622aea
Merge: 96243df2a 79092e9f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 21 11:26:24 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 96243df2a8b7d3b974265e9a7c65c140333ea87d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 21 11:26:13 2018 -0400
add some CUDA notes
Docs/ManagingJobs/managingjobs.tex
commit 79092e9f6b6f6cbf982cecae2ced4f3782942062
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 21 08:01:15 2018 -0700
Use flag to disable device offload
Microphysics/EOS/eos.F90
Source/driver/generic_fill.F90
Source/problems/bc_fill_1d.F90
Source/problems/bc_fill_2d.F90
Source/problems/bc_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit efaa91d8dc5dfb8c37ccca6c9f967c957c3591b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 21 07:03:34 2018 -0700
Reapply dtinv to the hydro update
Source/hydro/cuda_advection_util_nd.F90
commit 305a911942677afb6ce1086fdfcf913b96588090
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 21 06:46:08 2018 -0700
Add the sources_for_hydro term on the GPU
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/cuda_advection_util_nd.F90
commit 414ff375b5c4345b43b4d612c2e11473b0fc0cd5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jun 20 21:47:59 2018 -0700
use AMREX_DEBUG instead of NDEBUG
Source/gravity/Gravity.cpp
commit 53fc6e0f34b6b280ff1cfe12fbf60fe6ce372f8f
Merge: 7a4e0bbb1 51130b901
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 20 16:40:33 2018 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 7a4e0bbb1bea45aa9392cf620179b5a7ed2812f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 20 16:40:26 2018 -0700
Lose the scaling by 1/dt
Source/hydro/cuda_advection_util_nd.F90
commit 51130b901768fc27166068a98b4ba0b264cfd36d
Merge: c15f27bcb e18f8d7f2
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed Jun 20 13:58:04 2018 -0400
Merge branch 'development' of https://github.com/AMReX-Astro/Castro into development
commit c15f27bcbe2f6324a0a871974d1a436cba656321
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed Jun 20 13:55:56 2018 -0400
scripts used to run wdmerger on summitdev for scaling and inputs, probin
Docs/ManagingJobs/scaling/wdmerger/summitdev_201806/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/summitdev_201806/probin_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/summitdev_201806/scaling.txt
Docs/ManagingJobs/scaling/wdmerger/summitdev_201806/summitd-160MPI.run
Docs/ManagingJobs/scaling/wdmerger/summitdev_201806/summitd-320MPI.run
Docs/ManagingJobs/scaling/wdmerger/summitdev_201806/summitd-80MPI.run
commit e18f8d7f2ab0bf0673883493323090d1276e3531
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 20 12:30:00 2018 -0400
update changes
CHANGES
commit 235889dc0d6d114ac2c173c55dfa5a8d0cc6e742
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 20 08:32:07 2018 -0700
Sync up StarLord inputs
Exec/hydro_tests/Sedov/inputs.starlord
commit 6b8215e1260e3e7b3ea0535137dc2aa117bba416
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 20 08:27:48 2018 -0700
Sync up with how we handle the MOL updates
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/cuda_advection_util_nd.F90
commit e9c5596c00b05197a5880edeee7db4ba07637dcc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 20 08:06:37 2018 -0700
Update k_stage, not hydro_source
Source/hydro/Castro_hydro.cpp
commit 547dc287c48228906ad63c44da4cbe89f2ecbb34
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 20 07:28:49 2018 -0700
Fix QCSML dependence in CUDA Riemann solver
Source/hydro/cuda_riemann_nd.F90
commit 79a32af7c4e589d5115e986577afdea4e024a187
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 19 21:13:00 2018 -0700
Print figure of merit at the end of the run
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/main.cpp
commit 67329aa116cd821a1e8168f89152d6a57115c7b4
Merge: 3f51e9e17 24e53e798
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 19 10:32:16 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 3f51e9e17b22a7eab527119126015355e8d47157
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 19 10:32:02 2018 -0400
remove extra network_init
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadFront/Prob_1d.f90
Exec/radiation_tests/RadFront/Prob_2d.f90
Exec/radiation_tests/RadShestakovBolstad/Prob_1d.f90
Exec/radiation_tests/RadSlope/Prob_1d.f90
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
Exec/radiation_tests/RadSuOlsonMG/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
commit 24e53e798b95850d6f9b040231a07b619533ad7e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 19 07:01:50 2018 -0700
Disable tiling when CUDA is used
Source/driver/Castro.cpp
commit 211bbfb376794addb4f3809c41c07907a1d82d8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 19 06:48:23 2018 -0700
No enforce_min_density on the device
Source/driver/Castro.cpp
commit 81c278e8012ee320b683a7b6b00614c1d16afb2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 19 06:47:07 2018 -0700
summass on the device
Source/driver/Make.package
Source/driver/sum_utils.cpp
Source/driver/sums_nd.F90
commit ef4ed813d6e2811384a715c3b58ff1175a5c1fd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 18 20:51:36 2018 -0400
more commenting
Source/driver/set_variables.py
commit 15f35e52b58212380f8e74daab5b8821642bb2bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 18 19:48:59 2018 -0400
update comments
Source/driver/set_variables.py
commit 9efd093c3e0996b16e63ec99bf80373898efafb6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 10:56:42 2018 -0700
estdt on the device
Source/driver/Castro.cpp
Source/driver/timestep.F90
commit 54630b0ae5373569add428bac4b0ff0b28de4620
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 10:44:08 2018 -0700
thermo_src on the GPU
Source/driver/Castro_F.H
Source/sources/Castro_thermo.cpp
Source/sources/thermo_nd.F90
commit b3eb4cc1eaffede4185ee919e4d70cd45c04dfc2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 09:16:51 2018 -0700
no NaN check on the GPU
Source/driver/Castro_advance.cpp
commit 057172898a992ad4f415c676c30c2acd35a3ff13
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 08:45:27 2018 -0700
Move general null network to device
Microphysics/networks/general_null/Make.package
Microphysics/networks/general_null/network.template
commit 34ea6ff4072ed1c9ee426b2730092ee9b116f16b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 08:45:10 2018 -0700
Move gamma law EOS to device
Microphysics/EOS/gamma_law/gamma_law.F90
commit 89d51f70f7ce64e29d0318e7c43a041980d97e41
Merge: d7fa4790d 51e4a3231
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 06:50:47 2018 -0700
Merge branch 'gpu_hydro' of github.com:AMReX-Astro/Castro into gpu_hydro
commit d7fa4790d4b06990cf793472994ee4dfa439e123
Merge: 5799805cd 0c55a7140
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 18 06:50:32 2018 -0700
Merge branch 'development' into gpu_hydro
commit 0c55a7140b6162b4fdface0384c37dee810e6585
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 17 21:14:57 2018 -0400
fix uninitialized nadv
Source/driver/Castro_nd.F90
commit c9c21deb3a39698fcbcb63fe035625f88b82755a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 17 10:38:10 2018 -0700
Fix macro
Source/driver/Castro.cpp
commit 8bcebf0937a0659ac5d825fc1f5f8ad59bdf8532
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 21:21:21 2018 -0700
Add a couple things onto the GPU
Source/driver/Castro.cpp
Source/driver/Castro_util.F90
commit d6d3eb50a1ea76a5fe64391648d887b811bb7a45
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:43:01 2018 -0400
ifdef out some hydro we won't use on the GPU
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
commit 08eef48604b07038188d9033595afe9631d22084
Merge: e626ebab3 6ab68c9c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:24:34 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit e626ebab3b90e22bb71c85234d5f3516b1a82ce4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:24:28 2018 -0400
Avoid the ext_fill when using CUDA
Source/problems/Make.package
Source/problems/bc_fill_2d.F90
commit 4d80abd2fb95708275a79fe692afad55d5da917d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:15:49 2018 -0400
Move more variables to the device
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 6ab68c9c036465c28d714e2ce8e86b0ef39b59a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 15 16:20:37 2018 -0400
get this compiling again
Util/exact_riemann/GNUmakefile
Util/exact_riemann/dummy.probin.template
Util/exact_riemann/riemann_support.f90
commit 51e4a3231c3bb02895044398326ba5423f56ae2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 15 12:51:24 2018 -0400
Move statement out of ifdef
Source/driver/meth_params.F90
Source/driver/meth_params.template
commit 005e6275eba30e074247858262b995d8079effc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 15 12:42:05 2018 -0400
ifdef out some un-GPUified code
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
commit 63b0240428a23ca5664b7f3f36c3396db5ecdd40
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 15 12:25:17 2018 -0400
xl_ext, etc. on device
Source/driver/meth_params.F90
Source/driver/meth_params.template
commit 47b55d55aba77a0066f4f4be1adab11729e4652c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 21:55:40 2018 -0400
Add the host interface to call the EOS
Microphysics/EOS/eos.F90
commit 02cad7487ba18506a3469d96e7ac177c66ef4b5c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 21:45:20 2018 -0400
compute_temp, reset_internal_e to device
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util.F90
commit d6d522daec07c815abaaced60fdc623d96684ea5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 21:40:36 2018 -0400
Network and EOS to device
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_override.F90
Microphysics/EOS/eos_type.F90
Microphysics/networks/Make.package
Microphysics/networks/network.F90
commit 8eaab0b3bc81913d383c04e1d8c33e7f749bcbe5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 20:32:04 2018 -0400
Remove QCSML, no longer used
Source/hydro/cuda_advection_util_nd.F90
commit f71051ada0151150c588c0a3e364353dc0e34830
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 20:31:57 2018 -0400
primitive variables to device
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 93dfc8f034d14bcb0dfbbebc3c1a9ca8e1aecdfe
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 20:06:47 2018 -0400
ctoprim on the device
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
commit a2d24afac47d68d9942e15ff4c39a47df237479f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:55:28 2018 -0400
istage -> mol_iteration
Source/hydro/Castro_hydro.cpp
commit 368af2df9d4c0d8d0c2d0b24a4188a6923055231
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:52:57 2018 -0400
Add missing Castro_F.H signatures
Source/driver/Castro_F.H
commit 33c4d7ddb1e5611ffedadf910163b12a655f57c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:46:52 2018 -0400
Add MultiFab definitions
Source/hydro/Castro_hydro.cpp
commit 095c4cd085543302532719ccba97e543abef8ada
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:44:53 2018 -0400
Remove ctoprim call
Source/hydro/Castro_hydro.cpp
commit 42583e07998b8728f79f6dbad10a2bb112c5d56c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:41:47 2018 -0400
enforce_min_density on the device
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/hydro/advection_util_nd.F90
Source/hydro/cuda_advection_util_nd.F90
commit 62d876ad873acc4790732c07808c176b173eeb15
Merge: 403f17f6e 387406ad3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:29:46 2018 -0400
Merge branch 'development' into gpu_hydro
commit 403f17f6e9ed9c7d54fb63a00d255eda4ce642bb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 14 19:29:15 2018 -0400
retry and subcycle advance unavailable for CUDA
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit 387406ad3c99bcdd4dc0bba67586342994970bc1
Merge: 2d3424406 19dbfce9f
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Jun 14 12:20:08 2018 -0400
Merge branch 'development' of https://github.com/AMReX-Astro/Castro into development
commit 2d34244064055e451a21a1c75346eab7816f80ae
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Jun 14 12:16:48 2018 -0400
finish ifndef AMRE_USE_CUDA for prints and amrex_error calls in /driver
Source/driver/MGutils_1d.F90
Source/driver/MGutils_2d.F90
Source/driver/Make.package
Source/driver/extern_probin.template
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/set_indices.F90
Source/driver/set_variables.py
commit 19dbfce9fa3f699aa6e84ca02cc103d45e0855fc
Merge: 07427ca50 ca9cc7291
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Jun 14 00:08:48 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 07427ca5019ef10761fe8120b739d68856ea6af5
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Jun 14 00:06:32 2018 -0400
Fix number of components in generic_multi_fill.
Source/driver/generic_fill.F90
commit 0a90b6955de9dc3c73fe774ce4c859c466fa3e6d
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 23:02:57 2018 -0400
Revise dimensionality of bc array.
Source/problems/bc_fill_1d.F90
commit ca9cc7291f99e87a538a914ffe0a2cb5162fc9fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 13 22:18:05 2018 -0400
fix a valgrind issue
Source/driver/Castro_nd.F90
commit cf5411524a335a2a106695d299e01eb5980eac04
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 20:34:30 2018 -0400
Fix call to amrex_filccn.
Source/problems/bc_fill_nd.F90
commit 69e250d645dd35d78455c443395a128e40ce5821
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 20:33:08 2018 -0400
Fix call to amrex_filccn.
Source/problems/bc_fill_3d.F90
commit c99f477482f89fd157a12f0288da86b0408cd645
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 20:31:44 2018 -0400
Fix call to amrex_filccn.
Source/problems/bc_fill_2d.F90
commit 9c0a3d64659db23563b5dd7cd6fae6b5373bc568
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 20:30:13 2018 -0400
Fix call to amrex_filccn
Source/problems/bc_fill_1d.F90
commit ebb433d65bb20bf0b210b0957e8368df9a992111
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 20:16:03 2018 -0400
Add subroutine use statement.
Source/problems/bc_ext_fill_3d.F90
commit c1677b44062a63e84b5ac8930bd04848371b8e02
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 19:55:51 2018 -0400
Fix calls to interpolate_sub.
Source/driver/interpolate.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
commit e1c34983bdde481192e7efe935f3a1fdedd0582b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 19:40:49 2018 -0400
Fix variable in interpolate_sub.
Source/driver/interpolate.F90
commit 6b0c0300676199e9beb035e17e06b423dcf4ef1b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 19:08:34 2018 -0400
Update 3D BC Ext Fill for CUDA.
Source/problems/bc_ext_fill_3d.F90
commit cb86627b02cbb2fb2b5f14558b24f43500bac704
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 19:08:21 2018 -0400
Fix filcc bounds in 2D BC ext fill.
Source/problems/bc_ext_fill_2d.F90
commit 931d6c5e8d49eeddcf800db0b3f3d38482511215
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 18:52:38 2018 -0400
Update 1D BC Ext fill routines for CUDA.
Source/problems/bc_ext_fill_1d.F90
commit 323e895f693049a83c27f9a1d14cde3866de5219
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 18:43:19 2018 -0400
Update ND BC fill subroutines for CUDA.
Source/problems/bc_fill_nd.F90
commit 62ce57c7d6e54811e97a5accf3ad7bbe3fbaa368
Merge: acd7afe0a 3117c7441
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:51:26 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit acd7afe0ac2705789dfd77a2fa23a3492d460185
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:51:09 2018 -0400
In build system, update f90->F90.
Util/model_parser/GPackage.mak
Util/model_parser/Make.package
commit 0d308dfcf4eaa3cb9bbbb8869211ddfd61989ca9
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:49:02 2018 -0400
Removed unused grav_lo, grav_hi.
Source/problems/bc_fill_3d.F90
commit c8aff02d8f805465370ef6617aa5d3494c6f4fe3
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:47:39 2018 -0400
Update 2D BC fill routines for CUDA.
Source/problems/bc_fill_2d.F90
commit d9dbc0a26dc97f733f693ff605de0585cc40e10f
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:40:08 2018 -0400
Update 1D BC fill routines for CUDA.
Source/problems/bc_fill_1d.F90
commit 2b2312cc629b8a51c7c7aa376e966bb42fdee487
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:35:11 2018 -0400
Update external BC fill routines in 2D for CUDA.
Source/problems/bc_ext_fill_2d.F90
commit f89cb3f5dd9e2dd6ffff9258f10c66cb6d84d6ba
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:30:09 2018 -0400
Got rid of f90 version of the model parser.
Util/model_parser/model_parser.f90
commit ee109ec348cbc0893d577c59f026e90fc3bea96d
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:29:34 2018 -0400
Make npts_model managed in the model parser.
Util/model_parser/model_parser.F90
commit d05a39bf8877081941c32918aae19bb2c86a9673
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 13 17:28:02 2018 -0400
Add device subroutine versions of interpolate and locate.
Source/driver/Make.package
Source/driver/interpolate.F90
commit 3117c7441cb629fa6d5e7e4001d0de9b580573e8
Merge: 098108727 9c2d52287
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 13 15:16:39 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 098108727d2a0d228c7e569b255434e63310b682
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 13 15:16:21 2018 -0400
add a bash script for parallel vising
Exec/science/flame_wave/analysis/parallel
Exec/science/flame_wave/analysis/slice.py
commit 64bc34ddc602578765b057963824d064420f5108
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 13 14:23:16 2018 -0400
ifdef out some unused advance calls
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
commit 9c2d522878c4f6e97ed53ae612d8bde88e91be9f
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Wed Jun 13 12:45:43 2018 -0400
ifndef AMREX_USE_CUDA amrex_error calls and prints part of driver/
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
commit 5799805cd12cc27142f5001237d0d4210b1b4654
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 21:44:14 2018 -0700
[WIP] Start copying over hydro from StarLord
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Make.package
Source/hydro/cuda_Castro_mol_nd.F90
Source/hydro/cuda_advection_util_nd.F90
Source/hydro/cuda_flatten_nd.F90
Source/hydro/cuda_ppm_nd.F90
Source/hydro/cuda_riemann_nd.F90
commit 99727df9cd99823c8d2b20c1bd955a5c6592aa07
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Tue Jun 12 23:36:58 2018 -0400
ifndef AMREX_USE_CUDA on amrex_error calls and prints in hydro directory
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
commit 75e2448c2f34924b687f9e02c65b5be1581ddc6f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 19:58:37 2018 -0700
Get NGDNV in the C++
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
commit c4d1c9063b3ab8cbe17082365076b0a9b5467d9f
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 12 14:16:27 2018 -0400
Put time back into ca_hypfill for bc_fill_nd.
Source/problems/bc_fill_nd.F90
commit dca3d2112330ac9bc9dfa8cec0fc8eb9ffb34c4b
Merge: 6368f6ed5 33772db7b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 13:59:35 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 6368f6ed58556eafacad3da7caa72862b50dcfbc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 13:59:22 2018 -0400
Increase max_grid_size
Exec/hydro_tests/Sedov/inputs.starlord
commit 33772db7b23689f9f22adedd331e57f46467b3d9
Merge: c0ee5f52b 0c1b77d1a
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 12 13:33:12 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit c0ee5f52b4814d09a2d3ace74cd19df88acc421c
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 12 13:32:07 2018 -0400
Put time back into the 3d BCs.
Source/problems/bc_fill_3d.F90
commit 0c1b77d1a01f34fa076837993c78fbc628a726b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 13:26:52 2018 -0400
fix compilation
Source/hydro/Castro_advection_3d.F90
commit 2d9def35b73fbd0f329a947b4293699dd0107dc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 13:21:21 2018 -0400
fix compilatoin
Source/problems/bc_fill_nd.F90
commit d8a5e2b37aeabaa031c41d79df2cbfec4c721b48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 12:04:59 2018 -0400
add parallel
Exec/science/flame_wave/initial_model.f90
commit 027649de250b8388691bfa944e5712d66d0b1f79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 12:03:16 2018 -0400
tabs
Exec/Make.Castro
commit 4e63c9f2e637f695fbf5dbc34db5da7e8836b78d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 12:00:58 2018 -0400
Clean obsolete extern.f90
Exec/Make.Castro
commit a94399832cdfad880f3637c8f5be24ae995ffecc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 11:24:48 2018 -0400
Strip out the C++-to-F90 interfaces
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_util.F90
Source/driver/castro_c_interfaces_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit df804c2a847267a0291d3a923e9b5232e09823a9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 12 11:03:02 2018 -0400
Update 3D/ND BCs for CUDA
Source/driver/filcc_nd.F90
Source/driver/generic_fill.F90
Source/problems/bc_ext_fill_3d.F90
Source/problems/bc_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit fe9d89c6c6dd201fa5aeb5d045833dcac231873b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 11 22:06:17 2018 -0400
Update the parameter generation for CUDA
Exec/Make.Castro
Source/driver/extern_probin.template
Source/driver/parse_castro_params.py
commit 4f39f6e600a9c372a6847b3849fdd3d12c58403b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 11 21:51:48 2018 -0400
Some cleanup for getting on the device
Source/driver/Castro_nd.F90
Source/driver/Make.package
Source/driver/castro_c_interfaces_nd.F90
Source/driver/castro_cuda_interfaces_nd.F90
Source/driver/prob_params.F90
commit 3459c73bd204b7bf2d1b7c64c1294d4ee1f5684d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 11 21:08:37 2018 -0400
Move some meth_params variables to the device
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit db734f5cb946ae2c7f20039ba6538f32ae81850c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 23:42:39 2018 -0400
Add a success parameter to the burn_type
Microphysics/networks/burn_type.F90
commit 4cee2f603e34efb963bbc61eb9a2c241b9c6b3dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 14:42:33 2018 -0400
Lower blocking factor to 8
Exec/science/Detonation/inputs-collision
commit aae6471f70998845edd16ffaed70df0f9627147b
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Jun 7 14:34:23 2018 -0700
Move these diagnostics out of amrex/Tools/Postprocessing/F_Src/CASTRO_radiation
Diagnostics/Radiation/GNUmakefile
Diagnostics/Radiation/fgaussianpulse.f90
Diagnostics/Radiation/flgt_frnt1d.f90
Diagnostics/Radiation/fradshock.f90
Diagnostics/Radiation/fradsource.f90
Diagnostics/Radiation/fradsphere.f90
Diagnostics/Radiation/frhdshocktube.f90
commit 6dcdba8dbe083e62693f368ffcee59e3399fb89d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 4 13:22:07 2018 -0700
more amrex_errors
Source/hydro/Castro_advection_1d.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 6310ba68d3ba709ee8f89dbdbabc3a10b7df5727
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 4 13:20:25 2018 -0700
more amrex_errors
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
commit 6987daedfe82927d38e004576f222ca823707e15
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 15:59:19 2018 -0400
More amrex_error updates
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
commit ea4f1d2ce48c866d6b4a875a8fd954e207c5da5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 15:13:42 2018 -0400
amrex updates
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/wdmerger_util.f90
commit 9405b3b8adfc1e4eb0efbe5ca0c2bc1e2e92c7f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 14:57:16 2018 -0400
Update a call to amrex_error
Exec/science/wdmerger/wdmerger_util.f90
commit 03351d9994f5ae9ca1ae6e52d45c1e0fd3e9b57d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 10:07:06 2018 -0700
Remove dependence on F_BaseLib (#339)
* Modify Castro so that it no longer needs amrex/Src/F_BaseLib or amrex/Src/LinearSolvers/F_MG.
* Merge branch 'development' of https://github.com/amrex-astro/castro into development
* Part of converting from the use of dp_t to rt
* Forgot to commit these two -- part of the change away from F_BaseLib.
* More of the migration to not needing F_BaseLib.
Diagnostics/DustCollapse/fdustcollapse1d.f90
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Diagnostics/Sedov/fsedov1d.f90
Diagnostics/Sedov/fsedov2d_cart.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cartcoords.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cylcoords.f90
Diagnostics/Sedov/fsedov2d_sph_in_cylcoords.f90
Diagnostics/Sedov/fsedov3d_cyl.f90
Diagnostics/Sedov/fsedov3d_sph.f90
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/acoustic_pulse/Prob_2d.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_mach_reflection/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/initdata_others.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/hydro_tests/toy_flame/Problem.f90
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/flame_wave/initial_model.f90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Rotation_frequency.F90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_derive_nd.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Microphysics/networks/burn_type.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/network.f90
Microphysics/networks/sdc_type.F90
Microphysics/viscosity/constant/constant_viscosity.f90
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Enthalpy_nd.f90
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/MGutils_1d.f90
Source/driver/MGutils_2d.f90
Source/driver/extern_probin.template
Source/driver/interpolate.f90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/set_indices.F90
Source/driver/set_variables.py
Source/driver/sums_nd.f90
Source/driver/timestep.F90
Source/gravity/GR_Gravity_1d.f90
Source/gravity/GR_Gravity_2d.f90
Source/gravity/GR_Gravity_3d.f90
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_nd.f90
Source/gravity/gravity_sources_nd.F90
Source/gravity/pointmass_nd.f90
Source/gravity/prescribe_grav_nd.f90
Source/gravity/prescribe_phi_nd.F90
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/multid_slope_2d.f90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_2d.F90
Source/hydro/trans_3d.F90
Source/problems/Prob_1d.f90
Source/problems/Prob_2d.f90
Source/problems/Prob_3d.f90
Source/problems/Prob_nd.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
Source/radiation/rad_util.f90
Source/radiation/trace_ppm_rad_nd.F90
Source/reactions/React_nd.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.f90
Source/rotation/rotation_sources_nd.F90
Source/sources/ext_src_1d.f90
Source/sources/ext_src_2d.f90
Source/sources/ext_src_3d.f90
Source/sources/ext_src_nd.F90
Source/sources/sponge_nd.F90
Source/sources/thermo_nd.F90
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
Util/model_parser/model_parser.f90
Util/scripts/dpconvert.py
constants/constants_cgs.f90
commit 1e7364d49844dbcc6a0ea22238770423bf653d39
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 3 14:52:33 2018 -0400
Allow verbosity to turn off CFL violation warnings
Source/driver/Castro_F.H
Source/hydro/Castro_hydro.cpp
Source/hydro/advection_util_nd.F90
commit 9b1300bddd0a56d0861e289809a764bc826aea0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 3 11:55:44 2018 -0400
Revert "Merge branch 'development' of https://github.com/amrex-astro/castro into development"
This reverts commit 899b0006aef44564b31624df49f41bb5c1cfdc4b, reversing
changes made to 5fd035557cc69674cb013ee3528038cd1c0bebc4.
Diagnostics/DustCollapse/fdustcollapse1d.f90
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Diagnostics/Sedov/fsedov1d.f90
Diagnostics/Sedov/fsedov2d_cart.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cartcoords.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cylcoords.f90
Diagnostics/Sedov/fsedov2d_sph_in_cylcoords.f90
Diagnostics/Sedov/fsedov3d_cyl.f90
Diagnostics/Sedov/fsedov3d_sph.f90
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/acoustic_pulse/Prob_2d.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_mach_reflection/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/initdata_others.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/hydro_tests/toy_flame/Problem.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/flame_wave/initial_model.f90
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Microphysics/networks/burn_type.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/network.f90
Microphysics/networks/sdc_type.F90
Microphysics/viscosity/constant/constant_viscosity.f90
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Enthalpy_nd.f90
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/MGutils_1d.f90
Source/driver/MGutils_2d.f90
Source/driver/extern_probin.template
Source/driver/interpolate.f90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/set_indices.F90
Source/driver/set_variables.py
Source/driver/sums_nd.f90
Source/driver/timestep.F90
Source/gravity/GR_Gravity_1d.f90
Source/gravity/GR_Gravity_2d.f90
Source/gravity/GR_Gravity_3d.f90
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_nd.f90
Source/gravity/gravity_sources_nd.F90
Source/gravity/pointmass_nd.f90
Source/gravity/prescribe_grav_nd.f90
Source/gravity/prescribe_phi_nd.F90
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/multid_slope_2d.f90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_2d.F90
Source/hydro/trans_3d.F90
Source/problems/Prob_1d.f90
Source/problems/Prob_2d.f90
Source/problems/Prob_3d.f90
Source/problems/Prob_nd.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
Source/radiation/rad_util.f90
Source/radiation/trace_ppm_rad_nd.F90
Source/reactions/React_nd.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.f90
Source/rotation/rotation_sources_nd.F90
Source/sources/ext_src_1d.f90
Source/sources/ext_src_2d.f90
Source/sources/ext_src_3d.f90
Source/sources/ext_src_nd.F90
Source/sources/sponge_nd.F90
Source/sources/thermo_nd.F90
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
Util/model_parser/model_parser.f90
constants/constants_cgs.f90
commit 7faee306ea94046571c3886fca73a10b5a9aca3d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 3 11:55:33 2018 -0400
Revert "Part of converting from the use of dp_t to rt"
This reverts commit e389114b0b4c8c3d8c956d73c106026de1cfec5b.
Util/scripts/dpconvert.py
commit 61ede0d517aaa72c4e4eede762d96543c7e9435e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 3 11:55:25 2018 -0400
Revert "Forgot to commit these two -- part of the change away from F_BaseLib."
This reverts commit cd8d174c4b0ac46e4a357d13de694c23cb9b3143.
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
commit 6e8950e3e8c127466add576c2e4c9d2c68a2a624
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 3 11:55:18 2018 -0400
Revert "More of the migration to not needing F_BaseLib."
This reverts commit 6400b11f8587b3aa5226e9aacf2a6469da047234.
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Rotation_frequency.F90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_derive_nd.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/meth_params.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.f90
Source/rotation/rotation_sources_nd.F90
commit 6400b11f8587b3aa5226e9aacf2a6469da047234
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 20:36:02 2018 -0700
More of the migration to not needing F_BaseLib.
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Rotation_frequency.F90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_derive_nd.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/meth_params.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.f90
Source/rotation/rotation_sources_nd.F90
commit cd8d174c4b0ac46e4a357d13de694c23cb9b3143
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 18:27:26 2018 -0700
Forgot to commit these two -- part of the change away from F_BaseLib.
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
commit e389114b0b4c8c3d8c956d73c106026de1cfec5b
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 17:44:15 2018 -0700
Part of converting from the use of dp_t to rt
Util/scripts/dpconvert.py
commit 899b0006aef44564b31624df49f41bb5c1cfdc4b
Merge: 81306abc1 5fd035557
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 17:37:53 2018 -0700
Merge branch 'development' of https://github.com/amrex-astro/castro into development
commit 81306abc1eb6a7c5c7b30fe9b865fb6e475fd2af
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 17:37:25 2018 -0700
Modify Castro so that it no longer needs amrex/Src/F_BaseLib or amrex/Src/LinearSolvers/F_MG.
Diagnostics/DustCollapse/fdustcollapse1d.f90
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Diagnostics/Sedov/fsedov1d.f90
Diagnostics/Sedov/fsedov2d_cart.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cartcoords.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cylcoords.f90
Diagnostics/Sedov/fsedov2d_sph_in_cylcoords.f90
Diagnostics/Sedov/fsedov3d_cyl.f90
Diagnostics/Sedov/fsedov3d_sph.f90
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/acoustic_pulse/Prob_2d.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_mach_reflection/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/initdata_others.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/hydro_tests/toy_flame/Problem.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/flame_wave/initial_model.f90
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
Microphysics/EOS/gamma_law/gamma_law.F90
Microphysics/networks/burn_type.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/network.f90
Microphysics/networks/sdc_type.F90
Microphysics/viscosity/constant/constant_viscosity.f90
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Enthalpy_nd.f90
Source/driver/Castro_nd.F90
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/MGutils_1d.f90
Source/driver/MGutils_2d.f90
Source/driver/extern_probin.template
Source/driver/interpolate.f90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/set_indices.F90
Source/driver/set_variables.py
Source/driver/sums_nd.f90
Source/driver/timestep.F90
Source/gravity/GR_Gravity_1d.f90
Source/gravity/GR_Gravity_2d.f90
Source/gravity/GR_Gravity_3d.f90
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_nd.f90
Source/gravity/gravity_sources_nd.F90
Source/gravity/pointmass_nd.f90
Source/gravity/prescribe_grav_nd.f90
Source/gravity/prescribe_phi_nd.F90
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/multid_slope_2d.f90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_2d.F90
Source/hydro/trans_3d.F90
Source/problems/Prob_1d.f90
Source/problems/Prob_2d.f90
Source/problems/Prob_3d.f90
Source/problems/Prob_nd.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
Source/radiation/rad_util.f90
Source/radiation/trace_ppm_rad_nd.F90
Source/reactions/React_nd.F90
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.f90
Source/rotation/rotation_sources_nd.F90
Source/sources/ext_src_1d.f90
Source/sources/ext_src_2d.f90
Source/sources/ext_src_3d.f90
Source/sources/ext_src_nd.F90
Source/sources/sponge_nd.F90
Source/sources/thermo_nd.F90
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
Util/model_parser/model_parser.f90
constants/constants_cgs.f90
commit 5fd035557cc69674cb013ee3528038cd1c0bebc4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 2 14:16:25 2018 -0400
Drop to a lower CFL number
Exec/science/Detonation/inputs-collision
commit 90a1b88f550428fdcf61a9cf6e6bb7b0d4a0ca48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 1 10:11:04 2018 -0400
update changes
CHANGES
commit 2e93865d1cb0f2baaf0400eec0afe0a65e3737b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 31 21:44:39 2018 -0400
Update CHANGES
CHANGES
commit 1a21672f65b7391b8eeaa5b96f74862ae94547c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 31 18:43:36 2018 -0700
Fix logic for dealing with CFL violations during retries (#335)
castro.hard_cfl_limit now has the behavior that it is ignored during the initial
advance if you're using a retry, and is enforced during the retries. Thus the default
behavior is now that when a CFL violation is detected and retries are enabled, a retry
will be taken, and if a subcycle in that retry violates CFL stability, the run aborts.
Fixes #334
Source/driver/Castro_advance.cpp
commit 2d71c3d8efb4600581c73895fb42ddd98d30f21f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 31 19:35:22 2018 -0400
Add more subcycles, re-enable hard CFL limit
Exec/science/Detonation/inputs-collision
commit 66972e2d125d1d2875e17275fef8cc333002b71a
Merge: 3d43adb70 c66bcc379
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 31 10:59:01 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 3d43adb700b8dd60c0306b55f1e60f4a29c79a3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 31 10:58:55 2018 -0400
Switch to a gravitational acceleration version of the collision problem
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/probin-collision
commit c66bcc37908f37af2453a0097390f7526597c989
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 31 10:21:47 2018 -0400
update CHANGES
CHANGES
commit aa214d5818c528e36eba25ea93a0e5f8d089251c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 30 19:16:21 2018 -0400
this is Taeho's latest
Exec/science/planet/GNUmakefile
Exec/science/planet/Prob_3d.f90
Exec/science/planet/bc_ext_fill_1d.F90
Exec/science/planet/bc_ext_fill_2d.F90
Exec/science/planet/bc_ext_fill_3d.F90
Exec/science/planet/bc_fill_3d.F90
Exec/science/planet/inputs_3d
Exec/science/planet/newmodelcpp_T1800.hse
Exec/science/planet/newmodelcpp_T3000.hse
Exec/science/planet/probdata.f90
Exec/science/planet/probin
Exec/science/planet/taeho.net
commit a2ba936b599201d34227cecf34f90b3ea11df243
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 28 11:15:55 2018 -0400
fix relative path
Exec/hydro_tests/double_mach_reflection/GNUmakefile
commit f93c3f1d00a403c195287b3096f40cdfdf5ec7e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 28 11:10:40 2018 -0400
move some inputs
Exec/science/flame/flame_wave_tests/aprox13/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/aprox13/probin.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/README.md
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/triple_alpha_plus_cago/probin.boost
commit 3255206d120fbea18dccf6b9f7b5b89611d0eec3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 27 20:57:48 2018 -0400
new problem
CHANGES
commit 6b78e51593acda73f2620d153e8bc4b8a5a702c9
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sun May 27 09:28:37 2018 -0700
Add new pure hydro test problem -- double Mach reflection.
Exec/hydro_tests/double_mach_reflection/GNUmakefile
Exec/hydro_tests/double_mach_reflection/Make.package
Exec/hydro_tests/double_mach_reflection/Prob_2d.f90
Exec/hydro_tests/double_mach_reflection/bc_fill_2d.F90
Exec/hydro_tests/double_mach_reflection/inputs.2d
Exec/hydro_tests/double_mach_reflection/probdata.f90
Exec/hydro_tests/double_mach_reflection/probin.2d
commit 3d30775564081ddc844bbac973ec0475fe5f51c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 23 18:09:17 2018 -0400
an example with an aux variable
Microphysics/networks/general_null/gammalaw_aux.net
commit 54565ca249e6576e0bb02242fd3d5a727151d0b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 19:31:08 2018 -0400
Reset to the higher initial temperature to help the detonation along
Exec/science/Detonation/probin-collision
commit e3ae5b1a8918d25a353e126dbd4b42e5a24a9880
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 14:00:02 2018 -0400
Use post timestep regrid option
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/probin-collision
commit a2783a8c564f15f4c4388b19539263ac3034792a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 13:29:58 2018 -0400
Use a domain width that is a power of 2
Exec/science/Detonation/inputs-collision
commit 06538d3325c8aad27d641eb7518f98947604e5cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 12:39:48 2018 -0400
Use a smaller domain
Exec/science/Detonation/inputs-collision
commit 62f4d96bd6fc8132e4229332d9f1f087a4198714
Merge: 9d90a36ce c7aef1fa7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 12:38:39 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 9d90a36ce66778d35b439e3fea99700531f42fb9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 12:38:34 2018 -0400
Add custom stopping criteria to Detonation
Exec/science/Detonation/Prob.cpp
Exec/science/Detonation/Problem.H
Exec/science/Detonation/inputs-collision
commit c7aef1fa793c51a4bb39bbce49f1bde8c2bd838a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 10:54:49 2018 -0400
Use a colder initial temperature
Exec/science/Detonation/probin-collision
commit a43e222458616b180a15391be920c52a40e5830c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 03:12:35 2018 -0400
Earlier stop_time
Exec/science/Detonation/inputs-collision
commit 63e4edd404ae3f665df6c436c3c6be2dac30766c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 01:34:52 2018 -0400
Lower the dt_cutoff
Exec/science/Detonation/inputs-collision
commit 054146935b3663d7a872055928be3e49fcd1f91d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 22 01:34:45 2018 -0400
Use subcycling
Exec/science/Detonation/inputs-collision
commit c4f4e90906d67a57bf25bd9746ff17ce10802204
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 21 10:19:31 2018 -0400
Use maximum number of levels
Exec/science/Detonation/inputs-collision
commit 566dab10694ebb846ed4c70fe3e78677429f8c68
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 21 10:18:29 2018 -0400
Use PPM not PLM
Exec/science/Detonation/inputs-collision
commit bceb575033f58b5d3cee9d72eead6def1219fc92
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 21 10:18:20 2018 -0400
Use retry in detonation collision
Exec/science/Detonation/inputs-collision
commit 6c6c1bc76a70d1f70e4fbbaf23516b10b03f1f50
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 21 09:46:41 2018 -0400
Check in a collision setup for Detonation
Exec/science/Detonation/inputs-collision
Exec/science/Detonation/probin-collision
commit 0d56b737a0176bef244b0005b47ebbb7dcf3e76e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 21 02:18:26 2018 -0400
Initialize new-time reactions data after the first Strang burn
Source/driver/Castro_advance.cpp
commit 5524f90c6e89abd52556c268be68a48dc5066272
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 23:10:38 2018 -0400
Handle the case where we do a post-step regrid without use_retry = 1
Source/driver/Castro_advance.cpp
commit 0b36c9627b89324f6594a8639712d0fadc7278ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 23:00:08 2018 -0400
Always initialize an (empty) prev_state
Source/driver/Castro_advance.cpp
commit 6df7e78677ee869db7638e8d38d9ba150b4fa78f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 22:57:31 2018 -0400
Add an infall velocity to Detonation
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
Exec/science/Detonation/README
Exec/science/Detonation/probdata.f90
commit 3a7bc2add29523cca68c6bbfc99565158dc61bf9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 14:34:13 2018 -0400
Update Cray status at OLCF
Docs/ManagingJobs/managingjobs.tex
commit d19c1f68235d9b2b9f2944e200f4348d46aa653d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 11:04:07 2018 -0700
Update Cray status at NERSC
Docs/ManagingJobs/managingjobs.tex
commit a35996a3f118b18d995267130e8d68f46e42b277
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 13:45:47 2018 -0400
Add kinetic energy to the Detonation setup
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
commit db2de82356713fa502c5e72a18dcc1e116e63671
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 13:34:09 2018 -0400
frac is no longer used in this setup
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
Exec/science/Detonation/README
Exec/science/Detonation/probdata.f90
Exec/science/Detonation/probin-det-x.regrid
commit 86bf40b21ee1c3043e21a46a79df764a34330d99
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 20 13:25:22 2018 -0400
Fix typos
Exec/science/Detonation/README
commit 08e72ca0ee2a30963bc32f31738a5b70ea01cd3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 13:45:57 2018 -0400
IOProcessor to reduce parallel prints
Exec/science/flame_wave/initial_model.f90
commit 36dc15967e6028dadb9f914ec1c7155e9aca3cc9
Merge: c2b42c853 80928e690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 13:04:30 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit c2b42c8537db1e6570b3d1e09eeaee69ce3da122
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 13:04:16 2018 -0400
force cgs axes labels
Exec/science/flame_wave/analysis/slice.py
commit 80928e69056f7e9cd6b6917ccc3293a185e4a06c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 08:06:06 2018 -0700
looser tolerances
Exec/science/flame_wave/probin.boost.aprox13
commit 0cc367c0af3155049b5c2cf6a01f2acee180c92f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 10:51:29 2018 -0400
first pass at an aprox13 version
Exec/science/flame_wave/inputs_2d.boost.aprox13
Exec/science/flame_wave/probin.boost.aprox13
commit 0f92ddb492db9cb986636dcbf9d896c370acf177
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 07:28:36 2018 -0700
smaller CFL
Exec/science/flame_wave/inputs_2d.boost.hires
commit ab3bc1b668b04b23de6d575b1637cd15afa7278c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 19 07:28:25 2018 -0700
add limits to burning
Exec/science/flame_wave/inputs_2d.boost.wide
commit 2f5a9d58de14f3e991ce48fbff25d488ed697a1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 16 20:51:39 2018 -0400
some linting
Source/driver/parse_castro_params.py
commit f41507707f0a5bb06cb5e0e58b87e615c3ec36fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 16 20:11:45 2018 -0400
some linting
Microphysics/networks/general_null/write_network.py
commit 94c1b80484851f5800cca19353a3cf159aff067f
Merge: 94b4d1947 3ebd43065
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 15 11:29:22 2018 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 94b4d1947a1fb54e35bacafe61063771fb23d7b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 15 11:29:07 2018 -0700
new version for hires
Exec/science/flame_wave/inputs_2d.boost.hires
Exec/science/flame_wave/probin.boost.hires
commit 3ebd430652a63b2593f6b3d22e4a7897a485430e
Merge: da63ece64 6dbaf9674
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 15 12:03:05 2018 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit da63ece6464b5a813c1b4c7725fe0a1e34ef70c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 15 12:02:41 2018 -0400
add a routine to plot the grid
Exec/science/flame_wave/analysis/slice_grid.py
commit 6dbaf9674170ea990dca432032d629ca87f7f574
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 14 15:40:24 2018 -0400
move
Exec/science/flame_wave/old/inputs/inputs_2d.boost.base
Exec/science/flame_wave/old/inputs/probin.boost.base
commit 840699ed52831eccee9911c086d1d4ddd6650a4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 14 13:58:39 2018 -0400
add a tagging just on the buring layer
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost
Exec/science/flame_wave/problem_tagging_2d.f90
commit a8fe5afe576910c13a2df4df8ab5b29ab52f3e9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 13 14:26:30 2018 -0400
switch the conductivity cutoff back to 1.e4
the lower value impacts the timestep too much, and the density fall off
is so great in this region, that these differences don't matter to the
dynamics
Exec/science/flame_wave/inputs_2d.boost.wide
commit ff9954e9cec24a2eb8cd243a6c4c5957e645e309
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 12 18:43:58 2018 -0400
refine the cutoffs
now we diffuse down to rho = 1.e2
and we only burn in 1.e2 <= rho <= 5.e7
the lower limit corresponds to the sponge density
Exec/science/flame_wave/inputs_2d.boost.wide
commit 39d6dc91188e2ecbcf08a226a14ce2f894941bf3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 12 18:30:41 2018 -0400
add z velocity + better contouring
Exec/science/flame_wave/analysis/slice.py
commit c9f029fd02b51efe78d154bd1f2f75a5f8566c40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 16:50:41 2018 -0700
tweak perturbation size
Exec/science/flame_wave/probin.boost
commit dfe0d8ce91419f01ca627ab6559f069060115ce9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 16:16:00 2018 -0700
this is the wide version
Exec/science/flame_wave/inputs_2d.boost.base
commit d9257af9de6321956dc8d1ca536c9a73da28a533
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 18:36:12 2018 -0400
make the lower g our default
Exec/science/flame_wave/inputs_2d.boost.wide
Exec/science/flame_wave/old/inputs/inputs_2d.boost.g
commit 1757fa8c3c60f3d2bfc625208e8af613b26ebf46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 18:34:50 2018 -0400
move
Exec/science/flame_wave/old/inputs/inputs_2d
Exec/science/flame_wave/old/inputs/inputs_2d.boost
Exec/science/flame_wave/old/inputs/inputs_2d.boost.omega10
commit 2c38c5c3dd7a16c8ef50cb7926034c3eceeffcdd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 18:34:06 2018 -0400
move
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.aprox13
Exec/science/flame_wave/old/models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.cool
commit e7ba669b96cc332ddef20426f3312d66ddbddd13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 15:03:55 2018 -0400
tighten up the transition
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/probin.boost
commit a5df227ff56e594d0619cb05ee58c0bccaed2ce6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 7 09:29:18 2018 -0400
add MLMG note
CHANGES
commit 23b8778e3c4946d5ac78d3a2765b11735830b21b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 6 15:30:14 2018 -0700
these are the latest versions running @ NERSC
Exec/science/flame_wave/inputs_2d.boost.g
Exec/science/flame_wave/inputs_2d.boost.wide
commit c8e350242a2ad30b223d8dbee21d5d03317e0a87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 6 17:52:56 2018 -0400
add a version w/ lower g
Exec/science/flame_wave/inputs_2d.boost.g
commit 81f74aa147e4291ce97aadf1d1e46614b245f72c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 4 12:55:25 2018 -0400
make MLMG the default solver
* make the mlmg solver the default for diffusion and gravity
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/param_includes/diffusion_defaults.H
Source/driver/param_includes/diffusion_job_info_tests.H
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_job_info_tests.H
commit 1d1db472901e3efaf03277b1d6f3de77d62c4f22
Merge: 8b74010d8 1ba68c6ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 3 09:14:12 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 8b74010d814ccc2a51988d0feb2123f2a2a9e2bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 3 09:13:57 2018 -0400
remove print
Exec/science/flame/analysis/profiles.py
commit 1ba68c6ed524db31f59f4c4e7893349c28beeebb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 18:01:14 2018 -0400
add convergence results
Exec/unit_tests/diffusion_test/convergence_sph.txt
commit cf08d2d2fce5c6f7cdfec46e4cb7bb16bbc859b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 17:28:41 2018 -0400
for multilevel axisymmetric runs, we need diffusion.use_mlmg_solver = 1
otherwise things blow up fast
Exec/unit_tests/diffusion_test/inputs.2d.sph
commit 6e4460ac903b298b281a891576a8815f59e4cfd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 16:08:16 2018 -0400
make this multilevel
Exec/unit_tests/diffusion_test/inputs.2d.sph
Exec/unit_tests/diffusion_test/probin.2d
commit be60e6b6f5a4ca98921dab0d006c7251d1bb5fdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 15:45:04 2018 -0400
sync up params with flame_wave
Exec/science/flame/flame_wave_tests/inputs.1d.flame_wave.boost
commit 8f5401475271c6d619981586af5fff44e0fb82e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 15:24:40 2018 -0400
add test files
Exec/science/flame/flame_wave_tests/README.md
Exec/science/flame/flame_wave_tests/inputs.1d.flame_wave.boost
Exec/science/flame/flame_wave_tests/probin.boost
commit e740e842dc982665e79e03c53a65326585acc7df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 14:49:15 2018 -0400
zoom in on the profile
Exec/science/flame/analysis/profiles_zoom.py
commit 654e38360404b2485fb342ca2c4a2087d2cbc5b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 12:47:56 2018 -0400
update changes
CHANGES
commit 07d5860323fb2235146f621bde972d5338be556f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 11:52:04 2018 -0400
move
Exec/science/flame_wave/analysis/image_animator.py
Exec/science/flame_wave/analysis/multirays.py
Exec/science/flame_wave/analysis/plot_generator.py
Exec/science/flame_wave/analysis/profile2.py
commit 634660283d47c5b026ee0999507f77a18b153e91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 30 13:24:07 2018 -0400
update time
move to analysis/
Exec/science/flame_wave/analysis/slice.py
commit 71aa75972371eb961c340f78a86758a902203a60
Author: KiranEiden <32306975+KiranEiden@users.noreply.github.com>
Date: Mon Apr 30 19:46:04 2018 -0400
Added Python scripts for flame_wave visualization (#325)
plot_generator.py creates slices and projections, multirays.py generates 1D vertical ray plots from axisymmetric datasets, and image_animator.py builds animations from sets of images. All of them take command line arguments - launching the script with the -h or --help flag displays the options.
Exec/science/flame_wave/image_animator.py
Exec/science/flame_wave/multirays.py
Exec/science/flame_wave/plot_generator.py
commit 990ce56261ec2640ae1a54006c949032dc302661
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 29 17:38:58 2018 -0400
a new version with lower sound speed + more resolution
Exec/science/flame_wave/inputs_2d.boost.base
Exec/science/flame_wave/probin.boost.base
commit f872d0656b89817c2e8594a2262304505999e539
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 26 15:02:04 2018 -0400
add Gamma_1 as a derive (#323)
Source/driver/Castro_setup.cpp
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
commit 4fd8192cf172900bd2419e0cd58f58b64f7522a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:49:39 2018 -0400
sync up parameters with production inputs
Exec/science/flame_wave/inputs_2d.testsuite
commit 65607c50424c9206e30527e807617bb621357c69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:42:20 2018 -0400
set the model params
Exec/science/flame_wave/probin
commit 8da0c87ac1cb3e9c8cc8112dfcb2809dcc53ada8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:38:28 2018 -0400
model_name is no longer needed
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin
commit fe11d570341d69ea9874bbbb32799e41b0002768
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:33:00 2018 -0400
add state_nghost = 1 here for test suite coverage
Exec/hydro_tests/reacting_bubble/inputs_2d_test
commit 811329ff3c5c2812b1a9e789f36028cc2e8a89c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:24:54 2018 -0400
add limit_fluxes_on_small_dens to testing
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
commit be339e9f7281e1156baa66df4c0c30e5b3b29da0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:15:38 2018 -0400
add castro.rotation_include_centrifugal
this will be covered in the test suite now
Exec/science/convective_flame/inputs.2d.testsuite
commit 691e95a9951cfb1a855d7e508fa468b2687ceef6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 25 15:15:22 2018 -0400
we misspelled centrifugal
Exec/science/convective_flame/inputs.2d_good
commit a49517bcef75bc6868b83bf32b39645aa7f685a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 22 21:29:18 2018 -0400
add the 2-d axisymmetric diffusion problem + analytic solution
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/inputs.2d.sph
Exec/unit_tests/diffusion_test/prob_util.f90
commit 764130520d955c9bbb5413f6542e2a2e3b358fe2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Apr 18 10:30:37 2018 -0700
mempool_module --> amrex_mempool_module
Source/gravity/gravity_sources_nd.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/slope_nd.F90
Source/rotation/rotation_sources_nd.F90
commit 969525942354002d62e40bdd45fae109788fac24
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Apr 17 17:44:39 2018 -0700
Real --> amrex::Real
Exec/science/wdmerger/Problem_F.H
commit 225c33cd896d60d693a4e7e01ece2ce409d54567
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 14 13:16:03 2018 -0400
add the git describe status to build output
Exec/Make.Castro
commit 8c5f98e7c93fa68612844ecb1379bee0b94d4b83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 13 20:25:59 2018 -0400
slightly bigger perturbation
Exec/science/subchandra/probin
commit 7a5b65aac8fde9fd0bb2a607457f67cfdfa41a3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 13 18:26:26 2018 -0400
turn on reactions
Exec/science/subchandra/inputs_2d
commit 0f902ee89b499c9a12c2dcf2cb189499b2f7641c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 13 16:24:16 2018 -0400
add a perturbation
Exec/science/subchandra/Prob_2d.f90
Exec/science/subchandra/probdata.f90
commit 0abe4abcfc22ce4c1edbdb3c02286122f8045935
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 12 14:06:58 2018 -0400
Revert "Fix dimension agnostic"
This reverts commit d130b9e81039dc7ce0eb59a22cb9821945a61a6a.
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Source/problems/Make.package
Source/sources/Make.package
commit d54dda93506688b69772b15ea40afbe23f28adc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 12 11:47:34 2018 -0400
loosen tolerances a bit
Exec/science/flame_wave/probin.boost
commit d130b9e81039dc7ce0eb59a22cb9821945a61a6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 12 11:31:21 2018 -0400
Fix dimension agnostic
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Source/problems/Make.package
Source/sources/Make.package
commit a6c4eb0d9e3e124180f50b465caa1155f1f8699f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Apr 11 15:47:35 2018 -0700
DEBUG --> AMREX_DEBUG
Source/driver/param_includes/castro_defaults.H
Source/driver/parse_castro_params.py
commit f7adf3afb057b06266e31587897695eb0c5feb7a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Apr 11 15:42:04 2018 -0700
DIMENSION_AGNOSTIC --> AMREX_DIMENSION_AGNOSTIC
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_error_F.H
Source/driver/Castro_io.cpp
Source/sources/Castro_external.cpp
commit 9d0abae7203146ca127fac74d4e1bcab9c168525
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Apr 11 11:38:36 2018 -0700
PARTICLES and USE_PARTICLES --> AMREX_PARTICLES
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/particles/CastroParticles.cpp
commit 1451730555de60a0a7d5ca479eca2f28a91a7dd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 11 19:24:45 2018 -0400
start of a subchandra setup
the castro setup builds from StarGrav
the inputs model comes from Maestro, in the subch paper_II stuff
Exec/science/subchandra/GNUmakefile
Exec/science/subchandra/Make.package
Exec/science/subchandra/Prob_2d.f90
Exec/science/subchandra/inputs_2d
Exec/science/subchandra/probdata.f90
Exec/science/subchandra/probin
Exec/science/subchandra/sub_chandra.M_WD-1.00.M_He-0.040.hse.C.10240
commit 6a7654334d9eb2829a9f2c8a56a594ab52211f23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 11 19:05:38 2018 -0400
explicitly pick VODE
Exec/science/flame_wave/GNUmakefile
commit eb7da9c9d9025a78538182e7aad64a81d71ba366
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 10 17:30:41 2018 -0400
fix some module includes to use only
Source/driver/Castro_util.F90
Source/driver/Derive_nd.F90
Source/driver/sums_nd.f90
Source/driver/timestep.F90
commit 7147cfb9e5b97881022541d58154f87203c8107d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 10 12:38:40 2018 -0400
some use only fixes
Source/hydro/advection_util_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/multid_slope_2d.f90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_util.F90
Source/hydro/slope_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_3d.F90
commit d6af3eac4b43abcaa4b38ec893d389710c10e0c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 10 06:59:27 2018 -0700
declare missing var
Source/problems/bc_ext_fill_2d.F90
commit 4512b112f5edda4bf21f06a93a6934f400367307
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 10 06:57:21 2018 -0700
change the reflect in 2-d to be more consistent
some 'only' clauses too
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_ext_fill_3d.F90
commit 4cd0d5f2def473208bef740ec3dae0566d7d7b71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 10 08:33:06 2018 -0400
forth -> fourth
Source/radiation/_interpbndry/RadInterpBndryData_3d.F90
commit 835b62998c7d44d980a5d48662e7a15d69df730c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 9 19:05:56 2018 -0400
tighten T limits
add rho plot
add time
Exec/science/flame_wave/slice.py
commit 282938fab9adade54767769654a019ba068be2e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 7 15:48:17 2018 -0400
fix interface mismatches
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
commit 4e5549efc92d916dd8a0a1810ccc4654170ca862
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 4 20:30:36 2018 -0400
fill the model in some ghost cells to allow for BC interp
Exec/science/flame_wave/Prob_2d.f90
commit 9f57eb6af2f5f87c8e9eecb8c8a60945e5c1b2c3
Merge: cc88f4ac7 a4bec3cb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 3 10:08:11 2018 -0700
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit cc88f4ac797cde366e4d9cc8018fe15daad51902
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 3 10:07:59 2018 -0700
enable the new diffusion solver
Exec/science/flame_wave/inputs_2d.boost
Exec/science/flame_wave/inputs_2d.boost.omega10
commit a4bec3cb434bc5411fd0221c99dd28ea7a34f4e4
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Tue Apr 3 10:06:05 2018 -0700
Mlmg diffusion (#315)
* option to use MLMG for diffusion operator
* remove an old assertion
* add new parameter diffusion.mlmg_maxorder
Docs/runtime_parameters/runtime_parameters.tex
Exec/Make.Castro
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/diffusion_defaults.H
Source/driver/param_includes/diffusion_job_info_tests.H
Source/driver/param_includes/diffusion_params.H
Source/driver/param_includes/diffusion_queries.H
Source/gravity/Gravity.cpp
commit af61d2e87adacfd7ea8a326992ddc5c789f4549b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 2 18:17:32 2018 -0400
fix index bug
Exec/science/flame_wave/initial_model.f90
commit 94121287061cd47f1f2c3faea47becde715d8bca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 2 13:50:02 2018 -0400
switch to user upper boundary
remove prints
fix name clashes (when will Fortran get namespaces?(
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/inputs_2d.boost
Exec/science/flame_wave/slice.py
commit 5e9bd2f7a699a45447b92a1c9c3064f6c2e3552c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 2 12:09:22 2018 -0400
update CHANGES`
CHANGES
commit 55de1491b5dc5a69a15ff41b4276cc73f9e5e7a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 2 12:08:27 2018 -0400
less frequent output
Exec/science/flame_wave/inputs_2d.boost
Exec/science/flame_wave/inputs_2d.boost.omega10
commit 75ab366bcf2306e4f86d649e15594fefb377b58f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 2 12:07:35 2018 -0400
these are no longer relevant now that we automagically generate
the model
Exec/science/flame_wave/inputs_2d.boost.hot_ash
Exec/science/flame_wave/probin.boost.hot_ash
commit 531bce7e98289f4d0d03bdb9f904a7551c556709
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 1 12:49:18 2018 -0400
update CHANGES
CHANGES
commit 39b2bc29a717cf88d9911d6d55f447fbf4b5a318
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 31 15:54:16 2018 -0400
revise how runtime parameters are output to job_info (#314)
This now outputs all of the runtime parameters know to Castro (via _cpp_param_file)
to the job_info and indicates whether a run overrode the default
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/Castro_io.cpp
Source/driver/param_includes/castro_job_info_tests.H
Source/driver/param_includes/diffusion_job_info_tests.H
Source/driver/param_includes/gravity_job_info_tests.H
Source/driver/param_includes/particles_job_info_tests.H
Source/driver/parse_castro_params.py
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit eb4604e8b571524de6cc459ac1a2af75e442b074
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 29 13:01:17 2018 -0400
sync up with inputs_2d.boost
Exec/science/flame_wave/inputs_2d.boost.omega10
commit 20dd32e938b21982fbb024d0cba40df5afec19a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 29 11:05:01 2018 -0400
add frame of reference fig
Docs/CastroUserGuide.tex
Docs/Rotation/CastroRotation.tex
Docs/Rotation/frames.py
Docs/Rotation/tframes.png
commit 787d3b493947687671d17923699ed7e80bfaaff6
Merge: fecdd2b45 6a68c1f84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 27 20:31:26 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit fecdd2b45c46b266675fdcd79e514bf9ed517e73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 27 20:31:16 2018 -0400
spelling
Docs/Rotation/CastroRotation.tex
commit 6a68c1f844d5c577034efbff19e1e192625e7dd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 27 10:11:11 2018 -0400
more aggressive sponge
Exec/science/flame_wave/probin.boost
commit 3a20c2674374e932af684a06f7a73c7d0705ac00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 21:22:09 2018 -0400
rename for clarity
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost
commit 2b9b7a77bd4c532b725f12f6f02624027954fc14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 21:05:50 2018 -0400
wider lateral transition
Exec/science/flame_wave/probin.boost
commit 9be043f9f472977468fb34d2b73429ea89939e75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 20:59:47 2018 -0400
a wider transition
Exec/science/flame_wave/probin.boost
commit c45445adbf4115842b3a77988c1b276873f800c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 20:54:38 2018 -0400
this version makes the pressure in the atmosphere beneath the fuel
layer identical laterally. This is done by starting the integration
in the star instead of the base of the fuel layer.
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/probin.boost
commit 435996217a5e7f58fca4f88c19aa0a5f5e08a660
Merge: b4b5a2780 e8120973f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 19:11:12 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit e8120973fdff384b2136d8b01a059d97a7ff4fd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 19:10:53 2018 -0400
add some profile figs
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/profile2.py
commit b4b5a27803e5d47f9c2c2c9870f6a272d0fe5255
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 19:09:30 2018 -0400
we now build models in init
Exec/science/flame_wave/old_models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
Exec/science/flame_wave/old_models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.aprox13
Exec/science/flame_wave/old_models/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.cool
commit 11d4cac9f0803543f9101115b505e6f433c3169b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 13:51:15 2018 -0400
blend the two HSE models to create a transition region also in HSE
Exec/science/flame_wave/Prob_2d.f90
commit ff3bbcc7dc6c40dc5f140e20056c3f915d0a1858
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 26 12:37:07 2018 -0400
bigger T pert
engage sponge
Exec/science/flame_wave/inputs_2d.boost
Exec/science/flame_wave/probin.boost
commit c322f893e0cd3f259738017e73edb898503a26a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 25 21:04:03 2018 -0400
add an init_shrink
Exec/science/flame_wave/inputs_2d.boost
commit c5fb902c840a2216e7df8e905733b89493a972f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 25 20:47:02 2018 -0400
now allow for two different HSE models side-by-side
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/initial_model.f90
commit 4e2403d713ba8fdc68daebe98d35d80d8aea04e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 25 19:47:11 2018 -0400
this now automagically generates a base model -- no perturbation
Exec/science/flame_wave/Make.package
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/initial_model.f90
Exec/science/flame_wave/inputs_2d.boost
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost
commit 9e77987c8f16b460a6cf91e14b8591ef815e72cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 25 17:25:31 2018 -0400
start of a built-in initial model generator that can manage multiple HSE profiles
Exec/science/flame_wave/initial_model.f90
commit 615f2792f828a8cff93109d3320c5607f2a00adb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 21 14:48:15 2018 -0400
add cray compilation note
Docs/ManagingJobs/managingjobs.tex
commit f3cc0b8dc3361fbc7246612274484297bd479b21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 21 11:34:20 2018 -0400
separate out the hot ash to a separate inputs/probin
Exec/science/flame_wave/inputs_2d.boost.hot_ash
Exec/science/flame_wave/probin.boost
Exec/science/flame_wave/probin.boost.hot_ash
commit 1e0ec3bf2d33f3b56b63f66e223366eaf4408a00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 21 05:43:43 2018 -0400
use retry
Exec/science/flame_wave/inputs_2d.boost
commit f91da97f2f9d0636ff80c378b734e25279d13dfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 20 21:20:48 2018 -0400
use the cooler model + adjust the perturbation a little
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/probin.boost
commit 29243ddaceb71fc159335aaa534b0d3d2735676f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 20 20:57:38 2018 -0400
cooler model
Exec/science/flame_wave/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.cool
commit c5530d2e958f69c1da3c7937bfef04157bd61289
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 19 20:48:16 2018 -0400
add the ability to set the hot region to ash with a profile
that matches the temperature profile
Exec/science/flame_wave/GNUmakefile
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/README.md
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/probin.boost
commit 729a18dc9994242ee591268cee79b36269b903ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 19 20:12:16 2018 -0400
triple_alpha_plus_cago version
Exec/science/flame_wave/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
commit d1003c3ecab250091b88dedf570547e705e17a04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 19 20:10:27 2018 -0400
store the aprox13 version
Exec/science/flame_wave/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm.aprox13
commit 1ec81c59e79666f5a5be8ad948c063a21fc60343
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 17 08:37:41 2018 -0700
add retry
Exec/science/flame_wave/inputs_2d.boost.omega10
commit 9f17af16fe320e00ff6433147c105ec9ed06c14c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 14 17:02:29 2018 -0400
this now gets 4th order convergence
when run with acoustic_pulse and without computeTemp or clean_state
Exec/hydro_tests/acoustic_pulse/convergence.sh
Source/hydro/Castro_fourth_order.F90
Source/hydro/advection_util_nd.F90
commit 03041cd937de2953e283a39b38a5c36430c7c8f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 14 14:55:56 2018 -0400
somehow I got it into my head that the Laplacian has a 1/2 in it
I was wrong
Source/hydro/fourth_order.F90
commit 5b7c1787c0ac3becf36e636780c6dc4ba499fa9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 14 14:09:47 2018 -0400
use eos_gamma = 1.4 + make things double
Exec/hydro_tests/acoustic_pulse/Prob_2d.f90
Exec/hydro_tests/acoustic_pulse/probin
commit 898bd4ca17ee828a1bdfd93c40f4427598fa2549
Merge: b4a8691c1 240bda1ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 14 11:42:59 2018 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit b4a8691c135158fea4e258f4b79b06cbfc2f53b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 14 11:42:48 2018 -0400
boosted version
Exec/science/flame/inputs.1d.aprox13.boost
Exec/science/flame/probin.boost
commit 240bda1eed0d2e5f4c9ed890aca67aebf1e91aed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 13 17:50:40 2018 -0400
test slack
Exec/science/convective_flame/README
commit f86afbd3c7f997adfdddd146f491201ce8d72bb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 13 17:49:28 2018 -0400
update comments
Exec/science/convective_flame/README
commit 2bcf7edbe8ce86cb1ad1fe8fc70ef4f8160c4082
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 13 14:49:06 2018 -0400
a simple vis script using yt
Exec/science/flame_wave/slice.py
commit d5de4e71885ce7b7f85a086a9bfdb1e0f7486b84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 13 13:02:31 2018 -0400
since we allow retry, turn off hard cfl limit
Exec/science/convective_flame/inputs.2d_good
commit 280cee4b0e920f8ba6bf7edeff3c800b150ed078
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 11 12:26:29 2018 -0400
no longer need the initial model -- it is generated at runtime
Exec/science/convective_flame/convective_flame.hse.tanh.delta_0.040cm.dx_0.050cm
Exec/science/convective_flame/probin
commit de5ae27663c58142192266ffa8d913f13b6640d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 9 15:46:15 2018 -0500
fix a bounds issue
Exec/science/convective_flame/initial_model.f90
commit 119df5a9f9f444a79013272b4fc7d3db9d514481
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 9 14:48:43 2018 -0500
this seems to init, but doesn't work quite right yet
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/convective_flame/probin_good
commit a49d4d0cc275db814d725b3b535fba502497468f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 9 12:54:13 2018 -0500
require nx_model -- can't seem to get the grid size at init time
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/probdata.f90
Exec/science/convective_flame/probin_good
commit a1462763d394c9da804718133a4f6cf39bc4dca8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 9 11:33:44 2018 -0500
start of hooking in the initial model generator directly
Exec/science/convective_flame/Make.package
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/initial_model.f90
Exec/science/convective_flame/probdata.f90
commit b7bd3ab838982a19273d6e3357cbd5004742337c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 5 21:23:30 2018 -0500
Add a temperature stopping criterion
Also enable stopping criterion in 1D
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
commit c34bf8cd96085f7225042f28cef9dc8e94c264ad
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 5 20:57:12 2018 -0500
Add 1D 'collision' test
Exec/science/wdmerger/tests/wdmerger_collision_1D/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_collision_1D/inputs
Exec/science/wdmerger/tests/wdmerger_collision_1D/probin
commit 3cc25d43e8de636f96f98f02939f9fb336ebc7f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 4 16:24:06 2018 -0500
rename to reflect problem name
Exec/hydro_tests/KH/inputs.2d.p3
Exec/hydro_tests/KH/probin.p3
commit 018fac1529d7c54ab7d39f3948d1a1ba4b409f34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 2 14:06:19 2018 -0500
Hydro cleaning (#303)
This removes a bunch of slices from the innards of the hydro
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/fourth_order.F90
Source/hydro/multid_slope_2d.f90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
Source/radiation/trace_ppm_rad_nd.F90
commit 75acb727cb0c6d8ea46b8a9d3c1984ae096a929c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 1 14:05:06 2018 -0500
fix output file name
Exec/science/convective_flame/slice.py
commit 6eeb49e9ba8ecf1c6d5695fd36a1ebf726ac32a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 1 13:54:40 2018 -0500
nice default plot for this sim
Exec/science/convective_flame/slice.py
commit 0818ff4d9fdbcc2ddcb0ffce5f0e7e099d8a9497
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 28 09:31:54 2018 -0500
update for 18.03
CHANGES
commit e47366461cb8666fc30032f945725c60cc6510f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 27 19:48:11 2018 -0500
need to expand state before filling the sources the last time
this addresses #301
this may not be the most efficient solution
Source/driver/Castro_advance.cpp
commit b35e3bb078dc0b4a3b8d384844c907cf3d41698e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 26 10:22:06 2018 -0800
narrower domain
Exec/science/flame_wave/inputs_2d.boost
commit 0aa172c445a0bd63dac8d144b01e64e5e639cfb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 26 10:17:17 2018 -0800
job scripts for this run
Exec/science/flame_wave/job_scripts/edison.MPI.slurm
Exec/science/flame_wave/job_scripts/edison.xfer.slurm
commit 59421c7abcf437b4ebe00a6e22819d8494e8835e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 26 10:11:23 2018 -0800
sync up with the new version
Exec/science/flame_wave/inputs_2d.boost
commit 095e163aae827d00de3b2b8a84a048ab879c005d
Merge: ac7afcda9 2660d40d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 26 10:10:20 2018 -0800
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit ac7afcda9e09accc8318a62e9d45ce03e257489f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 26 10:10:02 2018 -0800
new inputs
Exec/science/flame_wave/inputs_2d.boost.omega10
commit 2660d40d2f48afff5dc3e7da0cfd605696985368
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 26 12:52:16 2018 -0500
update MOL
CHANGES
commit 4b642297f3eb2ef90c06a731a9b07ebf895ae80f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 25 10:15:15 2018 -0500
various fixes to MOL (#288)
This is a rewrite of the MOL driver. In particular, it addresses:
#287 (moving p divU to sources)
#286 (number of ghost cells for MOL)
#164 (treatment of sources with MOL)
#291 (initialization as true averages)
#137 (pradial weighting)
and prepares use for 4th order
Docs/FlowChart/FlowChart.tex
Docs/runtime_parameters/runtime_parameters.tex
Exec/hydro_tests/acoustic_pulse/GNUmakefile
Exec/hydro_tests/acoustic_pulse/Make.package
Exec/hydro_tests/acoustic_pulse/Prob_2d.f90
Exec/hydro_tests/acoustic_pulse/README
Exec/hydro_tests/acoustic_pulse/convergence.sh
Exec/hydro_tests/acoustic_pulse/inputs.2d.128
Exec/hydro_tests/acoustic_pulse/inputs.2d.256
Exec/hydro_tests/acoustic_pulse/inputs.2d.512
Exec/hydro_tests/acoustic_pulse/inputs.2d.64
Exec/hydro_tests/acoustic_pulse/probdata.f90
Exec/hydro_tests/acoustic_pulse/probin
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/Castro_fourth_order.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/Make.package
Source/hydro/fourth_order.F90
Source/hydro/outline.txt
Source/hydro/riemann_nd.F90
Source/sources/Castro_sources.cpp
Source/sources/Castro_thermo.cpp
Source/sources/Make.package
Source/sources/thermo_nd.F90
commit f1501706f1a46b445f2e735c15ef47e83dd90f44
Merge: 81f0eb2ae ea4a88632
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 22 13:21:21 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 81f0eb2aec537c09d82c61e8eaaf9be0164787ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 22 13:21:01 2018 -0500
lower CFL # -- this seems necessary after the merge of source
tracing on by default
Exec/science/convective_flame/inputs.2d_good
commit ea4a88632300edecfe992b7fa18d61de04a058d2
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Feb 22 12:51:15 2018 -0500
F interface lohi (#300)
making (lo, hi) the first arguments of the fortran subroutines
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Exec/hydro_tests/toy_convect/problem_tagging_2d.f90
Exec/radiation_tests/RadFront/Prob_2d.f90
Exec/science/convective_flame/problem_tagging_2d.f90
Exec/science/flame_wave/problem_tagging_2d.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/xrb_mixed/problem_tagging_2d.f90
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_error_F.H
Source/driver/castro_c_interfaces_nd.F90
Source/driver/timestep.F90
Source/gravity/Castro_pointmass.cpp
Source/gravity/Gravity.cpp
Source/gravity/Gravity_F.H
Source/gravity/pointmass_nd.f90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/problems/problem_tagging_1d.f90
Source/problems/problem_tagging_2d.f90
Source/problems/problem_tagging_3d.f90
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
commit 23b1985ec85bf3ca4dd69f0c85c6b07eebca9a62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 22 12:19:30 2018 -0500
update centrifugal
Exec/science/convective_flame/inputs.2d.test
Exec/science/convective_flame/inputs.2d_good
commit 06edfdeae85dd16012c186472765e09ba9d20955
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 21 20:30:17 2018 -0500
this doesn't seem to be used
Exec/science/convective_flame/convective_flame.hse.tanh.delta_0.040cm.dx_0.040cm
commit 8ee97ae60b24278b811f4826e83cfa395c7a349e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 21 20:28:51 2018 -0500
point to probin_good
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/probin_good
commit 113bbd030dc5e5a3cfaf6582d39ed41af96672ba
Merge: 89fe3d501 93aee0fe1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 21 12:10:23 2018 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 89fe3d50172e807f5fa1cafd21f04098293dea76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 21 12:02:55 2018 -0500
this is our new reference case
Exec/science/convective_flame/inputs.2d_good
Exec/science/convective_flame/probin_good
commit 93aee0fe1be4791ed9fcbe05d7e1a44ce16ba1ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 15 12:04:06 2018 -0500
fix source index
Source/radiation/trace_ppm_rad_nd.F90
commit 9c90d5c3bb21f2f7c65380ad8d400e9608c68b10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 15 10:13:28 2018 -0500
fix compilation
Source/hydro/Castro_advection_1d.F90
commit 7609fb4f81dd94e31d4faa03ad82e5d587b5c775
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 15 09:59:15 2018 -0500
update CHANGES
CHANGES
commit 239a050c0c1eaa7d7027315310eec963cc55263a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 15 09:57:41 2018 -0500
do source tracing on _all_ sources by default (#186)
remove ppm_trace_sources option and trace all sources by default
in addition to changing the default, this also traces all sources,
not just momentum sources
we no longer add source terms to states for ppm_type > 0
the tracing takes care of that
we no longer need srcQ in tracing
Docs/Hydrodynamics/Hydrodynamics.tex
Docs/runtime_parameters/runtime_parameters.tex
Exec/hydro_tests/reacting_bubble/inputs_2d
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/convective_flame/inputs.2d.testsuite
Exec/science/flame_wave/inputs_2d
Exec/science/flame_wave/inputs_2d.testsuite
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_2d.F90
Source/hydro/trans_3d.F90
Source/radiation/trace_ppm_rad_nd.F90
commit e470515210c9cbd9b7a78541e43416c5700910f0
Merge: 5a4503326 94cd97506
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 14 16:34:39 2018 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 5a450332676722d4266a5ca81b5f7bf7c037d902
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 14 16:34:25 2018 -0500
update amrvis to point to the github
Docs/GettingStarted/CastroGettingStarted.tex
commit 94cd975062caea70850abbedd3545df344f84c07
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 9 15:19:28 2018 -0500
Fix typo in comment
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.SDC
commit b038ce8ff11ddae457d4d1658ef4f3917b96fd7f
Author: Alan Calder <alan.calder@stonybrook.edu>
Date: Fri Feb 2 20:31:56 2018 -0500
update to user's guide (#282)
* Fixed typos in the URL for starkiller-astro
* Fixed wget URL for yt script and instructions for updating yt.
* Fixed wget URL for yt script and instructions for updating yt.
Docs/Visualization/CastroVisualization.tex
commit e03cb134c37d509748a249c694c52bb8a5c2cc7e
Merge: c20d9df0e 72a7ee141
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 1 11:25:42 2018 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 72a7ee141e74c20ceb1430414d88c072dc729c2e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 23 11:14:45 2018 -0800
Array --> Vector
Exec/science/wdmerger/Prob.cpp
commit c20d9df0e817245b6c18697507811c34c6368c88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 23 12:01:09 2018 -0500
note changes
CHANGES
commit a3babc27eb9b15cc97a8b2110e552ffc2b0a3610
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 21 19:50:09 2018 -0500
fix comment
Source/problems/bc_ext_fill_1d.F90
commit d79a681ccb55bb618d4cdd3be4273a24b1ca4bbb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 21 04:50:30 2018 -0500
Write out timestep duration to the AMR log
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit 9a8c759b7631b54e4087c23180ded28cf5a182cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 21 04:49:22 2018 -0500
Save the wall time at the beginning of a timestep
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit 59553d00834aeca28a1ba0b92c8d58753a07cb99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 20 14:50:39 2018 -0500
Split the approximate state RIemann solvers so we can access the full interface state (#283)
The approximate state Riemann solvers are now split into two parts: the main solver routine now returns the full interface state (indexed as the primitive state with NQ components) and a separate routine computes the fluxes and the reduced set of Godunov state (with NGDNV components). No changes to the test suite result. This closes #279
Source/hydro/Make.package
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.F90
commit 9119f4b15b92189a98a9362744744e628163e9cd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 19 16:33:54 2018 -0800
mlmg_msolve --> mlmg_nsolve
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/gravity/Gravity.cpp
commit 5bc49f043b61da8ed51a9120f185d66e0020e57a
Author: Alan Calder <alan.calder@stonybrook.edu>
Date: Thu Jan 18 14:12:44 2018 -0500
Fixed typos in the URL for starkiller-astro (#281)
Docs/GettingStarted/CastroGettingStarted.tex
commit 20aaae492bbf1d687c94dd29a29b9c716579cdac
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 17 10:44:18 2018 -0800
new runtime parameter gravity.mlmg_msolve=0 for M-Solve
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/gravity/Gravity.cpp
commit 2f450216dd7eef3128d5a4aeb6171b9781687aef
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 16 03:51:31 2018 -0500
Simplify relaxation by using a lagged application of the new rotation period
This was a previous approach; we revert to this approach because the effect of
re-calculating the source terms is negligible compared to simply waiting for the
next time step for the updated rotation period.
Exec/science/wdmerger/Prob.cpp
commit ada2cd18cd1d2c517c057e567da3d3cbd25286b3
Merge: c3f656dd7 9ca101df6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 16 02:04:23 2018 -0500
Merge branch 'wdmerger_relaxation_new' into development
commit c3f656dd7cc9c12713c69dc9ef34b9f17bac7311
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 15 21:03:03 2018 -0500
fix an indexing bug
Source/hydro/riemann_nd.F90
commit c79b5eb74fc983c799529e028bf25966598fd193
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 14 18:02:00 2018 -0500
Fix error in subroutine name
Source/rotation/Rotation_nd.f90
commit dd027ece828966d06bad27986c65b4c46d5d7f36
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 9 13:02:02 2018 -0500
Add option to disable initial orbital motion for TDE
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/wdmerger_util.f90
commit 5ab40b2e2f1444e5902b6806fa7ad4c12678d4fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 8 00:49:27 2018 -0500
Add parameter for disabling point mass
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/gravity/Gravity.cpp
commit 711934b4bc046304a1b8aa00619d33755d522205
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 7 06:13:06 2018 -0500
Add a TDE test setup
Exec/science/wdmerger/tests/tde/GNUmakefile
Exec/science/wdmerger/tests/tde/inputs
Exec/science/wdmerger/tests/tde/probin
commit b5416ef654cbb151f5027648e82485f015cda813
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 7 06:12:23 2018 -0500
Add wdmerger problem 5, a tidal disruption event setup
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.f90
commit 456c2a90856ae7df97d6f6bc31ec9622ffd6e790
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 2 13:59:50 2018 -0500
more updates to reflect latest code
Docs/FlowChart/FlowChart.tex
commit 67363497c8ef173a909523401619d447cd731464
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 2 11:13:52 2018 -0500
update initialization
Docs/FlowChart/FlowChart.tex
commit a8c610d3d84ba034eda3b86258f6ff1e146b867b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 2 10:35:47 2018 -0500
SDC_Source_Type, old_sources, and new_sources no longer exist
Docs/Software/CastroSoftware.tex
commit 3763d1affd278a83e09eae2926926e3db1883026
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 2 09:55:14 2018 -0500
update CHANGES
CHANGES
commit 9ca101df67e78ddc41a70acc1562fd96a424c8a4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 23 13:49:19 2017 -0500
For relaxation, only balance against gravitational force
Exec/science/wdmerger/Prob.cpp
commit 9f51d8552708f7d50412d0caf8e9946b9d612ed5
Merge: 5e8eb0f6f f9bb0ebe9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 22 08:19:54 2017 -0500
Merge branch 'development' into wdmerger_relaxation
Conflicts:
CHANGES
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit f9bb0ebe90248646432468b882e87e2cf0f05b0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 22 08:18:11 2017 -0500
Sync up rotation with gravity
Source/rotation/Castro_rotation.cpp
Source/rotation/rotation_sources_nd.F90
commit 5e8eb0f6f5c254dcd0fd5b82e2dd207d04467df4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 22 06:56:53 2017 -0500
Use initializer lists in reducerealsum
Exec/science/wdmerger/Prob.cpp
commit 0f0c130fc3139c42251925b5c83a2312df406204
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 22 06:30:58 2017 -0500
Fix some issues with multi-level relaxation
This still has problems for more than two levels though
Exec/science/wdmerger/Prob.cpp
commit 6bed48e349abf2cb4caa00fd61313508ce916bfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 21 10:17:34 2017 -0500
add a warning not to edit set_indices.F90
Source/driver/set_indices.F90
Source/driver/set_variables.py
commit 15a9ab80224d9a8064a9554d8a80abf29e65acdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 20 10:58:44 2017 -0500
initialize QRADHI
Source/driver/Castro_nd.F90
commit b24aad5b1b6188096dcb2b7f1d1d61e80be98a55
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 20 04:03:18 2017 -0500
Fix an ifdef
Source/driver/Castro_nd.F90
commit fa902aead62baf1829757c70c4fbbf7f465a8465
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 19 14:19:39 2017 -0500
Fix typo
Docs/FlowChart/FlowChart.tex
Docs/Hydrodynamics/Hydrodynamics.tex
Docs/radiation_notes/rad.tex
Exec/radiation_tests/RadSphere/README
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/_variables
Source/driver/set_indices.F90
Source/driver/set_variables.py
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/riemann_nd.F90
commit 300977b305cea60457e23b07f12804b667623b1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 19 14:04:41 2017 -0500
add changes
CHANGES
commit 1a24d2f0bde75119d62a410a91fbc49289bc10c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 19 14:00:30 2017 -0500
change how we set variables to index state arrays (#275)
We now list variable indices in a plain text file _variables. These are used as the index keys into state
arrays both in C++ (for conserved state) and Fortran (for all the states). This is the first part of a clean-up of how we define variables. This addresses part of #267. At the moment, we run the script set_variables.py manually to write the Fortran routines that C++ include file. We also do some checking to ensure that we are synced up between C++ and Fortran.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/_variables
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/parse_castro_params.py
Source/driver/set_conserved.H
Source/driver/set_indices.F90
Source/driver/set_variables.py
Source/radiation/Rad_nd.f90
Source/radiation/rad_util.f90
commit 03e2bac0c279185743f36927887197813886ac9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 10 16:52:54 2017 -0500
merge some of the CTU code into a dimension-agnostic version (#273)
This merges the main driver for the CTU hydro into a dimension agnostic driver,
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_nd.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Make.package
commit e5c2116ccd1d7f3a3cfee1d42d994de5d3002c49
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 9 00:47:19 2017 -0500
Add column numbers to diagnostic output
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit 7b86a38fcedf1bbf1aec2465b35efd3a2e7ab77c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 8 08:40:54 2017 -0500
Add rotational period to diagnostic outputs
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit 35a92b38c333b3e1ae1162ec5ccb9fa1d95b21e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 8 08:28:50 2017 -0500
Subtract off new-time sources before recalculating rotation source
Exec/science/wdmerger/Prob.cpp
commit 0fdeb99f05db07fb83e7abeb69235aeb976c77fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 8 08:25:49 2017 -0500
Zero out array between uses
Exec/science/wdmerger/Prob.cpp
commit 0b936b432c068d26905beda25919c6c669044c43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 7 12:11:10 2017 -0500
add function signature doc
Docs/FAQ/faq.tex
commit 913a37093ae8c665c057a6eae9c4574982cb2136
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 7 09:51:17 2017 -0500
add an example of dumping out a fab
Docs/FAQ/faq.tex
commit 52a085d5382ebcac895e92dd96a397a98c429619
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 5 17:52:32 2017 -0500
remove unused qbx
Source/hydro/Castro_hydro.cpp
commit 56287127e9c104832f61c36f3b7dbe9753513cbe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 4 11:00:40 2017 -0800
Remove parameter dtnuc_mode (#272)
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/timestep.F90
commit 9e292038113a2635387132825433859db1e5b5d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 21:24:46 2017 -0800
Describe the burning timestep limiter
Docs/Inputs/CastroInputs.tex
commit d60dee281ae6ecac62bb7b5450f1f7aa5af8d0e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 21:08:04 2017 -0800
Add description of diffusion timestep limiter
Docs/Inputs/CastroInputs.tex
commit ca016db58d7f4eeb51cdbe06afaff17936786411
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 20:59:48 2017 -0800
Use blue text for ifdef's
Docs/CastroUserGuide.tex
commit 2a7fe1f739ec34293ec2e03c0b25db6f27ac66cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 20:56:01 2017 -0800
Add description of MOL CFL criterion
Docs/Inputs/CastroInputs.tex
commit ce59a0c9d6d9063b1c9fa70d7ae2af0e8361f4ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 3 19:15:02 2017 -0500
changes got messed up
CHANGES
commit 7ebef4e0d052a12967246dd3a91525220b84ca41
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 16:12:21 2017 -0800
Pass the state for the source terms as an argument to the source constructor (#271)
This generalizes the algorithm so that one can choose which state MultiFab to send in for calculating the source terms. This is a step in the direction of enabling source term calculations at arbitrary times, which is useful for MOL, and also allows the old source terms to be either calculated with either S_old or Sborder (which can be useful if trying to reconstruct the source terms at a later time when Sborder is no longer available).
This changes results for diffusion if reactions are also enabled, since diffusion was previously using the unreacted S_old state, not Sborder.
Fixes #269
Fixes #268
Closes #168
CHANGES
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
commit 9a8e5446ff38b654678c3b502eb3bf3ac7a8e5fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 15:15:57 2017 -0500
Rework the relaxation process using the approach of Rosswog et al. (2004)
In the past, the wdmerger relaxation used a source-term based approach similar
to that of Rosswog, Speith and Wynn (2004) and Dan et al. (2011), that balanced
the rotation force against the gravitational and hydrodynamic forces. This was
recently changed to a simpler method for various reasons, some of which were
related to Castro code changes (e.g. no longer explicitly storing the hydrodynamic
force) and the desire to make it easier to simulate only a half-domain (z > 0)
for symmetric problems; and, because the earlier implementation was found to not
be that robust anyway. The reason for this is probably that we were not really
doing what Rosswog et al. recommended. Rather, we were doing a related but different
approach where we updated the rotation force for the next timestep to balance
against what the gravitational and hydrodynamic forces were in this last
timestep. This meant that the rotation update was always lagging by a timestep,
which led to an ineffective method.
This commit actually does what Rosswog et al. recommends. At the end of the
timestep, we calculate what the rotation source term should have been in
that timestep to balance the gravitational and hydrodynamic forces, and subtract
off the rotation source term that was applied and replace it with the more
accurate one. This means the relaxation step does not lag. Since we no longer
store the source terms individually, this requires a little bit of programming
legwork to do, but we achieve the desired result.
Exec/science/wdmerger/Prob.cpp
commit dddeda030872c1fb85ab38ba73cebd39ecd7cf65
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 11:06:40 2017 -0800
Remove deprecated use_colglaz parameter (#270)
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/radiation/Radiation.cpp
commit 31869faa2fd68734dbd027ebb3b1292b8cabe2a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 13:16:17 2017 -0500
Remove old, unused function declaration
Source/driver/Castro.H
commit 9ba533738bc1ae173ba62cac1b156ec340d1d2e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 04:31:32 2017 -0500
Update CHANGES
CHANGES
commit 5733e444c3a483c22635384e6f121152bc40533e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 02:39:19 2017 -0500
Pass the state for the source terms as an argument to the source constructor
This generalizes the algorithm so that one can choose which state MultiFab
to send in for calculating the source terms. This is a step in the direction
of enabling source term calculations at arbitrary times, which is useful for
MOL, and also allows the old source terms to be either calculated with either
S_old or Sborder (which can be useful if trying to reconstruct the source
terms at a later time when Sborder is no longer available).
This changes results for diffusion if reactions are also enabled, since
diffusion was previously using the unreacted S_old state, not Sborder.
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
commit c6fddfde195a53ee43cf6df8440290e6826eb9f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 01:24:19 2017 -0500
Remove obsolete ppm_reference parameter uses
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
Exec/science/planet/inputs_3d
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
commit 59a3c1fcb1926aab07a28bacf160595f146f2224
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 3 01:02:15 2017 -0500
Send source MultiFab as argument to source constructors
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.H
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
commit e278d91f1af5c067d2c98fbfa902d5f3d1c6f9ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 2 14:42:16 2017 -0500
changes for 17.12
CHANGES
commit 79cc339a1cd6622974e8d8b4c2f2389f85c954cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 2 14:27:20 2017 -0500
Avoid a hang in parallel if CFL is violated
Source/hydro/Castro_hydro.cpp
commit 4379d86a6c02c2ee2add26ae78a83f99d6972565
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 30 11:44:25 2017 -0800
Skip the advance if we detect a CFL violation (#261)
If we've detected a CFL violation, there is no point in continuing to do the advance; we can stop immediately and return, and then abort or retry. This saves a little time when we are doing a retry, but more importantly prevents bad failure modes when we attempt an advance with CFL > 1, such as NaN's being generated in the state.
This also corrects a hole that has been present in the subcycling logic: if we detect a CFL violation while subcycling, we must abort. In the future this will be relaxed to allow for recursive subcycling.
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_hydro.cpp
commit 807153c5371b94696e9525a3b67d306665bc6581
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 30 11:22:55 2017 -0800
Fix the reflux source term correction after a retry (#266)
As #264 illustrates, the source term correction after a reflux is incorrect if a retry happened in the last timestep. This was because we were correcting based on the original old-time, but really we needed to be correcting based on the last subcycled timestep of the retry. This fixes #264 by saving that last timestep's data in the event of a retry, and temporarily swapping it in before re-calculating the new-time source terms after a reflux.
* First cut at fixing the retry issue with source terms
* Clean up the logic for saving the prev_state
* Revert some accidental test changes
* Fix logic
* Use a MF copy rather than pointer swap
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit 12d3293dca4a0f5bd8718646c68687c14f1ea9a1
Merge: 42123cb01 43889a194
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 28 21:25:44 2017 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 42123cb01a22d712b8de4bf5430d3ed038ffdb4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 28 21:25:26 2017 -0500
QTHERM and NTHERM do not need to be module variables
also fix some OpenACC
Source/driver/Castro_nd.F90
Source/driver/meth_params.F90
Source/driver/meth_params.template
commit 43889a194dce5bb8c8dfe73599f5d791ed0f5a82
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 28 21:04:04 2017 -0500
Add a sponge based on pressure
The new parameters are sponge_lower_pressure and sponge_upper_pressure,
and they work in a way analogous to the density sponge.
CHANGES
Source/driver/Castro_nd.F90
Source/sources/sponge_nd.F90
commit 2d61ad88bb71a81db8519aea3e4494da4b8257ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 28 20:02:57 2017 -0500
The sponge can now drive towards a non-zero target velocity
The new parameters are sponge_target_{x,y,z}_velocity. The default behavior
is that these are set to zero, so the sponge still damps out all velocity
by default.
CHANGES
Source/driver/Castro_nd.F90
Source/sources/sponge_nd.F90
commit 1772e2222435351589a3ba05d8ce440878a37da2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 27 03:23:13 2017 -0500
Extend the lifetime of mass_fluxes
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit c99d26dece5a5d2d6a27082de3f1a86fcce5b818
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 26 21:24:19 2017 -0500
Store the most recent timestep length
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit 2c5f703b604e990bd090c13c27c370386e15def4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 26 15:35:22 2017 -0800
Fix the calculation of the source term predictor (#265)
For the momentum sources, the calculation of dS/dt was incorrect as a
result of #253, and was also incorrectly applied to all of the state
components. This reverts the behavior to the previous method, where
we only apply the source term predictor to the momentum and we
account for the predictor-corrector nature of the source terms.
Source/driver/Castro.cpp
commit 42ca04f87f3d4cd48d0f0d68bd93781030638e4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 16:11:00 2017 -0800
Shorten the lifetime of hydro_source (#254)
Now hydro_source only exists for the duration of the timestep, not permanently.
The indefinite lifetime of hydro_source was for an old wdmerger feature that
no longer exists.
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit 5cc09086a42e0c90a731487eb1101752bd5cf621
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 16:06:35 2017 -0800
Update the wdmerger_retry test to have a guaranteed retry (#263)
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit fa04567cc4694983c73dbc9528ebd8e019b939f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 16:04:35 2017 -0800
Move ctoprim to separate MFIter loop (#223)
The loop to do ctoprim is not slabbed like the PPM and Riemann solve are, so we get no real performance benefit from including it in the same MFIter loop. But we do take a performance hit because we are unnecessarily doing redundant work on ghost zones. This change removes the unnecessary ghost zone work, at the cost of allocating the whole array of primitive variables at one time.
* Fill q, qaux in a separate MFIter loop in MOL
* Fill q, qaux in a separate MFIter loop in CTU
* OMP the ctoprim loop
* Move compute_cfl up to C++
* Move ctoprim and the CFL check to separate functions
* Fix SDC compilation
* Apply the old sources to the hydro at the correct time
* Move Erborder and lamborder up to class scope
Source/driver/Castro.H
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_nd.F90
Source/hydro/advection_util_nd.F90
Source/sources/Castro_sources.cpp
commit 08935d9855358a5ed1ec7419bfb5b796ae63aba4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 18:25:46 2017 -0500
Fix amrex namespace issues in Castro.H
Source/driver/Castro.H
commit 99396d8d43b392e4390aa44acd2f5513bed7a1cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 15:49:58 2017 -0500
Insert some sanity checks when using MOL
Source/driver/Castro.cpp
commit d98191cdf19c04ccba13d8a47363cd3fbf255e09
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 15:45:02 2017 -0500
Apply dt/2 scaling of the source term predictor in initialize_do_advance
This works around an issue in the retry where we do not necessarily know the
retry timestep at the time where we would apply the source term predictor.
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit f568ac991fffc3689deeaf4eb045b785f9c00ef9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 14:25:45 2017 -0500
Fix time level setting in the retry source term predictor
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit 3f85cfe5096f036f444126e317a912c516b5bae4
Merge: c169b67ab 4be064c01
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 13:35:25 2017 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 4be064c01f07a58bfb6d0bc69b1d641c144b7c4c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 25 08:19:08 2017 -0800
Fix the source term predictor when doing a retry (#262)
* Fix the source term predictor when doing a retry
This fixes an issue where the sources going into the hydro were not
updated correctly during a retry. If we were using the source term
predictor, we wouldn't update to account for the smaller timesteps
(or the most recent data from the previous subcycled timestep).
* Add a missing conditional
* Fix logic of when to reset the predictor
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
commit bc06e9eba1450893abfb0566ac44a603236e78ed
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 24 13:16:02 2017 -0800
Remove SDC_Source_Type from StateData (#259)
A separate SDC_Source_Type is no longer needed, because now the standard
Source_Type StateData holds the new-time source terms, which is exactly
what SDC needed (the SDC in the name was something of a misnomer). SDC
now draws from the Source_Type.
This breaks checkpoint forward compatibility for previous runs using SDC.
The Castro checkpoint version number is incremented to 6.
CHANGES
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
commit c169b67ab4041f362d874f5bc80e10b2e714bdca
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 24 02:57:33 2017 -0500
Use a relaxation damping pegged to the dynamical timescale
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
Exec/science/wdmerger/wdmerger_util.f90
commit 8a123babb64aab16da16872570befd144b9789c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 24 02:04:20 2017 -0500
Use implicit damping for the radial damping
Exec/science/wdmerger/ext_src_nd.F90
commit 90f55439672731e4079d97b7f7181b83e2138fb8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 24 01:43:05 2017 -0500
Remove wdmerger relaxation_implicit parameter
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit 7439e9f659bfb1d5e318713a71d59d4baff63888
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 22 22:44:24 2017 -0500
Update for amrex TagBox change
Source/driver/Castro.cpp
commit a51acbcc850df96e31726a28e179247ed88a91e3
Merge: 368a6c0e6 cc8ad9a2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 21 14:56:59 2017 -0800
Merge pull request #257 from AMReX-Astro/tag_fnc
Remove some redundant work in apply_tagging_func
commit cc8ad9a2b6e00a9be1d040266d4200370df45c37
Merge: 121fb2ee7 368a6c0e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 21 14:51:56 2017 -0500
Merge branch 'development' into tag_fnc
commit 121fb2ee7af1ac4b35dae91862f179d745f1221d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 21 14:12:07 2017 -0500
Remove some redundant work in apply_tagging_func
Source/driver/Castro.cpp
commit 368a6c0e611398ad061dd20f5234b4e91a9fcba3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 14:01:50 2017 -0500
Fix number of ghost zones used in sources
Source/driver/Castro.H
Source/sources/Castro_sources.cpp
commit e3c00f739e7646046c31687d0f62c5fe218bab8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 19 11:08:40 2017 -0500
add note about bug fix
CHANGES
commit 59a3c4cc0547c483f45f39828aff80a2d0d43d98
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 08:06:30 2017 -0800
Apply the sources to the state's ghost zones (#255)
This fixes #213 -- it ensures the advances give a valid update for the ghost zones in the State_Type.
* Apply the sources to the state's ghost zones
* Fill State_Type ghost zones after the hydro update
Since the hydro update only works on the ghost zones, we must do a
FillPatch on the State_Type after the hydro update to ensure valid
data in the ghost zones.
* Do the clean_state on the ghost zones too
This is necessary because some of the zones will be on the physical
boundary or at coarse-fine interfaces and so do not have guaranteed
thermodynamic consistency.
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/sources/Castro_sources.cpp
commit 10a4caa43bd45cd339fff2b068520564020a636c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 03:32:10 2017 -0500
Remove some diagnostic prints
Exec/science/wdmerger/Prob.cpp
commit 30ff2482bf92232bb20c6fd4944ac011d59a1eb9
Merge: 5f04d2957 5d1a0b06e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 02:35:43 2017 -0500
Merge branch 'development' into wdmerger_half_domain
commit 5d1a0b06ec1cd8bcde548872c7a711f78e3a97f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 02:28:22 2017 -0500
Clean up some now-redundant wdmerger code
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit 8835f19d20c2fe8d5d86b201c853d5c21fdff02c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 02:23:11 2017 -0500
Remove custom BCs for wdmerger
These were not actually being used
Exec/science/wdmerger/bc_fill_nd.F90
commit d19fd94037c81e3ced41aa7709751d7cd3e978be
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 19 01:15:28 2017 -0500
Fail gracefully when using hybrid momentum with HLLC
Source/driver/Castro.cpp
commit e8d97116965358a85d558df5f80a0da9885c2665
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 18 18:36:54 2017 -0500
Update CHANGES
CHANGES
commit a4cf9e14762724c4f8926cad89dbd5e750f77602
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 18 18:30:23 2017 -0500
Remove parameter gravity.max_solve_level
This was added to work around convergence issues in the multigrid solve,
but those convergence issues have since been fixed, so the parameter is
no longer used.
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/_cpp_parameters
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/gravity/Gravity.cpp
commit 4f38ccef9ba2a8bdfa228a363aca6e4e0ad0c46a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 18 14:55:21 2017 -0800
Fill hydro source term ghost zones with valid data (#253)
* Compute source terms only on the valid domain
This is a temporary change only. It is intended to be part of a larger
change to use StateData to store the source terms.
* Rework the source terms into StateData
* Add note about FillPatch operation validity
* Restore Source_Type to have NUM_GROW ghost zones
This is necessary for a valid restart from previous checkpoints
* Use a FillPatch for the SDC_React_Type ghost zones
* Use FillPatch, not FillPatchAdd
* Move the zeroing of sources_for_hydro to the start of step
* Update CHANGES
* Fix SDC compilation issues
* Fix hybrid advection compilation issues
* Be more careful with ghost zone filling
* Fix name of sources state data
* Avoid using EXT_DIR for Source_Type; replace with FOEXTRAP
* Also replace EXT_DIR with FOEXTRAP for SDC
* Zero out ghost zones for safety
CHANGES
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/Castro_setup.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
commit e870121a02a9172207c876aee810357ed16cdd39
Merge: 3e8b2acda 4acda6c78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 19:20:45 2017 -0500
Merge pull request #199 from AMReX-Astro/mol
merge the mol hydro routines into a dimensionless version
commit 4acda6c78131728c5c4a92bf5f378f0999f1723f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 17 18:53:40 2017 -0500
Fix a comment typo
Source/hydro/Castro_mol_nd.F90
commit 52e0feec0dee23e09f04ed8453adfb78a3a61591
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 17 18:41:45 2017 -0500
Simplify another ghost zone indexing
Source/hydro/Castro_mol_nd.F90
commit af291825c2e9592e65d5e18b39e0dab1e6421a5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 17 18:36:50 2017 -0500
Simplify flatten indexing
Source/hydro/Castro_mol_nd.F90
commit fbcbe296cad61c0681c55aec4632bf270098e7f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 17 18:34:46 2017 -0500
Simplify shock indexing
Source/hydro/Castro_mol_nd.F90
commit f55f7258ed015c48b3aa870539257c11c3dbe962
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 17 18:31:03 2017 -0500
Remove obsolete comment
Source/hydro/Castro_advection_1d.F90
commit ebcce27026210ba9e93c3b41dae88f96c803bbb1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 18:21:02 2017 -0500
remove unneeded versions
Source/hydro/Castro_mol_1d.F90
Source/hydro/Castro_mol_2d.F90
Source/hydro/Castro_mol_nd.F90
Source/hydro/Make.package
commit 00a18acbb472ffc665c197ab2a47804a356bfa31
Merge: e17f4248a 1b84ea41e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 17:48:15 2017 -0500
Merge branch 'mol' of ssh://github.com/AMReX-Astro/Castro into mol
commit 1b84ea41e350b735f4d8270f5880e3ef3f735d7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 14:29:58 2017 -0500
fix radiation compilation
Source/hydro/Castro_mol_3d.F90
commit 0948f28b7df1cb226ec6ead2e6375f1dd1608d3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 14:23:47 2017 -0500
fix 3-d compilation
Source/hydro/Castro_mol_3d.F90
commit 145285f266ececa30552cc57035b1d32ec136e25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 13:59:20 2017 -0500
fix order of args -- this runs now
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_3d.F90
commit 2d4e500a078ca9ac89a8f8fbfc1e395165fc1643
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 12:09:12 2017 -0500
1-d updates -- doesn't run yet
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_mol_3d.F90
commit a5529480219932ab9fbfca85a429d068063aa088
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 11:02:42 2017 -0500
2-d compiles now:
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_mol_3d.F90
Source/hydro/Make.package
commit 471960691eda93e5b1bdf7c178307e33ad25f9b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 10:18:58 2017 -0500
fix some bounds for 1- and 2-d
Source/hydro/Castro_mol_3d.F90
commit 38bc88fcd311587457f0842138add11af1ee77c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 09:34:59 2017 -0500
this compiles now...
Source/hydro/Castro_mol_3d.F90
commit e697a2d2aaaa6368d206a71bd611cc80e0cdcc5d
Merge: c6f8f1cf9 3e8b2acda
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 09:20:08 2017 -0500
Merge branch 'development' into mol
commit 3e8b2acdad30de8afa367227ae6911fde408df22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 17 09:06:03 2017 -0500
add performance cite
CITATION
commit 0da5d29872468e892b21be718c3a49278d2c6c9a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Nov 16 15:12:31 2017 -0800
amrex renamed a funciton
Source/gravity/Gravity.cpp
commit faab9cc664095195058e11f846e6e73e0e96b184
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 16 15:20:21 2017 -0500
add two more definition comments
Microphysics/EOS/eos_type.F90
commit 17e9cdfb7a23682827bff218b88a6e5e91c17658
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 15 17:00:49 2017 -0500
Remove an obsolete safety check in wdmerger
Exec/science/wdmerger/Prob.cpp
commit 20019dd16fde0672e3cc9491116bea045bc1fd4f
Merge: 939828169 a2e18fa55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 15 13:13:05 2017 -0500
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 9398281691c22e2770c356220814f7d597bf4dc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 15 13:12:47 2017 -0500
revert this shortening, since we plot against the analytic solution
in the suite
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
commit a2e18fa5505d2402607ae55aeb81e2c48b8e668a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 15 10:25:29 2017 -0500
more problem shortening
Exec/hydro_tests/reacting_bubble/inputs_2d_test
Exec/hydro_tests/toy_flame/inputs.1d.testsuite
Exec/radiation_tests/Rad2Tshock/inputs.M2.test
Exec/radiation_tests/Rad2Tshock/inputs.M2.test.multid
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg.test
Exec/science/flame_wave/inputs_2d.testsuite
commit beed2d4cb5a47b68ecf56e3c40e25740a45b8b20
Merge: a0ef28b26 68d2579d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 20:28:35 2017 -0500
Merge pull request #252 from AMReX-Astro/source_param_remove
Remove the parameter castro.keep_sources_until_end
commit 68d2579d463abcd70001e7ea810301716f83f64b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 14 20:13:56 2017 -0500
Remove the parameter castro.keep_sources_until_end
This was added to assist with wdmerger due to the strategy of using
the source term data to calculate a relaxation step. This strategy
has been reworked and no longer needs the source term data, so this
parameter has been removed. Note that by default, the source term
data will be kept indefinitely anyway -- this is disabled only if
castro.update_sources_after_reflux = 0.
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Exec/science/wdmerger/Prob.cpp
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit a0ef28b26dccaecb6e2e64636a6d9713af93f301
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 20:11:25 2017 -0500
Particle docs (#251)
update docs for particles
Docs/CastroUserGuide.tex
Docs/GNUmakefile
Docs/Particles/Particles.tex
Docs/Particles/fluid_motion.png
Docs/Particles/tracer_trajectory.png
commit bc21b5f1a69884b1c5d99538a0fb0e6791c302d3
Author: taehoryu <30508125+taehoryu@users.noreply.github.com>
Date: Tue Nov 14 19:33:56 2017 -0500
Development : update "_cpp_parameters" and "CastroParticles.cpp" (#248)
Move some particle parameters into _cpp_parameters
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro.H
Source/driver/_cpp_parameters
Source/driver/param_includes/Make.package
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/particles_defaults.H
Source/driver/param_includes/particles_params.H
Source/driver/param_includes/particles_queries.H
Source/driver/parse_castro_params.py
Source/particles/CastroParticles.cpp
commit cea8ead5a48d8423549e97f6a8ae775001d60e57
Merge: 642de78eb 29d0cf7f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 19:01:19 2017 -0500
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 642de78eb6dfc6ca3c664cbb36d3d4a8bb3be259
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 19:01:10 2017 -0500
shorten this test
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
commit 2ad00d378235e9e102e08dc7f148c7d3b0d67dd5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 18:59:39 2017 -0500
shorten this test
Exec/gravity_tests/hydrostatic_adjust/inputs
commit bb2ee3c1b7a9b3777199cbdc26614d42e1d62ee7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 18:58:55 2017 -0500
shorten this test
Exec/science/bwp-rad/inputs_2d.test
commit 873706f5226c79916dc4b43731485040300cb7ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 18:58:07 2017 -0500
shorten this test
Exec/gravity_tests/StarGrav/inputs_2d.test
commit a96bcb184c725f9a1b4c4727172ece18c3f9cd48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 18:57:28 2017 -0500
shorten this test
Exec/hydro_tests/Sedov/inputs.3d.sph.testsuite
commit 29d0cf7f542860a91827db0503387e5cd0150742
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 14 18:01:53 2017 -0500
Add comment about hybrid momentum rotation source term
Source/rotation/rotation_sources_nd.F90
commit d00b3d5d7abe6393db127b3e346117356b08f15c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 14 16:50:29 2017 -0500
Update CHANGES
CHANGES
commit 819b683f10636d6f24cc4abc3b6b65ef9706af47
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 14 13:48:46 2017 -0800
Unify sources into a single MultiFab (#249)
* Recompute old diffusion source instead of relying on saved value
* Recompute old sponge source instead of relying on saved value
* Recompute old external source instead of relying on saved value
* Use S_old since Sborder is not always available
* Recompute old hybrid source instead of relying on saved value
* Add a unified source container
* Move the gravity source to the unified_src
* Move rotation to unified_src
* Move sponge to unified_src
* Add hybrid source to unified_src
* Add diffusion to unified_src
Note that this also removes a FillBoundary call for the old sources
so it may change the answer.
* Move the external source to unified_src
This may change results due to a FillBoundary removal
* Fix a few missed things
* Use only a single entry in old_sources/new_sources
* Devectorize old/new sources
* Depointerize old_sources/new_sources
* Remove coalesce_update_diagnostics parameter
* Remove update_state_between_sources parameter
* Update CHANGES
* Add note about time accuracy
* Only apply source terms if using at least one of them
* Clarify the changes for rotation
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/diffusion/Castro_diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_setup.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/gravity/Castro_gravity.cpp
Source/gravity/gravity_sources_nd.F90
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/hybrid_advection_nd.F90
Source/rotation/Castro_rotation.cpp
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/sponge_nd.F90
commit 3e6c544da06cc37c4eaad4f3e6bf4d39089e20ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 14 15:00:08 2017 -0500
Return the subcycled timestep value from subcycle_advance
Fixes #250
Source/driver/Castro_advance.cpp
commit d4d14bbba0e1de8ad941d0dc7936fcf3db1773df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 14:48:31 2017 -0500
add a start of a processing script
Exec/science/convective_flame/exploration/process.py
commit c6f8f1cf9a2dfd6407ce6148200f6022be53e361
Merge: 97fcc67bc d6a9c4cd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 14 09:10:01 2017 -0500
Merge branch 'development' into mol
commit d6a9c4cd1aeb5797dd0c55e985f3d401e2eb22c8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 13 13:09:57 2017 -0800
use mlmg solver for the regression tests at lbl
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
commit 557e60ecf68e70c9afad1d0e95c9ebc78f312552
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 13 12:20:19 2017 -0500
Use a much simpler method to update the wdmerger relaxation
Exec/science/wdmerger/Prob.cpp
commit e17f4248a9566ae465cebb4c09391343e9b54582
Merge: 97fcc67bc f3b4a7231
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 13 12:00:41 2017 -0500
Merge branch 'development' into mol
commit f3b4a723133c04ca9af4a86430d6c305479aad57
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 12 19:27:45 2017 -0500
Add C++ interface for obtaining inertial velocity
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/wdmerger_util.f90
commit 97fcc67bc25f3bb04ab11158924ea1ffe5888883
Merge: 1aca5d3f9 b0220fdc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 11 22:01:34 2017 -0500
Merge branch 'development' into mol
commit b0220fdc379e3aa7c516cccf3661dc8e1e4def08
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Nov 10 11:53:23 2017 -0800
MLMG: update due to amrex change
Source/gravity/Gravity.cpp
commit 778d12c4e8396b0fb2364091e586f2c02e320fa3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 10 14:02:11 2017 -0500
Update CHANGES with issue/PR numbers
CHANGES
commit 534107205ab41d0f7b6ddb1112f7ad786442c316
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 10 10:47:59 2017 -0800
Take correct post-restart timestep if step was limited to hit plot interval (#243)
* Take correct post-restart timestep if step was limited to hit plot interval
If a timestep was limited to hit a plot interval, a restart would see this shortened
dt when calculating the next dt, and would limit the timestep to change_max * dt.
This situation was worked around during normal evolution because we do not want to have
to catch back up to the longer timestep every time we stop to hit a plot interval.
This commit also ensures this behavior if we're restarting after a shortened timestep.
A new file is added to the checkpoint directory that stores the previous, longer timestep
in this situation. On a restart, we check if this file exists, and if so, read in that
longer timestep. This fixes the problem.
Fixes #242
* Update CHANGES
CHANGES
Source/driver/Castro_io.cpp
commit 253bb1d1ad2deb965560192d0d2c6517e66234c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 10 05:18:24 2017 -0500
Add parameter dxnuc_max to set an upper bound on dxnuc tagging
If dxnuc is used to refine zones above a certain burning instability threshold,
dxnuc_max can be used to set up an upper limit on the tagging. Zones that approach
order unity for dxnuc are essentially already ignited, so adding refinement to these
zones does not achieve the goal of suppressing numerically seeded ignitions, and
thus refinement for these zones may be unnecessary. Setting dxnuc_max allows the user
to further control the region of burning instability that is targeted for refinement.
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Tagging_nd.f90
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 979f876db7dd2032b5eebe7924e5ce6473bbf98d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 2 15:17:16 2017 -0400
a script to explore parameters
Exec/science/convective_flame/exploration/inputs.2d.template
Exec/science/convective_flame/exploration/probin.template
Exec/science/convective_flame/exploration/setup_explore.py
commit 6ca3d64c581e8d0555ba14b476da914cb1f404e5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Nov 8 09:49:40 2017 -0800
MLMG: it turns we have always been using agglomeration and consolidation due to a bug in AMReX
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/_cpp_parameters
Source/driver/param_includes/gravity_defaults.H
Source/gravity/Gravity.cpp
commit a44073e54e96cfe78a23090fd11e0762b1c83bb9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 7 16:24:25 2017 -0800
getFluxes -> getGradSolution
Source/gravity/Gravity.cpp
commit c2cacf82eda90d5efb4f5d3639b54ced9c15442e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 7 13:00:15 2017 -0800
2d mlmg is now supported. note that metric terms are handled in MLMG not in Castro.
Exec/Make.Castro
Source/gravity/Gravity.cpp
commit 4d4eaaaff041acb56085cbd006d5bc0aba9eefee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 6 21:52:00 2017 -0500
remove some git merge conflict noise
CHANGES
commit f36c4fa06d3cb29cc10be3a5abe52add9bc77d52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 5 12:32:03 2017 -0500
doc new MG
CHANGES
commit 568ad6e011599231a0e1995658cd6d2e6e9cdc85
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Sun Nov 5 09:29:02 2017 -0800
Use AMReX's new MLMG linear solver (#241)
* add mlmg to make and runtime parameters
* move use_mlmg_solver parameter to gravity namespace
* add two mlmg functions that currently just call F_MG
* MLMG wip
* finished implementation of solve_phi_with_mlmg
* solve_for_delta_phi_with_mlmg
* fix bc
* need to return the final residual norm after solve
* add gravity.mlmg_max_fmg_iter=20 parameter
* change default of gravity.mlmg_max_fmg_iter to 0. that is use vcycle only without any fcycle
* add gravity.mlmg_agglomeration flag
* compile MLMG by default in 3d
* add parameter gravity.mlmg_consolidation=1
* forgot to call set
* turn off gravity.mlmg_agglomeration and gravity.mlmg_consolidation by default
* tidy
* refactor
Docs/runtime_parameters/runtime_parameters.tex
Exec/Make.Castro
Source/driver/_cpp_parameters
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
commit 4bc6ec0b299d610ae5d7774f0eeceaf0229a40af
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 5 12:13:05 2017 -0500
Remove obsolote sponge parameter
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 9adc9bca4330606c5b6f8a22a2a6fadd0186ebfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 4 15:57:56 2017 -0400
a little more loosening and reduce AMR on the test suite case
Exec/science/flame_wave/inputs_2d.testsuite
Exec/science/flame_wave/probin
commit 2a1570399d7bca11d6a928b32f05e1e6dcf8d0fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 4 15:49:56 2017 -0400
default to GNU
Exec/science/flame_wave/GNUmakefile
commit 816da29cc79f6468cb308467e4e4c5fd769f2bbd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 4 10:31:44 2017 -0400
loosen tolerances
Exec/science/flame_wave/probin
commit aae549e4a8ec26b92e93820a7805d0d1c8c4279d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 3 10:29:11 2017 -0400
more intent fixes
Source/problems/bc_fill_3d.F90
commit 59aa8671a492ea571cbbce12042cc029c9083958
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 3 09:38:22 2017 -0400
rad should be in/out
Source/problems/bc_fill_3d.F90
commit b1719f58237d949cf3d5fa564f2bb81f99939c7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 3 09:27:24 2017 -0400
fix compilation
Source/problems/bc_fill_2d.F90
commit 284efa3f7c6263d51b905429c354ca496ba868d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 2 22:05:56 2017 -0400
fix intents on adv
Source/problems/bc_fill_3d.F90
commit c47190de64eb0e3169775279f21fe83666e60cbb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 2 13:42:45 2017 -0400
Set a default value for the sponge factor
Closes #240
Source/sources/sponge_nd.F90
commit 7b8d2e24a6094c41d461d228504fa23f62d08e8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 2 13:36:49 2017 -0400
Remove unused variables
Source/sources/Castro_sponge.cpp
commit fec9e22344b9e430915794ac4c6df5c4a352f3e3
Merge: 2649a13a9 b65041fb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 1 14:41:08 2017 -0400
Merge branch 'development'
commit b65041fb0f1e30e80fd72313ee0d1a2ead5af77d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 31 18:14:25 2017 -0400
update changes
CHANGES
commit 31baf572be26ae1916719d5c464022ee3db89898
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 31 17:27:56 2017 -0400
Migrate Source/ to use filccn instead of dimensional filcc
Source/driver/filcc_nd.F90
Source/driver/generic_fill.F90
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_fill_1d.F90
Source/problems/bc_fill_2d.F90
Source/problems/bc_fill_3d.F90
Source/problems/bc_fill_nd.F90
commit 1aca5d3f9070e54bcd9940015f6eb293e568f851
Merge: 6ab543c76 4644ac808
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 31 14:04:10 2017 -0400
Merge branch 'development' into mol
commit 6ab543c76a4c930459933ad6a2cc7611654f0fa7
Merge: 589b018f9 f51f311ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 31 14:04:03 2017 -0400
Merge branch 'mol' of ssh://github.com/AMReX-Astro/Castro into mol
commit 4644ac80843ab7f71cfdd4b117a09e47809f58df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 31 12:55:30 2017 -0400
finish the merge of the Riemann solvers (#239)
there is now a single `cmpflx` routine that is used regardless of dimensionality
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_mol_1d.F90
Source/hydro/Castro_mol_2d.F90
Source/hydro/Make.package
Source/hydro/riemann_1d.F90
Source/hydro/riemann_2d.F90
Source/hydro/riemann_3d.F90
Source/hydro/riemann_nd.F90
commit 09891bb336222f7b4140b8473f1deeec2bad5ee3
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Tue Oct 31 10:58:05 2017 -0400
add note about I/O error obtained in cori when running with more than 32 nodes
Docs/ManagingJobs/managingjobs.tex
commit f51f311ce08f5154d1ea9e3dd78da00a213f4f69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 30 20:48:21 2017 -0400
update todo
Source/hydro/Castro_mol_3d.F90
commit 7b8ea6939bceaf7e26c39509df4b1c7df8b855e7
Merge: e6fee5c18 5e457eafa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 30 18:17:07 2017 -0400
Merge branch 'riemann-cleaning' into mol
commit 5e457eafa498aa5d7fe69ae96b2c4de0909325d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 30 13:13:02 2017 -0400
finish the merge of the Riemann solvers
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_mol_1d.F90
Source/hydro/Castro_mol_2d.F90
Source/hydro/Make.package
Source/hydro/riemann_1d.F90
Source/hydro/riemann_2d.F90
Source/hydro/riemann_3d.F90
Source/hydro/riemann_nd.F90
commit 589b018f9292e910facd95ad9b2526d82349e958
Merge: 19577c17e e823a5275
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 30 11:30:11 2017 -0400
Merge branch 'mol' of ssh://github.com/AMReX-Astro/Castro into mol
commit 19577c17e03e899592a954251fa1a2d296b99c82
Merge: 95ab9167b 4f6faf985
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 30 11:07:33 2017 -0400
Merge branch 'development' into mol
commit 4f6faf9850fa7304e675aa89fa5f19ebf96e47c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 29 19:35:42 2017 -0400
Fix loop index typo
Source/driver/sums_nd.f90
commit a550aec444fe11a9dda53b4f0af5193285d90706
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 29 14:38:55 2017 -0400
Remove the ignition de-tagging functionality
Exec/science/wdmerger/Castro_prob_err.cpp
Exec/science/wdmerger/Castro_prob_err_F.H
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/Problem_Derives.H
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_derive_nd.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.f90
commit e6fee5c185ca9bde92a9888e366b05a93d48075d
Merge: e823a5275 ab59e5ac0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 24 19:16:02 2017 -0400
Merge branch 'development' into mol
commit ab59e5ac0e3aa3f2fb1abf348feb9ad34b0ce4ff
Merge: a03ed1b75 bea465208
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 24 18:18:08 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit a03ed1b75fa6e906ec20ebd033f1ae5eff09b0a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 24 18:17:52 2017 -0400
document the format of _cpp_parameters
Docs/runtime_parameters/rp_intro.tex
commit 15de328785f02d561bcbfa1aced559897097a5f1
Merge: 30d2c8542 730f6b89c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 24 15:49:36 2017 -0400
Merge pull request #238 from eftov/docs
Fix a typo in the Microphysics repo urls
commit 730f6b89cb822e15b7a20845e412d4de485be188
Author: eftov <b.fovet@gmail.com>
Date: Tue Oct 24 21:37:37 2017 +0200
Fix a typo in the Microphysics repo urls
Docs/GettingStarted/CastroGettingStarted.tex
commit bea465208f81154748c94362ee3890301e8a1971
Merge: c967910e4 c4683dc17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 23 18:02:22 2017 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit c967910e46a836c54b8bfa9ccf0e5fe677ffabe0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 23 18:02:02 2017 -0700
fix max_step
Exec/science/flame_wave/inputs_2d.boost
commit c4683dc1790789bf1172dca25b15a22539692052
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Mon Oct 23 10:42:08 2017 -0700
added scripts for cori knl, used for scaling. Also, the inputs and probin used (up to some change in grid size for 256) also when run for 1 level, change amr.max_level to 1
Docs/ManagingJobs/scaling/wdmerger/cori_201710/cori-nodes_128.knl.MPI.OMP.slurm
Docs/ManagingJobs/scaling/wdmerger/cori_201710/cori-nodes_16.knl.MPI.OMP.slurm
Docs/ManagingJobs/scaling/wdmerger/cori_201710/cori-nodes_32.knl.MPI.OMP.slurm
Docs/ManagingJobs/scaling/wdmerger/cori_201710/cori-nodes_64.knl.MPI.OMP.slurm
Docs/ManagingJobs/scaling/wdmerger/cori_201710/cori-nodes_96.knl.MPI.OMP.slurm
Docs/ManagingJobs/scaling/wdmerger/cori_201710/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/cori_201710/probin_test_wdmerger_3D
commit b7e715556e0402559a8176517d2a5903593a9a85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 23 10:28:04 2017 -0400
add FAQ about getting amrvis to work with nvidia
Docs/FAQ/faq.tex
Docs/GettingStarted/CastroGettingStarted.tex
commit a6334ea31b010d2e08896db5ff96b0927a69dafa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 22 12:52:13 2017 -0700
use the right probin
Exec/science/flame_wave/inputs_2d.boost
commit 50db06abbe1d4a1294787eef01bf7ec487ba7a22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 22 12:49:17 2017 -0700
new input set
Exec/science/flame_wave/inputs_2d.boost
Exec/science/flame_wave/probin.boost
commit e823a527571e140a415fd0259bab44b2cb04ee09
Merge: 23c8f9701 ae8c2c7e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 19:34:45 2017 -0400
Merge branch 'development' into mol
commit ae8c2c7e97351d88577e1c6f07903474e5732044
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 19:26:50 2017 -0400
index some build stuff
Docs/GettingStarted/CastroGettingStarted.tex
commit 8e784babb5883f5565b5d9a07df4eaa6e8fc0a61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 19:24:20 2017 -0400
add BLAS discussion
Docs/FAQ/faq.tex
Docs/castrosymbols.tex
commit ea3949e7c021854e6a6ee18ea9681eec0cdbe155
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 19:20:49 2017 -0400
remove levelset macros
Docs/CastroUserGuide.tex
commit fdffacfacc10212b3fd6dfba06a7da2114f598f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 19:07:59 2017 -0400
if USE_SYSTEM_BLAS=TRUE, then we don't compile blas directly, but link in
the library pointed to by BLAS_LIBRARY (defaults to -lopenblas)
Exec/Make.Castro
commit af8c9199ac7150a4b686153c1e8f8a2da5afff41
Merge: b4e74c415 803de6846
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 20:06:38 2017 -0400
Merge pull request #237 from AMReX-Astro/ArrayToVector
Array to vector
commit 803de6846d1ac58310de9d0ef4986994138f6711
Merge: 8f2da7b86 b4e74c415
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 19:44:06 2017 -0400
Merge branch 'development' into ArrayToVector
commit b4e74c415f4a6e09ea8b38252e62cff6f2fb2993
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 19:40:33 2017 -0400
QCSML is no longer needed
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
commit 8f2da7b86824f91333696dd754445754e95e0515
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 20 16:32:37 2017 -0700
more Array -> Vector
Source/radiation/Radiation.H
commit 46f61cf59035ad8aa330228695cba4d350eb2c50
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 20 16:22:28 2017 -0700
Array to Vector because amrex::Array is deprecated
Docs/Software/CastroSoftware.tex
Exec/science/flame/Prob.cpp
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/unit_tests/diffusion_test/Prob.cpp
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_io.cpp
Source/driver/Castro_setup.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/hydro/Castro_hydro.cpp
Source/problems/Prob.cpp
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGRadBndry.H
Source/radiation/MGRadBndry.cpp
Source/radiation/NGBndry.H
Source/radiation/RadBndry.H
Source/radiation/RadBndry.cpp
Source/radiation/RadMultiGroup.cpp
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/_interpbndry/RadBndryData.cpp
Source/reactions/Castro_react.cpp
Source/sources/Castro_sources.cpp
Util/ConvertCheckpoint/Embiggen.cpp
commit 98117ac0faae2e51b2485e440622f9c980efb869
Merge: 83284d769 c2d66a051
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 19:15:56 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 83284d769567d9c85ca5d72a55a065fa402232c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 19:15:13 2017 -0400
remove PArray -- it no longer exists
Docs/Software/CastroSoftware.tex
commit c2d66a0512a1d3ab46e7cc463f3120d8c015913a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 20 11:00:57 2017 -0400
Restore a comment explaining SDC hydro time-centering
Source/hydro/Castro_hydro.cpp
commit 759e7fa09282f1098d8858b1db7578e7b15fc383
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 19 14:32:34 2017 -0400
add a mailmap to condense contributions by name
.mailmap
commit cc4e81905ed89df612f8007e3ab1a9f971976500
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 22:24:09 2017 -0400
add the scaling scripts for wdmerger on titan
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/avg_time.sh
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/probin_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-OMP2-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI128-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI2-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPI64-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx2-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx4-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx4-OMP8-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_0amr/titan-512-MPIx8-OMP8-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/avg_time.sh
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/probin_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPI2-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPIx2-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPIx4-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-512-MPIx8-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-MPI128-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_1amr/titan-MPI512-OMP8-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/avg_time.sh
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/probin_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPI-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPI2-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPIx2-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPIx4-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/256_2amr/titan-512-MPIx4-OMP8-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/avg_time.sh
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/probin_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI1024-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI2048-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-OMP2-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI4096-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_0amr/titan-MPI512-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/avg_time.sh
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/inputs_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/probin_test_wdmerger_3D
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI1024-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-OMP2-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-OMP8-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI2048-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-OMP2-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-OMP4-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI4096-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/512_1amr/titan-MPI512-PE16.run
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/avg_time.sh
Docs/ManagingJobs/scaling/wdmerger/titan_20171011/castro-wdmerger-scaling.txt
commit acd99f7e41e03dcde16465c3b7b616bb5a76ab7f
Merge: b79a9c944 986a2d18d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 21:58:32 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit b79a9c94459c5648f5e69c9c7651a64999d6aa20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 21:58:21 2017 -0400
scripts for scaling
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/avg_time.sh
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI1024-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP16-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI2048-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level/titan-MPI4096-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/avg_time.sh
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI2048-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/1level_4x/titan-MPI4096-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-MPI2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1024/titan-1024-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-MPI2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_1536/titan-1536-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/avg_time.sh
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/inputs.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/probin.starlord
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/titan-512-MPI-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/titan-512-MPI2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/titan-512-OMP2-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/titan-512-OMP4-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/64_512/titan-512-OMP8-PE16.run
Docs/ManagingJobs/scaling/sedov/titan_20171011/castro-sedov-scaling.txt
commit 986a2d18dcdaa6cc774b8bdb6af0390697a2d844
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 15:42:45 2017 -0400
some cleaning + a BC centralization
Source/problems/Make.package
Source/problems/bc_ext_fill_3d.F90
commit 03a2da54a387ae5f8b7719844e946936bb19cb5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 15:41:57 2017 -0400
a little cleaning
Exec/science/planet/Prob_3d.f90
commit a4c9cabb4145a553babe7d7385f8c7e186f69680
Author: taehoryu <30508125+taehoryu@users.noreply.github.com>
Date: Wed Oct 18 15:10:53 2017 -0400
planet 3D (#232)
* planet 3D
* initialmodel file
Exec/science/planet/Prob_3d.f90
Exec/science/planet/bc_ext_fill_3d.F90
Exec/science/planet/bc_fill_3d.F90
Exec/science/planet/inputs_3d
Exec/science/planet/newmodelcpp.hse
commit 678f2656875757cecea37c4791071ffbe2a8282e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 19:10:07 2017 -0400
use an EXTRA_THERMO flag to disable composition derivs (#230)
* use an EXTRA_THERMO flag to disable composition derivs
* renamed
* comment on EXTRA_THERMO
* don't call composition_derivatives at all
CHANGES
Microphysics/EOS/Make.package
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.F90
commit a703a0e09e33eaf1acd915a5a7df746692ee2aee
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon Oct 16 16:25:35 2017 -0400
Adressing issue #221, removed QCSML. Now, a grep doesn't show the var… (#227)
* Adressing issue #221, removed QCSML.
Source/driver/Castro_nd.F90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/hydro/advection_util_nd.F90
Source/hydro/riemann_1d.F90
Source/hydro/riemann_2d.F90
Source/hydro/riemann_3d.F90
Source/hydro/riemann_nd.F90
commit 386e27c22c189891a538d53593b0b7d7a0f92dd5
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon Oct 16 15:33:44 2017 -0400
removed the set_special_tagging_flag, issue #200 (#228)
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_nd.F90
commit 129909785f8f3f4c09718a16dc00a5b525e3cf09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 13:09:07 2017 -0400
python3 fix
Docs/runtime_parameters/rp.py
commit 23c8f97011315971c894fedf2fe01bfb73aa2f7f
Merge: f4a405309 6e4aed2fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 11:43:14 2017 -0400
Merge branch 'development' into mol
commit f4a405309af173ff4f29a2a4465bf79db3755c15
Merge: 0ea71b71e 95ab9167b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 11:42:44 2017 -0400
Merge branch 'mol' of ssh://github.com/AMReX-Astro/Castro into mol
commit 6e4aed2fbef3c427a8043718faf7664b18fcaf73
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 15 11:36:44 2017 -0700
Turn off debug mode by default for all problems (#224)
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/toy_flame/GNUmakefile
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
commit 04331ca87f273b28f22827ddb005f151597013a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 13 08:50:58 2017 -0700
Use the correct (negative) scaling for the coarse pressure (#222)
* Use the correct (negative) scaling for the coarse pressure
* Update CHANGES
CHANGES
Source/driver/Castro.cpp
commit ec1532c009fb2d687563a9ed6aee3f35f71992f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 13 10:51:14 2017 -0400
fix typo
Docs/ManagingJobs/managingjobs.tex
commit 8d8e810323c78454e46007b39ef5df058ad9c056
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Thu Oct 12 19:37:00 2017 -0400
Const cf (#220)
* In regard to issue #30, checked functions in castro_c_interfaces_nd.f90 and Castro_util.F90 for cnsistency between const in C and intent(in) in Fortran ...etc.
* Finished with functions in Castro_nd.F90. But have a few questions about ca_set_amr_info when calling the function with hardcoded numbers. Also, about ca_set_special_tagging_flag ... it isn't clear to me when the value of the flag will change? .... see call in Castro.cpp
* Finished with driver/Derive_nd.F90 . Have some question though, regarding ca_derangmomx(y and z too) why is rho needed? Also, what does ca_dernull do?
* almost finished with driver directory... still missing sums_nd.f90
* finished with driver functions
* done with diffusion
* almost done with gravity
* finished gravity, starting hydro
* some fix in gravity, done with hydro and reactions
* change qaux for CTU , and diff in derdiffterm
* forgot to add advection_3d for the previous commit
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.cpp
Source/diffusion/Diffusion_nd.f90
Source/driver/Castro.cpp
Source/driver/Castro_F.H
Source/driver/Castro_error_F.H
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Derive_nd.F90
Source/driver/MGutils_1d.f90
Source/driver/MGutils_2d.f90
Source/driver/Tagging_nd.f90
Source/driver/sum_utils.cpp
Source/driver/sums_nd.f90
Source/driver/timestep.F90
Source/gravity/Castro_gravity.cpp
Source/gravity/GR_Gravity_1d.f90
Source/gravity/GR_Gravity_2d.f90
Source/gravity/GR_Gravity_3d.f90
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.f90
Source/gravity/pointmass_nd.f90
Source/gravity/prescribe_grav_nd.f90
Source/gravity/prescribe_phi_nd.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_mol_1d.F90
Source/reactions/React_nd.F90
commit a59ab7d9d5460a13ef8f3e00d7ea006746ab707c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 12 13:03:15 2017 -0400
add note about Cray 8.6.1
Docs/ManagingJobs/managingjobs.tex
commit 95ab9167bdf3f7d2118b2d4e189cd225f5d7b507
Merge: 8c67de3ad 8e5f001f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 12 12:00:58 2017 -0400
Merge branch 'development' into mol
commit 8e5f001f1f902fd565e011d0b07bffe3cbb4cfe4
Merge: 8a58dc3d8 5df0293e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 10 20:46:11 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 8a58dc3d83d1794e826293acc0fb656266f4b3de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 10 20:39:24 2017 -0400
this gives a flame with aprox13 that looks reasonable
Exec/science/flame/inputs.1d.aprox13
commit 5df0293e72a7400a3d202de812d96becf474efba
Merge: c7693c029 5b7c5999d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 10 20:16:54 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit c7693c0298c8a5ea0bd91ee3732c78df7e2f5222
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 10 20:16:42 2017 -0400
remove old SGS stuff
Exec/science/flame/sum_integrated_quantities.cpp
commit 5b7c5999d9fe3057b4ef1dd3507586a639db6b01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 9 20:13:53 2017 -0400
always compile in filcc_nd
Source/driver/Make.package
commit ee05e4f35533c80d8a2cd7cf571e1dc13e40b951
Merge: 347aa4eea 26d4f73dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 9 17:40:44 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 26d4f73ddff644cc628e378fc3328fa2c79b582b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 9 06:23:23 2017 -0700
Use a standalone BC fill for sources StateData (#215)
This PR creates new functions, ca_generic_single_fill and ca_generic_multi_fill. All these do is call filcc. These are useful for any generic fill of data with NUM_STATE (NVAR) components.
This PR also applies them to Source_Type, SDC_Source_Type, and SDC_React_Type. These are all NUM_STATE sized, and use the same BCs as the State_Type (normal linear extrapolation for everything but the velocity components).
Source/driver/Castro_F.H
Source/driver/Castro_setup.cpp
Source/driver/Make.package
Source/driver/generic_fill.F90
commit 347aa4eea4129cc2a992096253c5ef6fb9baccd4
Merge: c7293f394 26297d2e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 8 15:08:03 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 26297d2e5eac385b72e509397d893f123a34a594
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 21:46:24 2017 -0400
rename Conductivity_dir -> CONDUCTIVITY_DIR (#212)
* rename Conductivity_dir -> CONDUCTIVITY_DIR
* backwards compatibility
CHANGES
Exec/Make.Castro
Exec/hydro_tests/toy_flame/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
commit c7293f3940e32334021679944dc3ee24d17f3c23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 21:21:49 2017 -0400
backwards compatibility
Exec/Make.Castro
commit 7c3564a498ed2636538e685799bc44a72e461988
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 21:16:40 2017 -0400
rename Conductivity_dir -> CONDUCTIVITY_DIR
CHANGES
Exec/Make.Castro
Exec/hydro_tests/toy_flame/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
commit 53f5d1a5560dcaf144e5e513b92fcd1166cc72d1
Merge: d110da779 8b4da0720
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 20:29:57 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit d110da77977d7449da2ccb3b5796e12b6358ccf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 20:29:49 2017 -0400
fix typo
Docs/Radiation/CastroRadiation.tex
commit 8b4da072095f06e6c123a90e4aaf4afc7e3d32cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 14:01:17 2017 -0400
fix smallx init
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/Prob_3d.f90
commit b41990c6bb491d2313e994b09ab5cd284ccbbefe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 13:16:37 2017 -0400
update known compiler bugs
Docs/ManagingJobs/managingjobs.tex
commit 27e2b4e97b06eb26fd5472832cd7282bc53b5d22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 12:10:43 2017 -0400
fix compilation error
Exec/science/wdmerger/Castro_prob_err_F.H
commit db48963c4600c6e1179a8a6e50ca95205daae1cd
Merge: 6fe1afb7d 930b2d1cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 11:59:38 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 6fe1afb7df6166d8878c023829950fd9e7f61c63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 11:59:28 2017 -0400
3-d version
Exec/science/Detonation/Prob_3d.f90
commit 930b2d1cbdbd3754ebccce608e65577093d2db6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 7 11:49:07 2017 -0400
some OLCF compiler updates
Docs/ManagingJobs/managingjobs.tex
commit 6350a9a55b24e2c1760e4b9b30bf0a760ab74869
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 7 07:30:35 2017 -0700
Update the sponge source term (#195)
* Update the sponge source term
- The sponge is now always time centered; the option to change this is removed.
- The energy source term is now correctly time centered.
- The energy source term is now calculated in the same way we do it for other sources.
* Update the sponge factor for the new time
* Fix the corrector form (0.5 * new - 0.5 * old)
* Correctly update the sponge parameters for the corrector
* Restore the statement to skip the sponge if do_sponge=0
* Remove an obsolete S_new hook
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro_F.H
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/sources/Castro_sponge.cpp
Source/sources/sponge_nd.F90
commit 5f04d29573b640ac5b549e4c9921bbffb9b702af
Merge: f22dd1b08 592e11f1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 7 03:20:21 2017 -0400
Merge branch 'development' into wdmerger_half_domain
commit 592e11f1e321c6203281d99cc546f44763a52a8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 7 02:51:29 2017 -0400
Use a default small retry tolerance
Docs/runtime_parameters/runtime_parameters.tex
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
commit 9c6c16c378ac826eae7c2e168ebf2c3cc1983a5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 7 02:49:33 2017 -0400
Fix the ignition checking in wdmerger
Exec/science/wdmerger/Castro_prob_err.cpp
Exec/science/wdmerger/Castro_prob_err_F.H
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_F.H
commit 2100b3728a74cfca277961402bcea33499783adb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 7 02:48:36 2017 -0400
Always clamp subcycles to 10 maximum
Docs/runtime_parameters/runtime_parameters.tex
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 506d81036c4dc676c609df4f6402b1263d3c1061
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 6 23:57:53 2017 -0400
Add some new files I forgot to check in
Exec/science/wdmerger/Castro_prob_err.cpp
Exec/science/wdmerger/Castro_prob_err_F.H
Exec/science/wdmerger/Castro_prob_err_list.H
commit 58dfcb7460e78773536a336f0387cdefc9c7f305
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 6 22:18:33 2017 -0400
Disable burning-based AMR if a detonation is detected
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/Problem_Derives.H
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/problem_derive_nd.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/wdmerger_util.f90
commit f1a030bfc0ea514eab44feca5f0355b9d0aa668e
Merge: 5ead16657 af35f548b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 4 13:49:55 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit af35f548b2ac2884f173c23da26714972065ae01
Author: Brian Friesen <bfriesen@lbl.gov>
Date: Wed Oct 4 07:03:28 2017 -0700
Castro::estTimeStep(): fix missed "min" in OpenMP reduction pragma (#208)
Source/driver/Castro.cpp
commit fb32a5c8d340f19edd135fea16754fc24aed9163
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 4 05:26:09 2017 -0400
Add more user hooks for problem-specific tagging
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_error.cpp
Source/problems/Castro_prob_err.cpp
Source/problems/Castro_prob_err_F.H
Source/problems/Castro_prob_err_list.H
Source/problems/Make.package
commit 5ead166577ec0c2f9e7237f3b65d503a5353980f
Merge: 659021974 17bbef8e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 3 21:08:55 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 0ea71b71ee23f12d296db2ce3bf89d4c254a67eb
Merge: 8c67de3ad 659021974
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 3 21:06:34 2017 -0400
Merge branch 'development' into mol
commit 17bbef8e0475deccdf77e9b2398f06a5078c5311
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 3 17:55:23 2017 -0700
When we force a post-timestep regrid, recalculate dt and subcycle if necessary (#206)
In this situation we either have a completely new level, or new zones on an existing level, that was not factored in when we calculated the timestep at the beginning of the coarse timestep. Consequently we can easily run into situations like CFL violations or burning timestep constraint violations. In this case we calculate the timestep for this level, and subcycle if necessary to complete the advance safely.
Fixes #204
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit 6590219747e8bba7e797e3c2cee3ddcb65207bf4
Merge: eed4e9d9f 70bccae9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 3 20:46:54 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 70bccae9c5879641637fc57a99de446129a2bf9f
Merge: 7045e7e36 70090d73a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 3 20:14:12 2017 -0400
Merge branch 'subcycle_separation' into development
Conflicts:
Source/driver/Castro_advance.cpp
commit eed4e9d9f8ce232f48e21d86c8590f0ecad10f7b
Merge: 99f152f5a 7045e7e36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 3 18:11:08 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 8c67de3ad4cf80cf7b77d8ee5bff0b028b4c1a54
Merge: 1ac8cf22d 7045e7e36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 3 13:20:34 2017 -0400
Merge branch 'development' into mol
commit 7045e7e36721b2e45730d6572a250d3e68675f80
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 3 06:45:38 2017 -0700
Remove an incorrect gravity time level swap during a retry (#205)
This removes a time-level swap in gravity that was missed previously (PR #189)
CHANGES
Source/driver/Castro_advance.cpp
commit 70090d73a069b021115801e780d648b204dfc968
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 3 04:20:55 2017 -0400
Split off subcycle functionality into separate function
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
commit 93f7c50bb8a6c1ccfe556c4bab6f00b478066b45
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 3 04:11:40 2017 -0400
Remove an incorrect gravity time level swap during a retry
PR #189 did not correctly fix the issue described in #188 because it missed
an initial time level swap in the retry functionality. This is now fixed, so
that the first subcycle in a retry actually sees the same old gravity as the
rejected advance.
This changes results for problems that use retries with Poisson gravity.
CHANGES
Source/driver/Castro_advance.cpp
commit 3dcccbe7f724d267d00765d2cd58316eac57c86c
Merge: 654458b58 915f23576
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 3 04:10:54 2017 -0400
Merge branch 'development' into timestep_retry_fix
commit 2649a13a94c7d4be1705756be0517fe6ad82dbdf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 2 12:52:14 2017 -0400
update CHANGES
CHANGES
commit 915f23576239bf405716931fbdbe4bcac6c5f906
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 30 15:07:49 2017 -0400
Read in the wdmerger extrema after a restart
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_F.H
commit 99f152f5a2f734a0babcfee069c7a286f02d4838
Merge: eef57a7ea 484eab8c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 29 13:23:04 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 484eab8c43bacb51591cea7e86f34368feab6cd4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 28 03:08:07 2017 -0400
Fix the meaning of the ts_te stopping criterion
Exec/science/wdmerger/Prob.cpp
commit abe072a462db71c77d94eea5d0e33f0dea24cb26
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Sep 27 14:44:27 2017 -0700
fix comment that generated bad latex
Source/driver/_cpp_parameters
commit 9abc0d905f9adac4b62f99d1ababd8a29927cfcc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Sep 27 10:58:58 2017 -0700
fixed underscore errors so this builds again
Docs/runtime_parameters/runtime_parameters.tex
commit d50599470d34fd3b254d6afe7ca9cb79c3ceb0be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 26 06:31:39 2017 -0400
merge the logic for plotfiles and small plotfile (#201)
Source/driver/Castro.H
Source/driver/Castro_io.cpp
commit 2caef8d8d7b7b896c495ca694b07150570d30bef
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 26 05:19:37 2017 -0400
Use input parameter, not hardcoded value
Exec/science/wdmerger/Prob.cpp
commit 01610703f47d95b2f3871af2a1ebb9b1d903d07f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 26 04:48:42 2017 -0400
Update wdmerger collision stopping criterion
Now we use the burning instability criterion rather than the density.
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
commit eef57a7ea443e1b39dffed6bb96dc675416ed6b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 25 20:27:34 2017 -0400
merge the logic for plotfiles and small plotfile
Source/driver/Castro.H
Source/driver/Castro_io.cpp
commit f09924e8140b9d2ea50be2e6117a04e97e51a91f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 25 19:00:25 2017 -0400
fix cases where we do UFS:, assuming that only species follow.
check with ack "UFS:\w\)"
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/problem_derive_nd.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/science/flame_wave/Prob_2d.f90
Exec/science/planet/Prob_1d.f90
Exec/science/planet/Prob_2d.f90
Exec/science/xrb_mixed/Prob_2d.f90
commit 3d49fd1f7608d5a8b01e5ede2ca24a67132da83f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 25 03:33:50 2017 -0400
Add sponge density parameters to wdmerger probin
Exec/science/wdmerger/probin
commit f091f79406f33bd0050aaea99d0d4210ff16b3ea
Merge: 2a14c079e 4bcd4cde0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 21:14:29 2017 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 1ac8cf22d84cd18a3beea200faacb02e66485eed
Merge: 93d7a63e4 4bcd4cde0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 24 21:07:55 2017 -0400
Merge branch 'development' into mol
commit 4bcd4cde07d112d35658697814c4e75e392f5121
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 24 19:34:34 2017 -0400
update the runtime_parameters.tex after we rewrite the param stuff
Source/driver/mk_params.sh
commit 2a14c079e59eae5ec3b62c164bde667225696d0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 20:00:50 2017 -0400
Write a smallplotfile at the end
Source/driver/main.cpp
commit c6dfb9bc1b30267373d9c4df7a9851af6dd2c874
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 19:26:07 2017 -0400
Update CHANGES
CHANGES
commit b3d95f608f66f2b908388f2f8080d4863ad26000
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 19:09:54 2017 -0400
Do a wdmerger sum reduction after a restart at t=0
Exec/science/wdmerger/Prob.cpp
commit 57398212e6da2b585478c300a91d4aa49b86a064
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 19:08:57 2017 -0400
Set the old data behind by dt when resetting checkpoint time
Source/driver/Castro_io.cpp
commit d56664bfc252c1adadffee22b9f9fc4feebf1714
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 07:49:05 2017 -0400
Set level count when resetting checkpoint step
Source/driver/Castro_io.cpp
commit 4b199131fc83c34bf57271b35e21ad50459a74b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 04:06:27 2017 -0400
Add a density stopping criterion for wdmerger
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.H
commit 1863c0c19e01f81ed9c3c1e9271e84fe11f3bc07
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 24 02:55:35 2017 -0400
Add options to reset checkpoint time and step
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro_io.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit b6288ded55462426558720ebd97ab62547b32d07
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 23 00:39:52 2017 -0400
Add amrex namespace to Real
Source/driver/Castro.H
commit 052e3c5056e2526b657a2c2f28310ea62debbd49
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 22 04:29:57 2017 -0400
Add options to limit the timestep to hit plot intervals exactly
The AMReX behavior for the input parameter plot_per, which is the simulation
time between taking plot files, is to generate a plot if we passed a multiple
of plot_per in the last timestep. If the timestep is of the same order as
plot_per, though, the resulting time of the plotfile can actually be significantly
different than a multiple of plot_per. If the timestep is significantly larger,
some multiples can be skipped altogether. The new parameter, castro.plot_per_is_exact,
enforces that a timestep that would pass a multiple of this interval is shortened
so that it hits this interval exactly. Then every plot file will be an exact multiple
of plot_per, and there will be a plotfile for every multiple of plot_per.
The same holds true for small plotfiles with the parameter castro.small_plot_per_is_exact.
To prevent very small timesteps, which can mess up the hydrodynamics, the shortened
timestep is limited to be no smaller than 10^-4 * dtEst, where dtEst is the limited dt
from all other factors (e.g. CFL limiting).
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 93d7a63e4a42a4ceaf0b9faa89db800527341502
Merge: 95eb29e7b 61b3b70bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 20 17:01:49 2017 -0400
Merge branch 'development' into mol
commit 61b3b70bbcbbece2d5266334e73a7b961b5fbe85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 20 17:00:19 2017 -0400
fix blanket species initialization
Exec/science/flame_wave/Prob_2d.f90
commit 0d5542d431fd84fa95976479bba9609b3be5c258
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 20 12:08:14 2017 -0400
Update CHANGES
CHANGES
commit 5fe26b7fca31861849b4cb8143533efd8ff1c2b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 20 12:03:47 2017 -0400
add discussion of flux limiter (#193)
* add discussion of flux limiter
Docs/Hydrodynamics/Hydrodynamics.tex
Docs/refs.bib
commit 30d2c85428a72a4175c74882393423c5f246a5a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 20 08:49:34 2017 -0400
fix some comments from the PR
Docs/Hydrodynamics/Hydrodynamics.tex
commit 1776be33eddfadf3323fa984715c68a75d1a26c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 20 01:22:40 2017 -0400
Do not calculate n+1/2 potential on domain corners
There is no valid data there from the Poisson solve, so skip it (we do
not need the data here anyway; this is mainly to avoid generating NaNs).
(Partially) fixes #109
Source/gravity/gravity_sources_nd.F90
commit 8385a5271432d3504b3186e70cfe1beea50a5a3e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 20 01:22:34 2017 -0400
Add a function that determines if we're on a domain corner
Source/driver/Castro_util.F90
commit 54aefe3081c4ea82682fac3bf8f02dab50242792
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 20 00:54:47 2017 -0400
Handle symmetry boundaries correctly in calculating ghost zone potential
This error had no practical effects because the flux is always zero on a symmetry
boundary, so it didn't matter what the value of the potential was.
(Partially) fixes #109
Source/gravity/gravity_sources_nd.F90
commit 9a6cee344f0b8075c49281fd7795623e46c6bc0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 19 13:58:19 2017 -0400
add discussion of flux limiter
Docs/Hydrodynamics/Hydrodynamics.tex
Docs/refs.bib
commit 623939b51d6865883ab3a9d477a0bd0405d86388
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 19 09:19:57 2017 -0700
Do not swap gravity time levels on the first retry subcycle (#189)
* Use a MultiFab to store the fluxes during a timestep
The fluxes MultiFab holds this data normally when no subcycles occur.
But when subcycles occur, the fluxes MultiFab is intended to hold the
sum of the fluxes over all of the subcycles -- this is important for
getting refluxing right with AMR. But this introduces a problem because
the gravity source term references the fluxes MultiFab. A new MultiFab,
current_fluxes, has been introduced and it stores the hydro flux only
for a single timestep or subcycle.
Fixes #178
* Revert "Use a MultiFab to store the fluxes during a timestep"
This reverts commit b72573539a23af48d6c900dcda5ff7917a390e14.
* Store the mass flux for use in evaluating the gravity source
* Change when mass_fluxes is allocated in a reflux
* Do not swap gravity time levels on the first retry subcycle
The swapTimeLevels call for gravity copies the new data to the old data,
and sets the new data to a meaningless value. This makes sense for normal
evolution, but for subcycled evolution we must be careful because of the
way we use grad_phi. We do not simply recompute it from scratch during
the old-time level solve; rather, we use the saved value of it because
it contains data from the composite solve that is more accurate than the
level solve.
After the original level advance, during which we swapped the gravity
time levels, the old-time grad_phi is the correct composite data. So,
on the first subcycle of a retry iteration, we do not want to swap the
time levels -- everything is already OK (the new-time data does not have
the meaningless data in this case, but rather the new-time data from the
rejected advance, but this does not matter because the new-time data is
never re-used). On subsequent iterations, when we have advanced in time,
we want to swap the time levels as normal.
Source/driver/Castro_advance.cpp
commit 56b11b5ec4b323499831bbc20ed00ec105c2faf5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 19 05:51:19 2017 -0700
Add a README comment: all known bugs should have issues filed (#190)
Transparency about known bugs is important for helping users establish a judgment
about how reliable the code is. If they have done simulations using a given version
of the code they should be able to find out if there were any known issues relating
to the code modules they used. More broadly, setting an expectation of full transparency
about known issues helps establish a precedent in the community that it is acceptable
to make mistakes, and that being open about them improves confidence in the software
produced by the community as a whole.
README.md
commit 4193353c6aec93825eb1469190c6885bba87b6be
Merge: 6090d4490 f69597a73
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 19 01:36:09 2017 -0700
Merge pull request #191 from AMReX-Astro/smallplots
Add capability for small plotfile to have derived variables
commit f69597a739afe6772ee53ca997f853e3c0b5e518
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 19 04:32:43 2017 -0400
Add capability for small plotfile to have derived variables
Source/driver/Castro_io.cpp
commit 654458b581df6d39b219879d6d71228eda930c56
Merge: 5b52d23af 6090d4490
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 18 23:24:31 2017 -0400
Merge branch 'development' into timestep_retry_fix
commit 5b52d23afd5d93a1b8bc82e6e213ecd24713cf98
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 18 23:19:16 2017 -0400
Do not swap gravity time levels on the first retry subcycle
The swapTimeLevels call for gravity copies the new data to the old data,
and sets the new data to a meaningless value. This makes sense for normal
evolution, but for subcycled evolution we must be careful because of the
way we use grad_phi. We do not simply recompute it from scratch during
the old-time level solve; rather, we use the saved value of it because
it contains data from the composite solve that is more accurate than the
level solve.
After the original level advance, during which we swapped the gravity
time levels, the old-time grad_phi is the correct composite data. So,
on the first subcycle of a retry iteration, we do not want to swap the
time levels -- everything is already OK (the new-time data does not have
the meaningless data in this case, but rather the new-time data from the
rejected advance, but this does not matter because the new-time data is
never re-used). On subsequent iterations, when we have advanced in time,
we want to swap the time levels as normal.
Source/driver/Castro_advance.cpp
commit 95eb29e7b70b24d68738dbe0d8849da593e1dfd5
Merge: d85828265 6090d4490
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 18 20:29:43 2017 -0400
Merge branch 'development' into mol
commit 6090d44902584d7f7b0fc69fd8591bc94cf9de95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 18 20:22:46 2017 -0400
integrate ppm_temp_fix = 3 into the mainline (#187)
* most of the work toward implementing the temperature tracing
* more updates
* fix compilation
* fix compilation
* fix undefined dTs
* some compilation fixes
* fix the fix...
* fix some uninitiailzed quantities
* no longer needed
* sync up
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-y
Exec/hydro_tests/Sod_stellar/inputs-test1-helm-z
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
Source/hydro/trace_ppm_nd.F90
commit 981ccd76031ff8bc27d36255568cf6a35193a21c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 17 11:25:53 2017 -0400
update CHANGES
CHANGES
commit 146b5d0fd7333fcede332100de9007d5e2a29a65
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 17 08:22:35 2017 -0700
Use a MultiFab to store the mass fluxes during a timestep (#180)
* Use a MultiFab to store the fluxes during a timestep
The fluxes MultiFab holds this data normally when no subcycles occur.
But when subcycles occur, the fluxes MultiFab is intended to hold the
sum of the fluxes over all of the subcycles -- this is important for
getting refluxing right with AMR. But this introduces a problem because
the gravity source term references the fluxes MultiFab. A new MultiFab,
current_fluxes, has been introduced and it stores the hydro flux only
for a single timestep or subcycle.
Fixes #178
* Revert "Use a MultiFab to store the fluxes during a timestep"
This reverts commit b72573539a23af48d6c900dcda5ff7917a390e14.
* Store the mass flux for use in evaluating the gravity source
* Change when mass_fluxes is allocated in a reflux
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/gravity_sources_nd.F90
Source/hydro/Castro_hydro.cpp
commit 48d7c5f6c4aead6cd16597b9610b2aa1652d77b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 17 08:20:09 2017 -0700
Apply a small tolerance to the density floor when flux limiting (#185)
Source/hydro/advection_util_nd.F90
commit d858282651bc6e38a0b68e9cf925e30a764bcea7
Merge: ff3f88913 8f33b96b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 17 09:36:30 2017 -0400
Merge branch 'development' into mol
commit 8f33b96b79fab7b56d323e2a77f8baa0aba1dba5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 17 09:36:01 2017 -0400
Add guidelines for becoming a "core developer" of Castro (#183)
* add some contributor guidelines
* update CHANGES and discuss updating CHANGES in README.md
* add pointers to README.md on contribution
CHANGES
Docs/Preface/Preface.tex
README.md
commit ed0bc80cc7b40df7c7f41159f418885c515141ea
Merge: 9ea8b1046 4004d36bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 19:00:51 2017 -0400
Merge branch 'reorg' into development
commit 4004d36bbe677ad6e9af3f704fb924ec8d0ad7a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 19:00:25 2017 -0400
update CHANGES
CHANGES
commit 9ea8b1046ec0b914fb0c15c2ef63d7dac12f4a33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 18:58:46 2017 -0400
rename Network_dir -> NETWORK_DIR; EOS_dir -> EOS_DIR (#184)
* rename Network_dir -> NETWORK_DIR; EOS_dir -> EOS_DIR
* update to new names
Docs/Radiation/CastroRadiation.tex
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/RT_particles/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/reacting_bubble/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/hydro_tests/toy_flame/GNUmakefile
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/test_react/GNUmakefile
commit f22dd1b08d409962f104d8a8f29678fbdf2dae6d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 18:30:15 2017 -0400
[WIP] Start making wdmerger be able to use a half domain (z > 0 only)
This currently loads the data onto the grid fine, but there's some things
we haven't dealt with correctly yet. The relaxation step isn't dealing with
the symmetry boundary correctly, and the gravitational wave calculation hasn't
dealt with it at all.
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/wdmerger_util.f90
commit 40d9b7497cbc2d6e8f3f7acdfec558cf822cfe2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 18:05:47 2017 -0400
update to new names
Docs/Radiation/CastroRadiation.tex
commit 4a0c20bce45df2cae98e74225017757e4391cdfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 18:02:38 2017 -0400
rename Network_dir -> NETWORK_DIR; EOS_dir -> EOS_DIR
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/RT_particles/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/reacting_bubble/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/hydro_tests/toy_flame/GNUmakefile
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/science/wdmerger/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/test_react/GNUmakefile
commit ff3f88913c75509a645bf89fe9908e3045d463a0
Merge: bc153ac6a e3bb62221
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 14:18:42 2017 -0400
Merge branch 'development' into mol
commit e3bb62221cd21bffa01e1b427b8bf25657c17371
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 13:56:46 2017 -0400
Clamp temperatures in the reactions to 10^10 K
Exec/science/wdmerger/probin
commit 9b7f51e7e558f7bac8be8ff6b718a23d08999885
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 13:41:12 2017 -0400
Clamp number of wdmerger retries to 100
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 12db610710957bb48dd29c98baed11e6b9f030a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 13:28:08 2017 -0400
Get the wdmerger retry problem back in working order
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
commit 9753871a1a7a8c564d58548fd5069bb370cb2fa9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 13:24:34 2017 -0400
Add an option to not fail if we request too many subcycles
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit 98ffe4964e91c35188b16adb8619ee4d264b69ed
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 11:29:15 2017 -0400
Change when mass_fluxes is allocated in a reflux
Source/driver/Castro.cpp
commit e3b4e025ac37e75754f887fd12080b7a221cc2d3
Merge: 5e6f57a49 5e0d6e500
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 16 09:10:12 2017 -0400
Merge pull request #181 from adam-m-jcbs/development
Minor parameter change
commit 5e6f57a498c7a232e916a383f0591c9d0676ae43
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 00:49:37 2017 -0400
Add a small retry tolerance to wdmerger
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit e5681a56e0d3bd0e02977f88bc36ba273e8035ae
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 00:48:11 2017 -0400
Allow a user-specified tolerance factor for avoiding retries
Docs/runtime_parameters/runtime_parameters.tex
Source/driver/Castro_advance.cpp
Source/driver/_cpp_parameters
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
commit cf0813d1b46a555b622d4b904fd1b51f0edbb130
Merge: d58f60d02 004601291
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 15 23:40:06 2017 -0400
Merge branch 'development' into timestep_retry_fix
commit d58f60d02243374568986b18dda9effbc981e1cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 15 23:14:11 2017 -0400
Store the mass flux for use in evaluating the gravity source
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/gravity/gravity_sources_nd.F90
Source/hydro/Castro_hydro.cpp
commit 90f75cd73985c56e0886170f068e43e060909d2f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 15 21:36:57 2017 -0400
Revert "Use a MultiFab to store the fluxes during a timestep"
This reverts commit b72573539a23af48d6c900dcda5ff7917a390e14.
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hydro.cpp
commit bc153ac6ad70b6df293900f3adaddcec5880cbf6
Merge: d98cdd56f 004601291
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 15 15:37:28 2017 -0400
Merge branch 'development' into mol
commit 00460129119a13a9beca9eae2caf99f450041641
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 15 15:33:07 2017 -0400
remove unused variables
Source/hydro/riemann_1d.F90
Source/hydro/riemann_2d.F90
commit 62b70ed0bfd54313d68bc6af80348e41379c5e33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 15 15:31:48 2017 -0400
fix some indexing issues
Source/hydro/Castro_advection_2d.F90
commit 5e0d6e50014e6193e5f1bd3926849272d7500085
Merge: 6add73e2a 032bcccb7
Author: Adam M. Jacobs <ajacobs@pa.msu.edu>
Date: Fri Sep 15 14:39:23 2017 -0400
Merge upstream into Adam's fork
commit 6add73e2a44aeee175c1d32471e21722f3ceccdc
Author: Adam M. Jacobs <ajacobs@pa.msu.edu>
Date: Fri Sep 15 14:39:16 2017 -0400
Add CFL retries to convective_flame
Exec/science/convective_flame/inputs.2d.test
commit b72573539a23af48d6c900dcda5ff7917a390e14
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 15 01:09:58 2017 -0400
Use a MultiFab to store the fluxes during a timestep
The fluxes MultiFab holds this data normally when no subcycles occur.
But when subcycles occur, the fluxes MultiFab is intended to hold the
sum of the fluxes over all of the subcycles -- this is important for
getting refluxing right with AMR. But this introduces a problem because
the gravity source term references the fluxes MultiFab. A new MultiFab,
current_fluxes, has been introduced and it stores the hydro flux only
for a single timestep or subcycle.
Fixes #178
Source/driver/Castro.H
Source/driver/Castro_advance.cpp
Source/gravity/Castro_gravity.cpp
Source/hydro/Castro_hydro.cpp
commit 032bcccb7bc0e4cf6997463332ed0b6072d377f5
Merge: c100d1c8f fed7cf4f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 13 20:45:48 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit c100d1c8f7fb850f647939416e08a3ba86b474cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 13 20:45:09 2017 -0400
parallel initialization is now handled by AMReX when BL_USE_FORTRAN_MPI
is set (which is defined in FParallelMG.mak in F_BaseLib)
Source/driver/Castro_nd.F90
commit d98cdd56f53f239bfe5f2682953c789bef9418aa
Merge: 00f27e1e9 fed7cf4f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 13 10:29:21 2017 -0400
Merge branch 'development' into mol
commit fed7cf4f23f0bf7afec1cda09c2fc8b19b2aae79
Merge: 444bdb73b 9527e2f32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 13 10:27:20 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 9527e2f3269fd6f079972d8a356a30fecda25bcb
Merge: 04093930b 4c230243f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 13 10:26:27 2017 -0400
Merge pull request #177 from zingale/development
move pdivu into a subroutine
commit 4c230243f7be9f2d3fd191a98bac5c6b07078025
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 22:09:24 2017 -0400
move pdivu into a subroutine
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_mol_1d.F90
Source/hydro/Castro_mol_2d.F90
Source/hydro/Castro_mol_3d.F90
Source/hydro/advection_util_nd.F90
commit 04093930bb4acb15f88c376d99c37ce6b9764a46
Merge: 453685017 787eb31aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 18:32:29 2017 -0400
Merge pull request #176 from taehoryu/development
planet update (Sep12)
commit 787eb31aac1de9245ec1cdf000af5ec3f03db44b
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Sep 12 16:35:08 2017 -0400
original
Docs/GNUmakefile
commit d32d1cbf48a8030f6895c4ef3f6af6049ed57ccb
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Sep 12 16:26:45 2017 -0400
planet update (+tracer particle) Sep.12
Docs/GNUmakefile
Exec/science/planet/GNUmakefile
Exec/science/planet/Prob_2d.f90
Exec/science/planet/bc_ext_fill_2d.F90
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/inputs_2d
Exec/science/planet/newmodelcpp.hse
Exec/science/planet/particle_file
Exec/science/planet/probin
commit 4536850173677add5683721d4884e0e510bd208f
Merge: de4728ad7 14c0fe582
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 13:15:24 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit de4728ad7083eafe342719986d64e6b4111532d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 13:14:53 2017 -0400
fix compilation with new Riemann interface
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
commit 14c0fe582923211678397e94a0984e4a2e600a64
Merge: 326ec2be0 1f742ad5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 12:00:09 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 326ec2be0a6a7c0f6383fc4c25148914c55bdeb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 12:00:03 2017 -0400
fix typo
Exec/science/flame_wave/inputs_2d
commit 1f742ad5f6938e19a7394baa3a73daee8c778022
Merge: 13fc3f6fb 25a1c3144
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 11 17:57:57 2017 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 13fc3f6fbfe82063846c1bed97fa70622ce1a87f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 11 17:57:32 2017 -0700
add mechanism to post to slack when jobs start
Util/job_scripts/edison/edison.MPI.slurm
Util/job_scripts/edison/slack_job_start.py
commit 444bdb73b8e97dd4c6c369cc51c9676b7bda2e7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 11 09:37:58 2017 -0400
some comments
Source/driver/Castro_advance.cpp
Source/sources/Castro_sources.cpp
commit 25a1c31443c04ad9720a493d552bc005fbafdcc7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 21:25:51 2017 -0400
update changes
CHANGES
commit 00f27e1e9600466eeb7f5605a75a97cd7282f837
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 20:23:47 2017 -0400
some works on the merge
Source/hydro/Castro_mol_3d.F90
commit 6995246d0f447dec48f3e898daeb5c24ff60a397
Merge: dd0a4a5aa 51950c5d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 19:28:03 2017 -0400
Merge branch 'development' into mol
commit 51950c5d5d33afe1d3f1a238990c4ca379201715
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 18:49:24 2017 -0400
move 1-d divu into advection_util_module : divu
this also fixes some geometry bugs with divu in 1-d
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_mol_1d.F90
Source/hydro/advection_util_nd.F90
commit dd0a4a5aa8ffc287665695d67db550935e76b31c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 18:09:08 2017 -0400
more merge work
Source/hydro/Castro_mol_3d.F90
commit 6e9fe185d7df7c96f0599d5b1a5944f71a55ebb6
Merge: fe7ed1b10 4f84d83b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 16:32:19 2017 -0400
Merge branch 'development' into mol
commit 4f84d83b283a35551a1ea523f582294ce1e4f02a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 14:59:55 2017 -0400
simplify the setting of the interface states -- we don't need temporaries
for all variables
Source/hydro/Castro_mol_3d.F90
commit fe7ed1b107d1ad1e1648d6e8c98fa4a87d653a9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 14:42:19 2017 -0400
some MOL unification start
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_3d.F90
commit b2e3509bdb873e631d8372790da88402e7d14935
Merge: 28c6b07e2 33c7eb092
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 10:39:56 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 28c6b07e2bbd6091dbd6aae9f9c8318aed3881cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 10 10:39:42 2017 -0400
disable centrifugal
rename H_min -> X_min
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/inputs_2d
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/problem_tagging_2d.f90
commit 33c7eb0920fe2f9009ea7264f9cc126a0d7ab26e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 8 19:29:16 2017 -0400
Use implicit relaxation damping by default
Exec/science/wdmerger/probin
commit bd9fe30b74fd808e7d53975cfae2f47448c934c2
Merge: 3efdf4dde 37197c388
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 8 18:39:14 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 3efdf4dde4fb424b74110e9a2b50098a1ea11eb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 8 18:39:02 2017 -0400
update the notes on CCE compilers
Docs/CastroUserGuide.tex
Docs/ManagingJobs/managingjobs.tex
commit 37197c3885b45d6a368344b34e8e06304f1bc80d
Merge: 1c283eb6b b7245b151
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 8 09:35:34 2017 -0700
Merge pull request #171 from AMReX-Astro/x_limiter
Set a floor for timestep limiting due to changes in X
commit b7245b1514552995634490860d499dc7d3cd2840
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 8 11:23:20 2017 -0400
Set a floor for timestep limiting due to changes in X
The current implementation has the problem that it can drag the timestep
down to very small values due to changes in trace isotopes. Usually for
burning simulations we do not care about changes to abundances that are
very small in absolute terms. This limiter (which defaults to 1.e-3) is
the abundance below which the timestep limiter is not applied.
Source/driver/_cpp_parameters
Source/driver/meth_params.F90
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/timestep.F90
commit 1c283eb6b5af91e9563bbe6ab051740571a869e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 7 16:51:56 2017 -0400
Revise a comment
Exec/science/wdmerger/probin
commit 5d0010cbb29cf2e58bc8c22def430e85a47255d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 5 16:01:56 2017 -0400
Test against allocated status before deallocating BC variables
This should not be necessary, but GCC 6.1 seems to have an issue with allocating
the character variables on at least one system.
Source/driver/meth_params.F90
Source/driver/parse_castro_params.py
commit fd5d954873413c64a50d726b2340bfb3246ac2ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 2 19:54:04 2017 -0400
some compilation fixes. We need the proper EOS for this to
actually compile
Source/radiation/MGFLDneut_1d.f90
commit 5be4682166777fda0e5fcd1e573c43d7212e1771
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 2 19:46:33 2017 -0400
fix build when using a USERSuffix
Exec/Make.Castro
commit cdf40206aedebbbfb367bffe2346a66bcfc64cf8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 1 11:56:09 2017 -0400
remove the custom BCs -- we should just do a standard outflow here
instead of an inflow pegged at ambient.
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
commit b620efbee69c51597bcb7708ab137f0e8de61091
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 1 11:52:17 2017 -0400
propagate temp_ambient through all dimensions
also fix a bug in 3d where the composition was not initialized
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
commit bb48bed7854eefa39835ca76ea800b93bcd432d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 1 11:36:59 2017 -0400
remove some of the more obscure geometries
now we get rid of probtype and set the Sedov geometry based on
the grid geometry and dimensionality, looking at coord_type
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sedov/inputs.2d.cyl_in_cylcoords
Exec/hydro_tests/Sedov/inputs.3d.cyl
Exec/hydro_tests/Sedov/probdata.f90
Exec/hydro_tests/Sedov/probin.1d.cyl
Exec/hydro_tests/Sedov/probin.1d.sph
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cartcoords.gammae
Exec/hydro_tests/Sedov/probin.2d.cyl_in_cylcoords
Exec/hydro_tests/Sedov/probin.2d.sph_in_cylcoords
Exec/hydro_tests/Sedov/probin.2d.sph_in_cylcoords.testsuite
Exec/hydro_tests/Sedov/probin.3d.cyl
Exec/hydro_tests/Sedov/probin.3d.sph
Exec/hydro_tests/Sedov/probin.3d.sph.testsuite
Exec/hydro_tests/Sedov/probin.starlord
commit e6915e27fd6f69e2c859079f425ff9366496e6e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 1 10:09:33 2017 -0400
update changes
CHANGES
commit b0551c1a444d0e443a66bfec85c9c8ffa16ffb9f
Merge: 7940dc3fd a5469c8df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 29 13:43:51 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 7940dc3fda85b79666a67b0426eea61c797e6900
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 29 13:43:42 2017 -0400
more labels
Exec/science/flame/analysis/profiles.py
commit a5469c8df768d826b958859f6963ee1a48f3866a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 27 11:49:58 2017 -0400
update the sad state of compiling at NERSC
short version: only GNU works
Docs/ManagingJobs/managingjobs.tex
commit 272032ff6866d95ec339e36266bfe2173af9a7af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 26 18:22:33 2017 -0400
remove some OMP critical regions, following Nyx's lead
Source/driver/Castro.cpp
Source/hydro/Castro_hydro.cpp
commit 5282882be81635fd201cebae57619942fc31c3ae
Merge: 837805e27 ebe20edb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 25 20:58:04 2017 -0400
Merge pull request #163 from taehoryu/development
[planet] update (bc*.f90, initial model and python scripts making plots)
commit ebe20edb6505662c3f6e5be0501eabe2d9a2c60d
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Aug 25 20:46:20 2017 -0400
slice plots for 2D (Aug25)
Exec/science/planet/dataset_sliceplot.py
commit 93e10f59c15484ab3965b9975d0a9094da3ffac9
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Aug 25 20:46:06 2017 -0400
line plots (Aug25)
Exec/science/planet/dataset_lineplot.py
commit 3b682341699cb2af280eebc76318b05dc41bceb4
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Aug 25 20:41:26 2017 -0400
update input files (Aug25)
Exec/science/planet/inputs_1d
Exec/science/planet/inputs_2d
commit 2f0bf3e167ca68ad2ef74d3e0fcd66bb149da189
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Aug 25 20:41:04 2017 -0400
update bc*fill*.F90 (Aug25)
Exec/science/planet/bc_ext_fill_1d.F90
Exec/science/planet/bc_ext_fill_2d.F90
Exec/science/planet/bc_fill_1d.F90
Exec/science/planet/bc_fill_2d.F90
commit d7f01762a7893686b435371a6e1adee4f4fddaec
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Aug 25 20:40:24 2017 -0400
continuous rho and continuous P at the buffer boundary (Aug25)
Exec/science/planet/HotJupiter.cpp
commit 837805e2758c568a51f25405965369593b2297a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 24 10:12:01 2017 -0400
add labels
Exec/science/flame/analysis/flame_speed.py
commit 7912c06f579ac4b531d0e3824b997511f34daaa8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 23 12:25:00 2017 -0400
updated model
Exec/science/flame_wave/probin
commit 40c831227bd994d698a2dc98d9ed0791eae05596
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 23 12:24:19 2017 -0400
new model with aprox13
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/flame_wave.hse.tanh.delta_12.000cm.dx_10.000cm
Exec/science/flame_wave/flame_wave.hse.tanh.delta_12.000cm.dx_20.000cm
commit 210a129b3e5691947e1b83ef1d2fd8c76a32922d
Merge: 0274f8791 c515257c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 23 09:46:44 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit c515257c2c2b0a2d82ecbbb7dd81c74cbc01b7fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 22 14:19:11 2017 -0400
new analysis script
Exec/science/flame/analysis/flame_speed.py
commit beae5a539e808d31e9f88707505674f0fba767bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 22 14:18:20 2017 -0400
updated microphysics
Exec/science/flame_wave/GNUmakefile
commit 0274f8791c5271ec07086247dfd1110ad08632d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 20 14:15:37 2017 -0400
fix paths
Source/driver/mk_params.sh
Source/driver/parse_castro_params.py
commit 5bc20cca3893ae63c0ee82c5a9df6ef4972f98a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 20 13:55:55 2017 -0400
velocities are contained in passive for DIM < 3, so don't
redo tracing for those
Source/hydro/trace_nd.F90
commit 98b60fa49def1e4fdbcaf2b27e19a401140752b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 20 13:06:38 2017 -0400
diffusion should not require gravity
this moves the metric terms into driver
closes #161
Exec/Make.Castro
Source/diffusion/Diffusion.cpp
Source/driver/Castro_F.H
Source/gravity/Gravity_F.H
commit cdb1cc10680f04ec064248aa25aaf6177010d7b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 20 12:23:15 2017 -0400
update changes
CHANGES
commit d91ff0605ebe6ee6b541aa9bb5d6d745641486aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 20 12:15:54 2017 -0400
fix some logic with the passive variables
in particular, we always update all 3 velocity components (and
deal with the source terms) in the main section, so don't overwrite
this in the single loop over passive variables for DIM < 3
also fix some logic for the mass flux fix in radiation -- it should
only be 1-d
Source/hydro/trace_ppm_nd.F90
Source/radiation/trace_ppm_rad_nd.F90
commit c2d23f581f325c50efa3a08a5bea78967f1f4db7
Merge: c7f2053df 2d983557f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 20 11:57:55 2017 -0400
Merge branch 'development' into hydro-cleaning
commit 2d983557f2e0c6086a64dc2762bf4d5f93c4a81e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 19:42:44 2017 -0400
diffusion needs a gravity header
Exec/Make.Castro
commit c7f2053df26051f811c04aeb643bf8d25f580233
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 19:20:16 2017 -0400
fix compilation with the new tracing for radiation
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/radiation/Make.package
Source/radiation/trace_ppm_rad_nd.F90
commit c75a0170204cfa53234ee0f1dd4d509c87eaea4e
Merge: 46e9f59e3 968922c27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 18:39:16 2017 -0400
Merge branch 'hydro-cleaning' of ssh://github.com/AMReX-Astro/Castro into hydro-cleaning
commit 46e9f59e3c7e63943fb7c17143c4432cb916fa9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 18:35:00 2017 -0400
some cleaning
Source/hydro/trace_ppm_nd.F90
commit 87df5d400e4eac3aebda9105063db288eb02f3a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 18:34:37 2017 -0400
dimensionally agnostificate
Source/radiation/trace_ppm_rad_1d.f90
Source/radiation/trace_ppm_rad_2d.f90
Source/radiation/trace_ppm_rad_nd.f90
commit 968922c27f1684bb28cfbebb2618e3a4ce3075be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 14:02:11 2017 -0400
fix location
Exec/Make.Castro
commit 7eb54f1b65f83eca78a872f79b385fb09297f917
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 13:47:21 2017 -0400
update docs to reflect new directory structure
Docs/AMR/AMR.tex
Docs/Diffusion/CastroDiffusion.tex
Docs/Gravity/CastroGravity.tex
Docs/Software/CastroSoftware.tex
commit b8ef6805bed5757f5c92f86eb530141f16e3b814
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 13:37:00 2017 -0400
update runtime param docs
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit 19a37793b8bccfe61baa7c4c464488ddcd38ed34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 12:08:57 2017 -0400
update changes
CHANGES
commit 6f35421ae093f9c07d201f478cf79862207a7384
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 19 11:17:10 2017 -0400
rename
Source/sources/Castro_external.cpp
Source/sources/Castro_sources.cpp
Source/sources/Castro_sponge.cpp
Source/sources/Make.package
Source/sources/ext_src_1d.f90
Source/sources/ext_src_2d.f90
Source/sources/ext_src_3d.f90
Source/sources/ext_src_nd.F90
Source/sources/sponge_nd.F90
Source/sources/update_sponge_params.f90
commit ee70fcce2c126819bb24b25d7e08bac62ed61747
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 18 20:58:58 2017 -0400
throw an error if hybrid_momentum is used in 3-d
Exec/Make.Castro
commit b9754839e5e34fe87fb4bb5ca27066a43a94174f
Merge: 53c4fb06b e8cdf2abd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 18 19:51:17 2017 -0400
Merge branch 'development' into reorg
commit e8cdf2abdd1a5f4e8bba560cae41083f787bcc70
Merge: 8520282ad 7afd22739
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 18 19:50:47 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 7afd2273990772cb5a23d926346d93a3860252e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 17 11:48:50 2017 -0400
Do an even better job protecting against roundoff
Source/Castro_advance.cpp
commit 53c4fb06b25985da77e58f6b82840ab8189bca77
Merge: 99e02264c 8520282ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 17 09:06:53 2017 -0400
Merge branch 'development' into reorg
commit 8520282ad3e1c967b695abd39e5c1fcdf0d0f5bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 17 09:06:43 2017 -0400
formatting
Source/Src_nd/React_nd.F90
commit 2f108c6d0b4e94daf1d436609f3801cefe3bd0f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 17 01:24:11 2017 -0700
Add an inputs file similar to the one from StarLord
Exec/hydro_tests/Sedov/inputs.starlord
Exec/hydro_tests/Sedov/probin.starlord
commit 3692872d839e063b9883c10716944a6cde6f4f52
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 16 22:04:28 2017 -0700
Remove gamma-law EOS dependence from Sedov BC fill
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
Exec/hydro_tests/Sedov/probdata.f90
commit 99e02264c438b7bc1d200754ec2eb8cc43816ae0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 16 22:13:59 2017 -0400
much cleaner Make.Castro
Exec/Make.Castro
Exec/unit_tests/test_react/GNUmakefile
Exec/unit_tests/test_react/testburn.f90
commit ddb92b324e104e69c853bf1f689383d4411fadf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:37:17 2017 -0400
fix some logic
Exec/Make.Castro
commit 28218799b75fe53d347cc7e61d509ea011e45f27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:35:46 2017 -0400
fix some logic
Source/driver/Make.package
commit 82b44b86ee6c8607f167e075210507312bcc05e8
Merge: 0c8c6a683 8f97cbb80
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:27:50 2017 -0400
Merge branch 'development' into reorg
commit 8f97cbb8006c00d4b49c7278c66dd0efbee89259
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:26:56 2017 -0400
fix normalize call
Source/Src_2d/Castro_mol_2d.F90
commit 0c8c6a6838152e1c9f73e29bcc77f3ce5032e7ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:25:59 2017 -0400
fix normalize call
Source/hydro/Castro_mol_2d.F90
commit af11bc6446797569e5f4ec41b016fdc817211fbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:17:41 2017 -0400
this files are not use
Source/gravity/pointmass_1d.f90
Source/gravity/pointmass_2d.f90
commit a730a324593133f8098d596499819943036e981c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 15 22:16:54 2017 -0400
move sources into directories by physics topic
Exec/Make.Castro
Source/Make.package
Source/Radiation/Make.package
Source/Radiation/RadSrc_1d/Make.package
Source/Radiation/RadSrc_2d/Make.package
Source/Radiation/RadSrc_3d/Make.package
Source/Radiation/RadSrc_nd/Make.package
Source/Src_1d/Make.package
Source/Src_1d/TODO
Source/Src_2d/Make.package
Source/Src_2d/TODO
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/diffusion/Castro_diffusion.cpp
Source/diffusion/Diffusion.H
Source/diffusion/Diffusion.cpp
Source/diffusion/Diffusion_nd.f90
Source/diffusion/Enthalpy_nd.f90
Source/diffusion/Make.package
Source/driver/Castro.H
Source/driver/Castro.cpp
Source/driver/CastroBld.cpp
Source/driver/Castro_F.H
Source/driver/Castro_advance.cpp
Source/driver/Castro_error.cpp
Source/driver/Castro_error_F.H
Source/driver/Castro_io.H
Source/driver/Castro_io.cpp
Source/driver/Castro_nd.F90
Source/driver/Castro_setup.cpp
Source/driver/Castro_util.F90
Source/driver/Derive_F.H
Source/driver/Derive_nd.F90
Source/driver/MGutils_1d.f90
Source/driver/MGutils_2d.f90
Source/driver/Make.package
Source/driver/Tagging_nd.f90
Source/driver/_cpp_parameters
Source/driver/amrinfo.f90
Source/driver/castro_c_interfaces_nd.F90
Source/driver/castro_cuda_interfaces_nd.F90
Source/driver/extern_probin.template
Source/driver/filcc_nd.F90
Source/driver/interpolate.f90
Source/driver/io.f90
Source/driver/main.cpp
Source/driver/math.f90
Source/driver/meth_params.F90
Source/driver/meth_params.template
Source/driver/mk_params.sh
Source/driver/param_includes/Make.package
Source/driver/param_includes/castro_defaults.H
Source/driver/param_includes/castro_params.H
Source/driver/param_includes/castro_queries.H
Source/driver/param_includes/diffusion_defaults.H
Source/driver/param_includes/diffusion_params.H
Source/driver/param_includes/diffusion_queries.H
Source/driver/param_includes/gravity_defaults.H
Source/driver/param_includes/gravity_params.H
Source/driver/param_includes/gravity_queries.H
Source/driver/parse_castro_params.py
Source/driver/prob_params.f90
Source/driver/sum_integrated_quantities.cpp
Source/driver/sum_utils.cpp
Source/driver/sums_nd.f90
Source/driver/timestep.F90
Source/gravity/Castro_gravity.cpp
Source/gravity/Castro_pointmass.cpp
Source/gravity/GR_Gravity_1d.f90
Source/gravity/GR_Gravity_2d.f90
Source/gravity/GR_Gravity_3d.f90
Source/gravity/Gravity.H
Source/gravity/Gravity.cpp
Source/gravity/Gravity_1d.f90
Source/gravity/Gravity_2d.f90
Source/gravity/Gravity_3d.f90
Source/gravity/Gravity_F.H
Source/gravity/Gravity_nd.f90
Source/gravity/Make.package
Source/gravity/gravity_sources_nd.F90
Source/gravity/pointmass_1d.f90
Source/gravity/pointmass_2d.f90
Source/gravity/pointmass_nd.f90
Source/gravity/prescribe_grav_nd.f90
Source/gravity/prescribe_phi_nd.F90
Source/hydro/Castro_advection_1d.F90
Source/hydro/Castro_advection_2d.F90
Source/hydro/Castro_advection_3d.F90
Source/hydro/Castro_ctu_1d.F90
Source/hydro/Castro_ctu_2d.F90
Source/hydro/Castro_ctu_3d.F90
Source/hydro/Castro_hybrid.cpp
Source/hydro/Castro_hydro.cpp
Source/hydro/Castro_mol_1d.F90
Source/hydro/Castro_mol_2d.F90
Source/hydro/Castro_mol_3d.F90
Source/hydro/Make.package
Source/hydro/advection_util_nd.F90
Source/hydro/flatten_nd.F90
Source/hydro/hybrid_advection_nd.F90
Source/hydro/multid_slope_2d.f90
Source/hydro/ppm_nd.F90
Source/hydro/riemann_1d.F90
Source/hydro/riemann_2d.F90
Source/hydro/riemann_3d.F90
Source/hydro/riemann_nd.F90
Source/hydro/riemann_util.f90
Source/hydro/slope_nd.F90
Source/hydro/trace_nd.F90
Source/hydro/trace_ppm_nd.F90
Source/hydro/trans_2d.F90
Source/hydro/trans_3d.F90
Source/particles/CastroParticles.cpp
Source/particles/Make.package
Source/problems/Make.package
Source/problems/Prob.cpp
Source/problems/Prob_1d.f90
Source/problems/Prob_2d.f90
Source/problems/Prob_3d.f90
Source/problems/Prob_nd.F90
Source/problems/Problem.H
Source/problems/Problem.f90
Source/problems/Problem_Derive_F.H
Source/problems/Problem_Derives.H
Source/problems/Problem_F.H
Source/problems/bc_ext_fill_1d.F90
Source/problems/bc_ext_fill_2d.F90
Source/problems/bc_fill_1d.F90
Source/problems/bc_fill_2d.F90
Source/problems/bc_fill_3d.F90
Source/problems/bc_fill_nd.F90
Source/problems/problem_derive_nd.f90
Source/problems/problem_tagging_1d.f90
Source/problems/problem_tagging_2d.f90
Source/problems/problem_tagging_3d.f90
Source/problems/problem_tagging_nd.F90
Source/radiation/CastroRad_1d.f90
Source/radiation/CastroRad_2d.f90
Source/radiation/CastroRad_3d.f90
Source/radiation/Castro_radiation.cpp
Source/radiation/DumpModel1d.H
Source/radiation/DumpModel1d.cpp
Source/radiation/HABEC_1D.F90
Source/radiation/HABEC_2D.F90
Source/radiation/HABEC_3D.F90
Source/radiation/HABEC_F.H
Source/radiation/HypreABec.H
Source/radiation/HypreABec.cpp
Source/radiation/HypreExtMultiABec.H
Source/radiation/HypreExtMultiABec.cpp
Source/radiation/HypreMultiABec.H
Source/radiation/HypreMultiABec.cpp
Source/radiation/MGFLD.cpp
Source/radiation/MGFLDRadSolver.cpp
Source/radiation/MGFLD_1d.f90
Source/radiation/MGFLD_2d.f90
Source/radiation/MGFLD_3d.f90
Source/radiation/MGFLDneut_1d.f90
Source/radiation/MGFLDneut_2d.f90
Source/radiation/MGFLDneut_3d.f90
Source/radiation/MGRadBndry.H
Source/radiation/MGRadBndry.cpp
Source/radiation/Make.package
Source/radiation/NGBndry.H
Source/radiation/RAD_1D.F90
Source/radiation/RAD_2D.F90
Source/radiation/RAD_3D.F90
Source/radiation/RAD_F.H
Source/radiation/RadBndry.H
Source/radiation/RadBndry.cpp
Source/radiation/RadBndry_1d.f90
Source/radiation/RadBndry_2d.f90
Source/radiation/RadBndry_3d.f90
Source/radiation/RadDerive_nd.f90
Source/radiation/RadEOS_1d.f90
Source/radiation/RadEOS_2d.f90
Source/radiation/RadEOS_3d.f90
Source/radiation/RadHydro_nd.f90
Source/radiation/RadMultiGroup.cpp
Source/radiation/RadPlotvar.cpp
Source/radiation/RadPlotvar_1d.f90
Source/radiation/RadPlotvar_2d.f90
Source/radiation/RadPlotvar_3d.f90
Source/radiation/RadSolve.H
Source/radiation/RadSolve.cpp
Source/radiation/RadTests.H
Source/radiation/RadTypes.H
Source/radiation/Rad_nd.f90
Source/radiation/Radiation.H
Source/radiation/Radiation.cpp
Source/radiation/SGFLD.cpp
Source/radiation/SGRadSolver.cpp
Source/radiation/_interpbndry/Make.package
Source/radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/radiation/_interpbndry/RadBndryData.H
Source/radiation/_interpbndry/RadBndryData.cpp
Source/radiation/_interpbndry/RadBoundCond.H
Source/radiation/_interpbndry/RadInterpBndryData.H
Source/radiation/_interpbndry/RadInterpBndryData.cpp
Source/radiation/_interpbndry/RadInterpBndryData_1d.F90
Source/radiation/_interpbndry/RadInterpBndryData_2d.F90
Source/radiation/_interpbndry/RadInterpBndryData_3d.F90
Source/radiation/blackbody.f90
Source/radiation/energy_diagnostics.cpp
Source/radiation/filt_prim_1d.f90
Source/radiation/filt_prim_2d.f90
Source/radiation/filt_prim_3d.f90
Source/radiation/filter.f90
Source/radiation/fluxlimiter.f90
Source/radiation/kavg.F90
Source/radiation/notes.txt
Source/radiation/rad_params.f90
Source/radiation/rad_util.f90
Source/radiation/trace_ppm_rad_1d.f90
Source/radiation/trace_ppm_rad_2d.f90
Source/radiation/trace_ppm_rad_3d.f90
Source/reactions/Castro_react.cpp
Source/reactions/Make.package
Source/reactions/React_nd.F90
Source/rotation/Castro_rotation.cpp
Source/rotation/Make.package
Source/rotation/Rotation_frequency.F90
Source/rotation/Rotation_nd.f90
Source/rotation/rotation_sources_nd.F90
Source/source_terms/Castro_external.cpp
Source/source_terms/Castro_sources.cpp
Source/source_terms/Castro_sponge.cpp
Source/source_terms/Make.package
Source/source_terms/ext_src_1d.f90
Source/source_terms/ext_src_2d.f90
Source/source_terms/ext_src_3d.f90
Source/source_terms/ext_src_nd.F90
Source/source_terms/sponge_nd.F90
Source/source_terms/update_sponge_params.f90
commit cd5f1398c811a1fed598e3c8c61050d2e2c328e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 14 20:20:23 2017 -0400
more dimensional agnostification
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/Make.package
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_2d/Make.package
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Castro_ctu_3d.F90
Source/Src_3d/Castro_mol_3d.F90
Source/Src_3d/Make.package
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/advection_util_nd.F90
commit 9defcef89b7060fc169d85e0b79652754989dc6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 14 11:38:34 2017 -0400
update changes
CHANGES
commit a84c1d425c0b422cb6d1795e0070638b10a13855
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 13 21:14:02 2017 -0400
realclean, not clean
Exec/clean_probs.sh
commit ab105e8afedacf4beecf93bf3b1eb6d20ff34323
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 13 20:10:56 2017 -0400
in 1-d, we still need to add the sources for all quantities
Source/Src_nd/trace_ppm_nd.F90
commit 4034b11c6244b50ad3f634193d010d17c6235335
Merge: 6a4921a01 6b1f4aca3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 11 20:54:25 2017 -0400
Merge branch 'development' into hydro-cleaning
commit 6a4921a016597145a3501e0d756afffeb6b73497
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 11 00:35:52 2017 -0400
if we are not doing source term tracing, then we need to explicitly add
the gravitation accel in 1-d
Source/Src_nd/trace_ppm_nd.F90
commit 6b1f4aca377820ce4ec1546adbdb10bce98ea30f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 10 12:45:15 2017 -0400
a simple clean-up script
Exec/clean_probs.sh
commit 3454724130f254beb8a06e6a5a9ff2887fcfbfe0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 9 14:24:37 2017 -0400
for 1-d PLM, since we don't do the transverse stuff, we need to
add gravity
Source/Src_nd/trace_nd.F90
commit 08dff6261c2b25bd224e99e9a95aa135c443a7a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 9 13:36:58 2017 -0400
remove unneeded files
Source/Src_2d/trace_2d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 4fb9e86ec4b07d6305787a7698f4af29cae72f87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 9 13:32:41 2017 -0400
update interfaces for merged tracing
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Make.package
Source/Src_3d/Castro_advection_3d.F90
commit 3cdb462088d8e2b366f5da0475f0b06f1e1e75dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 9 12:43:25 2017 -0400
more work on merging the trace routines
Source/Src_1d/Castro_advection_1d.F90
Source/Src_nd/trace_nd.F90
Source/Src_nd/trace_ppm_nd.F90
commit 0d3e4fa5804e95a5c2b343e64787eda987112053
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 8 17:05:28 2017 -0400
more merge cleaning...
Source/Src_nd/trace_nd.F90
Source/Src_nd/trace_ppm_nd.F90
commit 280bb8a098e8473745a91e50cc4b7696f83b46fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 8 16:20:33 2017 -0400
fix include file
Source/Src_1d/Make.package
commit e0a5396ba72d435d6d2bf13f6403c34a77f6c106
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 8 16:02:26 2017 -0400
more trace consolidation
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_nd/trace_nd.F90
Source/Src_nd/trace_ppm_nd.F90
commit 5f0e245d93d83e30850575eabdb6f74a02e60010
Merge: c1a8742b2 13fccec8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 8 15:02:12 2017 -0400
Merge branch 'development' into hydro-cleaning
commit 13fccec8ef8f784b68e64dd7bc106f0d0acedf73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 8 13:43:03 2017 -0400
add a ca_network_finalize() method that calls the network's finalize
Microphysics/networks/general_null/network.template
Microphysics/networks/network.f90
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_nd.F90
commit 91c33ecbd5a8e4cd3bfa07636d12436b6d4bf347
Merge: 15ec7fa18 ba393d9ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 8 12:43:59 2017 -0400
Merge pull request #153 from taehoryu/development
Development
commit ba393d9cebbde1c88e67b0a1d1f57a8f3db4e950
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:38:15 2017 -0400
update:2D planet
Exec/science/planet/newmodelcpp.hse
commit 74a00cff9db76b84d95757f4cea854342df05c15
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:38:00 2017 -0400
update:2D planet
Exec/science/planet/inputs_2d
commit 789cb2552d8c135e3ad64cd19812244d8065663c
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:37:32 2017 -0400
update : using bisection method
Exec/science/planet/HotJupiter.cpp
commit 5291071c5e0c85966eb76dc29f2dfb7aa21b2316
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:37:03 2017 -0400
update: HSE BC
Source/Src_1d/bc_ext_fill_1d.F90
commit 08884b9436f4b86a86ef0f6c919e809d9ad949b7
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:36:30 2017 -0400
update:1D planet
Exec/science/planet/inputs_1d
commit 70bf95765c6514fd78bd87aa10dd0ded44d0d2c3
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:36:11 2017 -0400
update:1D planet
Exec/science/planet/bc_fill_1d.F90
commit fc2c02988eeab0d4d952febce3c78666eb3c4e52
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Tue Aug 8 09:35:49 2017 -0400
update:1D planet
Exec/science/planet/Prob_1d.f90
commit 15ec7fa18ed10e2463c0340bd2b615e81e1c9a12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 7 15:12:04 2017 -0400
some changes from Blaire -- allow for T_ambient to optionally be set
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/probdata.f90
commit e540aac9b3df38723d06ba6642eff48c24cc17d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 7 14:20:29 2017 -0400
add a "free" routine for meth_params to deal with the new allocates of the
strings. Closes #147
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/parse_castro_params.py
commit c1a8742b269f695dd3d061e82c54f617b82a4289
Merge: 5fcc9110e 3ce7dc29d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 7 09:11:18 2017 -0400
Merge branch 'development' into hydro-cleaning
commit 3ce7dc29d92a142db5492d7f73ef9d0757e17c4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 7 01:55:01 2017 -0400
Lower wdmerger species tolerances to 1.d-6
Exec/science/wdmerger/probin
commit 0f7c2a5e66740dc0d28dde896589ad3c8822c8db
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 7 00:22:37 2017 -0400
Do a better job protecting against roundoff
Source/Castro_advance.cpp
commit 5fcc9110e5e0ee99c63fe26ccee897cc1d4e7923
Merge: a0120acce d864fa7bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 6 09:08:31 2017 -0400
Merge branch 'development' into hydro-cleaning
commit a0120acce024c836003bc359b20dab71e21359c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 22:19:38 2017 -0400
some more work on merging the trace stuff
main trick is that we need to put the goemetry terms in
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Make.package
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/trace_nd.F90
commit 82176626603ae266dbe7ac1a3ac9fe74b31c71cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 21:18:13 2017 -0400
clean up some interfaces
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/trace_ppm_3d.f90
commit d864fa7bbd108c31611a99de5b2c08701bb13360
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 15:03:19 2017 -0400
if we are using Microphysics, also look for parameters in
Microphysics/networks
Exec/Make.Castro
commit 020b7a21982039710268b471e20d01dc16a1ff4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 11:33:41 2017 -0400
work on merging PLM
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
commit b53812bec9db2a9758ed112bcb410582d4e19f9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 11:32:18 2017 -0400
start of merging the PLM tracing
Source/Src_nd/Make.package
Source/Src_nd/trace_nd.F90
commit 5a19bedc6e8fadc32b0bfa605667932e167eb86c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 10:17:22 2017 -0400
note ppm merge
CHANGES
commit 81a70576713f74c5fc4946053c83435d9f6a5c66
Merge: e4c75a005 660479e12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 10:16:45 2017 -0400
Merge branch 'development' into hydro-cleaning
commit e4c75a005107ef7a5d11d0f4b5ce0eef7db0cdaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 5 10:16:37 2017 -0400
fix compilation
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
commit 660479e1298fb0d941784337c58b10e9b94f66f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 5 03:51:22 2017 -0400
Use simpler logic for stopping a job
Exec/science/wdmerger/Prob.cpp
commit fe95ddd9dca4ad58ef8df98becb90765b265fee0
Merge: 8848802a7 8386ce33e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 4 22:07:13 2017 -0400
Merge branch 'development' into hydro-cleaning
commit 8386ce33e1e57598c660367d9ae82ca3bedddfb0
Merge: 122884163 a1326f710
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 4 22:06:16 2017 -0400
Merge pull request #148 from AMReX-Astro/mol
unify Riemann solvers across dimensions
commit 8848802a75733dd2e40325436465bb9801290d2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 4 15:14:54 2017 -0400
forgot this file
Source/Src_nd/ppm_nd.F90
commit deb9bdffb45a08428398c580a137d904c13cbdeb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 4 13:12:10 2017 -0400
dimension-agnosticize the ppm stuff too
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/Make.package
Source/Src_1d/ppm_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_2d/Make.package
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Make.package
Source/Src_3d/ppm_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/slope_nd.F90
commit b0de0859cfdde28199c9c134d89fcbd0f4e950f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 4 11:18:23 2017 -0400
make slope dimension_agnostic
Source/Src_1d/Make.package
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/multid_slope_2d.f90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/slope_nd.F90
commit 12288416317e3a2ac484e79126aa13a5ac46d2b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 21:11:54 2017 -0400
clean up the interface
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/slope_3d.f90
commit a1326f7100c85b3bc5fc11793c009f1622606c0b
Merge: 87b5fcd0d 8f4a2e56a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 15:26:56 2017 -0400
Merge branch 'development' into mol
commit 8f4a2e56a2c5ef34d91833857af3678244c02253
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 15:19:06 2017 -0400
this file is not used
Exec/science/planet/sponge_2d.f90
commit 7111a684027ce77c98404d182826069adc60eb5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 15:04:46 2017 -0400
some cleaning of the HSE code
Exec/science/planet/Prob_2d.f90
commit 87b5fcd0dcf2d69c524efab32e1665fc17e1a4b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 15:04:46 2017 -0400
some cleaning of the HSE code
Exec/science/planet/Prob_2d.f90
commit 4c330672c6b0e299696ee80186b7f0de6468d358
Merge: 1404877f6 84984922a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 14:34:36 2017 -0400
Merge branch 'development' into mol
commit 84984922aa068b23f19a91ed6241beffcd76fd20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 14:10:11 2017 -0400
fix the fuel temperature -- if it is too hot, it burns ahead of the flame
Exec/science/flame/probin
commit 5bbb73af65fd9732b9c855f43911724b581cd4be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 14:03:22 2017 -0400
remove stray characters
Exec/science/flame/Prob.cpp
commit 693651a93dd33136e10627b859fcfbb24f8fc7a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 13:46:34 2017 -0400
looser species tols
Exec/science/flame/probin
commit 004f729b49b6243ef7de99cad7cbbc16c946cb07
Merge: 5f7fef908 5c2718b18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 13:43:45 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 5f7fef908d78a0eec402841fb478ed955430b1b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 13:43:28 2017 -0400
hack around the different network names for he4 and He4
Exec/science/flame/Prob.cpp
commit 5c2718b18e68be473818a8e1625f85bbfb991f6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 13:04:36 2017 -0400
add a scaling factor for conduction
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 1404877f68b092acdc698d996405d8a5f981d762
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 10:30:07 2017 -0400
fix radiation compilation
Source/Src_nd/riemann_nd.F90
commit d2f893a946035787fc4a8b48e14f81342986bb07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 3 09:51:17 2017 -0400
adapt interfaces to use qaux
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
commit 72a174321af3021ad46e0d26ef19c01f399c08b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 2 20:59:58 2017 -0400
more riemann interface fixing
Source/Src_3d/riemann_3d.F90
Source/Src_nd/riemann_nd.F90
commit 4c96d85de2b2fb0e68577b6f0f07061eb36ab5b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 2 12:14:34 2017 -0400
add a thermo consistency option
Source/Src_nd/meth_params.F90
Source/Src_nd/riemann_nd.F90
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit ffa0a815b1e5fb0848ebca515c4e5dba121eded4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 21:16:09 2017 -0400
comment up the CGF solver
Source/Src_nd/riemann_nd.F90
commit 248a5dec94e31dc2893b89ba0d969fefe7703ddf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 19:43:22 2017 -0400
fix extern now that we use VODE
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit cd6feb117015a7675f4403abe6e2be0908a7a623
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 19:43:22 2017 -0400
fix extern now that we use VODE
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit e08acf03e0235287ac40b0517df68c6973bd5659
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 14:48:51 2017 -0400
fix dimensioning of q2
Source/Src_2d/Castro_ctu_2d.F90
commit 25c91e5c411778a10d150144dcadd16c72570826
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 14:11:04 2017 -0400
make some indexing clearer
Source/Src_2d/Castro_advection_2d.F90
commit aacbef8218b91b01cb12b345cb547915de6f4e8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 13:46:39 2017 -0400
fix some dimensioning
Source/Src_2d/Castro_mol_2d.F90
commit f9809f62f96cb86fa9445736071d4a444aeb3409
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 12:38:07 2017 -0400
fix some compilation with radiation
Source/Src_nd/riemann_nd.F90
commit 82834a4a6e957261e6d21beaccb1e30ea2ae1627
Merge: 238f9a413 108b1566e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 12:17:24 2017 -0400
Merge branch 'mol' of ssh://github.com/AMReX-Astro/Castro into mol
commit 238f9a4132d80f651b82335edad25795e4a4f8b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 12:17:10 2017 -0400
centralize HLLC solver
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/riemann_nd.F90
commit 108b1566e4dc5168285823917f007002abdd7006
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 11:17:23 2017 -0400
update riemann
CHANGES
commit 47f781d0ae99966aac73735cb38e2dd62e9cf22c
Merge: ae06a15d7 bf558c742
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 09:49:38 2017 -0400
Merge branch 'development' into mol
commit bf558c742166b40f961a40fa04a29fe79d32a3c4
Merge: 97756eb68 49fdfee23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 09:49:04 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 49fdfee23e228846405a659b1443cfb9f9f14adf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 09:04:16 2017 -0400
new heading
CHANGES
commit ae06a15d7c5d67fe911c0684fe95e35ad4e0ac74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 20:44:31 2017 -0400
make the CGF Riemann solver nd
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/riemann_nd.F90
commit 858aab3f14ec79f3e241900220469101c25407f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 19:38:29 2017 -0400
fix compilation
Source/Src_3d/riemann_3d.F90
commit 0ffc37b5e9defe7ca1a9d2acb4968d494b2ed13f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 19:31:48 2017 -0400
fix some dimensions
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_nd/riemann_util.f90
commit ada8352a6812fb5abac79f7708abdcafa44bf423
Merge: 1f39de58c f344d87cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 19:21:40 2017 -0400
Merge branch 'mol' of ssh://github.com/AMReX-Astro/Castro into mol
commit f344d87ccbba6979abe23e5a1060e769828d47eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 19:05:02 2017 -0400
work on moving the CG riemann solver to an nd
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/Make.package
Source/Src_nd/riemann_nd.F90
commit 953fd44124d77744aa154deaa7df766ee7eb5e72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 15:34:46 2017 -0400
make shock() dimension-agnostic
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Castro_mol_3d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/advection_util_nd.F90
commit 052a51f12e9a23b9b08345bf34ef1ab43fe7d8ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 14:50:14 2017 -0400
a little cleaning
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/Castro_util.F90
commit 06316bf486f919de000fa7e098b054a05a959d43
Merge: 8e6030de1 97756eb68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 14:16:22 2017 -0400
Merge branch 'development' into mol
commit 97756eb68382cd2c54f3baea1b93651287fdbc17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 14:16:08 2017 -0400
some doc fixes
Docs/FlowChart/FlowChart.tex
commit 1f39de58cd2895e15c143686cc35f22f3e5e2294
Merge: 8e6030de1 6d961b87a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 14:01:45 2017 -0400
Merge branch 'development' into mol
commit 6d961b87a274e0803d3aa7ea16c9aac9e967fe8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 13:01:17 2017 -0400
we were not storing the transverse velocities in qint for cg
Source/Src_2d/riemann_2d.F90
commit 8e6030de1095a2adcf91d303063cb26216770dae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 12:39:25 2017 -0400
compilation fixes
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_mol_3d.F90
commit ec6255682e75609ec7cd94dd0cdb8d1db9764b40
Merge: aadbf11df 4fec25ca0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 11:37:26 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit aadbf11df9128aef82758d7ce8f1f955d2f091b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 31 10:42:12 2017 -0400
some analysis
Exec/science/flame/GNUmakefile
Exec/science/flame/analysis/profiles.py
commit 18fc89d0f134ac205bcd79776267d42e8098bdf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 30 14:08:58 2017 -0400
more ppm_temp_fix
Source/Src_1d/Castro_mol_1d.F90
Source/Src_3d/Castro_mol_3d.F90
commit f5796cb59f95aa00934eb7ea2a9b45b1d9173531
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 30 13:49:33 2017 -0400
implement ppm_temp_fix
Source/Src_2d/Castro_mol_2d.F90
commit 4fec25ca09056647e44c4eaf2b5e225342d94b32
Merge: abfc720b6 56c437e96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 28 19:56:14 2017 -0400
Merge pull request #146 from taehoryu/development
the planet problem, updated by July 28
commit 56c437e961af9c6d8b662400c7d090d64eb90622
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Jul 28 19:48:13 2017 -0400
the planet problem, updated by July 28 (re-updated)
Exec/science/planet/HotJupiter.cpp
Exec/science/planet/Prob_2d.f90
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/inputs_2d
Exec/science/planet/probin
Exec/science/planet/sponge_2d.f90
commit 0018e086a461c9dbc914e6d411109bd87706759a
Author: taehoryu <taeho.ryu@stonybrook.edu>
Date: Fri Jul 28 14:49:13 2017 -0400
the planet problem, updated by July 28
Exec/science/planet/HotJupiter.cpp
Exec/science/planet/Prob_2d.f90
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/inputs_2d
Exec/science/planet/newmodelcpp.hse
Exec/science/planet/probin
Exec/science/planet/sponge_2d.f90
commit abfc720b6f8bc4713e3059b36c2092211b731d81
Merge: 5d7d1fecf ff871675e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 28 13:34:41 2017 -0400
Merge pull request #145 from zingale/development
the planet problem, copied from zingale/planet
commit ff871675ee6a6a5a9c3e1848eac99a10c53b9d91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 28 13:24:45 2017 -0400
the planet problem, copied from zingale/planet
Exec/science/planet/GNUmakefile
Exec/science/planet/HotJupiter.cpp
Exec/science/planet/Make.package
Exec/science/planet/Prob_2d.f90
Exec/science/planet/README.md
Exec/science/planet/bc_fill_2d.F90
Exec/science/planet/inputs_2d
Exec/science/planet/newmodelcpp.hse
Exec/science/planet/notes/notes.tex
Exec/science/planet/planet.net
Exec/science/planet/probdata.f90
Exec/science/planet/probin
Exec/science/planet/sponge_2d.f90
commit 5d7d1fecfd3357c19a2a021d6be4ef9773b56af4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 28 12:47:37 2017 -0400
update CHANGES
CHANGES
commit cc389ccdb7295a349a9224529ecce22c11705b87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 22:01:32 2017 -0400
this is not used + we should use the AMReX one if ever needed
Util/random/GPackage.mak
Util/random/Make.package
Util/random/mt19937ar.f90
commit e163ce9a4b630d95bf1e7729dccf8152459bec67
Merge: b07b6211e 83dbb53df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 19:56:44 2017 -0400
Merge branch 'development' into starlord
commit b07b6211ecbf24e8bb588206e84bd4965798af1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 19:51:18 2017 -0400
add burning support
Util/regression_testing/Castro-SBU-amrex-tests.ini
commit 43bcb75be2c4f6e6b5a716026a64503a1514846b
Merge: 45318bca1 076b27483
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 19:38:20 2017 -0400
Merge branch 'starlord' of ssh://github.com/AMReX-Astro/Castro into starlord
commit 45318bca1b7345e24c493262c2465fd5dcbeea3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 19:38:02 2017 -0400
add keywords to tests for helm, gravity, rad, diffusion
Util/regression_testing/Castro-SBU-amrex-tests.ini
commit 83dbb53df493208cbae99154d664e84f0d0ac9fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 17:06:44 2017 -0400
fix allocation of character strings for new Fortran parmparse
Source/Src_nd/meth_params.F90
Source/parse_castro_params.py
commit b5bf084c1104600762c11f9597cab03bd7bf8a9d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jul 26 15:37:05 2017 -0700
update acoording to change in AMReX Fortran parmparse
Source/Src_nd/meth_params.F90
commit b5c824d5342924d7e8e422ecedcf22cad5a45f5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 16:31:17 2017 -0400
add note about convergence testing
Exec/unit_tests/diffusion_test/README.md
commit b5ff22a790bfcd37de57ebfc0dc5a29842ecfb37
Merge: 52bb0160b 434c29539
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 16:18:43 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 434c295399c13ed0c3f17f6d5d1f269ee2c2b0b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 15:00:36 2017 -0400
update changes
CHANGES
commit a5756eeb550defd2afd64ba4a27db96f7e21ff84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 14:58:54 2017 -0400
separate viscosity into its own directory
Exec/Make.Castro
commit 58dc4b294b64c2577e06056b96ce1ab2fe355b70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 14:52:22 2017 -0400
fix vis params
Microphysics/viscosity/constant/Make.package
Microphysics/viscosity/constant/_parameters
commit b71275bf48340467a4fc6eca310c1537d0c69e40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 14:47:45 2017 -0400
move into subdirectory
Microphysics/viscosity/constant/Make.package
Microphysics/viscosity/constant/_parameters
Microphysics/viscosity/constant/constant_viscosity.f90
commit 32a73aa28f69e0d890485d11639e43cbe405aa94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 14:36:31 2017 -0400
move the viscosity
Microphysics/conductivity/constant/Make.package
Microphysics/conductivity/constant/_parameters
Microphysics/conductivity/constant_opacity/Make.package
Microphysics/conductivity/constant_opacity/_parameters
Microphysics/conductivity/constant_opacity/constant_viscosity.f90
Microphysics/viscosity/Make.package
Microphysics/viscosity/_parameters
Microphysics/viscosity/constant_viscosity.f90
commit 847a5df27b250b6b20cfef6b1058a3cdeedae28d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 13:49:22 2017 -0400
fix compilation issue
Microphysics/conductivity/constant/constant_conductivity.f90
commit 964e90083feca4bc23b99a455cf2d9fb64e8393f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 13:39:10 2017 -0400
hook in new conductivity
Exec/Make.Castro
commit 630eda79056a8cbd8874d7a6d75c09b6c64f5860
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 13:38:38 2017 -0400
new conductivity interface consistent with StarKiller
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Enthalpy_nd.f90
Source/Src_nd/timestep.F90
commit 1872a06d1fb0fd610174179c2a6534f0798876c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 13:38:10 2017 -0400
new conductivity interface consistent with StarKiller
Microphysics/conductivity/Make.package
Microphysics/conductivity/conductivity.F90
Microphysics/conductivity/constant/constant_conductivity.f90
Microphysics/conductivity/constant_opacity/constant_conductive_opacity.f90
commit 1ce3c2a24d46924e09737e5aeb2c2d45251d6401
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 13:20:05 2017 -0400
fix bounds issue on srcU
Source/Src_3d/Castro_mol_3d.F90
commit 52bb0160b716cfe4450b8ab1fc517ac0e4b53f9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 24 15:16:43 2017 -0400
better parameters
Exec/science/flame/inputs.1d
commit f3e1ca9415b1fcb104d22fb350f39e68627e12b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 24 11:46:33 2017 -0400
add ack + citation paragraph
Docs/Preface/Preface.tex
commit 0bca418d1ab1526facb480fa088802b89f9fe099
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 24 10:40:45 2017 -0400
fix output name so test suite finds it properly
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
commit dd3bc5fd32d6ff884cfdb2fe9b910d7dd7964e1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 24 10:11:43 2017 -0400
fix compilation failure due to excess white space
(yes, really)
Exec/science/Detonation/Prob_1d.f90
commit 7cdf6e3e18e7e8105a9d7f197dc0da421e0a3262
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 22 15:36:06 2017 -0400
Loosen wdmerger species tolerances from 1e-10 to 1e-8
Exec/science/wdmerger/probin
commit 076b27483dcf8f98d32204b16942a0b4428f1a12
Merge: d3ef767ae 385326246
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 21 16:12:36 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit d3ef767ae2508104b6173fd24a3b1a17ebbf4986
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 21 16:12:02 2017 -0400
make riemannus public
Source/Src_2d/riemann_2d.F90
commit 726819d6952db406bfc4ec1eb7883e680b04adad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 21 16:11:32 2017 -0400
some comments
Microphysics/networks/sdc_type.F90
commit 3853262466a51a34a96f55c2c04aff33b7b8089f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 21 13:04:30 2017 -0400
switch to the EOS instead of relying on gamma_const -- this
allows other EOS-es to be used
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
commit b0dda6747870612be0cc94c7c94fd29b2a712394
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 19 21:05:52 2017 -0400
remove unused function
Source/Gravity.H
Source/Gravity.cpp
commit c4a28d91e066a597b2fc7212dd49997ab27c9065
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 19 20:55:31 2017 -0400
add note about params
CHANGES
commit 8c4b28f3a69f9488d32e997955a8a154d933695a
Merge: 04a7a0195 f74c85eaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 19 20:33:16 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 04a7a0195477f753c529fed4d975c207140f7aed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 19 20:32:33 2017 -0400
create the parmparse object in the proper namespace
we had hardcoded in "castro", so some parameters were not properly
imported into Fortran
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/parse_castro_params.py
commit f74c85eaa2b6fffe461045236f84f1b05dd7c4f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 18 09:34:10 2017 -0400
better stop time
Exec/science/Detonation/inputs-det-x.SDC
commit 25aa669922403276f70006510321d663b77ffa07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 14 19:30:13 2017 -0400
let us know which strang half we are in
Source/Castro.H
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_nd/React_nd.F90
commit 40435457fde878979e08565ed4632510a84108be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 14 17:05:25 2017 -0400
pass the sdc_iteration into the sdc_t struct for diaging
Microphysics/networks/sdc_type.F90
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_nd/Castro_nd.F90
Source/Src_nd/React_nd.F90
commit c79188a931ceca7232d654072d9fe00a954a74a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 13 22:07:34 2017 -0400
point to the script to download all the dependencies
README.md
commit 345b74c197e63a2b26f89ae5f2913e9cad1a2260
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 13 21:56:56 2017 -0400
fix comment
Util/scripts/get_castro_date.sh
commit 22349d2f28aa7f5a0cf9cb7936b3ace0077c6a7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 13 21:55:39 2017 -0400
a simple script to get everything needed to run Castro and show
the necessary environment settings
Util/scripts/get_castro.sh
commit cc00e3f92f5fdbabc60c4f1ff023d052b4f8df3b
Merge: 8a1393a1a 1a59201aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 13 13:38:45 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 8a1393a1a690be864c376681b65556edb3abbd40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 13 13:38:26 2017 -0400
update this for new locations + make it more flexible -- the date
is optional
Util/scripts/get_castro_date.sh
commit 1a59201aaea5ea28936865030225a65134feff8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 12 19:52:31 2017 -0400
fix compilation
Exec/unit_tests/test_react/testburn.f90
commit b56166579b85b3332032c4578c0fff307cb9cbf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 12 19:38:04 2017 -0400
fix compilation
Exec/science/flame/Prob_1d.f90
commit 2d511bcaa7e8ffac2b403accd5351950ece17884
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 12 18:34:55 2017 -0400
Fix constness of ints
Docs/Coding_Standards.md
commit 4661807638444d42dc92fe9f5899b67cca7f8af3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 12 14:22:33 2017 -0400
xgraph no longer supported
CHANGES
commit 25305320628db7e321b690776550e34c8e6bfd65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 12 14:20:18 2017 -0400
add an example of outputting a zone
Docs/FAQ/faq.tex
commit 5ede5f1eae059e276eba0b3199dae399b5f1da02
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 11 20:41:50 2017 -0400
Use VODE for wdmerger
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/probin
commit f896775104f4ff434c35c9f0f9c83df92cfd9499
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 11 16:36:42 2017 -0400
call the EOS in the RHS with Strang
Exec/science/Detonation/probin-det-x
commit 97024e58bef070deeedc9e4a38e63c3f4c00214e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 11 13:10:33 2017 -0400
we should be doing a constant volume burn for detonation
Exec/science/Detonation/inputs-det-x.SDC
Exec/science/Detonation/probin-det-x
commit eb41c9815ec17e6ec065c3e54a7adcc247f18bb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 11 11:44:32 2017 -0400
remove the XGRAPH stuff -- it was unsupported and we can use amrvis in 1-d now,
also fextract, yt, ...
Docs/Visualization/CastroVisualization.tex
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/StarGrav/inputs_1d
Exec/gravity_tests/hydrostatic_adjust/inputs-subchandra
Exec/hydro_tests/Sedov/inputs.1d.cyl
Exec/hydro_tests/Sod/Figure1/inputs-sod-1d
Exec/hydro_tests/Sod/Figure2/inputs-test2-1d
Exec/hydro_tests/Sod/Figure3/inputs-test3-1d
Exec/hydro_tests/Sod/inputs-double-rarefaction
Exec/hydro_tests/Sod/inputs-test2-1d
Exec/radiation_tests/Rad2Tshock/inputs.M2
Exec/radiation_tests/Rad2Tshock/inputs.M2.mg
Exec/radiation_tests/Rad2Tshock/inputs.M5
Exec/radiation_tests/Rad2Tshock/inputs.M5.mg
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadShestakovBolstad/inputs.common
Exec/radiation_tests/RadSlope/inputs
Exec/radiation_tests/RadSphere/inputs
Exec/radiation_tests/RadSuOlson/inputs
Exec/radiation_tests/RadSuOlsonMG/inputs.common
Exec/radiation_tests/RadThermalWave/inputs.1d
Source/main.cpp
Util/plot1d/Make.package
Util/plot1d/Misc.H
Util/plot1d/XGraph1d.H
Util/plot1d/XGraph1d.cpp
commit 5d1ac48d75c4fc86606c13fa550e63e659914a77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 10 19:36:14 2017 -0400
add smallx
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/inputs-det-x.SDC
Exec/science/Detonation/probdata.f90
Exec/science/Detonation/probin-det-x
commit 0700d5109fecacc0649dd7b5accdf79594d32a86
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 9 16:21:35 2017 -0400
Update the name of I/O parameter
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit b933fddf25c40a02eaff7280a58be5b1b92a45b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 9 06:07:58 2017 -0400
Remove internal energy flux limiting
CHANGES
Source/Src_nd/advection_util_nd.F90
commit 97dca5fab1b77fe1ff4dc202d500f7a8ffa4e05d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 9 05:39:07 2017 -0400
Clean up formatting in density flux limiter
Source/Src_nd/advection_util_nd.F90
commit 41273e244522684244f5ba8026408e2ce2e84d0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 9 05:36:30 2017 -0400
Only fix the flux register in the first subcycle after a post-step regrid
Source/Castro_advance.cpp
commit 80923240b7a9693ce6aa7a1d8ae365e29e886aee
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 9 05:36:04 2017 -0400
Fix the time used in fillpatch after a post-step regrid
Source/Castro.cpp
commit 9031434c5dfc9446f3de821edbd2fe6f290e26e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 18:36:07 2017 -0400
Fix the shock burning disabling for SDC
Source/Src_nd/React_nd.F90
commit b8b589fcac991a639dc6c476e8c1cae68db073d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 18:21:18 2017 -0400
Fix compilation failure
Exec/science/Detonation/Prob_2d.f90
commit fcec6d9972d51c4cfa9f3f434be26afdf86c0a12
Merge: d22f91fc5 d957d6f77
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 15:12:13 2017 -0700
Merge pull request #142 from KISSFORMISS/development
Fix the width and central position of temp transition definition
commit d957d6f774930d199553dcb307e12f65004b8834
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Sat Jul 8 18:07:43 2017 -0400
Sync up 2D-detonation with 1D-detonation
Exec/science/Detonation/Prob_2d.f90
commit 44c7febaada05688c8defae1d791f3fb33444254
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Sat Jul 8 17:53:58 2017 -0400
Fix the width and central position of temp transition definition
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/probin-det-x
commit d22f91fc58ed73ff9ec0fd6e1d27f973289d64d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 15:21:00 2017 -0400
Update coding standards
Docs/Coding_Standards.md
commit 01ab3394fdd712fd35e310e406e385e1db1e4c3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 15:11:03 2017 -0400
Clean up Detonation problem
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/probdata.f90
commit 1916da00ed7694378ea26ab5247512c617c02362
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 14:51:32 2017 -0400
Sync up 2D detonation with 1D
Exec/science/Detonation/Prob_2d.f90
commit 7e2f13d969465cab508eec0fc6e3ec49a3167df5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 14:48:24 2017 -0400
Remove superfluous tagging variables in probdata
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
commit b00b43ac7dd6a9f7bf98e83c1b49ccb1983cf653
Merge: e51a79488 564e9362f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 8 11:42:32 2017 -0700
Merge pull request #141 from KISSFORMISS/development
Bug fixing for Prob_1d.f90
commit 564e9362f7ed6135f87a3209ab3ff46758e235bd
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Sat Jul 8 14:34:52 2017 -0400
Bug fixing for Prob_1d.f90
Exec/science/Detonation/Prob_1d.f90
commit e51a79488825740749d7ba3598611b1b3064f564
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 7 11:07:32 2017 -0400
a bit more on flowcharting
Docs/FlowChart/FlowChart.tex
commit 4722e7305a97c77d74442b83467116b73ec94dae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 19:08:06 2017 -0400
fix formatting of the species information
Source/Castro_io.cpp
commit 517249604d312b0545a0e5b20e6f08361b4f1a13
Merge: b008b37f7 1fd33add0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 15:41:30 2017 -0400
Merge pull request #139 from KISSFORMISS/development
Smooth initial temp profile
commit 1fd33add0e05de2e18ff32cb419b9c5ce292b92f
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Thu Jul 6 15:32:44 2017 -0400
clean up conflict tags
Exec/science/Detonation/Prob_1d.f90
commit 70f6be133cc0684bc96b18a8416e4514cd61e4bd
Merge: b5213fc1d bc80f3f2f
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Thu Jul 6 14:56:11 2017 -0400
merge development into master
commit b5213fc1db9b210ae4385c64f98ecf2a9ead8ef9
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Thu Jul 6 14:11:40 2017 -0400
Make width and central position of temperature transition zone as runtime parameters
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/probdata.f90
Exec/science/Detonation/probin-det-x
commit b008b37f7b607bbe0e5987938b666b44ef17ceb1
Merge: 0b14e6065 9ad7df14e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 13:12:06 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 0b14e60650666c0778db717fd2e9ee9cf19a976d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 13:09:37 2017 -0400
fix compilation
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
commit 9ad7df14e4d9396a997802e067fdea3a46bce2b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 12:44:21 2017 -0400
simple script to allow for comparison of algorithms
Exec/science/Detonation/analysis/compare_plot.py
commit 3a3613d124df2b27b1a409c763623b8cd79cab85
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Thu Jul 6 11:23:28 2017 -0400
smooth temp transition
Exec/science/Detonation/Prob_1d.f90
commit c80f827747f3f94382d7f698ba651e2ba763f684
Merge: cf41d3d7e 324bdbfcd
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Thu Jul 6 11:21:42 2017 -0400
Merge branch 'development' of https://github.com/KISSFORMISS/Castro
commit bc80f3f2fb8e9dde2539d8c369030ff3921e3a49
Author: muhung <mu-hung.chang@stonybrook.edu>
Date: Thu Jul 6 09:38:43 2017 -0400
Smooth initial temp profile
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/inputs-det-x
commit 0872ab45cdceadd6ebe6e33ffb31fa8e42fc0765
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 09:13:25 2017 -0400
less output
Exec/science/Detonation/inputs-det-x.SDC
commit 324bdbfcd189a327ffbb338fcb0e31622d6e001b
Merge: 995a28313 218d56e36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 5 10:57:03 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 995a283136475bc442bdff408db6c76650003a43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 5 10:56:48 2017 -0400
USE_RAD = TRUE, not 1
Docs/Radiation/CastroRadiation.tex
commit 218d56e36423aff25394ad1644522b6aa235be32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 4 13:35:36 2017 -0400
a little more note to amrvis
Docs/GettingStarted/CastroGettingStarted.tex
commit 88c2ab65b861074a48eadcae1acb83c6c7e75626
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 4 08:26:51 2017 -0400
a little interface cleaning
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/riemann_util.f90
commit cf41d3d7ea8067b7d84855f023757b0508a0c193
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 16:22:55 2017 -0400
update changes
CHANGES
commit 3cae587e2337b00e9becb23175e7e59155ecf699
Merge: b3eabb35c c0ba7163d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 16:20:39 2017 -0400
Merge branch 'starlord' into development
commit b3eabb35cc6bc9fd5d70d93f6ab96dea0cbf96f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 12:30:45 2017 -0400
start of a coding standards document, addresses #74
Docs/Coding_Standards.md
commit c0ba7163d09f50151b1baa64dda5bb406d328685
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 12:30:45 2017 -0400
start of a coding standards document, addresses #74
Docs/Coding_Standards.md
commit 4710d8a90b0ab6eb16bdd542d7d0100ead3fb3cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 2 23:20:34 2017 -0400
remove unused variables
Util/model_parser/model_parser.f90
commit 687b5406f1b3449a50791c79fb32abc8a381f5aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 2 17:41:37 2017 -0400
some compilation fixes + remove some unused variables
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Castro_ctu_3d.F90
Source/Src_3d/Castro_mol_3d.F90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/flatten_nd.F90
Source/Src_nd/timestep.F90
commit 0b953229d82d3585c37c5d2a59438fad502d6701
Merge: 16e17b5b7 3202001ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 2 13:56:24 2017 -0400
Merge branch 'development' into starlord
commit 16e17b5b7410003191d22a7675060594c85fd3d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 2 13:38:54 2017 -0400
fix some bounds issues and clean up interfaces
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_advection_2d.F90
commit 3202001ecfb2ef5b6fb594bc4b78ba539f75f238
Merge: 357e8181c 32aeb83a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 30 02:19:26 2017 -0400
Merge branch 'starlord' into development
This merge is interface cleaning. All regression tests passed.
commit 32aeb83a94ccc1b2166b150bf393ae25f4aa94e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 29 14:42:34 2017 -0400
fix radiation flattening
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_ctu_3d.F90
Source/Src_3d/Castro_mol_3d.F90
Source/Src_nd/flatten_nd.F90
Source/Src_nd/riemann_util.f90
commit 48c9b370bdf7700adbd52af58fa7fa2d06fbf65c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 29 08:54:57 2017 -0400
fix compilation
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
commit c8243ed436d4a708ae010314aecf1ee27289161b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 29 03:46:12 2017 -0400
fix radiation compilation for new interfaces
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Castro_mol_2d.F90
commit fc08b8e33cd6da1f105c4c05421171848b74a0eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 29 03:27:44 2017 -0400
woo hoo! it compiles now
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
commit 441eb63ccc06dad0ba50c0cdb788c97a7f9d29cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 29 02:30:22 2017 -0400
fix interface
Source/Src_3d/Castro_mol_3d.F90
commit 9bf937025231a6bda59afdac4fe667cb01a281bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 28 14:49:59 2017 -0400
more interface work
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/riemann_2d.F90
commit 09de0e91052c73b0eb9a1e8e61da32bbf598fcb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 28 06:01:17 2017 -0400
more interface cleaning work -- doesn't compile right now
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/advection_util_2d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit bcbc1287b9461e2dd95a304181fecdec63ecf175
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 09:09:27 2017 -0400
update radiation flattening interface
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_ctu_3d.F90
Source/Src_nd/flatten_nd.F90
commit 5934bf40d478e8c0cc712691d3e6a34802377af8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 08:53:17 2017 -0400
update the hydro flattening interface (sync with StarLord)
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_ctu_3d.F90
Source/Src_3d/Castro_mol_3d.F90
Source/Src_nd/flatten_nd.F90
commit 88ad2cca369dfec123beae217f9e1b69eb1501a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 08:17:18 2017 -0400
more interface updates
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_3d/Castro_ctu_3d.F90
commit 68ddc328eb0d70f5e4b305d576b7b9949dcd591b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 07:25:37 2017 -0400
rename for consistency with MOL. Now CTU is the corner transport
upwind; MOL is method of lines
Source/Src_1d/Castro_ctu_1d.F90
Source/Src_1d/Make.package
Source/Src_2d/Castro_ctu_2d.F90
Source/Src_2d/Make.package
Source/Src_3d/Castro_ctu_3d.F90
Source/Src_3d/Make.package
commit 63e40f377ab79cb5794fdf1ad4ee8bd1a0d01665
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 06:11:21 2017 -0400
2-d interface
Source/Src_2d/Castro_mol_2d.F90
commit c9e9c771b35477ac78c979c1665833a6877f3498
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 05:40:12 2017 -0400
start of interface simplication to make CUDA / Max happy
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_3d/Castro_mol_3d.F90
commit 357e8181c6beaecd8d20aad09d4aa6833ee3baf2
Merge: edc8ffafd 590edf8f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 03:41:46 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit edc8ffafddfcdbefdeefce32695f06738f3dabf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 27 03:41:21 2017 -0400
update scripts to name output based on plotfile name -- this gives more flexibility
for the suite
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_2d_cyl_in_cart.py
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_3d_sph.py
commit 590edf8f674d70d5d1a2bb1b74399016013665e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 26 10:29:23 2017 -0400
fix how the old-time sources are included with MOL integration.
Closes #138
Source/Castro_advance.cpp
Source/Castro_sources.cpp
commit b9cdf2ff83c8e11ede551f599a712229657fdacf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 26 08:12:58 2017 -0400
turn off xgraph stuff -- it crashes and is unsupported
Exec/gravity_tests/hydrostatic_adjust/inputs
commit 4078ec2b1697a6277faa44f4e96296cbf6fea913
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jun 20 16:22:28 2017 -0700
blocking_factor is now IntVect
Source/Castro.cpp
commit c608fa32a3b19652084d81a9bff12cedfb744d69
Merge: 4b2b044cb c4e0e7ee5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 19 10:02:06 2017 -0400
Merge pull request #135 from AMReX-Astro/mol
fix the MOL update to only include flux divergence in source
this closes #134
commit c4e0e7ee5e138ee7b186308cc15875ee43dafa2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 18 22:29:08 2017 -0400
fix the source correction for MOL integration (we were not doing it at all)
Source/Castro_advance.cpp
commit a3615ba95491fdb0c651c8d63b1d73c6ae16a0c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 18 20:27:59 2017 -0400
fix hydro_source to be just -div{F(U)}
Source/Castro.H
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_mol_3d.F90
commit 8d82ae2ade2d9cf46860162138de68238966ee0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 17 21:20:59 2017 -0400
don't include dt in hydro_source for MOL
Source/Castro_advance.cpp
commit 384b04d1a3a9ffb78a25df8cb8551c7855fff5da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 17 21:02:50 2017 -0400
a little restructuring
Docs/FlowChart/FlowChart.tex
commit 4b2b044cbc141ff7b80a83f5b67ca77dc701677a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 17 19:58:09 2017 -0400
add sources_for_hydro
Docs/Software/CastroSoftware.tex
commit b4158dfa4863be393259005cc9f1d8547d8dda2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 17 19:03:16 2017 -0400
update some comments
Source/Castro_advance.cpp
Source/Src_nd/React_nd.F90
commit b512c5556a7ceab6ff8e71c9a92c1cb11f924da4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 14 22:49:49 2017 -0400
use 2nd order TVD MOL for now, until we fix the subcycling fill boundary
Source/Castro_setup.cpp
commit 496b389b88009eb13e34add1f988dda4a3141c9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 14 22:48:37 2017 -0400
print which MOL stage we are on
Source/Castro_hydro.cpp
commit 964f5f2cfd31f87121070383339db840335c4f3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 14 15:34:07 2017 -0400
add https alternative for starkiller
Docs/GettingStarted/CastroGettingStarted.tex
commit dd9a101c91ac8e1d8640ac963efda7f9f274fd6b
Merge: 267bfea5a da6e3342d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 18:15:57 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 267bfea5a5afe9aaada972d989fb4498381207d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 18:15:48 2017 -0400
test file
Util/regression_testing/Castro-SBU-amrex-tests.ini
commit da6e3342d177a780bf2e5332330ac7f700269ce0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 15:54:14 2017 -0400
missing ;
Source/Castro_advance.cpp
commit c0a3986183fc08b0e37681f25dd4046e3f01b863
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 15:01:48 2017 -0400
fix compilation with rad
Source/Castro_hydro.cpp
commit 024358073726a26ed328471321f1a967edf0e4fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 14:29:00 2017 -0400
make the different iteration counters class members and disentangle
them
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Castro_hydro.cpp
Source/Castro_sources.cpp
commit f27259f5e5cb4b32ee2bd8447b9e27bcc5002da4
Merge: b3bb7577a 3fbfe8eb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 12:18:03 2017 -0400
Merge branch 'development' into mol
commit 3fbfe8eb4b3bb3e28bceae45e4dd2b4f4e86b7cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 3 16:02:11 2017 -0400
Fix incorrect divide by rho
Source/Src_3d/riemann_3d.F90
commit 582c7086f356ce5dafd7636a24ca3ae341d73f89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 1 12:35:34 2017 -0400
update for 17.06
CHANGES
commit d022d22777a00dfa99717c9c7db237d524bac89a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 1 12:33:22 2017 -0400
fix compilation due to EOS interface changes
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/radiation_tests/RadSlope/Prob_1d.f90
commit ebf59495723e4f2ef59414f71fa2c72ebc8f140d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 1 11:52:42 2017 -0400
fix compilation
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
commit b3bb7577abe19f40dd083f279c8282d21512b6e2
Merge: a56493449 66bb2157e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 30 15:38:21 2017 -0400
Merge branch 'development' into mol
commit 66bb2157ea37f35b102aee604045da8e09aea51d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 30 11:37:23 2017 -0400
last compilation fix (?)
Exec/science/xrb_mixed/Prob_2d.f90
commit 0fab802f0f6c70f599519b4f906d71d40d3678ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 30 11:31:23 2017 -0400
fix compilation
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
commit 9761967339fb56caf441c1c43b4fb147bd1537b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 30 11:24:02 2017 -0400
fix compilation
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadBreakout/filt_prim_1d.f90
commit 2d6cbc0df23ee433a4681cca127d0f4b07d11125
Merge: fa06bab9d 237ee74db
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 30 11:05:55 2017 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit fa06bab9d2ced9ff9b3eca5601aed12a2aa21127
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 30 11:05:51 2017 -0400
Fix evrard_collapse and rotating_torus
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/probdata.f90
commit 237ee74db6f77eec4932a6c6b79c13c47b8f814d
Merge: a52fefb86 f8fce3387
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 18:12:07 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit a52fefb866ec854f40bb6ad6804a435cd95dee3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 18:11:23 2017 -0400
PGI doesn't play nice with DEBUG=TRUE
Util/regression_testing/Castro-SBU-amrex-tests-pgi.ini
commit f8fce3387846c5d6af55c503c17babadabfa39bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 18:07:45 2017 -0400
fix compilation
Exec/radiation_tests/RadSphere/Prob_1d.f90
commit 2081c0a82326647d9ce69e2f90696ef8235a6366
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 17:48:16 2017 -0400
fix compilation
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
commit 3160b015ea06e1ead92be914a66e730e03136b98
Merge: 9fd7e240d 8fdddeac0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 17:21:42 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 9fd7e240d5714d0ddf68a9d387ff2d52521ce2f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 17:21:18 2017 -0400
compilation
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/problem_derive_nd.f90
commit 8fdddeac08fbc74ecd336234ea5f2ce997e4ecd6
Merge: 05279c582 8003ec774
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 29 17:04:59 2017 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 05279c582096b8760e9793863799fa1b2b50abf5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 29 17:04:54 2017 -0400
Fix more compilation issues
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/probdata.f90
Source/Src_nd/hybrid_advection_nd.F90
commit 8003ec7743e5509351681fa84b2729f928c3ea65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:41:18 2017 -0400
compilation
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
commit 4894c8e428995c7407d06feea1996336d451fce5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:36:41 2017 -0400
more compilation fixes
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
commit 3477a465dac77f3ac5e518e1651d37f9565aef9e
Merge: 3d14d2f62 4c2a42794
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:19:31 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f51d08e5a0cdf05fa98394ec4394905f1e9775ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:19:06 2017 -0400
compilation fixes
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
commit 91c354c9cefde1ee47ef251e33e300a12082c0e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:17:18 2017 -0400
fix compilation
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
commit a552c2a4161826614e5c7f11a065ef1a4f73d823
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:15:04 2017 -0400
fix compilation
Exec/science/flame_wave/Prob_2d.f90
commit 4c2a427945b997d871b08924c7774848e910c3b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 16:11:01 2017 -0400
compilation
Exec/hydro_tests/double_bubble/model_stuff.f90
commit a6ca3f5f099dd17ec69600499631759437982ce4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 14:46:02 2017 -0400
fix compilation
Exec/unit_tests/diffusion_test/Prob_2d.f90
commit 97c308eb96262b675c86497bb08fc73123010e89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 14:40:58 2017 -0400
fix compilation
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
commit c9d54230de1742c2e7606e66b0d7092c17830ef9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 14:34:41 2017 -0400
fix compilation
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
commit 3d14d2f6248f6b6debc26b449eb5192535634146
Merge: fa0a03de5 741a9ff0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 13:43:57 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 741a9ff0c784d20e131068fb5d9cc265112cac47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 13:31:41 2017 -0400
some EOS interface fixes
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/bc_fill_1d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
commit a5649344918e212d1a5140f2a9d7a74924dad178
Merge: eb5a984bf 958bd73ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 13:01:04 2017 -0400
Merge branch 'development' into mol
commit fa0a03de5b2876658a618b5f84ae60a28e11d441
Merge: 326f5c299 958bd73ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 03:37:42 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 958bd73ce25d08028644911dfcd491a5a2b2e202
Merge: 14632f273 d5ef8f4c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 28 00:48:39 2017 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 14632f27320d99815dcc7023d7389eb466697b89
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 28 00:42:51 2017 -0400
Tighten up the use EOS statements
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Microphysics/EOS/eos.F90
Microphysics/networks/burn_type.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_util.F90
Source/Src_nd/Derive_nd.F90
Source/Src_nd/React_nd.F90
Source/Src_nd/timestep.F90
commit eb5a984bf16ad844c91989155cf04277b51af0b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 27 18:06:43 2017 -0400
fix AMR by adding the proper scaling of the fluxes for the flux registers
Source/Src_3d/Castro_mol_3d.F90
commit a27d2fde994fe91542bb9ed0d844207c6f16e944
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 27 13:00:55 2017 -0400
fix ctoprim interface
Source/Castro_hydro.cpp
commit b73292d6e4c1ee4237f4809bcccfb3761df767d5
Merge: 4f785226e f45a1fff6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 27 12:55:27 2017 -0400
Merge branch 'development' into mol
commit d5ef8f4c9eb5d08f47101a02c33a4637e575ab40
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 27 12:43:54 2017 -0400
BoxLib --> AMReX
Source/Castro_setup.cpp
commit f45a1fff66fb2ab91b63d7921e1789e9e8574a06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 27 11:48:57 2017 -0400
remove TAU -- that is not needed
Exec/Make.Castro
commit a5b87e1a99e29108a1535c3593257da30b8da1eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 25 17:50:59 2017 -0400
note about starkiller
CHANGES
commit 124053e0d7ac42e1c6078dc99aacac86a414d528
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 25 13:49:55 2017 -0400
updates to reflect Microphysics move
Docs/EOSNetwork/EOSNetwork.tex
Docs/GettingStarted/CastroGettingStarted.tex
commit 4f785226ed24abe49ccc0e90f0a8867f95c05d98
Merge: b87b61353 9cf20ee5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 25 09:44:13 2017 -0400
Merge branch 'development' into mol
commit 326f5c2996d3d43af6acd01f0ea31a0b273358d5
Merge: 7fdd9117b 9cf20ee5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 25 03:35:49 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 9cf20ee5f2bd894a50b47ad835ea1716c836ec0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 24 19:32:20 2017 -0400
fix compilation error
Source/Src_2d/Castro_advection_2d.F90
commit 37611f104809a0cbf746ec5ab8a69693d55395ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 23 14:31:05 2017 -0400
use a new logical data structure, mom_flux_has_p to keep track of
whether the pressure is part of the momentum flux. This addresses
issues #130 and #131
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/prob_params.f90
Source/Src_nd/riemann_util.f90
commit 7fdd9117b9fbd9d066abc535ee3867ec8eb87009
Merge: 69f1b535c 0ae0c1ecd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 23 03:35:14 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b87b61353cce5660e56790eaa7272ac9591eb730
Merge: e6b5fcb66 0ae0c1ecd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 21 16:19:54 2017 -0400
Merge branch 'development' into mol
commit 0ae0c1ecde0946d82407864fda6cfbcf892916b9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 21 16:18:39 2017 -0400
Clean up formatting on a couple modules
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_util.F90
commit a75f6cc48f2cef51905d344be42ea01dfa4ed109
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 20 20:55:09 2017 -0400
Fix indexing bug in hydro flux limiter
Source/Src_nd/advection_util_nd.F90
commit 57d504ae76c45bce44210d106c85d37ab42bde83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 19 22:22:17 2017 -0400
fix srctoprim wrapper
Source/Src_nd/castro_c_interfaces_nd.F90
commit 19e3a0179eb1f8559f7e6d8acad5296df66db139
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 19 21:51:03 2017 -0400
more interface splitting
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_nd/Castro_util.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/castro_c_interfaces_nd.F90
commit fbb4a90f7b846cd3422e35c667c2b0c049d3ef56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 19 21:06:40 2017 -0400
more interface splitting
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_util.F90
Source/Src_nd/castro_c_interfaces_nd.F90
commit 71c90e66cfa28c1e7e73976e26910546ada1b724
Merge: 2722273a8 ce815217f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 19 20:55:46 2017 -0400
Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro into development
commit 2722273a832576bbc1c52a939fd3f8968c312915
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 19 20:55:38 2017 -0400
updates
Source/Castro.cpp
commit e6b5fcb66072a460044e21e4ca89f2fd03697f14
Merge: 052a6988f ce815217f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 19 11:54:18 2017 -0400
Merge branch 'development' into mol
commit ce815217ffc658cce190b1761e08445813f1cf24
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 19 11:54:10 2017 -0400
uniqueIndex -> tileIndex
Source/Castro.cpp
commit 27fd6abd5eae05decc2b0d30a304b083f64a3ab9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 19 11:52:42 2017 -0400
Revert "Remove an errant update"
This reverts commit 4967293eddb4d308c2eb2389fa350baf7f399e8f.
Source/Castro.cpp
Source/Castro_F.H
commit 052a6988f82bcd27613e402f79f0b95fb24857f2
Merge: 535414f40 4967293ed
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 19 11:46:35 2017 -0400
Merge branch 'development' into mol
commit 4967293eddb4d308c2eb2389fa350baf7f399e8f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 19 11:46:29 2017 -0400
Remove an errant update
Source/Castro.cpp
Source/Castro_F.H
commit 535414f40d4fdffa63e4a4a7b6b27f0e29a3102b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 19 11:42:09 2017 -0400
Remove commented out debugging prints
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Src_3d/Castro_mol_3d.F90
commit 69f1b535cd52ed134da96b51782ca629d4f1ff05
Merge: f38724bfc e455dedd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 19 03:36:46 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 0f28354301c1189eaa517ec252d2ec380a3e1101
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 18 13:17:57 2017 -0400
define hydro_source
Source/Castro_advance.cpp
commit 696ec29bc6478b5022a65f37cad1ae05d688dd50
Merge: 3b6f27e8d e455dedd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 18 12:28:19 2017 -0400
Merge branch 'development' into mol
commit e455dedd6e7d7d4cbd43db6d084ebb37c47733be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 18 12:28:02 2017 -0400
add intents
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_util.F90
Source/Src_nd/hybrid_advection_nd.F90
commit 7308b6a0ab0d0ab58f4d383c7ee8443636da1c5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 18 12:00:12 2017 -0400
fix compilation
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit e473939a62bcd36655a2ce0fdbcf84bb203624a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 18 10:25:09 2017 -0400
this is the proposed splitting of the interfaces for CUDAfication
Source/Src_nd/Castro_util.F90
Source/Src_nd/Make.package
Source/Src_nd/castro_c_interfaces_nd.F90
Source/Src_nd/castro_cuda_interfaces_nd.F90
commit 3b6f27e8d7900c3e30ce5883a72a7ee01a26a158
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 17 16:24:33 2017 -0400
sync with development
Source/Castro_hydro.cpp
Source/Src_nd/meth_params.F90
commit 51d2b4b902f4ca101fbb0c8833d66cddd98802ec
Merge: 3259581d7 768658212
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 17 16:19:33 2017 -0400
Merge branch 'development' into mol
commit 768658212c8869a581af807ae646b52cb8ce48ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 17 16:13:56 2017 -0400
switch some interfaces over to ca_ -- this is our new conveNtion
-- anything called from C++ will be prefixed by ca_
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_hybrid.cpp
Source/Castro_hydro.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
Source/Gravity.cpp
Source/Radiation/RadSrc_nd/Rad_nd.f90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_util.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit f38724bfc5a9a0c8ade0ab092956e4d03ce7e8e9
Merge: e483990c5 1d97438cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 17 03:36:50 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 1d97438cd7750cc70c2e984fdccc10f9cd036f55
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 17 02:04:29 2017 -0400
Fix logic for general regridding case
Source/Castro.cpp
commit b28530b439f453154f026d390c08cace49b186a6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 17 01:40:44 2017 -0400
Only do interpolation on phi if level == lbase
Source/Castro.cpp
commit a81947b3b96f82ba8ec16540d271c4b197e8c432
Merge: 056324824 3f142df6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 17 01:33:26 2017 -0400
Merge branch 'development' of github.com:AMReX-Astro/Castro into development
commit 05632482469c53703b7bb9a7bd5f772a8ff3807e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 17 01:32:39 2017 -0400
Take some steps to avoid MPI deadlocks
Source/Castro.cpp
commit 3f142df6ad07cf75470e85e178eae8b3a8d796d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 16 14:23:43 2017 -0400
add Lupe
Docs/Preface/Preface.tex
commit 3f9944c253407dee5c60384c7048901e73254348
Merge: e655cde40 d59a7119d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 16 10:50:56 2017 -0400
Merge pull request #125 from AMReX-Astro/rad-front-test
Rad front test
commit d59a7119dc587f56aea0a4366530f949800d7bdd
Merge: 44fb25fa6 e655cde40
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Tue May 16 10:26:23 2017 -0400
Merge branch 'development' into rad-front-test
commit e655cde40909a0668e8c665db67f3685e48933cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 16 03:23:31 2017 -0400
Remove obsolete reflux_strategy parameter
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit d87ae9d96e60418c57e6b4565de91a8495b7f603
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 16 02:06:38 2017 -0400
Enable post-timestep regrids in wdmerger
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
commit 44fb25fa69bb8f84976d8856bfaf78399fb80064
Author: Maria Barrios Sazo <guadabsb15@gmail.com>
Date: Mon May 15 18:52:44 2017 -0400
radiation front test
Exec/radiation_tests/RadFront/GNUmakefile
Exec/radiation_tests/RadFront/Make.package
Exec/radiation_tests/RadFront/Prob_1d.f90
Exec/radiation_tests/RadFront/Prob_2d.f90
Exec/radiation_tests/RadFront/README
Exec/radiation_tests/RadFront/inputs1d
Exec/radiation_tests/RadFront/inputs2d
Exec/radiation_tests/RadFront/probdata.f90
Exec/radiation_tests/RadFront/probin
Exec/radiation_tests/RadFront/radEnergyProf.ipynb
commit e483990c51dc560e5939684ebc4b973cc3c80c79
Merge: 06ec61ea5 4ca78913a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 11 03:36:56 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 4ca78913ab4bdf1678513e418222d8ebeb830655
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 10 10:18:54 2017 -0400
need to explicitly include list for compilation
Source/Radiation/HypreMultiABec.H
commit 830d51c9ef22824888192f7e11d65f0541f665b8
Merge: 15386daf1 42aad4f60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 9 19:46:17 2017 -0400
Merge branch 'megafortran' into development
commit 15386daf1aa00af1e534c8846895999690bc02c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 9 19:45:54 2017 -0400
remove deprecated MICROPHYSICS_DIR -- it's been almost a year now
Exec/Make.Castro
commit 42aad4f60f5f046f9413710ac1613856870d487a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 9 12:15:32 2017 -0400
sorting start
Exec/Make.Castro
commit 06ec61ea5a35b096ce9a024814d0856c2e81876b
Merge: 7deb0cdf3 8e63f75e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 9 03:38:31 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 8e55bde7a5530f51d7b82917ff31aef9c93d1ba5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 22:48:24 2017 -0400
this doesn't compile
Exec/Make.Castro
commit 8e63f75e3abb8a10adf3ce6bd9940518a9409b96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 20:15:35 2017 -0400
rename the Castro sources as ca_F90EXE_sources and ca_f90EXE_sources
to allow for future mangling
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/Make.package
Exec/gravity_tests/StarGrav/Make.package
Exec/gravity_tests/evrard_collapse/Make.package
Exec/gravity_tests/hydrostatic_adjust/Make.package
Exec/gravity_tests/uniform_cube_sphere/Make.package
Exec/hydro_tests/HCBubble/Make.package
Exec/hydro_tests/KH/Make.package
Exec/hydro_tests/Noh/Make.package
Exec/hydro_tests/RT/Make.package
Exec/hydro_tests/RT_particles/Make.package
Exec/hydro_tests/Sedov/Make.package
Exec/hydro_tests/Sod/Make.package
Exec/hydro_tests/Sod_stellar/Make.package
Exec/hydro_tests/Vortices_LWAcoustics/Make.package
Exec/hydro_tests/double_bubble/Make.package
Exec/hydro_tests/gamma_law_bubble/Make.package
Exec/hydro_tests/gresho_vortex/Make.package
Exec/hydro_tests/oddeven/Make.package
Exec/hydro_tests/reacting_bubble/Make.package
Exec/hydro_tests/riemann_test_zone/Make.package
Exec/hydro_tests/rotating_torus/Make.package
Exec/hydro_tests/symmetry/Make.package
Exec/hydro_tests/test_convect/Make.package
Exec/hydro_tests/toy_convect/Make.package
Exec/hydro_tests/toy_flame/Make.package
Exec/radiation_tests/Rad2Tshock/Make.package
Exec/radiation_tests/RadBreakout/Make.package
Exec/radiation_tests/RadShestakovBolstad/Make.package
Exec/radiation_tests/RadSlope/Make.package
Exec/radiation_tests/RadSphere/Make.package
Exec/radiation_tests/RadSuOlson/Make.package
Exec/radiation_tests/RadSuOlsonMG/Make.package
Exec/radiation_tests/RadThermalWave/Make.package
Exec/science/Detonation/Make.package
Exec/science/bwp-rad/Make.package
Exec/science/convective_flame/Make.package
Exec/science/flame/Make.package
Exec/science/flame_wave/Make.package
Exec/science/wdmerger/Make.package
Exec/science/xrb_mixed/Make.package
Exec/unit_tests/diffusion_test/Make.package
Source/Radiation/Make.package
Source/Radiation/RadSrc_1d/Make.package
Source/Radiation/RadSrc_2d/Make.package
Source/Radiation/RadSrc_3d/Make.package
Source/Radiation/RadSrc_nd/Make.package
Source/Radiation/_interpbndry/Make.package
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Make.package
commit 3757e49c58ddd6270d4648d6a5d3198ba09bcd5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 19:51:29 2017 -0400
update to free-form
Source/Radiation/_interpbndry/Make.package
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_1D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_2D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_3D.F
Source/Radiation/_interpbndry/RadInterpBndryData_1d.F90
Source/Radiation/_interpbndry/RadInterpBndryData_2d.F90
Source/Radiation/_interpbndry/RadInterpBndryData_3d.F90
commit 50378f5eec28215b175dd3bb3b5335bfaba6b7a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 18:23:12 2017 -0400
clean up the makefile to make it clearer
Exec/Make.Castro
commit 0fdae44083034c63227faf9326ef0462e345f692
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 13:06:12 2017 -0400
a bit more on the solver type
Docs/Radiation/CastroRadiation.tex
commit 7deb0cdf3caeff622026ff8fa5482711de115c17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 10:18:13 2017 -0400
update new locations + new test
Util/regression_testing/Castro-SBU-amrex-tests-pgi.ini
commit 773a8f285365f213b7596def79db1af2f3f52f87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 09:02:42 2017 -0400
add note
CHANGES
commit 3259581d7951d9e09ad6b755b13106bcaff19759
Merge: bc29e6500 4fc14d21a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 09:01:16 2017 -0400
Merge branch 'development' into mol
commit 4fc14d21af5b51095b44b5177eb9304a47415a5e
Merge: c9b159201 551c579a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 8 08:59:35 2017 -0400
Merge pull request #122 from AMReX-Astro/post_timestep_regrid
Add post timestep regrid functionality
commit 551c579a9329c521b35bfd38121ec79ea0f46984
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 7 22:07:37 2017 -0400
Fix the MPI communication for regridding
Source/Castro.cpp
commit c4c14932e4d58af12c9bc0fddf3f06a27b81b5f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 7 19:13:45 2017 -0400
Add Detonation test of post-step regrid
Exec/science/Detonation/inputs-det-x.regrid
Exec/science/Detonation/probin-det-x.regrid
commit c9b1592016dc005dc20e8c9c16313635aaeae860
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 7 18:55:31 2017 -0400
Fix Detonation multi-D aspect ratios
Exec/science/Detonation/inputs-det-x
Exec/science/Detonation/inputs-det-x.SDC
Exec/science/Detonation/inputs-det-x.test
commit 492cd5bc8447e132cac59f763e74049c3c35adac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 7 17:17:41 2017 -0400
AMReX versions of the test files
Util/regression_testing/Castro-SBU-amrex-tests-pgi.ini
Util/regression_testing/Castro-SBU-amrex-tests.ini
Util/regression_testing/boxlib/Castro-SBU-tests.ini
Util/regression_testing/boxlib/Castro-tests.ini
commit e926fbb34e2922f82739ce1ff5660ca196cbcbd2
Merge: 61402cc31 6d227dfd5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 7 16:47:06 2017 -0400
Merge branch 'development' into post_timestep_regrid
commit 61402cc31fef37014ef352a116cdbaac8024f28b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 7 16:42:46 2017 -0400
Ensure that after a post-step regrid, the FluxRegister is updated
If a regrid occurs after a step, it will in generate create new grids on
the fine level (the level itself may even be newly created). This means that
when the fine level then takes a step immediately afterward, it needs to
throw out the previous coarse fluxes and re-initialize them. This relies on
the fact that we are saving the coarse fluxes.
As part of this change, the flux register CrseInit and FineAdd operations
were moved to their own Castro methods.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 6d227dfd51768b2d2df6d76e622715b2548c2b24
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 6 22:19:07 2017 -0700
Restore RadBoundCond
Source/Radiation/HABEC_F.H
commit 93305d14a54e7cbb9d9bf1315af402b5714f2a43
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat May 6 20:54:27 2017 -0700
MultiFab* derive_dat --> auto derive_dat
Source/CastroParticles.cpp
commit d9995975b414de7e46bf802aeed31696ebcf9b5d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 6 16:34:28 2017 -0700
more headers are parsable by C parser
Exec/science/flame/Problem_F.H
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/Problem_F.H
commit a59bcaa02207b352e76d0ac89e0546cec43a756c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 6 16:09:14 2017 -0700
fix some type mismatch
Source/Radiation/RadSrc_nd/Rad_nd.f90
commit e5f4d07456331f9abc55ddf3da1652875d1568cc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 6 15:52:04 2017 -0700
make a number of headers parsable by a C parser
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive_F.H
Exec/hydro_tests/gamma_law_bubble/Problem_Derive_F.H
Exec/hydro_tests/reacting_bubble/Problem_Derive_F.H
Exec/hydro_tests/toy_flame/Problem_F.H
Source/Radiation/HABEC_F.H
commit 517754dbe910984512f7805663a9ae66609b7b3e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 6 10:51:26 2017 -0700
add a number of extern "C" so that the headers can be parsed by a C parser
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive_F.H
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
Exec/hydro_tests/gamma_law_bubble/Problem_Derive_F.H
Exec/hydro_tests/reacting_bubble/Problem_Derive_F.H
Exec/hydro_tests/toy_flame/Problem_F.H
Exec/science/flame/Problem_F.H
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/Problem_F.H
Exec/unit_tests/diffusion_test/Problem_Derive_F.H
Source/Castro_F.H
Source/Castro_error_F.H
Source/Derive_F.H
Source/Gravity_F.H
Source/Problem_F.H
Source/Radiation/HABEC_F.H
Source/Radiation/RAD_F.H
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
commit f44c3fb8cb7eb5a356f9a01ba53b73e97694d1d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 5 12:19:49 2017 -0400
Missed a boxlib
Exec/science/wdmerger/Prob.cpp
commit 68091031b50e60b6628600e2e9ec450a472c8b67
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 5 01:51:05 2017 -0400
Restore optionality of make variables
Exec/science/wdmerger/GNUmakefile
commit 844b65007740fbc747635be767f5da4ccfc96034
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 5 01:50:48 2017 -0400
Move wdmerger tests into subdirectories
Exec/science/wdmerger/tests/wdmerger_2D/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_2D/inputs_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_2D/probin_test_wdmerger_2D
Exec/science/wdmerger/tests/wdmerger_3D/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D
Exec/science/wdmerger/tests/wdmerger_collision/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_collision/inputs_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_collision/probin_test_wdmerger_collision
Exec/science/wdmerger/tests/wdmerger_retry/GNUmakefile
Exec/science/wdmerger/tests/wdmerger_retry/inputs_test_wdmerger_retry
Exec/science/wdmerger/tests/wdmerger_retry/probin_test_wdmerger_retry
commit fe6db3a3efa0f226f0b6c6be650a45107694e9d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 5 01:21:04 2017 -0400
BoxLib -> AMReX
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/problem_tagging_nd.F90
commit c57657e255b4d459b65e867427a73a7be79f322b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 2 21:36:45 2017 -0400
update github loc
Docs/GettingStarted/CastroGettingStarted.tex
Docs/Preface/Preface.tex
README.md
commit ce74c727c832360aadf116160e0e79ec0feb6da5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 2 18:29:16 2017 -0400
get this compiling with AMReX
Util/ConvertCheckpoint/Embiggen.cpp
Util/ConvertCheckpoint/GNUmakefile
Util/ConvertCheckpoint/Make.package
commit 4e4e3e1cc40af180316974b7317de503754f1c40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 2 18:04:34 2017 -0400
grown factor in Fortran
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
commit d7ca7306a4b15d6d46c075cc129dff15e8d4ef4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 20:17:05 2017 -0400
more boxlib -> amrex
Docs/FAQ/faq.tex
Docs/Software/CastroSoftware.tex
Docs/runtime_parameters/rp_intro.tex
commit bc29e6500b0d42ffabc9dea0505e46affea5ab79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 14:32:20 2017 -0400
remove k_mol from the constructor and do an explicit resize
Source/Castro.cpp
Source/Castro_advance.cpp
commit d1c00d17e624f6a1e3bb78c817e3a0ea5d360f99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 14:08:06 2017 -0400
this now compiles!!
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Src_1d/Castro_mol_1d.F90
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_mol_3d.F90
commit 061ecd0ef0424d1782105a257f6ef9decb846cf1
Merge: 3eb30dd71 37f47de92
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 13:34:48 2017 -0400
Merge branch 'development' into mol
commit 37f47de92c435f5f4fcd2fb2cb2e4ecc8377920c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 11:20:17 2017 -0400
update some docs BoxLib -> AMReX
Docs/GettingStarted/CastroGettingStarted.tex
Docs/Preface/Preface.tex
Docs/castrosymbols.tex
commit 8e3cd0f01f4730521ee676f5116d93065391e84b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 11:09:22 2017 -0400
AMReX
CHANGES
commit 2c5e35c4bd2317e1b76082d036cbc20b2ccb28e6
Merge: 1c48470a2 189dfcd65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 11:08:56 2017 -0400
Merge branch 'master' into development
commit 1c48470a24e298e6eeba2cb36ce40bb909d40bc8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 11:07:10 2017 -0400
boxlib -> AMReX
README.md
commit 189dfcd65ebe6a8834aa91b185fba0bc36522ed0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 1 09:03:10 2017 -0400
17.05
CHANGES
commit 611400903ba9335dda105ae891afbab8df2e4616
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 1 02:43:36 2017 -0400
Add post timestep regrid functionality
If the flag use_post_step_regrid is set to one, then a hook is
activated to check at the end of each timestep if any spatial
stability criteria have been violated. If so, we send a signal
to the Amr class that we want a regrid to occur immediately after
the end of the timestep. If this regrid results in a new fine
level being created, that fine level will immediately take its
timestep, rather than waiting for the next coarse step. In this way,
the fine grid will hopefully have enough resolution to not violate
the stability criterion.
At present the only stability criterion we have is the check against
numerically seeded detonations.
Note that for Poisson gravity, there is an added difficulty because
normally we do a multilevel solve to get the gravitational field in
sync after a regrid. We cannot do this here because the regrid occurs
after the coarse level has advanced, so the time levels are not in sync.
Consequently we simply rely on spatial interpolation to fill in the field.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 3b323abc2b2e4d8dfa3c1253bd66adf1b93a4a62
Merge: 999badb32 a91e9ad70
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 21:44:10 2017 -0400
Merge branch 'amrex-development' into post_timestep_regrid
commit a91e9ad702da110405c26259bd92511a7c1cddcd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 21:41:41 2017 -0400
Update params script for amrex::Real
Source/param_includes/castro_defaults.H
Source/parse_castro_params.py
commit 999badb3256c19e50c68f6d1439cd481afaf177a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 20:56:38 2017 -0400
Split off default tagging into separate function
Source/Castro.H
Source/Castro.cpp
commit 480a33a632757632070605aadead41741ea6db39
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 19:53:25 2017 -0400
Only swap time levels on the current level, not fine levels
This is in anticipation of the ability to add new levels at the end of
a timestep, not just at the beginning. This will mean that we need to
swap every time an advance is entered, because the level will not have
existed at the beginning of the coarse level timestep and so would
not have been swapped.
This commit should not change anything because we never need fine level
data before the fine level advance has begun.
Source/Castro_advance.cpp
commit 66a8e8cd357730bce94513783fce7795f83475a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 19:08:36 2017 -0400
Add a couple missed amrex updates
Exec/science/wdmerger/Prob.cpp
commit 301756bfeb71c3c10d0d4134512b01d8a4cf53a7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 18:57:03 2017 -0400
Update wdmerger for amrex changes
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/bc_fill_nd.F90
Exec/science/wdmerger/sum_integrated_quantities.cpp
commit ba7205fd050c6263f663a13df3f852ed6a92d962
Merge: dfd7c762a 7fce9198a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 30 17:32:03 2017 -0400
Merge branch 'amrex-development' into wdmerger
commit 7fce9198ac3c7b3d3d5d594671624334d9682e72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 19 18:13:24 2017 -0400
use the new build info stuff to add flags to the job_info
Exec/Make.Castro
Source/Castro_io.cpp
commit e33daee97e922aa8674d33ec59f4a1d8ffbe4ebb
Merge: 931cbba57 97ec99bd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 19 14:52:31 2017 -0400
Merge branch 'amrex-development' of ssh://github.com/BoxLib-Codes/Castro into amrex-development
commit 931cbba57e5559f863f5f564103feceb176d5cad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 19 14:52:22 2017 -0400
BoxLib -> AMReX
Source/Castro_io.cpp
commit 97ec99bd93e28bc72c710a591773cdacd59b9fe9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Apr 19 08:34:04 2017 -0700
PROBINIT --> amrex_probinit
Exec/science/flame/Prob_1d.f90
commit 3eb30dd718ab0644670ab2e9c425a7721bbbf3d5
Merge: 0057594cb 85201c8bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 15:28:00 2017 -0400
Merge branch 'development' into mol
commit 0057594cb3cd17cb58c1d856cef400dd3d4e27ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 13:29:43 2017 -0400
add MOL note
CHANGES
commit 5eabc90a4a2d58d0d1fe6f3845105453f0c9e6bc
Merge: 0a8d8c778 d77c71d47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 13:27:36 2017 -0400
Merge branch 'development' into mol
commit 7f2f937f2b8e7c3c2d942d185ebdab5536734989
Merge: 1e8f8b54b 85201c8bf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Apr 18 10:16:15 2017 -0700
Merge branch 'development' into amrex-development
commit 85201c8bf886e59eba0013ab7da24eb43a065aee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 11:15:06 2017 -0400
fix analytic sol out
Exec/radiation_tests/RadSphere/testsuite_analysis/radsphere.py
commit 6ed6e8d0054e4f7c73bee2dd189a89aed7160066
Merge: f51e5f18c d77c71d47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 11:14:05 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f51e5f18cf3b88a4b7fad3c14486be692f3f9aef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 11:13:55 2017 -0400
fix exec location
Exec/radiation_tests/RadSphere/testsuite_analysis/radsphere.py
commit d77c71d47a6a785e3d3c9ee6bec8594ca1538b70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 11:13:07 2017 -0400
fix compilation
Exec/radiation_tests/RadSphere/Tools/fradsphere.f90
commit 0a8d8c7789cd6f960af92cd82b0758dd68c40f79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 09:44:03 2017 -0400
fix hybrid_momentum compilation
Source/Src_3d/Castro_mol_3d.F90
commit fcc85b1fef60a51be343df238c7fce1cc23788e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 18 09:29:14 2017 -0400
some radiation fixes -- note radiation not yet supported
Source/Src_2d/Castro_mol_2d.F90
Source/Src_3d/Castro_mol_3d.F90
commit 630fee16b7ccd3f4fc1ae58b34a59d869ab28095
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 17 20:55:11 2017 -0400
weight the fluxes in the flux register by the integrator weights
Source/Castro_hydro.cpp
commit f73b2bf86b36750372d64289c23c4ddf04863eaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 17 13:56:42 2017 -0400
update compute_cfl to be MOL compatible
Source/Src_nd/advection_util_nd.F90
commit 1395a85d0b6cdbc6b0c844767609ec425b01ab8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 17 13:17:02 2017 -0400
update some comments
Source/Castro_hydro.cpp
commit fab63ae5d586cec21c12ddd1d6e26c3841f601cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 17 13:12:25 2017 -0400
fix the buffering of the ppm reconstructed interface states -- we need
storage for all components, since we use the slab pointers to alternate
the storage from one k3d iteration to the next. Previously we were
overwriting one variable's data with the next.
Source/Src_3d/Castro_mol_3d.F90
commit 1e8f8b54b754e9782d4450481ae7f2243b03ef1a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 13 10:51:17 2017 -0700
BoxLib:: --> amrex::
Source/Castro_advance.cpp
commit 5bf9a73c5f529a4e13ec2dc1d4ff913a8a34dc59
Merge: fe77dba5c ad589fd74
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 13 10:27:15 2017 -0700
Merge branch 'development' into amrex-development
Conflicts:
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
commit ac34b580c43eb41fe20411994c6b7a1b5d7d21af
Merge: 7e3486de6 ad589fd74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 13 09:16:21 2017 -0400
Merge branch 'development' into mol
commit ad589fd74c19760c6b723bab5fe31a80e4a8d05d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 13 05:03:27 2017 -0400
Add some protects against nonsense retry attempts
First, ensure that we're not about to do an integer overflow by requesting
more timesteps than integer counter can accept.
Second, check that we are not requesting more timesteps than a user-defined
maximum number. This is checked against the new parameter castro.retry_max_subcycles.
The parameter defaults to 1000.
Third, check that the subcycled timestep is not smaller than the user-defined
minimum timestep, castro.dt_cutoff.
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit fe77dba5ca49deb322175b1a12ac7689dea72518
Merge: 1ef640dba d814b59fa
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Apr 12 10:45:04 2017 -0700
Merge branch 'development' into amrex-development
Conflicts:
Source/Castro.H
commit 7e3486de6d95bf263c878e3c1ad7c3bffd8da350
Merge: 8378054c9 d814b59fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 10 09:13:18 2017 -0400
Merge branch 'development' into mol
commit d814b59fa7ae0534929ac2f7e2861f57087113a4
Merge: 99bd205dd 812930df5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 9 20:08:44 2017 -0700
Merge pull request #118 from ickc/KH-p5
Exec/hydro_tests/KH/*.p5: fix problem number and filename reference
commit 812930df5051d7f567b520b50945bd8eb5000d8b
Author: Kolen Cheung <christian.kolen@gmail.com>
Date: Sun Apr 9 19:56:24 2017 -0700
Exec/hydro_tests/KH/*.p5: fix problem number and filename reference
Exec/hydro_tests/KH/inputs.2d.p5
Exec/hydro_tests/KH/probin.p5
commit 99bd205dd80ae4dfa863d1f186548870651dcbff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 9 18:36:32 2017 -0400
QVAR -> NQ to make these all radiation compatible too
Source/Src_nd/advection_util_nd.F90
commit efd0bf1e610b50cd065c4befb7fcdeb6c56c57f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 4 01:49:05 2017 -0400
Move output_at_completion to a Castro parameter
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.H
Source/_cpp_parameters
Source/main.cpp
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 1ef640dbaf7bdbfac0d2da5f89235a72764bf842
Merge: f276a08d1 fdaf8b7cf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Apr 3 08:24:34 2017 -0700
Merge branch 'development' into amrex-development
Conflicts:
Source/Castro_gravity.cpp
Source/Gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
commit 8378054c95cd0320cb78b3d87c91494d7221c62d
Merge: 3fad6cafa fdaf8b7cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 3 11:06:36 2017 -0400
Merge branch 'development' into mol
commit fdaf8b7cf20b1c0b6d429c0e95f291a5f5b629d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 3 11:05:40 2017 -0400
add 17.04 changes
CHANGES
commit 3fad6cafae7fc5e46a6298434f4f1f02c579cd3c
Merge: d603d57ef 84c5df78c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 3 10:25:27 2017 -0400
Merge branch 'development' into mol
commit 84c5df78c9cb73331892b64ff5fa111542003fb3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 2 17:47:23 2017 -0400
Use the potential-based energy source term for gravity again
Experimentation has shown that with AMR, the best version is the potential-based
formulation. This is different from the previous implementation because we are now
using the version in Appendix B from Katz et al. (2016), which splits the term
up into a cell-centered and cell-edge term
Source/Src_nd/gravity_sources_nd.F90
commit 96308841d919bc3a0d92f4c525e62187ddeb1dcf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 2 15:46:25 2017 -0400
Revert "Rewrite gravity source in terms of edge-centered gravity"
This reverts commit a0477353a7aaef83cc9956fa64638f8111ce3969.
Source/Castro_F.H
Source/Castro_gravity.cpp
Source/Gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
commit 1c023b7a5352c5616a895d0eeaef1d16dacc7d0a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 2 15:45:20 2017 -0400
Revert "Fix an illegal ghost zone access"
This reverts commit a360ffa1c2d4aaa3f59a1756748d61d4c811e6ff.
Source/Src_nd/gravity_sources_nd.F90
commit f276a08d1de048c622001d611643a808a30efd1c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 29 12:46:18 2017 -0700
amrex update
Source/Gravity.cpp
commit d603d57ef1c4c9144c9552324dd80540dcbddb4f
Merge: 3fa0063ff adf88b611
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 26 20:37:29 2017 -0400
Merge branch 'mol' of ssh://github.com/BoxLib-Codes/Castro into mol
commit 3fa0063ffc1b30b3c8d07b86716ad34e9011d967
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 26 20:37:12 2017 -0400
remove some unneeded declarations, fix some bounds
Source/Castro_hydro.cpp
Source/Src_3d/Castro_mol_3d.F90
commit adf88b611479f4f08bb91056a5810d180f55c73e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 26 14:56:12 2017 -0400
sanity check
Source/Castro_hydro.cpp
Source/Src_3d/Castro_mol_3d.F90
commit 3ac7b655f04121d61be8b73354dfe04884c5da7f
Merge: c3607a6b5 cdc0378c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 26 14:40:52 2017 -0400
Merge branch 'mol' of ssh://github.com/BoxLib-Codes/Castro into mol
commit cdc0378c195324a2fbfcd1d409ec2a8728e95057
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 26 14:19:46 2017 -0400
do all reconstruction before RIemann
Source/Src_3d/Castro_mol_3d.F90
commit 160a580f24dcca2ca8e537eb6f5edd622100b7e3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Mar 26 07:14:48 2017 -0700
update .gitignore
.gitignore
commit c3607a6b536ba3c34d3f8b60ce3100c09b37e01d
Merge: 291c5169f 2b035f84c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 24 12:00:32 2017 -0400
Merge branch 'mol' of ssh://github.com/BoxLib-Codes/Castro into mol
commit 291c5169f48edbb520608fe33bd1d539d3f1d8c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 24 12:00:25 2017 -0400
remove unneeded module
Source/Src_2d/Castro_mol_2d.F90
commit 2b035f84c8c450c2186f9c42f25cfa40e8d85b82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 24 11:24:38 2017 -0400
more bounds fixes
Source/Src_3d/Castro_mol_3d.F90
commit fbbbf801f897a1dcc8ea44c55e38f1413f2f1201
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 24 11:01:30 2017 -0400
fix some allocations
Source/Src_3d/Castro_mol_3d.F90
commit 44a316aca3a31fa251a4eeb10ee5cbf22bdacbd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 24 09:56:50 2017 -0400
some cleaning
Source/Src_2d/Castro_mol_2d.F90
commit 403d4c04fd4e3b7f0b125b3517a82b8695896702
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 23 21:27:46 2017 -0400
compiles, but doesn't run
Source/Src_3d/Castro_mol_3d.F90
commit 9f9eef8185da980299f91035de759c6aa3e74c64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 23 21:09:40 2017 -0400
mostly there...
Source/Src_3d/Castro_mol_3d.F90
commit 119b0c10124ffd28fc46b0eff3f4d396b3bf3c34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 23 15:33:56 2017 -0400
work in progress
Source/Src_3d/Castro_mol_3d.F90
Source/Src_3d/Make.package
commit d8bf48f0a3a25467479ace9b98aad2d358ee5330
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 23 13:46:50 2017 -0400
use split ppm
Source/Src_3d/Castro_advection_3d.F90
commit 9b75d0babd321b6cb954728ce2dba8617f30006e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 23 09:37:17 2017 -0400
get radiation compiling with MOL
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/trace_ppm_1d.f90
commit 80bff5107de7ec24d41ba6d7fe466221936282e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 22:37:00 2017 -0400
split the reconstruction and integtration
Source/Src_3d/ppm_3d.f90
commit 5a82cc99a0d919712425f32ad7b67377676cde37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 15:23:26 2017 -0400
fix indexing issues
Source/Src_1d/Castro_mol_1d.F90
commit 2974e0d8a059cb60acee87e85f814e76613eaf43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 14:52:53 2017 -0400
first cut
Source/Src_1d/Castro_mol_1d.F90
Source/Src_1d/Make.package
commit 64b50cd7bdee52cab60b7cb101ceba0e030acf28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 22 13:19:24 2017 -0400
split the reconstruction from integration for MOL
Source/Src_1d/ppm_1d.f90
Source/Src_1d/trace_ppm_1d.f90
commit ed7ba094f08e2318c754929a5cdec3505150bd37
Merge: 912d7c40f c73505a6a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 22 08:42:49 2017 -0700
Merge branch 'development' into amrex-development
Conflicts:
Source/Castro.cpp
commit a3eee86851dc7371dc3b5c19b48153ab96774ce1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 21 14:34:40 2017 -0400
add the method-of-lines timestep constraint
Source/Src_nd/timestep.F90
commit 1d6533f8b64914b19c6477b73741c8b892726a4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 21 14:13:41 2017 -0400
more tableaus
Source/Castro_setup.cpp
commit 12ed1e3af0aadc4c67613fad85d45ad825371f43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 20 13:41:03 2017 -0400
for the final update, we need to build from Sburn, which is no
longer in S_new (since we've been using S_new for scratch).
Also, add tableau's for 1st and 2nd order
Source/Castro_advance.cpp
Source/Castro_setup.cpp
commit 76a510e888fdaeb0eaf3dbd3f706ec7ed6ae30e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 20 11:11:10 2017 -0400
remove debugging code
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit ab55b940659183d26aa9ee6b19316e845d067e3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 20 10:36:11 2017 -0400
dimensioned q1 and q2 incorrectly
Source/Src_2d/Castro_mol_2d.F90
commit 833198f07d19b6ff014645a49c95ed42fb4d9ca6
Merge: d2e05538a c73505a6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 19 20:43:16 2017 -0400
Merge branch 'development' into mol
commit d2e05538a4f8ce823faecab0e5d81b9f36b9dc55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 19 20:02:15 2017 -0400
need a clean_state() after we create the final MOL update.
also switch to using S_new as our work array for the new stages,
to make Max happy
Source/Castro_advance.cpp
commit c73505a6a76a871fe35eab58b48cc7fbbb3f7d19
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 19 02:25:58 2017 -0400
Fix the negative density reset diagnostics
Source/Castro.cpp
commit fe7f0e7e3471bb2a4c7f6f1e6124e0064e93d2fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 22:22:05 2017 -0400
fix hydro update diagnostic
Source/Castro_hydro.cpp
commit a9aa2313a888d43bb8d88f9d0f517f0416426c86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 20:25:43 2017 -0400
fix the construction of the input to the next stage
and zero out k_mol on init
Source/Castro_advance.cpp
commit 37030187bcb01027eb9c56ed28a76bdd29cb828e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 18:40:32 2017 -0400
fix Sborder init
Source/Castro_advance.cpp
commit 0eacc1dfbb16818334b3d8a679ab78a58c3d9112
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 18:25:37 2017 -0400
add k_mol to the initializer list
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 4e987125cada265e29eb3a057a747639c524e5d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 16:02:48 2017 -0400
add the initialization of Sborder for later stages
fix a dt in the final update
Source/Castro_advance.cpp
commit 4b503e31f0fe10786cf1235fc058ff60b837df1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 15:30:19 2017 -0400
iterate over do_advance
Source/Castro_advance.cpp
commit 4aec5f8d498539c1a8e30b4478e07d7ba832a81a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 14:43:15 2017 -0400
construct S_new as the weighted sum of the k_mol
Source/Castro_advance.cpp
commit 1996c38c6e89457b465d918eacc39792884454f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 14:01:49 2017 -0400
store the update result in k_mol
add logic for different stages in the main do_advance
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 0791b5d9e2899566a34b7382b456ded85aa41492
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 12:52:59 2017 -0400
don't apply old sources to the new state for MOL integration
Source/Castro_sources.cpp
commit d6cfd221d489831253ed33288a262b960c9d30b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 12:49:43 2017 -0400
don't need a FillBoundary on sources for MOL
Source/Castro_hydro.cpp
commit 21c4b7bf707791968fa16167f63ad1a905ef83cf
Merge: 28c0aa1a2 a22c0d302
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 08:19:07 2017 -0400
Merge branch 'development' into mol
commit a22c0d3026357d1bbd904fadafc8cf62d9533223
Merge: 6c85e10bb 266b69552
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 08:18:51 2017 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 6c85e10bb42b4c695f62d530060988f6c1b6c15f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 17 08:18:43 2017 -0400
remove marginpar
Docs/FlowChart/FlowChart.tex
commit 28c0aa1a2d4684804af1157cab21f1797b4f736e
Merge: 7af499eb4 266b69552
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 16 21:23:48 2017 -0400
Merge branch 'development' into mol
commit 7af499eb49ee824ac8f810b4fbad0ee697d7d0a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 16 21:23:27 2017 -0400
lots of compilatoin fixes
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Src_2d/Castro_mol_2d.F90
commit b1a5ff2ee82754a712cf63d29d4d642536c0979e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 16 14:17:42 2017 -0400
allocate new MultFabs
Source/Castro.H
Source/Castro_advance.cpp
commit 2839b029d6abca13e3b517050a0f92a667fbec64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 22:41:01 2017 -0400
add a Butcher tableau
Source/Castro.H
Source/Castro.cpp
Source/Castro_setup.cpp
commit 266b695523883dd59a2c775d94051b10a056d7e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 18:46:37 2017 -0400
fix typo
Docs/FlowChart/FlowChart.tex
commit a094a0fc66c06ab9351dd4007e2ea1cab066aeaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 16:28:59 2017 -0400
add a summary table
Docs/FlowChart/FlowChart.tex
commit d7bf3a0bc94b46eab07a42494bb768fee0c71a44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 14:50:38 2017 -0400
a bit more clarity on what is updated when:
Docs/FlowChart/FlowChart.tex
Docs/Software/CastroSoftware.tex
commit f69653e94d90fbef3bb9ac9ebe5c326f68af860c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 12:02:59 2017 -0400
new separate driver for MOL
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Src_2d/Castro_mol_2d.F90
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 9ce64f53ad7efeaf465fa7dedf1114d353ed891d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 15 11:04:24 2017 -0400
fix compilation with shocks
Source/Src_2d/Castro_mol_2d.F90
commit 619d5adc78867b1c6473d68c24e6d4afff1ef643
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 20:23:49 2017 -0400
fix indexing error
Source/Src_2d/Castro_mol_2d.F90
commit 82fdc53bcccae9731fffacb0e0b1d0961a2c6fef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 20:07:41 2017 -0400
first cut at the mol stage
Source/Src_2d/Castro_mol_2d.F90
Source/Src_2d/Make.package
commit ed93f0d26ad933037a127ac82bacdc5869429280
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 17:08:42 2017 -0400
new interface
Source/Src_2d/Castro_mol_2d.F90
commit 068ba689a88dc0fb2846ca4791e7a3ebefd95cd8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 17:08:23 2017 -0400
remove unused variable
Source/Src_2d/Castro_2d.F90
commit 912d7c40fa7c54e913f74a163d642271d75069e0
Author: Andrew Myers <atmyers2@gmail.com>
Date: Tue Mar 14 10:20:35 2017 -0700
Updating the Castro tracer particles for AMReX.
Source/Castro.cpp
commit fe71593bcc05437c576a33e2189f241ce6c68ef8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 13:11:43 2017 -0400
rename some routines ctu to show that they are the ctu unsplit advection
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
commit 7e45b8768aac4a275dba3135f8e52ffb3ff21f86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 11:17:20 2017 -0400
sync with the main trace
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
commit ea1e7ea74ae325890c60512643712e2f074411f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 14 10:17:58 2017 -0400
split the ppm reconstruction and integration into separate routines
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit d02f41c905f4e9d52cf40590c7a66d4bff497925
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 10 21:24:08 2017 -0800
Must use the distribution map passed in, not build a new one. This worked in BoxLib because the distribution maps were cached.
Source/Radiation/HypreABec.cpp
commit f7d069753a11f97c08d969d744d9257adc6a23a6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 10 10:31:01 2017 -0800
fix some migration issues
Exec/science/flame/Prob.cpp
Exec/science/flame/Problem.H
Exec/science/flame/Problem_F.H
Exec/science/flame/sum_integrated_quantities.cpp
Exec/unit_tests/diffusion_test/Prob.cpp
Exec/unit_tests/diffusion_test/Problem_Derive_F.H
Source/Castro.H
Source/Prob.cpp
Source/param_includes/castro_params.H
commit 24ff9140e2bd428b016f85e7942220cc43bd3efd
Author: Andrew Myers <atmyers2@gmail.com>
Date: Thu Mar 9 13:35:37 2017 -0800
migration step 3.
Source/Gravity.cpp
commit ddb686c3faf623f8c1c47cd7d1328d2d3b8efa02
Author: Andrew Myers <atmyers2@gmail.com>
Date: Thu Mar 9 12:49:51 2017 -0800
migration step 2
CHANGES
Docs/Software/CastroSoftware.tex
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/StarGrav/probdata.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/hydrostatic_adjust/ext_src_1d.f90
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
Exec/gravity_tests/hydrostatic_adjust/probdata.f90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/probdata.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/HCBubble/probdata.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/KH/probdata.f90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT/probdata.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/RT_particles/probdata.f90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
Exec/hydro_tests/Sedov/probdata.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod/probdata.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/probdata.f90
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/probdata.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_bubble/bc_fill_2d.F90
Exec/hydro_tests/double_bubble/model_stuff.f90
Exec/hydro_tests/double_bubble/probdata.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
Exec/hydro_tests/gamma_law_bubble/probdata.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/probdata.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/oddeven/probdata.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/initdata_others.f90
Exec/hydro_tests/reacting_bubble/probdata.f90
Exec/hydro_tests/reacting_bubble/problem_derive_nd.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/riemann_test_zone/probdata.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/probdata.f90
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/symmetry/probdata.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/test_convect/probdata.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/probdata.f90
Exec/hydro_tests/toy_convect/problem_tagging_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/hydro_tests/toy_flame/Problem.f90
Exec/hydro_tests/toy_flame/probdata.f90
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/bc_fill_1d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/Rad2Tshock/probdata.f90
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadBreakout/filt_prim_1d.f90
Exec/radiation_tests/RadBreakout/probdata.f90
Exec/radiation_tests/RadShestakovBolstad/Prob_1d.f90
Exec/radiation_tests/RadShestakovBolstad/probdata.f90
Exec/radiation_tests/RadSlope/Prob_1d.f90
Exec/radiation_tests/RadSlope/probdata.f90
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/radiation_tests/RadSphere/Tools/analytic.f90
Exec/radiation_tests/RadSphere/Tools/radbc.f90
Exec/radiation_tests/RadSphere/probdata.f90
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
Exec/radiation_tests/RadSuOlson/probdata.f90
Exec/radiation_tests/RadSuOlsonMG/Prob_1d.f90
Exec/radiation_tests/RadSuOlsonMG/probdata.f90
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
Exec/radiation_tests/RadThermalWave/Tagging_nd.f90
Exec/radiation_tests/RadThermalWave/probdata.f90
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/probdata.f90
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/bwp-rad/probdata.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/bc_fill_2d.F90
Exec/science/convective_flame/bc_fill_3d.F90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/probdata.f90
Exec/science/convective_flame/problem_tagging_2d.f90
Exec/science/flame/Prob_1d.f90
Exec/science/flame/Problem.f90
Exec/science/flame/probdata.f90
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/problem_tagging_2d.f90
Exec/science/xrb_mixed/Prob_2d.f90
Exec/science/xrb_mixed/probdata.f90
Exec/science/xrb_mixed/problem_tagging_2d.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Exec/unit_tests/diffusion_test/prob_util.f90
Exec/unit_tests/diffusion_test/probdata.f90
Exec/unit_tests/test_react/testburn.f90
Source/Castro_advance.cpp
Source/Radiation/HABEC_F.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/RadPlotvar.cpp
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/HABEC_1D.F90
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_1d/MGFLDneut_1d.f90
Source/Radiation/RadSrc_1d/RAD_1D.F90
Source/Radiation/RadSrc_1d/RadBndry_1d.f90
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_1d/RadPlotvar_1d.f90
Source/Radiation/RadSrc_1d/filt_prim_1d.f90
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/HABEC_2D.F90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_2d/MGFLDneut_2d.f90
Source/Radiation/RadSrc_2d/RAD_2D.F90
Source/Radiation/RadSrc_2d/RadBndry_2d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_2d/RadPlotvar_2d.f90
Source/Radiation/RadSrc_2d/filt_prim_2d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/HABEC_3D.F90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/RadSrc_3d/MGFLDneut_3d.f90
Source/Radiation/RadSrc_3d/RAD_3D.F90
Source/Radiation/RadSrc_3d/RadBndry_3d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
Source/Radiation/RadSrc_3d/RadPlotvar_3d.f90
Source/Radiation/RadSrc_3d/filt_prim_3d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Radiation/RadSrc_nd/RadDerive_nd.f90
Source/Radiation/RadSrc_nd/RadHydro_nd.f90
Source/Radiation/RadSrc_nd/Rad_nd.f90
Source/Radiation/RadSrc_nd/blackbody.f90
Source/Radiation/RadSrc_nd/filter.f90
Source/Radiation/RadSrc_nd/fluxlimiter.f90
Source/Radiation/RadSrc_nd/kavg.F90
Source/Radiation/RadSrc_nd/rad_params.f90
Source/Radiation/RadSrc_nd/rad_util.f90
Source/Radiation/Radiation.H
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_1D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_2D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_3D.F
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_1d/Prob_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/bc_fill_1d.F90
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_2d/Prob_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
Source/Src_2d/ext_src_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/Prob_3d.f90
Source/Src_3d/advection_util_3d.F90
Source/Src_3d/bc_fill_3d.F90
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/slope_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_util.F90
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Enthalpy_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/Prob_nd.F90
Source/Src_nd/Problem.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/Rotation_frequency.F90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/amrinfo.f90
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/ext_src_nd.F90
Source/Src_nd/filcc_nd.F90
Source/Src_nd/flatten_nd.F90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
Source/Src_nd/interpolate.f90
Source/Src_nd/io.f90
Source/Src_nd/math.f90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/pointmass_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/prescribe_phi_nd.F90
Source/Src_nd/prob_params.f90
Source/Src_nd/problem_tagging_nd.F90
Source/Src_nd/riemann_util.f90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/sponge_nd.F90
Source/Src_nd/sums_nd.f90
Source/Src_nd/timestep.F90
Source/Src_nd/update_sponge_params.f90
Util/scripts/dpconvert.py
commit 24914f5cc2b5b18665fa30c004c88f4bb6f602fb
Author: Andrew Myers <atmyers2@gmail.com>
Date: Thu Mar 9 11:16:59 2017 -0800
migration stage 1
CHANGES
Docs/Software/CastroSoftware.tex
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/probdata.f90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/StarGrav/probdata.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/hydrostatic_adjust/ext_src_1d.f90
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
Exec/gravity_tests/hydrostatic_adjust/probdata.f90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/probdata.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/HCBubble/probdata.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/KH/probdata.f90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT/probdata.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/RT_particles/probdata.f90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
Exec/hydro_tests/Sedov/probdata.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod/probdata.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/probdata.f90
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/probdata.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_bubble/bc_fill_2d.F90
Exec/hydro_tests/double_bubble/model_stuff.f90
Exec/hydro_tests/double_bubble/probdata.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
Exec/hydro_tests/gamma_law_bubble/probdata.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/probdata.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/oddeven/probdata.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/initdata_others.f90
Exec/hydro_tests/reacting_bubble/probdata.f90
Exec/hydro_tests/reacting_bubble/problem_derive_nd.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/riemann_test_zone/probdata.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/probdata.f90
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/symmetry/probdata.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/test_convect/probdata.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/probdata.f90
Exec/hydro_tests/toy_convect/problem_tagging_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/hydro_tests/toy_flame/Problem.f90
Exec/hydro_tests/toy_flame/probdata.f90
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/bc_fill_1d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/Rad2Tshock/probdata.f90
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadBreakout/filt_prim_1d.f90
Exec/radiation_tests/RadBreakout/probdata.f90
Exec/radiation_tests/RadShestakovBolstad/Prob_1d.f90
Exec/radiation_tests/RadShestakovBolstad/probdata.f90
Exec/radiation_tests/RadSlope/Prob_1d.f90
Exec/radiation_tests/RadSlope/probdata.f90
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/radiation_tests/RadSphere/Tools/analytic.f90
Exec/radiation_tests/RadSphere/Tools/radbc.f90
Exec/radiation_tests/RadSphere/probdata.f90
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
Exec/radiation_tests/RadSuOlson/probdata.f90
Exec/radiation_tests/RadSuOlsonMG/Prob_1d.f90
Exec/radiation_tests/RadSuOlsonMG/probdata.f90
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
Exec/radiation_tests/RadThermalWave/Tagging_nd.f90
Exec/radiation_tests/RadThermalWave/probdata.f90
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/probdata.f90
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/bwp-rad/probdata.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/bc_fill_2d.F90
Exec/science/convective_flame/bc_fill_3d.F90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/probdata.f90
Exec/science/convective_flame/problem_tagging_2d.f90
Exec/science/flame/Prob_1d.f90
Exec/science/flame/Problem.f90
Exec/science/flame/probdata.f90
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/problem_tagging_2d.f90
Exec/science/xrb_mixed/Prob_2d.f90
Exec/science/xrb_mixed/probdata.f90
Exec/science/xrb_mixed/problem_tagging_2d.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Exec/unit_tests/diffusion_test/prob_util.f90
Exec/unit_tests/diffusion_test/probdata.f90
Exec/unit_tests/test_react/testburn.f90
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Castro_sources.cpp
Source/Derive_F.H
Source/Gravity.cpp
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/HABEC_1D.F90
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_1d/MGFLDneut_1d.f90
Source/Radiation/RadSrc_1d/RAD_1D.F90
Source/Radiation/RadSrc_1d/RadBndry_1d.f90
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_1d/RadPlotvar_1d.f90
Source/Radiation/RadSrc_1d/filt_prim_1d.f90
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/HABEC_2D.F90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_2d/MGFLDneut_2d.f90
Source/Radiation/RadSrc_2d/RAD_2D.F90
Source/Radiation/RadSrc_2d/RadBndry_2d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_2d/RadPlotvar_2d.f90
Source/Radiation/RadSrc_2d/filt_prim_2d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/HABEC_3D.F90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/RadSrc_3d/MGFLDneut_3d.f90
Source/Radiation/RadSrc_3d/RAD_3D.F90
Source/Radiation/RadSrc_3d/RadBndry_3d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
Source/Radiation/RadSrc_3d/RadPlotvar_3d.f90
Source/Radiation/RadSrc_3d/filt_prim_3d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Radiation/RadSrc_nd/RadDerive_nd.f90
Source/Radiation/RadSrc_nd/RadHydro_nd.f90
Source/Radiation/RadSrc_nd/Rad_nd.f90
Source/Radiation/RadSrc_nd/blackbody.f90
Source/Radiation/RadSrc_nd/filter.f90
Source/Radiation/RadSrc_nd/fluxlimiter.f90
Source/Radiation/RadSrc_nd/kavg.F90
Source/Radiation/RadSrc_nd/rad_params.f90
Source/Radiation/RadSrc_nd/rad_util.f90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_1d/Prob_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/bc_fill_1d.F90
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_2d/Prob_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
Source/Src_2d/ext_src_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/Prob_3d.f90
Source/Src_3d/advection_util_3d.F90
Source/Src_3d/bc_fill_3d.F90
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/slope_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_util.F90
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Enthalpy_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/Prob_nd.F90
Source/Src_nd/Problem.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/Rotation_frequency.F90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/amrinfo.f90
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/ext_src_nd.F90
Source/Src_nd/filcc_nd.F90
Source/Src_nd/flatten_nd.F90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
Source/Src_nd/interpolate.f90
Source/Src_nd/io.f90
Source/Src_nd/math.f90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/pointmass_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/prescribe_phi_nd.F90
Source/Src_nd/prob_params.f90
Source/Src_nd/problem_tagging_nd.F90
Source/Src_nd/riemann_util.f90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/sponge_nd.F90
Source/Src_nd/sums_nd.f90
Source/Src_nd/timestep.F90
Source/Src_nd/update_sponge_params.f90
Util/scripts/dpconvert.py
commit 8ce1eac9ec99d3f65f4df2c75cd26d8cc7c5363a
Merge: b83d7bc49 0a0e6fcfc
Author: Andrew Myers <atmyers2@gmail.com>
Date: Thu Mar 9 10:01:50 2017 -0800
merging development into amrex-development.
commit 0a0e6fcfc668fd80669f209a83bc65272c3d455b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 08:51:43 2017 -0500
increment
CHANGES
commit 109f5b2fd3269003ab5ed253c34a9fd997454f3a
Merge: f3b47fcc3 79f2e3ef1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 28 14:43:55 2017 -0500
Merge pull request #111 from BoxLib-Codes/posthook
implement a post_simulation hook
commit 79f2e3ef177e6c4380e0d740d8d2727bbc5acdf9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 28 14:39:02 2017 -0500
use the standard set for the other problem-specific hooks.
Now the problem_post_simulation() routine is #ifdef-ed out
but DO_PROBLEM_POST_SIMULATION. This can be enabled on
a problem-level basis by USE_POST_SIM=TRUE in the GNUmakefile
Exec/Make.Castro
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/diffusion_test/Prob.cpp
Source/Castro.H
Source/Prob.cpp
Source/main.cpp
commit dd043e696b78f8b4eb93ad00ef6267476809560e
Merge: aec9a7468 d1091ed5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 28 13:35:46 2017 -0500
Merge branch 'development' into posthook
commit d1091ed5b22921d29df48334cab5d02574175c56
Merge: 6e9c29630 f3b47fcc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 28 13:35:31 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f3b47fcc3798b92a7987388261604618586d6a0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 26 20:27:51 2017 -0500
Correct error in grav source to hybrid momenta
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
commit aec9a7468ce2bf3e77d5398f049ba20eddd3175c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 19:03:12 2017 -0500
add post_simulation
CHANGES
commit 8363ae28fca0d118fc0c9a5e3badb3c01317d44c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 18:15:00 2017 -0500
use a unique pointer
Exec/unit_tests/diffusion_test/Prob.cpp
commit 713074237cc716d181e8afc135493df03c91bf17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 17:43:00 2017 -0500
comment out some example instructions
Source/Prob.cpp
commit 82aa125610a7c38a0ab449f1aeb5b13b411cca6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 17:39:11 2017 -0500
account for multiple levels, pretty print
Exec/unit_tests/diffusion_test/Prob.cpp
commit 7fb2fe6e24123f006e9e5f7ad3fa25cb96b1be2e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 16:25:34 2017 -0500
new post_simulation
Exec/unit_tests/diffusion_test/Prob.cpp
commit b1c8e8dcbca286d1f2701fda95ec1203a48f2307
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 16:25:08 2017 -0500
support arbitrary time for the analytic solution
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Exec/unit_tests/diffusion_test/prob_util.f90
commit dfd7c762adc03ed161217d8bd534aadb821235df
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 26 14:33:17 2017 -0500
Copy over the wdmerger_retry test
Exec/science/wdmerger/inputs_test_wdmerger_retry
Exec/science/wdmerger/probin_test_wdmerger_retry
commit 2a01bfef7ca5ed475237b21934c8eb69f3381241
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 13:27:28 2017 -0500
add the analytic solution as a derived variable
Exec/unit_tests/diffusion_test/Make.package
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/Problem_Derive_F.H
Exec/unit_tests/diffusion_test/Problem_Derives.H
Exec/unit_tests/diffusion_test/extra_derives_2d.f90
Exec/unit_tests/diffusion_test/prob_util.f90
commit fbcef90a300f965ca420ff1b28de33ca1c0a9ec6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 13:10:02 2017 -0500
explicitly name the bind
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
commit 18217432ab8837bbf31893bf26086bbb1fdf5826
Merge: 08deb0074 378e7bc51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 26 12:47:11 2017 -0500
Merge branch 'development' into posthook
commit 915fb7ce62fefbbb8c05530838ede6ec372df8ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 25 19:24:23 2017 -0500
Move wdmerger source files to Castro
Exec/science/wdmerger/GNUmakefile
Exec/science/wdmerger/Make.package
Exec/science/wdmerger/Prob.cpp
Exec/science/wdmerger/Prob_nd.F90
Exec/science/wdmerger/Problem.H
Exec/science/wdmerger/Problem.f90
Exec/science/wdmerger/Problem_Derive_F.H
Exec/science/wdmerger/Problem_Derives.H
Exec/science/wdmerger/Problem_F.H
Exec/science/wdmerger/Rotation_frequency.F90
Exec/science/wdmerger/bc_fill_nd.F90
Exec/science/wdmerger/binary.f90
Exec/science/wdmerger/ext_src_nd.F90
Exec/science/wdmerger/initial_model.f90
Exec/science/wdmerger/inputs_2d
Exec/science/wdmerger/inputs_3d
Exec/science/wdmerger/inputs_test_wdmerger_2D
Exec/science/wdmerger/inputs_test_wdmerger_3D
Exec/science/wdmerger/inputs_test_wdmerger_collision
Exec/science/wdmerger/probdata.f90
Exec/science/wdmerger/probin
Exec/science/wdmerger/probin_test_wdmerger_2D
Exec/science/wdmerger/probin_test_wdmerger_3D
Exec/science/wdmerger/probin_test_wdmerger_collision
Exec/science/wdmerger/problem_derive_nd.f90
Exec/science/wdmerger/problem_io.f90
Exec/science/wdmerger/problem_tagging_nd.F90
Exec/science/wdmerger/sum_integrated_quantities.cpp
Exec/science/wdmerger/wdmerger_util.f90
commit 378e7bc517e22f7d86757509dbdc650215a51534
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 25 17:43:51 2017 -0500
Fix declaration of temporary grad_phi
Source/Castro_gravity.cpp
commit e5892ed8937b0865e8798a54ff4e8b8040a33c05
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 25 05:40:19 2017 -0500
Permit disabling of self-gravity
Exec/Make.Castro
commit 0fda1a238739384b4c55faac64df05aaef462496
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 25 01:35:11 2017 -0500
Permit disabling of (comp - level) phi correction
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro_gravity.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
Source/param_includes/gravity_defaults.H
Source/param_includes/gravity_params.H
Source/param_includes/gravity_queries.H
commit 08deb00747ae2d6ea3549787e3564c2921faf4ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 24 20:11:38 2017 -0500
post_simulation is static, so we can access it directly from Castro::
also, proof-of-concept implementation of post_simulation that outputs
the min/max of the variables
Source/Prob.cpp
Source/main.cpp
commit 0549b4aa667c13022edb66ba474840f2756303b9
Merge: cc972138a 8c5b79b41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 24 11:57:48 2017 -0500
Merge branch 'development' of ssh://github.com/zingale/Castro into posthook
commit 6e9c2963015c8a16b5bc174fa3dc38c884c57412
Merge: 8c5b79b41 cc972138a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 24 08:53:33 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit cc972138addf99bf081597f73f8495ad30451719
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 24 01:21:23 2017 -0500
Revert so grad_phi is size BL_SPACEDIM
Source/Gravity.cpp
commit a360ffa1c2d4aaa3f59a1756748d61d4c811e6ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 24 00:47:27 2017 -0500
Fix an illegal ghost zone access
Source/Src_nd/gravity_sources_nd.F90
commit 8c5b79b41204e27e06fcfe31ab83d24bfffd455e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 22:31:32 2017 -0500
start of the post_simulation() hook
Source/Castro.H
Source/Prob.cpp
Source/main.cpp
commit 8bae38cac99d32d9e595aa9180ec795f7a796e9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 19:47:03 2017 -0500
note change to the mass fraction output
CHANGES
commit 8b95250e950cdce81784edcb3858c86d2cb640bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 18:56:48 2017 -0500
all -> ALL
Exec/science/Detonation/inputs-det-x.SDC
commit 9c203f9d343ef0a8c06eb29b9b18184df636d991
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 18:54:01 2017 -0500
all -> ALL
Exec/science/Detonation/inputs-det-x
commit c756a0a2d54923650a72ca5a01f2e5d7ff07db35
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 23 18:51:31 2017 -0500
remove dupe of species mass fraction
Source/Castro_setup.cpp
commit c28ddf9354f71a3b0663a2643dee8caaeec806b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 23 05:19:06 2017 -0500
Fix a scoping issue without self-gravity
Source/Castro.cpp
commit a0477353a7aaef83cc9956fa64638f8111ce3969
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 23 04:48:55 2017 -0500
Rewrite gravity source in terms of edge-centered gravity
When AMR is being used, edge-centered gravity is much more accurate
than the previously-used cell-centered potential, due to the fact that
the edge-centered gravity on refinement boundaries comes directly from
the multigrid, which uses a special stencil on the boundary to account
for the change in resolution. For non-Poisson gravity (e.g. monopole),
there is no change (we are constructing an edge-centered gravity by
averaging adjacent cell centers).
Source/Castro_F.H
Source/Castro_gravity.cpp
Source/Gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
commit ee9a01832faec2d6b36a1c122d8eb5f353663106
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 22 03:15:28 2017 -0500
Merge the const_grav and general gravity source terms
Also a fair bit of cleanup in the code.
Source/Castro_gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
commit ea31c503e89dcb7f1bfbb22e193b30f16050dbd4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 22 03:15:05 2017 -0500
Fix issues with SELF_GRAVITY define
Exec/Make.Castro
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Gravity.H
Source/Make.package
commit 1b59f694a3fc8c47e87426119962800f64154a24
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 21 11:23:43 2017 -0500
Fix logic that should only exist with PoissonGrav
Source/Castro_gravity.cpp
commit 0b3da9fa82d77f8334aa56606e184634a6054417
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 21 09:21:50 2017 -0500
note diffusion variables
CHANGES
commit dfe6411cda355956e74bf81b296edff0e04874bf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 20 19:50:23 2017 -0500
Disallow sync solves if composite solves disallowed
Source/Castro.cpp
commit 206a92b0b13eb950fb2754960ca746b768c100eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 20 19:39:04 2017 -0500
Do not save the comp_minus_level data if we're syncing
The comp_minus_level_phi data is useful for getting an answer for the
gravitational potential which is approximately correct, in that it provides
a lagged approximation to the composite solution. However, it is also incompatible
with the approach of doing a sync solve at the end of the timestep, because
the sync solve relies on the only difference between the coarse and fine
grids being the mismatch that develops on the coarse-fine interface. So,
a compromise solution is to use the comp_minus_level data when calculating the
forcing on the coarse grid (so that we get the most accurate force prior
to the sync solve occurring), but to then subtract it from the potential so
that the coming sync solve can proceed correctly.
Source/Castro_gravity.cpp
commit c2290fbbe12d2fb40cfd0b431d9fa336dc6eea9f
Merge: 0d5101d12 9c7029207
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 20 16:51:38 2017 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit 9c70292078ddf7d511ebdc741abf8d62bea7c3eb
Merge: c86d7fdcf caa13ff0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 11:40:20 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit c86d7fdcfdb5282b59c102c03e6cc1215c424dac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 11:40:07 2017 -0500
store the diffusion term in the plotfile, closes #104
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_nd/Derive_nd.F90
commit caa13ff0f15620baa7f7637c61749445e9ae0afb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 10:53:59 2017 -0500
a little about derived variables
Docs/Visualization/CastroVisualization.tex
commit 33945335ad59e832cc5f0d38692cd9bed0215c80
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 10:46:42 2017 -0500
fix formatting
Docs/Diffusion/CastroDiffusion.tex
commit 71d1e2f5a36ae1fe6b72d662af4a75214464d93d
Merge: 3124c078d 220ccad18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 10:02:44 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 3124c078d7627f4296e79e784fd1d0fff02911da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 10:02:40 2017 -0500
fix param
Docs/Diffusion/CastroDiffusion.tex
commit 220ccad183373608a2dad404170f1c6dc1f55cf7
Merge: e1c4a9c73 2e08a13d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 09:58:23 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit e1c4a9c732785bd0b77295cb4c83071be7aef7aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 09:58:07 2017 -0500
also store the diffusion coefficient
Source/Castro_diffusion.cpp
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Diffusion_nd.f90
commit 2e08a13d1673be5c636bc67870bab209112ca3a8
Merge: b15dda4fc 36dc146cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 09:56:16 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b15dda4fcd4a03e2d4e7091e0b71d65374cff912
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 20 09:46:53 2017 -0500
fix typo
Docs/Diffusion/CastroDiffusion.tex
commit 0d5101d12a9ff7e07847d2a970ab7e1dbb551101
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 20 00:57:11 2017 -0500
Include c-f grad(phi) mismatch in sync solve BCs
Source/Gravity.cpp
commit 1f22d560f151b1a4853b77ef9876d3cc4b7f614c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 19 23:20:16 2017 -0500
Remove the new refluxing method
The newer refluxing method, which attempted to do gravitational
sync solves at the end of every fine timestep rather than at the
synchronization time, has been shown to provide very little benefit
but does add computational expense, so it has been removed. The
parameter reflux_strategy has also been removed.
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.cpp
Source/Castro_advance.cpp
Source/_cpp_parameters
commit 36dc146cbc986ab4550ff92bbc31b880b62d299f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 19 23:03:50 2017 -0500
Permit preprocessing on Derive_nd
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Make.package
commit 6a1aeb60761dadda2170f65b0a0f9bd809036b20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 19 22:44:15 2017 -0500
only output thermal_conductivity if diffuse_temp != 0
Source/Castro_setup.cpp
commit b55ee4a9f1234b8db40f237dfbf6dbd6c626656f
Merge: 764bf3019 069139cd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 19 22:19:05 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 764bf30196480f64c7b90077683cc7a47d4ab2bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 19 22:18:50 2017 -0500
store thermal conductivity with diffusion
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_nd/Derive_nd.f90
commit 069139cd6e06f4b73d85f65a1913e889c5881b2c
Merge: adcc459d7 136691096
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 19 21:20:21 2017 -0500
Merge pull request #105 from zingale/development
move more diffusion parameters into _cpp_parameters
commit 13669109690f542e10007c171ee4735ea52eb529
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 19 20:29:59 2017 -0500
move more diffusion parameters into _cpp_parameters
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.F90
Source/Src_nd/React_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit adcc459d7bc43caa5879328beba225adb48aed3b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Feb 15 13:39:33 2017 -0500
Add command to link the Cuda libraries using the PGI compiler.
Docs/ManagingJobs/managingjobs.tex
commit ae0ec13850e8f3c63801b9dcee3cba9d1c790fec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 15 11:25:28 2017 -0500
fix typot
Docs/ManagingJobs/managingjobs.tex
commit 6dd39cca7ee5ea356492d78baf24337d59d8d171
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 15 11:24:05 2017 -0500
magic incantation to get PGI working at OLCF
Docs/ManagingJobs/managingjobs.tex
commit 7f3d9948a19e9ea4ec9e3d1c80feddc73928d943
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 15 10:01:09 2017 -0500
note about python at OLCF
Docs/ManagingJobs/managingjobs.tex
commit 5dd3ac0a693a1bf1c9a79495c5fd6139d94d7c9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 7 19:16:01 2017 -0500
simple script to find the speed of the detonation as a function of time
Exec/science/Detonation/analysis/shock_speed.py
commit 9953c394b099e41a2bff3561d028501cdaebf83c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 2 14:58:41 2017 -0500
turn on radiation, enable plot variables for rad diagnostic
Exec/science/bwp-rad/inputs_2d
commit 25b87007f8fc34759a09261b2d15f8cacef0968c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 2 09:33:00 2017 -0500
update tag
CHANGES
commit d3dbcc22a1534d5c792de87521000d8fb7003bfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 28 19:54:37 2017 -0500
better parametrs
Exec/science/flame/inputs.1d
commit 2190cff93812f1b0d86ab182f96657f9d8727c58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 28 19:47:15 2017 -0500
new setup for testing realistic flames
Exec/science/flame/GNUmakefile
Exec/science/flame/Make.package
Exec/science/flame/Prob.cpp
Exec/science/flame/Prob_1d.f90
Exec/science/flame/Problem.H
Exec/science/flame/Problem.f90
Exec/science/flame/Problem_F.H
Exec/science/flame/README
Exec/science/flame/inputs.1d
Exec/science/flame/probdata.f90
Exec/science/flame/probin
Exec/science/flame/sum_integrated_quantities.cpp
commit b83d7bc4983612f621f9f5d8434138d7351d1f97
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 27 10:03:53 2017 -0800
gfortran 4.8.4 has a bug causing it to crash when compiling riemann_2d.F90. This simple change makes it compile.
Source/Src_2d/riemann_2d.F90
commit ed863f3a3c174a86bc2f05e0ae65d712671356a0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 27 09:56:42 2017 -0800
migration step 10
Exec/gravity_tests/hydrostatic_adjust/Problem_Derive_F.H
Exec/gravity_tests/uniform_cube_sphere/Problem.H
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
Exec/hydro_tests/gamma_law_bubble/Problem_Derive_F.H
Exec/hydro_tests/reacting_bubble/Problem_Derive_F.H
Exec/hydro_tests/test_convect/Problem.H
Exec/hydro_tests/toy_convect/Problem.H
Exec/hydro_tests/toy_flame/Problem.H
Exec/hydro_tests/toy_flame/Problem_F.H
Exec/science/xrb_mixed/Problem.H
Source/Castro.H
Source/Castro_F.H
Source/Castro_error_F.H
Source/Derive_F.H
Source/Diffusion.H
Source/Gravity.H
Source/Gravity_F.H
Source/Radiation/HABEC_F.H
Source/Radiation/HypreABec.H
Source/Radiation/HypreExtMultiABec.H
Source/Radiation/HypreMultiABec.H
Source/Radiation/MGRadBndry.H
Source/Radiation/RAD_F.H
Source/Radiation/RadBndry.H
Source/Radiation/RadSolve.H
Source/Radiation/Radiation.H
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/Radiation/_interpbndry/RadBndryData.H
Source/Radiation/_interpbndry/RadInterpBndryData.H
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/gravity_defaults.H
Source/param_includes/gravity_params.H
Util/plot1d/XGraph1d.H
commit aa93f319b0e7966fc4e1eeb50289affe6f8fd623
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 26 12:39:41 2017 -0800
parmparse has been added to amrex base
Source/Src_nd/Make.package
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/parmparse_fi.cpp
Source/Src_nd/parmparse_mod.f90
Source/Src_nd/string_mod.f90
commit ca4b5332c24624c48ed76427dd2def1d2ae0446f
Merge: 8fd33b6d1 71d603970
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 26 13:12:30 2017 -0500
Merge pull request #97 from atmyers/master
Writing particle information to the plotfiles using the standard BoxLib format
commit 71d603970d49eb455c58b4f09b2bc855facc142e
Author: Andrew Myers <atmyers2@gmail.com>
Date: Wed Jan 25 21:41:27 2017 -0800
Use a wrapper function to write plot files and add a comment for clarity.
Source/Castro.H
Source/CastroParticles.cpp
Source/Castro_io.cpp
commit 8fd33b6d10f5a06835454dc2ca029009e93347f7
Merge: b4523e8f3 d0b90be7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 25 20:15:34 2017 -0800
Merge pull request #98 from jaharris87/development
Allow sponge to be active in an interior region
commit d0b90be7a945d108b10158c1e4053d161b763492
Author: Austin Harris <jaharris87@users.noreply.github.com>
Date: Wed Jan 25 17:28:28 2017 -0800
Allow sponge to be active in an interior region
Source/Src_nd/sponge_nd.F90
commit b4523e8f3e8af79452cccfccd83c42331d13b860
Merge: fac74a2bb 2e86a57f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 25 08:26:11 2017 -0800
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit fac74a2bbdc9170de4dd09b369fb253cb3b70afb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 25 08:25:57 2017 -0800
sparsify output
Exec/science/flame_wave/inputs_2d
commit afe7adbdf388877f8b361e1d5bf63975bf3a6550
Author: Andrew Myers <atmyers2@gmail.com>
Date: Mon Jan 23 11:07:37 2017 -0800
Writing particle information to the plotfiles using the standard BoxLib format.
Source/Castro_io.cpp
commit 2e86a57f8c795c8d42c314dd17f7709c8aa7d17a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 21 22:18:03 2017 -0500
add note about internal energy source
Docs/Hydrodynamics/Hydrodynamics.tex
commit 9b134c86e1ce272c7746f11742d49c18dd898e05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 21 22:07:27 2017 -0500
clean up some of the internal energy stuff
Docs/Hydrodynamics/Hydrodynamics.tex
commit b4f56aea3281b521c2c6f84619a426ac365336d2
Merge: 44867efd5 0217e64d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 20 18:12:09 2017 -0500
Merge branch 'development' into radmerge
commit 44867efd591aebdd367248f0d542b503e2b52c1a
Merge: 1d16e5839 5e194b447
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 20 18:09:23 2017 -0500
Merge branch 'radmerge' of ssh://github.com/BoxLib-Codes/Castro into radmerge
commit 1d16e58399775c1c191c7eeac921bdb6ca64ed82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 20 18:08:57 2017 -0500
fix path to analytic solution
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test1-helm.py
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test2-helm.py
Exec/hydro_tests/Sod_stellar/testsuite_analysis/test3-helm.py
commit bb03abee6247915012c5e7a8aea29dd5c9465c33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 20 18:07:15 2017 -0500
fix path to analytic solution
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_2d_cyl_in_cart.py
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
Exec/hydro_tests/Sedov/testsuite_analysis/sedov_3d_sph.py
commit 0217e64d4e23cd852233daea9ee7d7dbba6533c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 17 20:21:52 2017 -0500
add docs for grav_source_type
Docs/Gravity/CastroGravity.tex
Docs/Rotation/CastroRotation.tex
Docs/refs.bib
commit 31623f62166a7348aa7ae2437bd028051007adb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 17 20:03:00 2017 -0500
clean up some runtime parameter definitions and index them
Docs/Gravity/CastroGravity.tex
commit 04c02bd5c7e38a73da97ce9d8ee1f4ab22be7915
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 17 15:52:39 2017 -0500
add cases where benchmarks were updated
Util/regression_testing/hash_pairings.txt
Util/regression_testing/test_pairings.py
commit a810ec1e297ab2c1b2b73a883289340113c0caf9
Merge: 3425e28ce 734d30611
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 17 15:43:00 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 3425e28cea836f8f2074834dac3b5ae3d22119f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 17 15:42:15 2017 -0500
script to scrape the test suite web output and produce a list,
by date, of the git hashes for Castro, BoxLib, and Microphysics
that work together. These are only from days that all tests passed.
Util/regression_testing/hash_pairings.txt
Util/regression_testing/test_pairings.py
commit 734d3061106656e2f5ad0c5b3e7d3ae1bb754a9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 15 15:18:00 2017 -0500
add issue reference
CHANGES
commit 823e1805e2d30da9a5215b52816c257bbac029a8
Merge: 73ee9d1e2 a125f9dd8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 14 19:07:34 2017 -0500
Merge pull request #94 from BoxLib-Codes/diag
Diagnostics updates
commit a125f9dd8d45d34b9bdc44f0f0b2b1f257025a0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 13:20:02 2017 -0500
Update CHANGES with diagnostics changes
CHANGES
commit 5f6ac155fc2696625800483cd3bee5af0a4d089b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 13:16:14 2017 -0500
Put ext_src first to simplify logic
Source/Castro.H
commit 34e13a5441be3bdb254925b0c41cad4d95115df5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 13:15:18 2017 -0500
Print eint added in diagnostics
Source/Castro_sources.cpp
commit 4a9b8a1365fc934de03019011ae451bc25a3fc95
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 13:14:04 2017 -0500
Print energy reset diagnostics on all levels
Source/Castro.cpp
commit f1e7c99d3fc238bace0ab0a67d26443d22b1c156
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 13:13:31 2017 -0500
Use new diagnostics for internal energy resets
Source/Castro.cpp
commit 6e72187c116679599cb4c4836f5ea331e6d1fe59
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 13:06:27 2017 -0500
Use the new diagnostics for negative density resets
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/advection_util_nd.F90
commit 403915b9d45c0454f91ca8505b0406d9ab4a4adc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 12:39:22 2017 -0500
Do the new diagnostics for the hydro
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
commit c41f2c2f90616b4de8dac7fb91ec4e131e4bb5ad
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 12:27:38 2017 -0500
Allow source-term diagnostics to be coalesced
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro_sources.cpp
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit c234b6d142170b44cc97ffc0af56d082cfd0b4ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 09:03:59 2017 -0800
print_energy_diagnostics -> print_update_diagnostics
Source/Castro.cpp
Source/Castro_hydro.cpp
Source/Castro_sources.cpp
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit d6d891c74704ab74c86220ac85989b84a23417fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 14 08:58:19 2017 -0800
Use the generic diagnostic routine for all sources
Source/Castro.H
Source/Castro_F.H
Source/Castro_gravity.cpp
Source/Castro_rotation.cpp
Source/Castro_sources.cpp
Source/Castro_sponge.cpp
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/sponge_nd.F90
commit 1757292790cfcec482ff5d612416fed8e1ebadcf
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 13 13:01:26 2017 -0800
Give names to the various source terms
Source/Castro.H
Source/Castro.cpp
Source/Castro_setup.cpp
commit 227770555db5a60a34ab51f08c6128e316ae34e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 13 12:37:15 2017 -0800
Add routines to generically evaluate source term effect
Source/Castro.H
Source/Castro_sources.cpp
commit 73ee9d1e25d78449c2e09976e89a1a82425a6f81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 13 18:03:23 2017 -0500
update to reflect we now do git describe for job_info
CHANGES
Source/Castro_io.cpp
Source/Castro_setup.cpp
commit c36ddc81d07c903fc4075b4f2ab5afa04bc94c13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 11 18:16:12 2017 -0500
rmeove -- redundant with rad
Exec/science/bwp/GNUmakefile
Exec/science/bwp/Make.package
Exec/science/bwp/Prob_2d.f90
Exec/science/bwp/SolarLike_0.2M.hse.1280
Exec/science/bwp/inputs_2d
Exec/science/bwp/probdata.f90
Exec/science/bwp/probin
Exec/science/bwp/probin.dens_sponge
commit a1a3673b73f0390487429a7cca45e9c3a415cdb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 11 18:16:00 2017 -0500
copy over from the non-rad
Exec/science/bwp-rad/probin.dens_sponge
commit cdc6bd2c055b23b0b7f1e5aadaa1530e0ca102e4
Merge: 9b976b30d 5e194b447
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 11 14:05:14 2017 -0500
Merge pull request #91 from BoxLib-Codes/radmerge
eliminating LHH.H
commit 5e194b447e11607f82a333b334cd081505ad5a40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 21:21:29 2017 -0500
fix some dataPtr() components
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/RAD_F.H
Source/Radiation/RadSolve.cpp
Source/Radiation/Radiation.cpp
commit 9a8e97e5d91f32085eacf2a616d95f86b368cac6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 16:58:53 2017 -0500
remove LHH.H
Source/Radiation/HABEC_F.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/LHH.H
Source/Radiation/Make.package
commit c144501e9639ed9db9d31682877299fe351ad8c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 16:57:13 2017 -0500
finish the updates
Source/Radiation/HABEC_F.H
Source/Radiation/HypreMultiABec.cpp
commit 4c46f7a1d8aa154001d81e3e25f6cf8e8e05bf2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 16:26:15 2017 -0500
more updates since I'm not paying attention to a teleconference as much as I should be
Source/Radiation/HABEC_F.H
Source/Radiation/HypreABec.cpp
commit 401361840a0ca2052b6b5c260279648d39fc886f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 15:41:28 2017 -0500
more progress
Source/Radiation/HABEC_F.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreMultiABec.cpp
commit b018f02f530dd2b9ae132897a338c7f709c7a72a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 15:32:01 2017 -0500
update notes on naming
Source/Radiation/notes.txt
commit 7648cfef78fc449ba22542a18191d16c380797be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 15:09:47 2017 -0500
more LHH cleaning
Source/Radiation/HABEC_F.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/MGFLD.cpp
Source/Radiation/RAD_F.H
commit 632be4556e192e3204934252d4f61c1179912ccd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 14:43:21 2017 -0500
DIMS.H is redundant with ArrayLim.H
Source/Radiation/_interpbndry/DIMS.H
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_1D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_2D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_3D.F
commit 838f0552f7a0b1bcb003f49dc9499777eb6a1862
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 14:39:40 2017 -0500
get rid of references to BL_USE_ARLIM
Source/Radiation/MGFLDRadSolver.cpp
Source/Radiation/MGRadBndry.cpp
Source/Radiation/RadBndry.cpp
Source/Radiation/RadSolve.cpp
Source/Radiation/Radiation.cpp
Source/Radiation/SGRadSolver.cpp
commit 8f649ee0c61b02867f010d447dac0b1a2c9d2cc8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 14:17:59 2017 -0500
more macro cleaning
Source/Radiation/HABEC_F.H
Source/Radiation/MGRadBndry.cpp
Source/Radiation/RAD_F.H
Source/Radiation/RadSolve.cpp
commit c3c57805096a9eac8b0ae2a3d5b88bb58ba0dddb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 12:34:46 2017 -0500
remove some of the dimlist stuff
Source/Radiation/MGFLD.cpp
Source/Radiation/RAD_F.H
Source/Radiation/Radiation.cpp
commit 9b976b30de6c692aa070f2fce220d46a55eea521
Merge: 69268a371 f91299eef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 10 09:50:21 2017 -0500
Merge branch 'development' into radmerge
commit f91299eef103ecdc419502a2c1d7d110d4f460ad
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 10 00:01:00 2017 -0500
Add a narrative description of the reflux updates
Docs/AMR/AMR.tex
Docs/Gravity/CastroGravity.tex
commit 69268a37190e64609cff4fba8f29ea1a8d3bff6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 9 19:01:26 2017 -0500
get rid of intS
Source/Radiation/HABEC_F.H
Source/Radiation/LHH.H
commit d0d703909ad6bad36d785cabb0298d08f20bb9b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 22:02:41 2017 -0500
some more restricting on where LHH.H is needed
Source/Radiation/MGFLD.cpp
Source/Radiation/RadSolve.H
Source/Radiation/Radiation.cpp
commit bec43cf77f20b8a00941a4e83bb64b21dd622bce
Merge: e338098e0 17f2ba82a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 21:58:37 2017 -0500
Merge branch 'development' into radmerge
commit e338098e0b4e44d6dc686e694ddaa7f09ba4e8f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 21:53:37 2017 -0500
get rid of intS
Source/Radiation/RAD_F.H
Source/Radiation/RadBndry.cpp
commit 466d58cfa5566aeab3524391b9e275af1fa775f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 21:04:37 2017 -0500
remove an include
Source/Radiation/RadBndry.cpp
commit ee27aeb915a1afd7b71778e761f8f3ac21583d42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 21:01:54 2017 -0500
bind(C)
Source/Radiation/RAD_F.H
Source/Radiation/RadPlotvar.cpp
Source/Radiation/RadSolve.cpp
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_1d/MGFLDneut_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_2d/MGFLDneut_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/RadSrc_3d/MGFLDneut_3d.f90
commit 17f2ba82a280882f375f50fc705ff0224ed8cade
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 19:01:52 2017 -0500
remove check on dimensionality and ppm_temp_fix -- no longer needed
Source/Castro.cpp
commit db9d1b6260ffea6065ce67c04b08b917b0ec98fa
Merge: 633d56328 1493f8672
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 8 18:45:33 2017 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit 633d56328126887f551445a35a2b3d294a903115
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 8 18:45:27 2017 -0500
Fix dimensional logic for pressure scaling
Source/Castro.cpp
commit 1493f86724ffc6da4d3b0738fae2436cd3cc8358
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 18:28:13 2017 -0500
update changes
CHANGES
commit 5a38f08f080cc70b9d247dc0a5114e2fceb824db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 18:27:03 2017 -0500
port the ppm_temp_fix stuff to 1-d -- it is now in sync with 2- and 3-d
closes #25
Source/Src_1d/riemann_1d.F90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 797c82526cfe928b50edab0c556fe4580e077659
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 16:54:16 2017 -0500
update GCC
Docs/ManagingJobs/managingjobs.tex
commit 2e6a99e2980f76a88d94c280402636b917df73e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 14:36:05 2017 -0500
document ppm_temp_fix -- addresses part of issue #25
Docs/Hydrodynamics/Hydrodynamics.tex
commit 8bba43cadbca8e55fadb98598cb22fae12bf8f69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 13:35:52 2017 -0500
some cleaning and comments
Docs/Hydrodynamics/Hydrodynamics.tex
commit 05d0c2350dc96a4aefabab366e0e6160a7e28a0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 12:48:27 2017 -0500
fix a lot of indexing
Docs/Hydrodynamics/Hydrodynamics.tex
commit fe9a802b3573974342a814dbc9619c208ec5f9b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 12:39:44 2017 -0500
fix sorting of index
Docs/CastroUserGuide.tex
commit 95c077f5044ba395a91b67d1fedb0be91ed44ef6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 11:18:59 2017 -0500
new tables for qaux and the Godunov keys
Docs/CastroUserGuide.tex
Docs/Hydrodynamics/Hydrodynamics.tex
commit 023f503065081800bd4748fa4d6b2f2b4460ab9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 10:28:34 2017 -0500
rename
Docs/GNUmakefile
Docs/Hydrodynamics/Hydrodynamics.tex
commit 9543523573f112947fc12f111396e1c008da2674
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 8 10:23:27 2017 -0500
update default
Docs/runtime_parameters/runtime_parameters.tex
commit 9a575c020966fde7c09638535fe77ccaa70c0d54
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 7 03:34:05 2017 -0500
Check to make sure we're actually doing the sources
Source/Castro.cpp
commit 3c912da4c47ce9087e26b0e13e24a4da1e8704e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 6 20:50:50 2017 -0500
Replace some ifdefs with dimensional logic
Source/Castro.H
Source/Castro.cpp
commit b04ea78c98ae22efaf2c7eb2ae50be7d60fc7830
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 6 20:31:57 2017 -0500
remove a magic number to a parameter in the extrema test. Closes issue #13
Source/Src_1d/ppm_1d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_3d/ppm_3d.f90
commit 3a07cd2251e0516322eccdb190871d7c44ce81a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 20:21:44 2017 -0500
get rid of Fab
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/LHH.H
Source/Radiation/MGRadBndry.cpp
Source/Radiation/RadBndry.cpp
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
commit 6a1b0b69294207c6c2f8678897c34c1d293405f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 20:09:29 2017 -0500
get rid of Iv
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/LHH.H
commit e969506dc65c651899ae06013c13259703a745e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 19:53:12 2017 -0500
some more LHH.H cleaning
Source/Radiation/HABEC_F.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.H
Source/Radiation/NGBndry.H
commit ed515ecad2ce1476960c6f3f2ab6e72fed7042e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 19:45:41 2017 -0500
split the RadTest class out of LHH.H (we'll get rid of that separately)
Source/Radiation/LHH.H
Source/Radiation/Make.package
Source/Radiation/RadMultiGroup.cpp
Source/Radiation/RadTests.H
Source/Radiation/Radiation.cpp
commit 96b7c3c729dd693750be260f5fd01c2cee7a75a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 19:39:21 2017 -0500
LHH.H is not needed here
Source/Radiation/Radiation.H
commit 9c9af26b6d57f34a533cdc8afaa949554edfec65
Merge: 98fd271e0 e55148c17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 19:35:25 2017 -0500
Merge branch 'development' into radmerge
commit d18457ee64be5f0a3bb437bce772a5266e2114f4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 5 15:13:22 2017 -0800
migration step 9
Exec/hydro_tests/test_convect/sum_integrated_quantities.cpp
Exec/hydro_tests/toy_convect/sum_integrated_quantities.cpp
Exec/hydro_tests/toy_flame/Prob.cpp
Exec/science/xrb_mixed/sum_integrated_quantities.cpp
Source/Castro.H
Source/Castro.cpp
Source/CastroParticles.cpp
Source/Castro_F.H
Source/Castro_io.cpp
Source/Radiation/HypreMultiABec.H
Source/sum_utils.cpp
Util/plot1d/XGraph1d.cpp
commit e55148c1766c929271f39a319103963cb385a78a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 10:37:02 2017 -0500
update to reflect time-center sponge
CHANGES
commit 2482b880466c0a0ed6bf69056d7755398b12753b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 10:33:33 2017 -0500
change time_center_sponge default to 1
also update the parameter writing scripts to use real(rt) instead of double precision
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/parse_castro_params.py
commit be8893354967d9591e14d704e48540c959b0c565
Merge: dabe49a93 8cb9c1caf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 5 10:21:24 2017 -0500
Merge pull request #88 from BoxLib-Codes/c_real
switch all double precision declarations and constants to c_real
commit 8cb9c1cafb60075d4c27623028078347c56c8ccc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 22:02:29 2017 -0500
also convert the double precision stuff in the problem directories
to c_real
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/probdata.f90
Exec/gravity_tests/DustCollapse/update_sponge_params.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/StarGrav/probdata.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/probdata.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/hydrostatic_adjust/ext_src_1d.f90
Exec/gravity_tests/hydrostatic_adjust/extra_derives.f90
Exec/gravity_tests/hydrostatic_adjust/probdata.f90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/probdata.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/HCBubble/probdata.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/KH/probdata.f90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT/probdata.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/RT_particles/probdata.f90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
Exec/hydro_tests/Sedov/probdata.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod/probdata.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/probdata.f90
Exec/hydro_tests/Sod_stellar/trace_ppm_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/Vortices_LWAcoustics/probdata.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/double_bubble/bc_fill_2d.F90
Exec/hydro_tests/double_bubble/model_stuff.f90
Exec/hydro_tests/double_bubble/probdata.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
Exec/hydro_tests/gamma_law_bubble/extra_derives_2d.f90
Exec/hydro_tests/gamma_law_bubble/probdata.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/probdata.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/oddeven/probdata.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/initdata_others.f90
Exec/hydro_tests/reacting_bubble/probdata.f90
Exec/hydro_tests/reacting_bubble/problem_derive_nd.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/riemann_test_zone/probdata.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/rotating_torus/probdata.f90
Exec/hydro_tests/rotating_torus/problem_tagging_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/symmetry/probdata.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/test_convect/ext_src_2d.f90
Exec/hydro_tests/test_convect/probdata.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/ext_src_2d.f90
Exec/hydro_tests/toy_convect/probdata.f90
Exec/hydro_tests/toy_convect/problem_tagging_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/hydro_tests/toy_flame/Problem.f90
Exec/hydro_tests/toy_flame/probdata.f90
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/Rad2Tshock/Tools/bc.f90
Exec/radiation_tests/Rad2Tshock/bc_fill_1d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/Rad2Tshock/probdata.f90
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadBreakout/filt_prim_1d.f90
Exec/radiation_tests/RadBreakout/probdata.f90
Exec/radiation_tests/RadShestakovBolstad/Prob_1d.f90
Exec/radiation_tests/RadShestakovBolstad/probdata.f90
Exec/radiation_tests/RadSlope/Prob_1d.f90
Exec/radiation_tests/RadSlope/probdata.f90
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/radiation_tests/RadSphere/Tools/analytic.f90
Exec/radiation_tests/RadSphere/Tools/fradsphere.f90
Exec/radiation_tests/RadSphere/Tools/radbc.f90
Exec/radiation_tests/RadSphere/probdata.f90
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
Exec/radiation_tests/RadSuOlson/probdata.f90
Exec/radiation_tests/RadSuOlsonMG/Prob_1d.f90
Exec/radiation_tests/RadSuOlsonMG/probdata.f90
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
Exec/radiation_tests/RadThermalWave/Tagging_nd.f90
Exec/radiation_tests/RadThermalWave/probdata.f90
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/Detonation/probdata.f90
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/bwp-rad/probdata.f90
Exec/science/bwp/Prob_2d.f90
Exec/science/bwp/probdata.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/convective_flame/bc_fill_2d.F90
Exec/science/convective_flame/bc_fill_3d.F90
Exec/science/convective_flame/hydrostatic_bc_2d.f90
Exec/science/convective_flame/hydrostatic_bc_3d.f90
Exec/science/convective_flame/probdata.f90
Exec/science/convective_flame/problem_tagging_2d.f90
Exec/science/flame_wave/Prob_2d.f90
Exec/science/flame_wave/probdata.f90
Exec/science/flame_wave/problem_tagging_2d.f90
Exec/science/xrb_mixed/Prob_2d.f90
Exec/science/xrb_mixed/probdata.f90
Exec/science/xrb_mixed/problem_tagging_2d.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Exec/unit_tests/diffusion_test/probdata.f90
Exec/unit_tests/test_react/testburn.f90
commit 5a217c54fff0d82432990f0a3721dc600e092de7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 18:17:58 2017 -0500
update c_real
CHANGES
commit d81ce237d9942ab2357fc17dce63670a020c092f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 18:15:30 2017 -0500
update docs on c_real
Docs/Software/CastroSoftware.tex
commit e53b3dcce95676173c6441b11765d11c8d95dee9
Merge: d6c78ae7a dabe49a93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 17:44:58 2017 -0500
Merge branch 'development' into c_real
commit dabe49a93d27bc68843d5d73161e57f1ada17a34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 17:43:46 2017 -0500
fix how constants are handled (in particular, the '-' in the exponent
Util/scripts/dpconvert.py
commit d6c78ae7a4a2b6c7ab88bf00737c0e27aee5bbba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 13:35:09 2017 -0500
switch all double precision declarations and constants to
use the BoxLib-compatible c_real type so we support single
and double precision options. This was updated using
dpconvert.py. This addresses issue #34
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/HABEC_1D.F90
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_1d/MGFLDneut_1d.f90
Source/Radiation/RadSrc_1d/RAD_1D.F90
Source/Radiation/RadSrc_1d/RadBndry_1d.f90
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_1d/RadPlotvar_1d.f90
Source/Radiation/RadSrc_1d/filt_prim_1d.f90
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/HABEC_2D.F90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_2d/MGFLDneut_2d.f90
Source/Radiation/RadSrc_2d/RAD_2D.F90
Source/Radiation/RadSrc_2d/RadBndry_2d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_2d/RadPlotvar_2d.f90
Source/Radiation/RadSrc_2d/filt_prim_2d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/HABEC_3D.F90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/RadSrc_3d/MGFLDneut_3d.f90
Source/Radiation/RadSrc_3d/RAD_3D.F90
Source/Radiation/RadSrc_3d/RadBndry_3d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
Source/Radiation/RadSrc_3d/RadPlotvar_3d.f90
Source/Radiation/RadSrc_3d/filt_prim_3d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Radiation/RadSrc_nd/RadDerive_nd.f90
Source/Radiation/RadSrc_nd/RadHydro_nd.f90
Source/Radiation/RadSrc_nd/Rad_nd.f90
Source/Radiation/RadSrc_nd/blackbody.f90
Source/Radiation/RadSrc_nd/filter.f90
Source/Radiation/RadSrc_nd/fluxlimiter.f90
Source/Radiation/RadSrc_nd/kavg.F90
Source/Radiation/RadSrc_nd/rad_params.f90
Source/Radiation/RadSrc_nd/rad_util.f90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_1d/Prob_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/bc_fill_1d.F90
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_2d/Prob_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
Source/Src_2d/ext_src_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/Prob_3d.f90
Source/Src_3d/advection_util_3d.F90
Source/Src_3d/bc_fill_3d.F90
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/slope_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_util.F90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Enthalpy_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/Prob_nd.F90
Source/Src_nd/Problem.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/Rotation_frequency.F90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/amrinfo.f90
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/ext_src_nd.F90
Source/Src_nd/filcc_nd.F90
Source/Src_nd/flatten_nd.F90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
Source/Src_nd/interpolate.f90
Source/Src_nd/io.f90
Source/Src_nd/math.f90
Source/Src_nd/meth_params.F90
Source/Src_nd/parmparse_mod.f90
Source/Src_nd/pointmass_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/prescribe_phi_nd.F90
Source/Src_nd/prob_params.f90
Source/Src_nd/problem_tagging_nd.F90
Source/Src_nd/riemann_util.f90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/sponge_nd.F90
Source/Src_nd/string_mod.f90
Source/Src_nd/sums_nd.f90
Source/Src_nd/timestep.F90
Source/Src_nd/update_sponge_params.f90
commit 6c27058c5fca9aaedd7e260dfba123682d0378dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 12:57:21 2017 -0500
rename to prevent forthcoming real type name clashing
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
commit 1a90b18eee93c49110167f81f02ca915c6ff7534
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 4 10:14:54 2017 -0500
add real*8 support, fix how we handle functions, fix how we handle
numerical constants too
Util/scripts/dpconvert.py
commit 2b2c9f567b0a45980ea6a627614fa71b9354fef6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 21:32:49 2017 -0500
properly indent the use statement
Util/scripts/dpconvert.py
commit 0be29896de061d4537c17de1905ca4f30553ae5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 20:03:25 2017 -0500
this successfully inserts the `use bl_fort_module` statement
Util/scripts/dpconvert.py
commit d80440f2a3dbfa7f05775da37b26b714d3122dc5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 3 12:35:32 2017 -0800
update to amrex
Source/Castro.cpp
commit 6f5dfa6c28eb527134b07520a639cb554923b790
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 3 12:33:28 2017 -0800
using namespace amrex
Exec/hydro_tests/test_convect/sum_integrated_quantities.cpp
commit 1584ce23919636d7c5a893c4bbdd81ee63d8718e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 3 12:28:00 2017 -0800
fix binding for gravity_tests/uniform_cube_sphere
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
commit 78781b9b02345a895928b82c6c94c0a12b8ad336
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 3 12:28:00 2017 -0800
fix binding for gravity_tests/uniform_cube_sphere
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
commit 2b775a598dc56e3752f9059e9df1406ef5d2562f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 14:38:07 2017 -0500
preserve spacing and handle constants too
Util/scripts/dpconvert.py
commit 13814ba4107023d360625cb27a14341a65bde895
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 3 11:17:07 2017 -0800
update to amrex
Source/Castro.cpp
commit 39a34306851b5875fd31f6173b1f22439cc71cba
Merge: 7542c86bd c7c0a52ee
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 3 11:12:44 2017 -0800
Merge tag '17.01' into amrex-development
Castro 17.01
Conflicts:
Source/Castro.cpp
Source/Castro_advance.cpp
commit 68c1d054389bfece60aef9fe433a4c1dc720ffe0
Merge: 24ef4bfff c7c0a52ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 11:58:54 2017 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 24ef4bfffbbe169a7d6fabc8e0544eb1c40cf2e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 11:58:11 2017 -0500
start of a script to change all of the double precision declarations
to the new c_real format. The only missing piece is that we need
to smartly add the "use" statement to each program scope.
Util/scripts/dpconvert.py
commit c7c0a52eed2abacbfd0ad211d8066e533a11f27a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 10:09:30 2017 -0500
update for release
CHANGES
commit f276231c64bf10e17ca6d1e4d647c4fd75472a8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 31 20:02:47 2016 -0500
update CHANGES
CHANGES
commit 98fd271e0298c121205cbb9a88483c1e34469056
Merge: ac1518a95 76fe2c02a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 31 18:44:48 2016 -0500
Merge branch 'development' into radmerge
commit 76fe2c02aacee942e66bccbc3813544e55596e18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 31 18:43:57 2016 -0500
this changeset puts the radiation flux limiter, lambda, inside qaux (#87)
* adds QLAMS component to meth_params
* rely on lambda coming in through qaux up through umeth.
* updates tracing routine to take qaux and not lambda
* updates the trans routines to get lambda from qaux
* NQAUX initialization now depends on the number of radiation groups, so it is initialized in Castro.cpp
* cmpflx now gets lam through qaux
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Castro_setup.cpp
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Radiation/RadSrc_nd/RadHydro_nd.f90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit ac1518a95e0b6678f4e4fa30d893d06610e6baa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 20:04:25 2016 -0500
get 3-d compiling
Source/Src_3d/Castro_3d.F90
Source/Src_3d/riemann_3d.F90
commit ba0d9306968afe85cb0f0cc8deeaf5ad5f919996
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 14:39:22 2016 -0500
almost done...
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/trans_3d.F90
commit ff49eca7ab86387945d7859dbc987bcc4935e016
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 14:10:38 2016 -0500
update the cmpflx interface
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/riemann_2d.F90
commit 60f67940906dcac8a4d742165f7677b6471a5634
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 13:38:35 2016 -0500
more compilation work
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/trans_2d.F90
commit aa586faebef7166d3dad952215d6f4dde940a7e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 12:35:00 2016 -0500
fix bounds of lam
Source/Src_1d/riemann_1d.F90
commit 036c59e16e40cc4bcf4e383835494f252715e909
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 12:27:59 2016 -0500
fix up NQAUX initialization
Source/Castro.cpp
Source/Castro_setup.cpp
Source/Radiation/RadSrc_nd/RadHydro_nd.f90
Source/Src_1d/riemann_1d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit b957281594433b427770edf76faa2031be19dac6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 11:00:11 2016 -0500
some compilation fixes
Source/Castro_F.H
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Src_nd/advection_util_nd.F90
commit ed7d367ab61875796aa7472479f70c2b6fef0e43
Merge: a11af064d e1de20e6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 10:48:48 2016 -0500
Merge branch 'development' into radmerge
commit e1de20e6e67ef8cc6ef952964d96352006ba57b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 09:52:30 2016 -0500
BS has a hard time integrating networks unless you make the tolerances
loose. This problem is enhanced by the change to integrate mass
fractions instead of molar fractions -- now the heavy species
have the same absolute tolerance as the light species, causing
difficulties. Switch to VODE which is more robust.
Exec/science/Detonation/GNUmakefile
commit a11af064dc4d7d5b576858a69135f0f506627fb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 30 09:52:30 2016 -0500
BS has a hard time integrating networks unless you make the tolerances
loose. This problem is enhanced by the change to integrate mass
fractions instead of molar fractions -- now the heavy species
have the same absolute tolerance as the light species, causing
difficulties. Switch to VODE which is more robust.
Exec/science/Detonation/GNUmakefile
commit 7542c86bdec16979e8ad8ace7f5da3f98fb5ac8d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 29 22:33:43 2016 -0800
migration step 8
Exec/Make.Castro
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/radiation_tests/Rad2Tshock/Castro_error.cpp
Exec/radiation_tests/RadThermalWave/Castro_error.cpp
Exec/unit_tests/test_react/main.cpp
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_error.cpp
Source/Castro_io.cpp
Source/Castro_react.cpp
Source/Castro_rotation.cpp
Source/Castro_setup.cpp
Source/Radiation/Castro_radiation.cpp
Source/Radiation/energy_diagnostics.cpp
Source/main.cpp
Util/ConvertCheckpoint/Embiggen.cpp
commit ac126fd932e24f102aa95fb318d812f2c2f698e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 29 22:19:08 2016 -0500
work on the trans routines
Source/Src_2d/trans_2d.F90
Source/Src_3d/trans_3d.F90
commit 95502bc5661b7cc54f9c73880c66cb688947fce4
Merge: c6aeb5f83 ce9ba27df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 29 15:26:05 2016 -0500
Merge branch 'development' into radmerge
commit c6aeb5f83932cda33f8739fe3daba4111935352a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 29 14:08:39 2016 -0500
update interfaces
Source/Src_3d/Castro_advection_3d.F90
commit ce9ba27df7eb5f035b1b4ef6ea1685a5ef569b57
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 29 14:01:46 2016 -0500
Fix an issue for the old refluxing method
Source/Castro_advance.cpp
commit a6fc505da77e2f78991946ae37b04e4cc18bc711
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 29 13:45:52 2016 -0500
update the trans routines (2-d) to get lambda from qaux
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/trans_2d.F90
commit 734689c91ce866d02d83428d9c0032b5d14c19da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 29 12:16:56 2016 -0500
update tracing routine to take qaux and not lambda
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_advection_3d.F90
commit caa06d5f4d7c2b208644cf5affb4618519bc22d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 29 11:00:26 2016 -0500
a little cleaning
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_advection_3d.F90
commit 27054c93aecef85f1199755d9aef00acc84a9023
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 29 05:27:29 2016 -0500
Generalize and correct the recent reflux fix
Source/Castro.H
Source/Castro_advance.cpp
commit 995abc39207816cca6b0db5fdf5cd2687dd55e76
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 28 19:08:31 2016 -0800
probinit --> amrex_probinit
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/StarGrav/Prob_1d.f90
Exec/gravity_tests/StarGrav/Prob_2d.f90
Exec/gravity_tests/StarGrav/Prob_3d.f90
Exec/gravity_tests/evrard_collapse/Prob_3d.f90
Exec/gravity_tests/hydrostatic_adjust/Prob_1d.f90
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/hydro_tests/HCBubble/Prob_3d.f90
Exec/hydro_tests/KH/Prob_nd.F90
Exec/hydro_tests/Noh/Prob_nd.F90
Exec/hydro_tests/RT/Prob_2d.f90
Exec/hydro_tests/RT/Prob_3d.f90
Exec/hydro_tests/RT_particles/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_1d.f90
Exec/hydro_tests/Sedov/Prob_2d.f90
Exec/hydro_tests/Sedov/Prob_3d.f90
Exec/hydro_tests/Sod/Prob_1d.f90
Exec/hydro_tests/Sod/Prob_2d.f90
Exec/hydro_tests/Sod/Prob_3d.f90
Exec/hydro_tests/Sod_stellar/Prob_1d.f90
Exec/hydro_tests/Sod_stellar/Prob_2d.f90
Exec/hydro_tests/Sod_stellar/Prob_3d.f90
Exec/hydro_tests/Vortices_LWAcoustics/Prob_2d.f90
Exec/hydro_tests/double_bubble/Prob_2d.f90
Exec/hydro_tests/gamma_law_bubble/Prob_2d.f90
Exec/hydro_tests/gresho_vortex/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_2d.f90
Exec/hydro_tests/oddeven/Prob_3d.f90
Exec/hydro_tests/reacting_bubble/Prob_2d.f90
Exec/hydro_tests/riemann_test_zone/Prob_2d.f90
Exec/hydro_tests/rotating_torus/Prob_nd.F90
Exec/hydro_tests/symmetry/Prob_1d.f90
Exec/hydro_tests/symmetry/Prob_2d.f90
Exec/hydro_tests/symmetry/Prob_3d.f90
Exec/hydro_tests/test_convect/Prob_2d.f90
Exec/hydro_tests/toy_convect/Prob_2d.f90
Exec/hydro_tests/toy_flame/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_1d.f90
Exec/radiation_tests/Rad2Tshock/Prob_2d.f90
Exec/radiation_tests/Rad2Tshock/Prob_3d.f90
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadShestakovBolstad/Prob_1d.f90
Exec/radiation_tests/RadSlope/Prob_1d.f90
Exec/radiation_tests/RadSphere/Prob_1d.f90
Exec/radiation_tests/RadSuOlson/Prob_1d.f90
Exec/radiation_tests/RadSuOlsonMG/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_1d.f90
Exec/radiation_tests/RadThermalWave/Prob_2d.f90
Exec/radiation_tests/RadThermalWave/Prob_3d.f90
Exec/science/Detonation/Prob_1d.f90
Exec/science/Detonation/Prob_2d.f90
Exec/science/bwp-rad/Prob_2d.f90
Exec/science/bwp-rad/Prob_3d.f90
Exec/science/bwp/Prob_2d.f90
Exec/science/convective_flame/Prob_2d.f90
Exec/science/convective_flame/Prob_3d.f90
Exec/science/flame_wave/Prob_2d.f90
Exec/science/xrb_mixed/Prob_2d.f90
Exec/unit_tests/diffusion_test/Prob_2d.f90
Source/Src_1d/Prob_1d.f90
Source/Src_2d/Prob_2d.f90
Source/Src_3d/Prob_3d.f90
Source/Src_nd/Prob_nd.F90
Util/ConvertCheckpoint/probinit.f90
commit 9c1e9bda9fb25cb6958f435df35cea7314aefa28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 22:03:12 2016 -0500
a little cleaner
Source/Src_3d/trans_3d.F90
commit f2da2e15cb65b0a8b5d2404e998495866554473e
Merge: 1d9c22ca6 9a871c6c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 21:32:13 2016 -0500
Merge branch 'development' into radmerge
commit c4da74f711c735bf098b5ce8c9b7064085e51b81
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 28 18:25:08 2016 -0800
rename to avoid confusion
Source/Radiation/HypreABec.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreMultiABec.H
Source/Radiation/HypreMultiABec.cpp
commit 9a871c6c008b21fd0a5d7f4185273c10b7ae8a7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 21:21:33 2016 -0500
we were using the wrong gamma (should be using gas, not rad) in
the tracing
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
commit 1d9c22ca61b6446b45f4d52e61d0396a0a81d8d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 20:50:30 2016 -0500
rely on lambda coming in through qaux up through umeth. We still
need to convert the trace, trans, and cmpflx routines
Source/Castro_hydro.cpp
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
commit 598e68a572cae7b6b31128cd512b139bb043745f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 20:32:49 2016 -0500
QLAM -> QLAMS cause there are ngroups components
Source/Src_nd/Castro_nd.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 110bb078dce0ee06efc43d69644df96f5b33ed34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 20:13:50 2016 -0500
add QLAM
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 9164ee3dba58b1ce3f1d8325134af913af2b3ab0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 18:29:47 2016 -0500
expand the diffusion docs
Docs/Diffusion/CastroDiffusion.tex
commit bf56c1a02cd94bececdc47cab064445a7b98cd81
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 28 12:26:36 2016 -0800
fix a bug by using the correct distribution map
Source/Castro.cpp
commit e2509ee15918e0f4d04086b47cdb5ce1d1e8bfe9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 28 10:43:47 2016 -0800
fix new bug
Source/Gravity.cpp
commit 7da26bed05d9697173b3ab55b3a7db0e2990d1d0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 28 08:02:29 2016 -0800
migration step 6
Source/Castro.H
Source/Castro.cpp
Source/CastroBld.cpp
Source/CastroParticles.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_gravity.cpp
Source/Castro_hydro.cpp
Source/Castro_io.cpp
Source/Castro_react.cpp
Source/Castro_sources.cpp
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Radiation/HypreABec.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.H
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/MGFLD.cpp
Source/Radiation/MGFLDRadSolver.cpp
Source/Radiation/MGRadBndry.H
Source/Radiation/MGRadBndry.cpp
Source/Radiation/NGBndry.H
Source/Radiation/RadBndry.H
Source/Radiation/RadBndry.cpp
Source/Radiation/RadSolve.cpp
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
Source/Radiation/SGRadSolver.cpp
Source/Radiation/_interpbndry/RadBndryData.H
Source/Radiation/_interpbndry/RadBndryData.cpp
Source/Radiation/_interpbndry/RadInterpBndryData.H
Source/Radiation/_interpbndry/RadInterpBndryData.cpp
Util/ConvertCheckpoint/Embiggen.cpp
Util/plot1d/XGraph1d.cpp
commit c21ab5a8254207e21294d21d9184ea3716f863ba
Merge: a3f67602b 7ea5fd219
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 26 21:51:44 2016 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit a3f67602b5a13c483e88480e6b3d7a82bc4b7387
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 26 21:50:29 2016 -0500
Fix a couple issues with the new reflux algorithm
First, the scaling wasn't correct when the refinement varied across levels;
second, the update_sources_after_reflux option was broken because it modified
the fluxes MultiFAB but the code was assuming it was still unchanged for later
refluxes.
Source/Castro.cpp
Source/Castro_advance.cpp
commit 7ea5fd2196f25436005d1559b3666250720f242d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 26 14:08:42 2016 -0500
add Cori note from Brian
Docs/ManagingJobs/managingjobs.tex
commit 7721bbb27bb427dd634fdbb1def45fef9862bf6b
Merge: bd42fbd88 4bd3add35
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 22 10:04:00 2016 -0800
Merge branch 'development' into amrex-development
Conflicts:
Source/Gravity.cpp
commit ebb3deabb7d8295279e8cb9ba8b058bd5cc618ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 22 09:00:39 2016 -0500
update to bind(C) to get this compiling
Exec/hydro_tests/toy_flame/Problem.f90
Exec/hydro_tests/toy_flame/Problem_F.H
commit bd42fbd88cfc9f8924de718dd1eadc2ddf23b322
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 21 22:03:02 2016 -0800
migration step 5
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/hydro_tests/toy_convect/sum_integrated_quantities.cpp
Exec/hydro_tests/toy_flame/Prob.cpp
Exec/hydro_tests/toy_flame/sum_integrated_quantities.cpp
Exec/radiation_tests/Rad2Tshock/Castro_error.cpp
Exec/radiation_tests/RadThermalWave/Castro_error.cpp
Exec/science/xrb_mixed/sum_integrated_quantities.cpp
Exec/unit_tests/test_react/main.cpp
Source/Castro.H
Source/Castro.cpp
Source/CastroBld.cpp
Source/CastroParticles.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_error.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_hydro.cpp
Source/Castro_io.cpp
Source/Castro_pointmass.cpp
Source/Castro_react.cpp
Source/Castro_rotation.cpp
Source/Castro_setup.cpp
Source/Castro_sources.cpp
Source/Castro_sponge.cpp
Source/Diffusion.H
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Radiation/Castro_radiation.cpp
Source/Radiation/HypreABec.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreExtMultiABec.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.H
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/LHH.H
Source/Radiation/MGFLD.cpp
Source/Radiation/MGFLDRadSolver.cpp
Source/Radiation/MGRadBndry.H
Source/Radiation/MGRadBndry.cpp
Source/Radiation/NGBndry.H
Source/Radiation/RadBndry.H
Source/Radiation/RadBndry.cpp
Source/Radiation/RadMultiGroup.cpp
Source/Radiation/RadPlotvar.cpp
Source/Radiation/RadSolve.H
Source/Radiation/RadSolve.cpp
Source/Radiation/RadSrc_1d/DumpModel1d.cpp
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
Source/Radiation/SGFLD.cpp
Source/Radiation/SGRadSolver.cpp
Source/Radiation/_interpbndry/RadBndryData.H
Source/Radiation/_interpbndry/RadBndryData.cpp
Source/Radiation/_interpbndry/RadInterpBndryData.H
Source/Radiation/_interpbndry/RadInterpBndryData.cpp
Source/Radiation/energy_diagnostics.cpp
Source/Src_nd/parmparse_fi.cpp
Source/main.cpp
Source/sum_integrated_quantities.cpp
Source/sum_utils.cpp
Util/ConvertCheckpoint/Embiggen.cpp
Util/plot1d/XGraph1d.H
Util/plot1d/XGraph1d.cpp
commit 58deac1be19e47bb10da066e29d9de7a704e5e46
Merge: 79ead0dae 90066f64a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 21:02:19 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 79ead0dae7c2da20294273298845c631d2b4d017
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 21:01:49 2016 -0500
switch problem_restart and problem_checkpoint to bind(C)
closes #85
Source/Castro_io.cpp
Source/Problem_F.H
Source/Src_nd/Problem.f90
commit 90066f64a401dc4ca9cd867f4253ec453bf1a24c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 20:54:11 2016 -0500
no need for a Problem_F.H here
Exec/hydro_tests/test_convect/Problem_F.H
commit ba84ded0fe0a5fc577a2dda3bbe488a7ab26c4b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 19:08:31 2016 -0500
use all vel components in the KE computation (for consistency)
Source/Src_1d/Castro_advection_1d.F90
commit 5e1f7684e4f6cb818a79b65bf52ca6df39a21a86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 19:00:21 2016 -0500
pass qaux in directly to riemann
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
commit 12fed01fd057b87f28896d1e2a6fa5b02dcd233b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 21 15:51:46 2016 -0800
migration step 4
Exec/Make.Castro
Util/ConvertCheckpoint/GNUmakefile
commit 8945ac60b055cf839528586a4fcaa5cc7583460f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 17:55:02 2016 -0500
instead of passing multiple thermo quantities into cmpflx, pass qaux
directly.
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/riemann_3d.F90
commit 5970240348ab1966478660d53889046d7b93fbdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 17:35:08 2016 -0500
QVAR -> NQ
Source/Src_3d/Castro_advection_3d.F90
commit 1c390d126c2114d9a8f759b26b0eaa5c1abd2ca1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 21 13:23:50 2016 -0800
migration: fix diffusion
Source/Castro_diffusion.cpp
Source/Diffusion.cpp
commit 70d2f73e7593f8806c6cb1e239dc2651b24ac8e1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 21 11:24:08 2016 -0800
migration step 3
Exec/Make.Castro
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/hydrostatic_adjust/bc_fill_1d.F90
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/hydro_tests/Noh/bc_fill_nd.F90
Exec/hydro_tests/RT_particles/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_1d.F90
Exec/hydro_tests/Sedov/bc_fill_2d.F90
Exec/hydro_tests/Sedov/bc_fill_3d.F90
Exec/hydro_tests/double_bubble/bc_fill_2d.F90
Exec/hydro_tests/gamma_law_bubble/bc_fill_2d.F90
Exec/hydro_tests/reacting_bubble/bc_fill_2d.F90
Exec/hydro_tests/test_convect/bc_fill_2d.F90
Exec/hydro_tests/toy_convect/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/Castro_error.cpp
Exec/radiation_tests/Rad2Tshock/bc_fill_1d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_2d.F90
Exec/radiation_tests/Rad2Tshock/bc_fill_3d.F90
Exec/radiation_tests/RadThermalWave/Castro_error.cpp
Exec/science/convective_flame/bc_fill_2d.F90
Exec/science/convective_flame/bc_fill_3d.F90
Exec/unit_tests/test_react/main.cpp
Source/Castro.H
Source/Castro.cpp
Source/CastroBld.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_error.cpp
Source/Castro_error_F.H
Source/Castro_io.cpp
Source/Castro_react.cpp
Source/Castro_rotation.cpp
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Diffusion.H
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Radiation/Castro_radiation.cpp
Source/Radiation/HypreABec.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/MGFLDRadSolver.cpp
Source/Radiation/MGRadBndry.cpp
Source/Radiation/NGBndry.H
Source/Radiation/RAD_F.H
Source/Radiation/RadBndry.cpp
Source/Radiation/RadMultiGroup.cpp
Source/Radiation/RadSolve.H
Source/Radiation/RadSolve.cpp
Source/Radiation/RadSrc_1d/DumpModel1d.cpp
Source/Radiation/RadSrc_1d/HABEC_1D.F90
Source/Radiation/RadSrc_1d/RAD_1D.F90
Source/Radiation/RadSrc_2d/HABEC_2D.F90
Source/Radiation/RadSrc_2d/RAD_2D.F90
Source/Radiation/RadSrc_3d/HABEC_3D.F90
Source/Radiation/RadSrc_3d/RAD_3D.F90
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
Source/Radiation/SGRadSolver.cpp
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_1D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_2D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_3D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/Radiation/_interpbndry/RadBndryData.H
Source/Radiation/_interpbndry/RadBndryData.cpp
Source/Radiation/_interpbndry/RadBoundCond.H
Source/Radiation/_interpbndry/RadInterpBndryData.H
Source/Radiation/_interpbndry/RadInterpBndryData.cpp
Source/Radiation/energy_diagnostics.cpp
Source/Src_1d/bc_fill_1d.F90
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
Source/Src_3d/bc_fill_3d.F90
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/filcc_nd.F90
Source/Src_nd/parmparse_fi.cpp
Source/main.cpp
Util/ConvertCheckpoint/Embiggen.cpp
Util/plot1d/Misc.H
Util/plot1d/XGraph1d.H
Util/plot1d/XGraph1d.cpp
commit e5a22a05682cd93755ce439059c6bab6b0a04575
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 21 10:39:29 2016 -0800
some BoxLib:: --> amrex::
Source/Castro.cpp
Source/Castro_gravity.cpp
Source/Diffusion.cpp
Source/Gravity.cpp
commit 17248b2b0264535d774a60a09e1796e155a5cbac
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 21 09:48:59 2016 -0800
migration step2: radiation
Source/Castro_io.cpp
Source/Radiation/HypreABec.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreExtMultiABec.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.H
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/MGFLDRadSolver.cpp
Source/Radiation/MGRadBndry.cpp
Source/Radiation/NGBndry.H
Source/Radiation/RadBndry.cpp
Source/Radiation/RadPlotvar.cpp
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
Source/Radiation/SGRadSolver.cpp
Source/Radiation/_interpbndry/RadBndryData.H
Source/Radiation/_interpbndry/RadBndryData.cpp
Source/Radiation/_interpbndry/RadInterpBndryData.cpp
commit 2f89c3990bbe46861f361c0829c2bdd22d83bede
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 10:23:07 2016 -0500
fix compilation
Source/Src_3d/Castro_advection_3d.F90
commit d1fa69b45696781ab3eb23d8673fb24aeb397efb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 08:36:55 2016 -0500
merge the radiation umeth and consup
Source/Radiation/RadSrc_3d/Make.package
Source/Radiation/RadSrc_3d/RadHydro_3d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Make.package
commit c519d8716d7d9c11f5c5c662479410169b2acf08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 08:27:33 2016 -0500
pure hydro works with the merge
Source/Radiation/RadSrc_3d/RadHydro_3d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
commit 681c79eddc6b06ff3c96ec95462a1c23609b3ba0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 21 06:54:16 2016 -0500
finish first cut at umeth_3d sync
Source/Src_3d/Castro_advection_3d.F90
commit ea61590a71bfb9f2ab366fa96dc815cfd25bce6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 20 21:53:06 2016 -0500
update CHANGES
CHANGES
commit 4d5c70bfe081e01a101b58933ccf76c4dd032d28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 20 21:52:11 2016 -0500
save my spot in merging the umeth_3d routines
Source/Radiation/RadSrc_3d/RadHydro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
commit 8746e1a417d977c9819e1dbd8e8cc1b48a18b5f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 20 11:49:48 2016 -0500
fix some indices
Source/Src_1d/Castro_advection_1d.F90
commit 78b8fb4f4e4ffc0f1e2de764ed6cf27f2120a88d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 20 09:18:54 2016 -0500
add in missing Erscale
Source/Src_2d/Castro_advection_2d.F90
commit d8fe22c0f8e3f2229196c4e8d74225aa18fc8f14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 19 22:23:42 2016 -0500
fix some dimensioning
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
commit 69fdd5576ec0cf3debc6e374dc8069aa6d10cb4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 19 16:05:50 2016 -0500
get the 2-d consup and umeth rad stuff merged
Source/Radiation/RadSrc_2d/Make.package
Source/Radiation/RadSrc_2d/RadHydro_2d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Make.package
commit 2bfa10f82696a62e5d7bac83b3a44ded7a66546f
Merge: 34639184a e28397c59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 19 10:27:49 2016 -0500
Merge branch 'radmerge' of ssh://github.com/BoxLib-Codes/Castro into radmerge
commit 624e19838d8237633424ae6ff574980e979dfdae
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Dec 16 10:27:37 2016 -0800
AMReX:: --> amrex::
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
commit e28397c59abb8873786ee95a550f359c2cea5a97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 15 20:09:47 2016 -0500
sync umeth up for rad / pure hydro
Source/Radiation/RadSrc_2d/RadHydro_2d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_advection_2d.F90
commit c34bd01c0d3a7ddc9630ee94e00c71c8b8c52a23
Merge: 9aa51143f 4bd3add35
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 15 18:48:44 2016 -0500
Merge branch 'development' into radmerge
commit baf1d88e2e0268700b7d9bdaf28ef77f345d0147
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 15 13:48:54 2016 -0800
migration step 2: non-radiation hydro with gravity, reaction and diffusion
Source/Castro.H
Source/Castro.cpp
Source/Castro_diffusion.cpp
Source/Castro_gravity.cpp
Source/Castro_react.cpp
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 4bd3add356b2bfc37b45c0d4c905e1197347c7a8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 15 12:46:03 2016 -0800
fix more index bug
Source/Gravity.cpp
commit c2c05459148e971491647042af8b440801194d3a
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date: Thu Dec 15 12:32:21 2016 -0800
fix index bug
Source/Gravity.cpp
commit 39d11c419ec877204ed359bde837e362391cee47
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 15 09:45:35 2016 -0800
migration step 2: pure hydro
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_hydro.cpp
Source/Castro_rotation.cpp
Source/Castro_sources.cpp
Source/Castro_sponge.cpp
Source/Diffusion.H
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 7f5c381aa116409e75458c814cc43ebfc5b5967c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 23:25:28 2016 -0500
start of some notes explaining what the different routines in radiation do
this will eventually be part of the docs
Source/Radiation/notes.txt
commit 92fed5f043c619e96cc72ec799b642bf268af596
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 22:12:45 2016 -0500
add a note about what HABEC means
Source/Radiation/RadSrc_1d/HABEC_1D.F90
Source/Radiation/RadSrc_2d/HABEC_2D.F90
Source/Radiation/RadSrc_3d/HABEC_3D.F90
commit e223919cee637211066ac0bb36508996d7edd18e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 14 12:22:39 2016 -0800
migration step 1
Diagnostics/DustCollapse/GNUmakefile
Diagnostics/Sedov/GNUmakefile
Exec/Make.Castro
Exec/radiation_tests/RadSphere/Tools/GNUmakefile
Util/ConvertCheckpoint/GNUmakefile
Util/exact_riemann/GNUmakefile
commit 34639184af714ad29549c3d3dc62e3b8e249223f
Merge: 9aa51143f 056d378b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 14:34:33 2016 -0500
Merge branch 'development' into radmerge
commit 056d378b62b0bb755676f925906d85c44d07aae4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 14:15:51 2016 -0500
for regression testing
Exec/radiation_tests/RadBreakout/inputs.1d.test
commit 561501bd33038ea2459097ed288b6f08bc57f07b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 14:03:14 2016 -0500
remove the implementation of filtering in 1-d, since the only
problem that uses it is RadBreakout, and it already has this
routine as a custom version in it. This way, this stays as
a stub that problems can override
Source/Radiation/RadSrc_1d/filt_prim_1d.f90
Source/Radiation/RadSrc_2d/filt_prim_2d.f90
Source/Radiation/RadSrc_3d/filt_prim_3d.f90
commit 9aa51143f5d26220cb2a538aec46947037a25e3d
Merge: 8daac9269 cd5701f68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 13:12:54 2016 -0500
Merge branch 'development' into radmerge
commit cd5701f686b43c90e40dfedddcbfcb769547a32d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 13:10:50 2016 -0500
this problem is unsupported -- we don't have access to the microphysics
that this requires, so we cannot compile or test it. It shall live
on in git's memory
Exec/radiation_tests/RadCoreCollapse/Castro_error.cpp
Exec/radiation_tests/RadCoreCollapse/GNUmakefile
Exec/radiation_tests/RadCoreCollapse/Make.package
Exec/radiation_tests/RadCoreCollapse/Prob_1d.f90
Exec/radiation_tests/RadCoreCollapse/Prob_2d.f90
Exec/radiation_tests/RadCoreCollapse/Prob_3d.f90
Exec/radiation_tests/RadCoreCollapse/Tagging_nd.f90
Exec/radiation_tests/RadCoreCollapse/bc_fill_2d.F90
Exec/radiation_tests/RadCoreCollapse/bc_fill_3d.F90
Exec/radiation_tests/RadCoreCollapse/filt_prim_1d.f90
Exec/radiation_tests/RadCoreCollapse/inputs.1d.mgfld
Exec/radiation_tests/RadCoreCollapse/inputs.2d.mgfld
Exec/radiation_tests/RadCoreCollapse/inputs.3d.mgfld
Exec/radiation_tests/RadCoreCollapse/modelInput
Exec/radiation_tests/RadCoreCollapse/probdata.f90
Exec/radiation_tests/RadCoreCollapse/probin.1d.mgfld
Exec/radiation_tests/RadCoreCollapse/probin.2d.mgfld
Exec/radiation_tests/RadCoreCollapse/probin.3d.mgfld
commit 8daac92698d171c420ac5c188ad04526f69fce2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 13:04:51 2016 -0500
remove the radiation specific umeth and consup routines in 1-d
Source/Radiation/RadSrc_1d/Make.package
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
Source/Radiation/RadSrc_2d/RadHydro_2d.F90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/Make.package
commit a9559a05739d03286935f68c8b77d4cc4216cfe2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 10:59:20 2016 -0500
get this working again
Exec/radiation_tests/RadBreakout/Prob_1d.f90
Exec/radiation_tests/RadBreakout/filt_prim_1d.f90
Exec/radiation_tests/RadBreakout/inputs.1d
Exec/radiation_tests/RadBreakout/probdata.f90
Exec/radiation_tests/RadBreakout/probin.1d.87a.23
commit 1a6129827a68c61a99c113b8aae2bea7bc8ae3f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 14 10:20:13 2016 -0500
fix compilation issue
Source/Src_1d/Castro_advection_1d.F90
commit 8717d97a1f7bf6496c2bc8d1ff15b27a7e9acd6e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 14 02:30:18 2016 -0500
Add a missing module variable
Source/Src_3d/Castro_advection_3d.F90
commit 7216011fae78cdae6a29c9239ef75e53fcfcc1d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 14 01:02:55 2016 -0500
Fix a bug for the custom weighting
Source/Castro_react.cpp
commit 5da56acfd915202fc2304cd1132d3d9b49d59a0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 19:34:36 2016 -0500
remove unused variable
Source/Src_3d/Castro_3d.F90
commit 95f400314f280f09d1897cefbc917ff065756977
Merge: b83d343a9 4c6e6781c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 19:30:08 2016 -0500
Merge pull request #80 from BoxLib-Codes/radmerge
work on syncing up the consup routines
commit 4c6e6781c85c591818861234b4e990d5fe6455a3
Merge: 625f9f2e1 b83d343a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 18:25:19 2016 -0500
Merge branch 'development' into radmerge
commit b83d343a999663d4295c3ff2a3528270ea91a3af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 18:22:53 2016 -0500
use NQ to simplify
Source/Src_nd/advection_util_nd.F90
commit 625f9f2e118cbac5d239401181725717a28472cf
Merge: abcf182d5 1620b6ccf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 15:11:42 2016 -0500
Merge branch 'development' into radmerge
commit abcf182d5fb510555d5b7eaba80fa92d02582c10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 14:23:47 2016 -0500
fix compilation
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
commit 61c384716d057b16da88d01431f9e2db03fbb7f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 14:16:55 2016 -0500
finish the sync of consup
Source/Radiation/RadSrc_2d/RadHydro_2d.F90
Source/Radiation/RadSrc_3d/RadHydro_3d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Castro_advection_3d.F90
commit d8eafc4ec1ffd8a9939387076ff31df1be04dae9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 13:06:22 2016 -0500
fix compilation
Source/Src_2d/Castro_advection_2d.F90
commit b92e394964e047a8aab0b767d22c1b9bf583a753
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 13 12:39:17 2016 -0500
more consup merging
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
Source/Radiation/RadSrc_2d/RadHydro_2d.F90
Source/Src_1d/Castro_advection_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
commit 1620b6ccf24c2f34a0596bdc5acdfab3832d37ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 21:07:25 2016 -0500
syncing up
Util/job_scripts/edison/edison.MPI.OMP.slurm
Util/job_scripts/edison/edison.MPI.slurm
commit 5159c0905fd1b6c342b0326efb188a746ddfffda
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 20:16:07 2016 -0500
add issue tracking
CHANGES
commit 0cc25d972c1e3779a13376567a63b32121c88805
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 17:34:34 2016 -0500
rename to allow preprocessing
Source/Radiation/RadSrc_2d/Make.package
Source/Radiation/RadSrc_2d/RadHydro_2d.F90
Source/Radiation/RadSrc_3d/Make.package
Source/Radiation/RadSrc_3d/RadHydro_3d.F90
commit 602d471e348ce6d9327d361aaea98d7386f9be48
Merge: aa6006979 26d145630
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 15:35:21 2016 -0500
Merge branch 'development' into radmerge
commit 26d1456309f45dd278578fcd82906e17d90b7a1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 14:37:11 2016 -0500
get the compiler version output into job_info once again
Exec/Make.Castro
Source/Castro_io.cpp
commit aa60069799ef074e7eac5c42a1cc97b6b66aa28e
Merge: feaeb900b baa79b822
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 10:30:05 2016 -0500
Merge branch 'development' into radmerge
commit baa79b822c877a9986d6c682ac0f47961667b8b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 10:29:46 2016 -0500
sync up with minor release
CHANGES
commit f9aaf3ece5b0625ffa4d82e49fd437b153364c51
Merge: 25ca1dfbc cdefa0b63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 10:29:32 2016 -0500
Merge branch 'master' into development
commit cdefa0b63d8dad26e1c1712e98fb737d046929f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 10:28:18 2016 -0500
update for intermediate release
CHANGES
commit fe581ff8746f25b739efeca0211e6c9e6957d800
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 16:58:20 2016 -0500
initialize QRADVAR after restart. Closes #76
Source/Castro.cpp
commit 7ae0331a42f38d263e4e4075135f39cd601ef5a6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Dec 11 21:24:47 2016 -0800
pass grids into radiation restart because at that time of restart grids have not been stored in Amr
Source/Castro_io.cpp
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
commit feaeb900b23bcb90651cfaa36f7ff5ca68a532a9
Merge: 4d9b26285 25ca1dfbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 10:18:34 2016 -0500
Merge branch 'development' into radmerge
commit 25ca1dfbc1a74dbf35eecc9f43485bb8fa0109cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 09:41:04 2016 -0500
make Max happy
CHANGES
commit a3525978b8753354b9e139a564766360268a9445
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 12 09:36:57 2016 -0500
add note about rad restart
CHANGES
commit 294872cc915ae9718da73bad18013120d72382c9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Dec 11 21:24:47 2016 -0800
pass grids into radiation restart because at that time of restart grids have not been stored in Amr
Source/Castro_io.cpp
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
commit 4d9b262851e3703e58f44e96c0c203a21b501643
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 11 18:38:26 2016 -0500
forgot to add the radiation pressure gradient
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
commit e4fb99a3ddea20fa87a48972310b96698ec19c87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 11 17:59:26 2016 -0500
scale radiation fluxes
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
commit 2915b75a1be634297056b5852bf340cd2e9d2c11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 11 17:49:25 2016 -0500
threadsafety fix
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
commit 1643aadf6d765f0a8e5aea72a70cb1cfd07cb900
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 11 15:55:47 2016 -0500
fix compilation
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
commit e654af2b8856d480078a67a894bd2aacd1d13142
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 11 15:23:13 2016 -0500
more work on merging
Source/Radiation/RadSrc_1d/Make.package
Source/Radiation/RadSrc_1d/RadHydro_1d.F90
commit ec571affc032e43dfd9ac0e56841d1a38b7a110a
Merge: 1f8e3d0ed e30143a51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 10 20:38:06 2016 -0500
Merge branch 'development' into radmerge
commit e30143a51d558b353757b03a2b3c0a0f7db9332d
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Fri Dec 9 21:44:21 2016 -0500
Escape underscore in _cpp_parameters.
Source/_cpp_parameters
commit 3c3a114d7ea65a2811f835498a0522d4c89e28eb
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Fri Dec 9 19:42:23 2016 -0500
Escape the underscore.
Docs/runtime_parameters/runtime_parameters.tex
commit 5ea26f2c14a69463747a063099ec75d4181180fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 20:46:56 2016 -0500
update parameters
Docs/runtime_parameters/runtime_parameters.tex
commit 1f8e3d0ed7bbdd6cae935def9b10a60d7e72d32a
Merge: 7ec7157fe 45807cdbd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 18:36:09 2016 -0500
Merge branch 'development' into radmerge
commit 7ec7157fe1a958800d100f2aab09f62717dba2f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 18:12:19 2016 -0500
start of work merging the consup and consup rad
Source/Radiation/RadSrc_1d/RadHydro_1d.f90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
commit 45807cdbda48732a183e2e02bab0f786cc1883d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 16:58:20 2016 -0500
initialize QRADVAR after restart. Closes #76
Source/Castro.cpp
commit b1160d6d4310f0394e36f51d21125ec9bb0a034f
Merge: 68e6a3eec 9cf06e885
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 14:37:55 2016 -0500
Merge pull request #75 from BoxLib-Codes/radmerge
add the shock variable stuff into 1-d to sync with 2- and 3-d.
commit 68e6a3eecedb73188fe8025d5056489619fe2545
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 14:32:30 2016 -0500
revert makefile that was accidentally changed
Exec/science/Detonation/GNUmakefile
commit 9cf06e88515fcccea494c1532577fcb800a8e062
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 12:57:40 2016 -0500
add the shock variable stuff into 1-d to sync with 2- and 3-d.
closes #72
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_advection_1d.F90
commit 551d71be0f965726df8d033f14244102f310ba42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 12:26:45 2016 -0500
add 1-d shock detection
Source/Src_1d/riemann_1d.F90
commit 980c744a6587cb2fc3cca7954b73a41a49398915
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 6 20:14:30 2016 -0500
more switches to bind(C)
Source/Radiation/MGFLD.cpp
Source/Radiation/RAD_F.H
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/SGFLD.cpp
commit e0886bfc755d13e756de7e5326c1d2d6986ef300
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 6 13:27:56 2016 -0500
eliminate all of the BL_FORT calls in Radiation.cpp in favor
of F2003 bind(C)
Source/Radiation/MGFLD.cpp
Source/Radiation/RAD_F.H
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_1d/filt_prim_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_2d/filt_prim_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/RadSrc_3d/filt_prim_3d.f90
Source/Radiation/RadSrc_nd/Rad_nd.f90
Source/Radiation/RadSrc_nd/fluxlimiter.f90
Source/Radiation/Radiation.cpp
Source/Radiation/SGFLD.cpp
commit d590b518b3d95c765626da1c8d75ce7b64c867ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 6 09:17:40 2016 -0500
update to reflect now static member variables
Source/Castro.cpp
commit c13be4223f05d1c4c6ca1fcdcaed85b507ca46da
Merge: dcaa47771 3b6c51922
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 6 09:12:40 2016 -0500
Merge branch 'development' into runparams
commit 3b6c51922308d08ad557a9e170050118d1ca1108
Merge: 919053728 3ed56cc7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 6 09:08:53 2016 -0500
Merge pull request #69 from BoxLib-Codes/radmerge
merge computeTemp from radiation to hydro
commit dcaa477713b52de02cf56ee965dd8e956c523202
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 21:35:43 2016 -0500
finish making the transport parameterizations scalars
Source/Radiation/MGFLD.cpp
Source/Radiation/SGFLD.cpp
commit 42a945ec1ea41ced7ec2d3f8ce3b051d7ec1769a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 21:09:17 2016 -0500
start working on making the various c_v and kappas scalars instead
of arrays of length 1. This is part of issue #42
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
commit 9190537288c8169d91ac5ecea1e0f76f1e2b7164
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 19:33:59 2016 -0500
simplify verbose output of parameters
Source/Radiation/Radiation.cpp
commit 3ed56cc7ff881c85c7ce94035a80d3b3029ea4c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 14:44:59 2016 -0500
fix compilation of SuOlsonMG
Source/Radiation/MGFLD.cpp
commit c02b3c39c34d33c689024b888e335addeae88d77
Merge: 0aa7e715e 843d47eca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 12:50:11 2016 -0500
Merge branch 'development' into radmerge
commit 843d47eca750033c79a8534e6f993d40c669cb5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 12:19:32 2016 -0500
fix typo in makefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
commit 0aa7e715e34c905523164d154f0b39bd4a1ad053
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 11:37:55 2016 -0500
add comment about change
CHANGES
commit 597ec0aa3993c398333e64205fe6dd4ab1e8632d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 10:45:39 2016 -0500
finish the computeTemp merge -- closes #64
Source/Castro.cpp
Source/Radiation/MGFLD.cpp
Source/Radiation/Radiation.H
commit 18dbfd1f70678a0bd112c40a7e55981a644d98f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 5 10:26:15 2016 -0500
save a snapshot of the computeTemp (issue #64) work.
Source/Castro.cpp
Source/Radiation/Castro_radiation.cpp
Source/Radiation/MGFLD.cpp
Source/Radiation/RAD_F.H
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
commit 5528fd51bd6ad65fe848d18bf9c18e369897a46a
Merge: 14007376e d69d556a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 21:55:33 2016 -0500
Merge branch 'development' into radmerge
commit d69d556a508c2e25ae874345d1ff9040da1d9790
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 21:35:03 2016 -0500
more simplificaiton
Util/job_scripts/edison/edison.MPI.slurm
commit 3178358150960c8413340be68212853bc395fec4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 18:03:35 2016 -0500
simplify the logic for finding the chk file to restart from by writing
a function. This has been tested a bit but needs further testing
through slurm
Util/job_scripts/edison/edison.MPI.slurm
commit 9d0ffc2020e75a03e83984cf20205515f3e8cfb3
Merge: 673c2aa01 49aaf5a55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 10:47:05 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 673c2aa0131d67f055f3c958fc2d3c3439407b1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 10:40:14 2016 -0500
add some notes about chainslurm
Docs/ManagingJobs/managingjobs.tex
commit 49aaf5a556338155de7ae2987ee76ff046bc5dfd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 4 07:20:38 2016 -0800
use --parsable to fix the job chaining for multiple jobs with slurm
Util/job_scripts/edison/chainslurm.sh
commit a2a6596071ecf6f09950c8eafc96134d03a4cbf9
Merge: 6851d6eac e491d3326
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 3 18:56:56 2016 -0800
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 6851d6eac13b363a8a08cd9f6cd7487450348688
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 3 18:56:41 2016 -0800
remove this util
Exec/science/flame_wave/hse_check.py
commit e491d33267df3171daf0cb1c50aa2aeb5398aa1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 3 21:36:21 2016 -0500
update some edison-specific Intel compiler info
Docs/ManagingJobs/managingjobs.tex
commit 9bcfb662d8e610acb1a3feae0c7eb0e7eb47bc65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 2 08:46:18 2016 -0500
don't need probdata
Source/Src_2d/bc_ext_fill_2d.F90
commit dbad3cc13d1b940b59d2ace8f16c6438cfbcdf87
Merge: aa9c0e21f c203e74ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 2 00:56:20 2016 -0500
Merge pull request #67 from BoxLib-Codes/hse_bc
Hse bc fixes in 2d
commit c203e74ab551ad6c2969fd0ea5600dc1d35d75b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 2 00:51:10 2016 -0500
fix the p_above when we are interpolating T
Source/Src_2d/bc_ext_fill_2d.F90
commit 770275563fa4de7d598b9af8d8fc32a4713d9fa9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 15:51:59 2016 -0500
restructure the HSE BC to make it safer at corners
Source/Src_2d/bc_ext_fill_2d.F90
commit aa9c0e21fb29fdb9c523d80706c8ca2bcf24c63a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 14:43:46 2016 -0500
stereoscopic spherical rendering FTW
Util/yt/vol-wd-spherical-stereo.py
commit 76be0575d99bf13878d6db2f3304321d1ec0bc60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 13:36:28 2016 -0500
fix the orientation -- not sure why this is needed
Util/yt/vol-wd-spherical.py
commit 8f17e0c8bd7209fc0567bb935171c01ff66e7f64
Merge: 94bec03db fd8f3689f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 09:26:56 2016 -0500
Merge branch 'master' into development
commit fd8f3689fc82c1b0c1be0e4a4234177dc6c4287c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 09:26:14 2016 -0500
update changes
CHANGES
commit 94bec03db1f69ade05a17d3ab106c02cc733cb68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 21:02:50 2016 -0500
switch some interfaces over to bind(C)
Source/Radiation/MGFLD.cpp
Source/Radiation/RAD_F.H
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
Source/Radiation/Radiation.cpp
commit 740d99aaf0c26d049e1f25d10c0024ef461f4c8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 16:15:00 2016 -0500
clean up the modules to prevent inheriting non-network stuff
Microphysics/networks/network.f90
commit b29086151eb4f9e867dce034c95d4ae6fe245288
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 16:05:14 2016 -0500
don't let us inherit nspec or naux through eos_module
Microphysics/EOS/eos_type.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.F90
Source/Src_3d/riemann_3d.F90
commit 6c84a034a2fd84396ca9eec46a416fd65f640d9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 12:56:53 2016 -0500
update clean_state
Docs/FlowChart/FlowChart.tex
commit 8509ca194ecc4061fcd41e474e0fd859562845ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 12:51:27 2016 -0500
include the fine level in the abs_eps calculation for solve_for_delta_phi
closes #60
Source/Gravity.cpp
commit 49198b120906256cfac4c1b7949c6d5e4bc08d07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 12:48:15 2016 -0500
work around a corner ghost cell problem (reports as issue #65).
Now it our starting state for integration is ZERO, then we interpolate
from the initial model and integrate from that. We should still understand
why the corner is a problem however.
Source/Src_2d/bc_ext_fill_2d.F90
commit b277c902ca1fd088a0cb7b85276c86d1b670dec5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 12:31:21 2016 -0500
more diagnostics
Source/Src_2d/bc_ext_fill_2d.F90
commit 22b05f2e0cde781ce3bd17f0a819fbfc800025f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 10:25:21 2016 -0500
some info about the conditions of the failure
Source/Src_2d/bc_ext_fill_2d.F90
commit 2045687ae4b7466fc71c99fde2d8791363e4773e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 09:11:35 2016 -0500
changes for the past month
CHANGES
commit a184b42f3e07368f4d343809bf53706664c71bc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 29 21:07:47 2016 -0500
sync up the clean_state functions -- in particular the computeTemp
bit
Source/Castro.cpp
commit 9420a164cf6caf9ad35d0f4bde3a96da87156dbf
Merge: ebefdf119 0241b41d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 29 15:11:40 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit ebefdf11957f4adf33b6fb0d62c4cae82bdfd427
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 29 15:11:29 2016 -0500
enable aion_inv
Microphysics/EOS/eos_type.f90
Microphysics/networks/network.f90
commit 0241b41d953a7d9b1b109accad0925e2182da171
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 29 13:54:39 2016 -0500
update to support branches and microphysics
Util/scripts/get_castro_date.sh
commit 08f12fb70d61e5f648dbff847d14893be1a2843e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 21:53:38 2016 -0500
better rounding
Exec/science/Detonation/inputs-det-x.SDC
commit 56c5089a456c9c4b83fc453d7c241c84dfb7f6fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 21:51:59 2016 -0500
bigger domain
Exec/science/Detonation/inputs-det-x.SDC
commit 07099e1f97ea749e1f137aa3bc9baab5ae3a2311
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 13:42:56 2016 -0500
add profiling info
Docs/FAQ/faq.tex
commit f70ad656de1e7a3191720ee565fee2ba80452fa6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 12:21:29 2016 -0500
fix index for SDC + radiation
Source/Castro_hydro.cpp
commit 214ca3c97b960d35a23fb873c1f188255d94c00d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 12:05:10 2016 -0500
decrease plot frequency
Exec/science/Detonation/inputs-det-x.SDC
commit 86152cc854685a13cd31263350f0dc8b359636e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 11:52:53 2016 -0500
fix compilation -- the BaseFab copy of the fluxes for SDC was missing
arguments
Source/Castro_hydro.cpp
commit 7185d6ecefd309fad108ec8464942d2ba348390b
Merge: 027cf7d8f 68e4a3104
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 11:51:16 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 027cf7d8fa84f243ededf39cffdc65176a349b63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 11:51:02 2016 -0500
add SDC inputs, use a numerical Jacobian
Exec/science/Detonation/inputs-det-x.SDC
Exec/science/Detonation/probin-det-x
commit 68e4a310466ee87cce816cd33badf3df9eedb14c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 11:28:50 2016 -0500
comment out a radiation part with SDC
Source/Castro_hydro.cpp
commit 8943f82641bd58de1fe83d10c7992465b61e5a18
Merge: a61bea4c3 6b60ae721
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 27 17:07:53 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit a61bea4c33ad9a02296a3224c9221dd23edfbbf2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 27 17:07:42 2016 -0500
add a note about "make help"
Docs/FAQ/faq.tex
commit 6b60ae7217f93010f2e1798be1667575ed67817b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 27 14:25:15 2016 -0500
Strip out remaining levelset code
Exec/Make.Castro
Source/Castro_error_F.H
commit e1490a593bc24774b18c335d50d10ffe0beacaf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 27 14:15:16 2016 -0500
add a readme
Util/yt/README.md
commit cd1af032dfa41195e5510de4b4ed95204b305555
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 27 13:03:31 2016 -0500
remove some remnants of levelsets
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_error.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
commit 607e26e26976555da85fa58f51c0f995c337604e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 27 11:30:01 2016 -0500
Simplify with loop over state types
Source/Castro.cpp
commit 70a0691c4e23b4a02a9a1d391529b59342a30e8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 27 11:27:18 2016 -0500
Fill ghost zones when fillpatching into new level from old
Fixes #62
Source/Castro.cpp
commit 1c6b6c123e8420ae13d7a813be7bc22e9c848006
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 26 21:37:11 2016 -0500
Use clean_state after burn for consistency
Source/Castro_react.cpp
Source/Src_nd/React_nd.F90
commit 548a26b183d5b8f70a154f533baed7a7ea558601
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Nov 26 17:14:01 2016 -0800
remove duplicated include locations
Exec/Make.Castro
commit dd14bba9b3ec423d4b0538a1fec15ab2b93b8033
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 26 19:10:57 2016 -0500
remove references to FCOMP
Docs/GettingStarted/CastroGettingStarted.tex
Docs/Radiation/CastroRadiation.tex
commit 7a245678c7a6bc73e81f6408d82408b1244a90d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 26 14:03:54 2016 -0500
Sync up computation of 1D numpts after restart
Source/Castro.cpp
commit ad293c720bbb1cc7ecfddfb0d81ae9c79d2f3790
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 26 01:37:16 2016 -0500
Get fluxes MF correct for SDC
Source/Castro_hydro.cpp
commit 783c6e5a4c5568b7484c19c839c59f7662575d5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 26 01:21:18 2016 -0500
Don't attempt retry iterations in SDC
Source/Castro_advance.cpp
commit a8a64f33a70a239f3ee60cffc26cf113d29c1f19
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 25 23:46:18 2016 -0500
Use ghost zones in computeTemp
Source/Castro.cpp
commit b2832ea3b721251bbefcc296e90289dd62fc2c91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 25 20:00:32 2016 -0500
simplify the build system according to the new BoxLib style
(no FCOMP)
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/evrard_collapse/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/gravity_tests/uniform_cube_sphere/GNUmakefile
Exec/hydro_tests/HCBubble/GNUmakefile
Exec/hydro_tests/KH/GNUmakefile
Exec/hydro_tests/Noh/GNUmakefile
Exec/hydro_tests/RT/GNUmakefile
Exec/hydro_tests/RT_particles/GNUmakefile
Exec/hydro_tests/Sedov/GNUmakefile
Exec/hydro_tests/Sod/GNUmakefile
Exec/hydro_tests/Sod_stellar/GNUmakefile
Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile
Exec/hydro_tests/double_bubble/GNUmakefile
Exec/hydro_tests/gamma_law_bubble/GNUmakefile
Exec/hydro_tests/gresho_vortex/GNUmakefile
Exec/hydro_tests/oddeven/GNUmakefile
Exec/hydro_tests/reacting_bubble/GNUmakefile
Exec/hydro_tests/riemann_test_zone/GNUmakefile
Exec/hydro_tests/rotating_torus/GNUmakefile
Exec/hydro_tests/symmetry/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/hydro_tests/toy_flame/GNUmakefile
Exec/radiation_tests/Rad2Tshock/GNUmakefile
Exec/radiation_tests/RadBreakout/GNUmakefile
Exec/radiation_tests/RadCoreCollapse/GNUmakefile
Exec/radiation_tests/RadShestakovBolstad/GNUmakefile
Exec/radiation_tests/RadSlope/GNUmakefile
Exec/radiation_tests/RadSphere/GNUmakefile
Exec/radiation_tests/RadSuOlson/GNUmakefile
Exec/radiation_tests/RadSuOlsonMG/GNUmakefile
Exec/radiation_tests/RadThermalWave/GNUmakefile
Exec/science/Detonation/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/bwp/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/unit_tests/diffusion_test/GNUmakefile
Exec/unit_tests/test_react/GNUmakefile
commit ff129e7c617b4ee369c633b86e1320b63a8b19ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 25 19:47:12 2016 -0500
some notes on the updates to BoxLib
CHANGES
commit 927e3327079f04b6562a54a9624eb441ac248a8c
Merge: 5bbd064a0 862ab80e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 25 19:43:47 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 5bbd064a0b483ae4e3afb8564370ad063e227e2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 25 19:43:18 2016 -0500
add notes about PGI + GCC support
Docs/ManagingJobs/managingjobs.tex
commit 862ab80e25d884641557228a972f2e115d7604f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 25 17:56:39 2016 -0500
clean_state now calls computeTemp
Source/Castro.cpp
commit af6370b84c211133226381216805dc6d353f3414
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 22 19:15:55 2016 -0500
spherical rendering for 360 degree youtube
Util/yt/vol-wd-spherical.py
commit b66f51d1729823b9ed91bb0229b07c75ee0a2c43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 22 19:07:57 2016 -0500
update to the new C++ 11 interface for array
Source/Diffusion.cpp
commit c56a9d7220138be1c7293a6aa778c95b879e739c
Merge: 2c762ff18 83b122829
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 22 11:17:52 2016 -0800
Merge branch 'development' into experimental
commit 83b122829f47a51518f7a971e91b7775ca6178e1
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Mon Nov 21 18:10:08 2016 -0500
Changes in inputs_2d.test to be more similar to the just hydro inputs and also should not fail running. probin also changed accordingly, and it is the same as the probin.dens_sponge file I had
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_2d.test
Exec/science/bwp-rad/probin
Exec/science/bwp-rad/probin.dens_sponge
commit ad7011e7aa71a53f6803809d321c647449b4c21e
Merge: 10a10a4c3 693df04ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 19 11:02:52 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 10a10a4c3ab57fa583268692bfa67a14a34aaa62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 19 11:02:47 2016 -0500
comments
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Src_nd/React_nd.F90
commit 693df04ffa640232a45938b219a8426a892e839c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 18 13:09:00 2016 -0500
a little more integration strategy
Docs/FlowChart/FlowChart.tex
commit 97d0f436f6b48aa6e47f55d54f0f058a3bd64f18
Merge: 02f07caba 0b2840cb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 18 12:34:11 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 02f07cabaf163ed475e53862f164e626593f6845
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 18 12:33:45 2016 -0500
make signs conform to the SDC notes. No changes expected
Source/Castro_react.cpp
Source/Castro_sources.cpp
Source/Src_nd/React_nd.F90
commit 0b2840cb6f65b58851fd5d1ff3a6ca1e956b6817
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 18 11:28:28 2016 -0500
Incorporate Jacobian into default burn weighting
Source/Src_nd/React_nd.F90
commit 5e9d8d70ec6c82683659dac19e3b3e853b37a3b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 18 11:15:07 2016 -0500
Only trigger retry if strictly violating CFL
Source/Src_nd/timestep.F90
commit 7947b7e2aed5a392f6b7552ed364e1ae75cb4c45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 17 21:26:10 2016 -0500
fix formatting
Docs/Software/CastroSoftware.tex
commit 7ed0d9e08e13df8809fd36d31369deb779c40a0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 17 21:20:27 2016 -0500
clarify what hydro_source loks like
Docs/Software/CastroSoftware.tex
commit 839891216b0b49753a1cf626b024d1a78770ecb1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 17 11:22:28 2016 -0500
Fix error string
Source/Castro_hydro.cpp
commit 4239b3d37d54b9b5f89f1e072357bd8324e65e73
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 16 01:21:26 2016 -0500
Allow final checkpoint/plotfile to be disabled
Source/main.cpp
commit 54982c08e035a05c38d06a8764c6703180b1a356
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Tue Nov 15 14:11:21 2016 -0800
updated the initial model, inputs and probin sponge parameters that have been using for the runs.
Exec/science/bwp-rad/SolarLike_0.2M.hse.1280
Exec/science/bwp-rad/inputs_2d
Exec/science/bwp-rad/inputs_3d
Exec/science/bwp-rad/probin.dens_sponge
commit cc0d95be5e1a09001370996eedf23d0b1b420646
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 15 09:36:15 2016 -0500
style
Docs/EOSNetwork/EOSNetwork.tex
Docs/FAQ/faq.tex
Docs/GettingStarted/CastroGettingStarted.tex
Docs/MAESTRO_restart/MAESTRO_restart.tex
commit adcc36a7405b1ae3159850b70e526e1241e50bd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 15 09:10:56 2016 -0500
fix typo
Docs/FlowChart/FlowChart.tex
commit 6a6bffc5bf890a6696bd1f36f1b2608ae06f8400
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 21:58:15 2016 -0500
a little more flow charting
Docs/FlowChart/FlowChart.tex
commit f0629958bb564cf530e43a2e6b44cfefcd7a2821
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 21:40:03 2016 -0500
a little more clarity
Docs/FlowChart/FlowChart.tex
commit c311267f537fe30b56faaea860ca6d7302beb4a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 20:52:57 2016 -0500
some notes on new_source
Docs/Software/CastroSoftware.tex
commit a4bf1f95ed5ba27e82495a1c351c7f30b1dd7b6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 20:38:52 2016 -0500
add comment
Source/Castro_sources.cpp
commit 4efba84ff6b12d15ba54cc6efb5a428343c897b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 19:26:49 2016 -0500
add some info about the different source multifabs
Docs/Software/CastroSoftware.tex
commit 61ae00cf1d107d8e15a4842290f2752be595f49d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 14:35:38 2016 -0500
fix note about ghost cells when RADIATION is enabled
Docs/Software/CastroSoftware.tex
commit eddb33d35c93b05ee22796d76351d2557be4e529
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 14:06:07 2016 -0500
add the option to check ghost cells for NaNs
Source/Castro.H
Source/Castro.cpp
commit 087112e009351e5e41e2110b7e4756e79287d382
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 09:16:13 2016 -0500
remove debugging prints
Source/Src_1d/Castro_1d.F90
commit f3901a43cab2f712009f8e79e821e20cafadbb46
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 14 05:51:59 2016 -0500
Don't reflux for uniform grid simulations
Source/Castro.cpp
commit e28b114baacf7a47c0825195b9ae79553c6dd138
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 13 21:04:31 2016 -0500
fix the dimensioning of q() in ca_umdrv
Source/Src_1d/Castro_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_3d/Castro_3d.F90
commit 2c762ff1810d102817919dbd72fae3023cc338ce
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 8 14:53:06 2016 -0800
update according to BoxLib changes in Array class and C++11
Exec/Make.Castro
Source/Castro.H
Source/Gravity.cpp
commit cf473e9e851d83af3cd52aab4d0ff3eed9bfeae9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 8 11:13:04 2016 -0800
fix deprecated access declarations
Source/Radiation/_interpbndry/RadBndryData.H
commit ca384cff08365d512da1c36b7b84bbd7204a388d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 7 21:43:01 2016 -0500
don't actually need self_heat here
Microphysics/networks/sdc_type.F90
commit cc86a4bb09bb422404e1364b9ee48a95d7b1d118
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 7 12:31:57 2016 -0500
add c binding name for PGI
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
commit 8a6efd520e82c20dc527d51a079114c39a159fba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 15:03:03 2016 -0400
define self_heat for SDC
Microphysics/networks/sdc_type.F90
commit ae303f0fbf7ca8ee2f246cda6ef85c1a68b923fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 11:15:19 2016 -0400
update note about tracking mass loss
Docs/FlowChart/FlowChart.tex
commit 1687f87896e11647171e73c5505602f7f2dc2d2d
Merge: 21581e5be 64df004bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 10:04:56 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 64df004bb9e2627f7bb8c4779d1bffbe602e091d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 21:49:52 2016 -0400
use USERSuffix
Exec/Make.Castro
commit 539e065c765e940ce2fb5c0130938f4f827efa31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 21:17:46 2016 -0400
override optionsSuffix to add SDC if USE_SDC=TRUE
Exec/Make.Castro
commit e0f3054fcd5075faaab34821a507dd70a325bb72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 21:09:28 2016 -0400
fix typo to get this compiling
Microphysics/networks/sdc_type.F90
commit df76cd43e27645fc0e4fcd943feadfa5de6308ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 20:57:43 2016 -0400
fix compilation
Source/Castro_sources.cpp
commit 14f5c6ba98049480a246b911af8f7a4f41962555
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 19:15:56 2016 -0400
more flow charting
Docs/FlowChart/FlowChart.tex
commit 569cf292bc0747e7e8eb0b717b67338c36024853
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 18:24:22 2016 -0400
fix a comment typo
Source/Castro_react.cpp
commit f16132046d92c28f1cf486072fc6da9992da1c6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 14:41:55 2016 -0400
a little more on the main driver
Docs/FlowChart/FlowChart.tex
commit cd7146e183aa1a2f51236f8eb67412b1a56fa28f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 13:31:55 2016 -0400
more flow charting
Docs/FlowChart/FlowChart.tex
commit 21581e5be45980b35e04ca401a3fd5bf9cd01463
Merge: 8aaaff4a6 d64c13140
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 14:48:22 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit d64c13140d8db5a8d73c301ca3b7f1543b2b4610
Merge: fe1708e32 a10aa99b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 1 14:36:39 2016 -0400
Merge branch 'master' into development
commit a10aa99b27d6a66dc4dba18993ca76ee86fae546
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 1 14:36:27 2016 -0400
Add a few comments to CHANGES
CHANGES
commit 8aaaff4a6531891f451e2152355f88d60a88fd94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 14:35:50 2016 -0400
comment
Source/Castro_advance.cpp
commit fe1708e32a858c296ff047a795ca01da4ae0a08d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 14:27:47 2016 -0400
remove levelset
Docs/FlowChart/FlowChart.tex
commit ff334e392e60a6555baa4b42f85f1f6bf5f39d35
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 14:21:54 2016 -0400
remove fixed marginpar
Docs/FlowChart/FlowChart.tex
commit 0491175740ed1c9e915c9d76396a5c70678f95be
Merge: 881abe4e2 f65aefa11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 09:56:36 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 881abe4e23453f2ffc4792cced581af805dd1a0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 09:56:25 2016 -0400
update
CHANGES
commit f65aefa119fb11b01ca8862bb666fc8aac00fab6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 31 19:30:29 2016 -0400
switch the solver from 104 to 100 (AMG) -- this converges more easily
Exec/science/bwp-rad/inputs_2d.test
commit 2474da9fbe7efab1b3c46b89a9f74d7d42d92cbe
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 30 01:23:02 2016 -0400
Directly silence buildinfo removal
Exec/Make.Castro
commit 57a53c0d58ab5f4d6e07b75be735fafefc6f500a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 29 15:52:16 2016 -0400
Do nothing in reactions if do_react == 0
Source/Castro_react.cpp
commit 984ddc7fab2de1a5389baf882a53faabf6d06d83
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 29 15:32:05 2016 -0400
Fill ghost zones of state in initData
Source/Castro.cpp
commit e30929bf2a2a0880f761964f69aecd5997d09490
Merge: 6aefa9c00 6354ed701
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 28 13:38:29 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 6aefa9c008b9282f4b5670d0994b0c1943ded8f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 28 13:38:06 2016 -0400
fix -y extrapolation catch-all for non-gravity
Source/Src_2d/bc_fill_2d.F90
commit 6354ed70148131fb076e3c323153621ee6770935
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 27 23:56:07 2016 -0400
Initialize class members after restart
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
commit 3394ad70f79130009983b6215e39e17e511c07be
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 27 23:22:06 2016 -0400
Use clean_state more consistently
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_sources.cpp
commit 270f463b91b6bf5b714ffefdcb8f0077028bc773
Merge: 8d305d360 fed0d2efb
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Oct 27 16:24:23 2016 -0700
Merge branch 'development' of https://github.com/BoxLib-Codes/Castro into development
commit 8d305d360c7906348a263ba2068b3a8f07b728e1
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Oct 27 16:23:47 2016 -0700
Move regression testing file from BoxLib to here.
Util/regression_testing/Castro-tests.ini
commit fed0d2efbd72648b3240319f876ac6b4acddc835
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 27 18:00:03 2016 -0400
move this here from BoxLib
Util/regression_testing/Castro-SBU-tests.ini
commit a6e3ca3372e80df1bf1efa79ff205380eb1c2ec6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 26 11:33:29 2016 -0400
But don't zero phi for PoissonGrav
Source/Castro_gravity.cpp
commit 752dd90cad3de3c95c05841aec4f0fba084cff3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 26 10:53:45 2016 -0400
Fix the location of the phi zeroing
Source/Castro_gravity.cpp
Source/Gravity.cpp
commit 978f3eef44c0134899c44331da02778b1f5d1398
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 26 10:41:20 2016 -0400
Always initialize phi to zero
Source/Gravity.cpp
commit a5ce7a43b916c93780dba9e36b95d9fdd93f81a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 26 10:35:18 2016 -0400
Fix incorrect gravity ifdef
Source/Castro_advance.cpp
commit 21dd8d50c98ca7781bc9239561dc54a599901b43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 24 10:52:51 2016 -0400
fix compilation
Source/Src_2d/bc_fill_2d.F90
commit 3a11e557b3b9de13d6ceb960b27f3c8501c0d376
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 23 18:25:53 2016 -0400
Redo clean_state change since there are diffs anyway
Source/Castro.cpp
commit 7156d632d5c7a18f6b330d163f0ab34a0dca3698
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 23 18:05:56 2016 -0400
Do not act for sources we don't use
Source/Castro.H
Source/Castro_sources.cpp
commit d52355494fd8a99feddfc02dd243ea64fa341718
Merge: a9f273a2a 4de22ae69
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 23 16:20:52 2016 -0400
Merge branch 'development' into reflux
commit 4de22ae692aa36b7dc0877c66c8e6bc768fcd1c3
Merge: 5c1b9d9a9 57499ad5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 22 09:12:55 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 57499ad5e4dfe9481e23673e9fbd53956ec7203e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 21 21:10:19 2016 -0700
call AmrLevel::postCoarseTimeStep to sync up StateData times; this may result in roundoff difference
Source/Castro.cpp
commit 5c1b9d9a9eb7a24c84febfcb36287f73d57d03fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 21 12:39:30 2016 -0400
add default extrapolation to reactfill, grav?fill, rot?fill for
EXT_DIR BCs at the lower boundary. These can easily be overwritten,
but this is a safer default than doing nothing
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
commit d0b838b4de43e7df9af67235cd0adc520881ebd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 21 10:08:50 2016 -0400
fix 3-d comp
Exec/gravity_tests/DustCollapse/probdata.f90
commit 3ce1db7e06ae10a531f69756d4d4d1154c44cac8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 20 22:25:59 2016 -0400
add interpolation of temperature and velocity reflection options to the
HSE BC
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 86dd8c810a08f5b46f1dae0d893d0929daded310
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 20 22:25:32 2016 -0400
switch to the centralized HSE BC
Exec/science/flame_wave/bc_fill_2d.F90
Exec/science/flame_wave/inputs_2d
Exec/science/flame_wave/inputs_2d.testsuite
commit 7ca637f296f4631005941ddb75e14e1763efe04c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 20 18:43:29 2016 -0400
remove unused parameters -- fixes compilation
Exec/gravity_tests/DustCollapse/probdata.f90
commit a9f273a2a86d3948dd536c6b840316fa94518a37
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 20 10:44:40 2016 -0400
Sync radiation up with pure hydro
Source/Castro_advance.cpp
commit c9fa27996133fe8d9b801ff7af4f88791f335f70
Merge: 51e8281e0 1e5eed9b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 20 10:25:25 2016 -0400
Merge branch 'development' into reflux
commit 1e5eed9b0910c86a8ee45790556f462e281c6560
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 21:30:05 2016 -0400
smaller test problem
Exec/science/flame_wave/inputs_2d.testsuite
commit d1b967907396c2dc182f4531fc2f9ddf6820f324
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 20:20:03 2016 -0400
add a test suite inputs
Exec/science/flame_wave/inputs_2d.testsuite
commit 31273f135b607232cde7c4a646d00d3532ba92e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 20:18:58 2016 -0400
add a test suite file
Exec/science/convective_flame/inputs.2d.testsuite
commit 57c0146fd6e27ff056233bfa581569822d6f3264
Merge: a3b822ec0 ef24c8c0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 18:38:37 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit a3b822ec0a4ac820ee31fec6b192ad67a5648907
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 18:36:32 2016 -0400
start hooking in a general external boundary -- right now HSE + interpolation.
This is 2-d only right now.
addresses issue #38
Exec/science/xrb_mixed/Prob_2d.f90
Exec/science/xrb_mixed/bc_fill_2d.F90
Exec/science/xrb_mixed/inputs_2d
Exec/science/xrb_mixed/probdata.f90
Exec/science/xrb_mixed/probin
Source/Src_2d/Make.package
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit ef24c8c0eade1c6e40f609042d976ecc2ba36055
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 18:36:32 2016 -0400
start hooking in a general external boundary -- right now HSE + interpolation.
This is 2-d only right now.
addresses issue #28
Exec/science/xrb_mixed/Prob_2d.f90
Exec/science/xrb_mixed/bc_fill_2d.F90
Exec/science/xrb_mixed/inputs_2d
Exec/science/xrb_mixed/probdata.f90
Exec/science/xrb_mixed/probin
Source/Src_2d/Make.package
Source/Src_2d/bc_ext_fill_2d.F90
Source/Src_2d/bc_fill_2d.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 8a6009bbcbf4f4ed535756ab09a13d32e3a041df
Merge: f2f8d85ef b0f659275
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 17:56:07 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f2f8d85effe61896e36f1b0966eba1240133da13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 17:55:32 2016 -0400
always compile in the model_parser -- it doesn't add much, and we will
rely on it for some ext bc behavior
Exec/Make.Castro
Exec/gravity_tests/StarGrav/GNUmakefile
Exec/gravity_tests/hydrostatic_adjust/GNUmakefile
Exec/hydro_tests/reacting_bubble/GNUmakefile
Exec/hydro_tests/test_convect/GNUmakefile
Exec/hydro_tests/toy_convect/GNUmakefile
Exec/science/bwp-rad/GNUmakefile
Exec/science/bwp/GNUmakefile
Exec/science/convective_flame/GNUmakefile
Exec/science/flame_wave/GNUmakefile
Exec/science/xrb_mixed/GNUmakefile
Exec/science/xrb_mixed/bc_fill_2d.F90
commit b0f659275719a9637cef6e80e7411dedbc4ef315
Merge: ad2dc3ac4 c61e8e6be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 17:23:52 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit ad2dc3ac430cae8df4c61eefeaa5a46fff560895
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 17:23:36 2016 -0400
g was removed -- put it back so things compile
Source/Src_2d/trans_2d.F90
commit c61e8e6be47ffe3fcc4d2debe3a8af6a71c5fc10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 17:21:43 2016 -0400
output wanrings to stderr
Source/parse_castro_params.py
commit 03d990832e18c867d15d9a76a78ae84a2d2a80c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 15:57:45 2016 -0400
add HSE_INTERP
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 85c3a5eeedb7c666851eac921969bcd70f91fa27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 13:41:19 2016 -0400
add a note about SELF_GRAVITY
CHANGES
commit 7e4305c1706f36e363410e4cd74f4fa88bbb872b
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 09:04:48 2016 -0700
Move Castro_advection_1d.f0 --> Castro_advection_1d.F90 to be consistent with 2d and 3d
Source/Src_1d/Castro_advection_1d.F90
Source/Src_1d/Make.package
commit ca5334e89d51b07a6aac7689e017f1ba18657c4e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 09:03:13 2016 -0700
Rename Castro_sums_nd.f90 --> sums_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/sums_nd.f90
commit baaa83e3fb4ba37ff77db2a2d67ea346adbd7dbd
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 08:50:41 2016 -0700
Was missing a semicolon.
Source/Castro_gravity.cpp
commit 3072861d7864f63d10b082f5aa6385aa44084656
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 08:47:18 2016 -0700
CASTRO --> Castro so it is easier to replace.
Source/Src_1d/Prob_1d.f90
Source/Src_2d/Prob_2d.f90
Source/Src_3d/Prob_3d.f90
commit 5d57fb87094202ee3eeac8cc77b8878c2a206af9
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 08:47:04 2016 -0700
Wrap more stuff inside ifdef.
Source/Src_nd/meth_params.F90
commit bbb99b076c9f1f36c39615987ae268964075a8e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 07:57:15 2016 -0700
Wrap more lines inside ifdefs to make cleaner conversion.
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
commit 51e8281e03ba645beddd9c419c6c0bb41588198c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 19 10:39:08 2016 -0400
Revert a clean_state call to make diffs cleaner
Source/Castro.cpp
commit dbd7e673ad248beda4d87b1968b29d42980046a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 19 06:39:03 2016 -0700
oops -- had non-curly instead of curly bracket. Fixed now.
Source/sum_integrated_quantities.cpp
commit b125110d9cdd5e5ee787a5de2a367239c6f55c69
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 23:07:58 2016 -0700
More fixes for the SELF_GRAVITY ifdef
Source/Castro.cpp
Source/sum_integrated_quantities.cpp
commit 46bcbb99f270b919cbde0a9071b1043307a50bf2
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:56:52 2016 -0700
We also wrap calls to get_numpts and make_radial data by ifdef SELF_GRAVITY.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_io.cpp
commit 707f57824bfdd72a5be358fbc2213e582490c4ad
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:47:02 2016 -0700
comp_minus_level_phi and comp_minus_level_grad_phi should be wrapped
by ifdef SELF_GRAVITY
Source/Castro.H
Source/Castro.cpp
commit ce7eca07e4f2638888ddec83d5167abae1fa96b2
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:32:27 2016 -0700
Oops -- left a buggy ifdef in there -- now ok.
Source/Castro.cpp
commit 3df258f05b4e133b7f5a63dbefb2006e1e41efbd
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:28:26 2016 -0700
Add versions of ca_gsrc and ca_corrgsrc that work for constant gravity,
ie. don't require us to pass in phi and grav as arrays
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
commit 1a2b8b93d93a2c1479f94771dbaa3854e5982d41
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:27:51 2016 -0700
Remove unused variables.
Source/Src_2d/riemann_2d.F90
commit 88725d0acdf161c6e7cde4965243d2db4105c2e8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:24:09 2016 -0700
Remove unused variable.
Source/Src_2d/trace_ppm_2d.f90
commit 7bb187c5c159f925c5bf4e25e10f1b3292f894a2
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 22:22:29 2016 -0700
wrap GDLAMS and GDERADS in ifdef RADIATION
Source/Src_nd/meth_params.F90
commit da825ca61b81065d9998754edebf38851baf9a0c
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 21:34:23 2016 -0700
Wrap the sponge functionality in ifdef SPONGE (set in Make.Castro)
so that we can strip it out later.
Exec/Make.Castro
Source/Castro.H
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Castro_sources.cpp
Source/Castro_sponge.cpp
commit 127db500a268bb443d0fcad35c56e0d35bb1453d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 21:33:53 2016 -0700
Removed unused "int ng"
Source/Castro_gravity.cpp
commit 52bb37dbc9d2b04d1b7ed67fc4943c089cb50a76
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 21:19:42 2016 -0700
Remove unused variable.
Source/Src_nd/timestep.F90
commit ec9efa390e57e51e4bfc97792e8459b9f8bff6bc
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 21:16:06 2016 -0700
Replace ngdnv by NGDNV in a few files to be consistent with the rest
that already use NGDNV
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.template
commit 99ce2003b3ba0dbfda104de86ff9ae8b4f6f3aef
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 20:23:15 2016 -0700
For now we will enforce in Make.Castro that if USE_GRAV = TRUE in the GNUmakefile
then both GRAVITY and SELF_GRAVITY will be defined.
Exec/Make.Castro
commit 0049de5e904e24a89bbf203785a8b4729c000c10
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 20:22:03 2016 -0700
Replace ifdef GRAVITY by ifdef SELF_GRAVITY where appropriate.
For now we will enforce in Make.Castro that if USE_GRAV = TRUE in the GNUmakefile
then both GRAVITY and SELF_GRAVITY will be defined.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_error_F.H
Source/Castro_io.cpp
Source/Castro_setup.cpp
Source/Castro_sources.cpp
Source/sum_integrated_quantities.cpp
Source/sum_utils.cpp
commit 78d24f6a25dbbba454dab01704c76c7ad4ee0e71
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 20:20:47 2016 -0700
1) Remove some unused variables
2) wrap QDLAMS and QDERADS in ifdef RADIATION
Source/Src_1d/riemann_1d.F90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trans_3d.F90
commit 01e01cd149d1275978fe4dc8cd387655d1b85958
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Oct 18 20:04:58 2016 -0700
Remove unused variables
Source/Src_3d/Castro_3d.F90
commit 4af31da3e42326bf13cea526524f6cbb316210f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 18 16:00:20 2016 -0400
get integer parameters for the EXT_DIR BC stuff in meth_params
-- this will be used to implement universal HSE BCs
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 30d7ed939bf675d4af43b42c737236a98bb97123
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 18 15:21:59 2016 -0400
don't put string parameters on the GPU
Source/Src_nd/meth_params.F90
Source/parse_castro_params.py
commit 311dc246ec9a2e2fc7ec14953934d0f18f805039
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 18 10:35:30 2016 -0400
Ensure that we are using the right old-time grad phi
Source/Castro_gravity.cpp
commit e1568e29d584d7c86ae99a531aafe3ff709989d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 11 10:37:31 2016 -0400
Revert to original usage of FluxRegisters
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 9245bc4f15519d8c2f9cab73db9b70726a4770db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 16 11:07:41 2016 -0400
move strings into F90 meth_params
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/parse_castro_params.py
commit 399e7258790e0ef87cbc52b0d673ed44fd8cfbb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 15 20:18:07 2016 -0400
add a string query too
Source/Src_nd/parmparse_fi.cpp
Source/Src_nd/parmparse_mod.f90
commit d97e1821390f139ac5fb5daea2951d0e3b426b57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 15 20:03:30 2016 -0400
this adds a parmparse get for strings -- seems to work based on
simple tests
Source/Src_nd/parmparse_fi.cpp
Source/Src_nd/parmparse_mod.f90
Source/Src_nd/string_mod.f90
commit 32b13a50324420f4e4765a3256072e74c7ffac6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 15 13:14:36 2016 -0400
write print-% to make output safe
Exec/Make.Castro
commit 253a06402c38681d0d5bb5d7f31234647245e4b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 14 20:27:06 2016 -0400
add string_c_to_f
Source/Src_nd/string_mod.f90
commit 74b9d2255ca193f10e30095dfee32a399b6dbe12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 14 11:35:59 2016 -0400
new runtime parameters to interpret external BCs
Source/_cpp_parameters
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
commit 8cd2f9112c922a25d161758244bbdf0f9aceeef7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 14 11:31:24 2016 -0400
put the includes in the new sub-directory
Source/parse_castro_params.py
commit 4d2997d14603768b644fe86812e4d7e72ae35f9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 11 15:57:16 2016 -0400
sync up with the xrb_mixed version since that handles the transverse terms
correctly
Exec/hydro_tests/test_convect/bc_fill_2d.F90
commit 5437403945d822107b98158e780aed6e98eab548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 10 11:53:28 2016 -0400
we had name clashing with nq and NQ -- why didn't GNU complain?
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trans_3d.F90
commit 107c6a211206982db3f960f031b7c3c570c9937b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 10 10:29:52 2016 -0400
Move the fluxregister back up to the class constructor
Source/Castro.H
Source/Castro.cpp
commit 5f7e0fd03dc121dfde5efdfb7af33e12858676b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 9 21:25:33 2016 -0400
Move the reflux scalings to the class level
Source/Castro.H
Source/Castro.cpp
commit c767153d83cf9757615617fdf02272929ad8c3b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 7 20:56:27 2016 -0400
fix location of radiation sources
Exec/Make.Castro
commit b4e8fa5a9db5155abd6b28d13cdf2d2004c403e7
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Oct 7 12:56:41 2016 -0700
1)Move radiation-only files out of Src* and into Source/Radiation/RadSrc*
2)Update Exec/Make.Castro to reflect this change.
Exec/Make.Castro
Source/Radiation/RadSrc_1d/CastroRad_1d.f90
Source/Radiation/RadSrc_1d/DumpModel1d.H
Source/Radiation/RadSrc_1d/DumpModel1d.cpp
Source/Radiation/RadSrc_1d/HABEC_1D.F90
Source/Radiation/RadSrc_1d/MGFLD_1d.f90
Source/Radiation/RadSrc_1d/MGFLDneut_1d.f90
Source/Radiation/RadSrc_1d/Make.package
Source/Radiation/RadSrc_1d/RAD_1D.F90
Source/Radiation/RadSrc_1d/RadBndry_1d.f90
Source/Radiation/RadSrc_1d/RadEOS_1d.f90
Source/Radiation/RadSrc_1d/RadHydro_1d.f90
Source/Radiation/RadSrc_1d/RadPlotvar_1d.f90
Source/Radiation/RadSrc_1d/filt_prim_1d.f90
Source/Radiation/RadSrc_1d/trace_ppm_rad_1d.f90
Source/Radiation/RadSrc_2d/CastroRad_2d.f90
Source/Radiation/RadSrc_2d/HABEC_2D.F90
Source/Radiation/RadSrc_2d/MGFLD_2d.f90
Source/Radiation/RadSrc_2d/MGFLDneut_2d.f90
Source/Radiation/RadSrc_2d/Make.package
Source/Radiation/RadSrc_2d/RAD_2D.F90
Source/Radiation/RadSrc_2d/RadBndry_2d.f90
Source/Radiation/RadSrc_2d/RadEOS_2d.f90
Source/Radiation/RadSrc_2d/RadHydro_2d.f90
Source/Radiation/RadSrc_2d/RadPlotvar_2d.f90
Source/Radiation/RadSrc_2d/filt_prim_2d.f90
Source/Radiation/RadSrc_2d/trace_ppm_rad_2d.f90
Source/Radiation/RadSrc_3d/CastroRad_3d.f90
Source/Radiation/RadSrc_3d/HABEC_3D.F90
Source/Radiation/RadSrc_3d/MGFLD_3d.f90
Source/Radiation/RadSrc_3d/MGFLDneut_3d.f90
Source/Radiation/RadSrc_3d/Make.package
Source/Radiation/RadSrc_3d/RAD_3D.F90
Source/Radiation/RadSrc_3d/RadBndry_3d.f90
Source/Radiation/RadSrc_3d/RadEOS_3d.f90
Source/Radiation/RadSrc_3d/RadHydro_3d.f90
Source/Radiation/RadSrc_3d/RadPlotvar_3d.f90
Source/Radiation/RadSrc_3d/filt_prim_3d.f90
Source/Radiation/RadSrc_3d/trace_ppm_rad_3d.f90
Source/Radiation/RadSrc_nd/Make.package
Source/Radiation/RadSrc_nd/RadDerive_nd.f90
Source/Radiation/RadSrc_nd/RadHydro_nd.f90
Source/Radiation/RadSrc_nd/Rad_nd.f90
Source/Radiation/RadSrc_nd/blackbody.f90
Source/Radiation/RadSrc_nd/filter.f90
Source/Radiation/RadSrc_nd/fluxlimiter.f90
Source/Radiation/RadSrc_nd/kavg.F90
Source/Radiation/RadSrc_nd/rad_params.f90
Source/Radiation/RadSrc_nd/rad_util.f90
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Make.package
commit ffd4a006c15062858e6bd843cb77134eeb939a0d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Oct 7 12:16:02 2016 -0700
Move the files which are only included if USE_RAD = TRUE (hence RADIATION is defined) out of Source
and into Source/Radiation. This makes Source more organized.
Exec/Make.Castro
Source/Make.package
Source/Radiation/Castro_radiation.cpp
Source/Radiation/HABEC_F.H
Source/Radiation/HypreABec.H
Source/Radiation/HypreABec.cpp
Source/Radiation/HypreExtMultiABec.H
Source/Radiation/HypreExtMultiABec.cpp
Source/Radiation/HypreMultiABec.H
Source/Radiation/HypreMultiABec.cpp
Source/Radiation/LHH.H
Source/Radiation/MGFLD.cpp
Source/Radiation/MGFLDRadSolver.cpp
Source/Radiation/MGRadBndry.H
Source/Radiation/MGRadBndry.cpp
Source/Radiation/Make.package
Source/Radiation/NGBndry.H
Source/Radiation/RAD_F.H
Source/Radiation/RadBndry.H
Source/Radiation/RadBndry.cpp
Source/Radiation/RadMultiGroup.cpp
Source/Radiation/RadPlotvar.cpp
Source/Radiation/RadSolve.H
Source/Radiation/RadSolve.cpp
Source/Radiation/RadTypes.H
Source/Radiation/Radiation.H
Source/Radiation/Radiation.cpp
Source/Radiation/SGFLD.cpp
Source/Radiation/SGRadSolver.cpp
Source/Radiation/_interpbndry/DIMS.H
Source/Radiation/_interpbndry/Make.package
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_1D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_2D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_3D.F
Source/Radiation/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/Radiation/_interpbndry/RadBndryData.H
Source/Radiation/_interpbndry/RadBndryData.cpp
Source/Radiation/_interpbndry/RadBoundCond.H
Source/Radiation/_interpbndry/RadInterpBndryData.H
Source/Radiation/_interpbndry/RadInterpBndryData.cpp
Source/Radiation/energy_diagnostics.cpp
commit e499f2287b593df31706c9ec5d7c7d3fb32beb16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 7 13:22:22 2016 -0400
switch to ArrayLim.H
Source/Src_1d/HABEC_1D.F90
commit 7aef40bd73001d7d976cb4f4875250b146526f73
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 6 10:34:37 2016 -0400
Fix logic for how long to keep the source terms
Source/Castro.cpp
Source/Castro_advance.cpp
commit a70463ce550b03a8152ff948ae9ba4cb114f0874
Merge: cfe7d8145 b194076bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 6 01:16:33 2016 -0400
Merge branch 'development' into reflux
commit cfe7d81450ea747707195eb37e93757c17d88659
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 6 00:49:57 2016 -0400
Fix the reflux logic for old method
Source/Castro.cpp
commit b194076bca2191c1b029a482886dd376e61cc9fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 5 17:01:59 2016 -0400
hook in param_includes
Exec/Make.Castro
commit 98d9c12e92703af2dc0fbf58409f9f84499502b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 5 16:56:10 2016 -0400
Make
Source/Make.package
Source/param_includes/Make.package
commit 1c6935831488589889c3d49c3d9934f046ac95a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 5 16:55:23 2016 -0400
move location
Source/param_includes/castro_defaults.H
Source/param_includes/castro_params.H
Source/param_includes/castro_queries.H
Source/param_includes/diffusion_defaults.H
Source/param_includes/diffusion_params.H
Source/param_includes/diffusion_queries.H
Source/param_includes/gravity_defaults.H
Source/param_includes/gravity_params.H
Source/param_includes/gravity_queries.H
commit e73c56a7f82a1e6c8b97d3c28bdad40dbeb56410
Merge: a2624fec6 f2dfffb59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 5 14:19:05 2016 -0400
Merge branch 'unified_code' into development
commit f2dfffb59ecb778529fd9a85f5662fd64470f1c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 5 09:42:16 2016 -0400
use NQ to allocate primitive states
closes #47
Source/Src_1d/Castro_1d.F90
Source/Src_1d/riemann_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trans_3d.F90
commit cc0b28a2896324bb4eae597d409980fd0381865c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 5 09:17:51 2016 -0400
fix NQ for radiation
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 77cc137c15596a875dfdc3c2ff82e57d56bd3faa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 4 22:48:00 2016 -0400
define NQ in Fortran -- this will be the number of primitive variables
for both hydro and radiation. This way we can dimension things just as
NQ regardless of whether there is radiation.
NQ is first initialized in Castro_nd to QVAR and then in the radiation
init (if it is called) to add QRADVAR
$acc device updates are in both locations
this is part of #47
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 386592ce83e6d00608cecd689d3c42edbb3b4a96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 4 21:50:09 2016 -0400
get rid of radhydro_params_module and move all of this into meth_params_module
this is part of #47
Source/RAD_F.H
Source/Radiation.cpp
Source/Src_1d/Castro_1d.F90
Source/Src_1d/RadHydro_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_1d/trace_ppm_rad_1d.f90
Source/Src_2d/Castro_2d.F90
Source/Src_2d/RadHydro_2d.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trace_ppm_rad_2d.f90
Source/Src_2d/trans_2d.F90
Source/Src_3d/Castro_3d.F90
Source/Src_3d/RadHydro_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trace_ppm_rad_3d.f90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Make.package
Source/Src_nd/Rad_nd.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/flatten_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/rad_util.f90
Source/Src_nd/radhydro_params.f90
commit a2624fec6335c086266b913fea83e48036e28c0e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Oct 4 12:38:57 2016 -0700
update due to changes in BoxLib Particle
Exec/Make.Castro
Source/Castro.H
Source/CastroParticles.cpp
commit 6d8751d10daa56e9fae31f9c389e5f16f6e8bac2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 3 12:25:46 2016 -0400
update changes
CHANGES
commit a1f03bc934fd9ecd2ca534c3587713527795779c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 1 23:54:08 2016 -0400
Fix the time passed to the source terms
Source/Castro_advance.cpp
commit 2c960948600aedc7d2d0cead2262cef3a02fa756
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 1 23:51:15 2016 -0400
Eliminate prepare sources routines
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Castro_rotation.cpp
Source/Castro_sources.cpp
commit b2de4a057d3bff828e50dadc836d5111f37dcba6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 1 12:59:47 2016 -0400
Move the reflux back to post_timestep
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_sources.cpp
commit 4fa1f4e607c1f863b3ad51a9471a4b7def49a68a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 30 13:17:16 2016 -0400
remove separate ergdnv and lamgdnv
closes #50
Source/Src_1d/Castro_1d.F90
Source/Src_1d/RadHydro_1d.f90
Source/Src_1d/riemann_1d.F90
commit 3785355a07e8f1b4607dfa6ece5df3b55e1a60f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 30 09:50:15 2016 -0400
add a little to the CHANGES
CHANGES
commit 7d1a28af2af4ec710c55d6bc32e68ff9ff6ba5dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 15:17:13 2016 -0400
compiles!
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Make.package
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Make.package
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Make.package
Source/Src_3d/RadHydro_3d.f90
commit 1e9b7a00fe8b42ffb5a0e61847a10a025cde12ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 14:38:26 2016 -0400
remove rad-specific umdrv
Source/Src_1d/CastroRad_1d.f90
Source/Src_2d/CastroRad_2d.f90
Source/Src_3d/CastroRad_3d.f90
commit f2c971d9ee666445f976054769858f7c41d3f549
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 14:34:13 2016 -0400
finish the merge of the Fortran -- it all compiles, so it should work ;)
Source/Src_1d/Castro_1d.F90
Source/Src_2d/Castro_2d.F90
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/Castro_3d.F90
commit fae87b076b2227e672877c81b71ad031267b72ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 14:08:48 2016 -0400
make cpp
Source/Src_3d/Castro_3d.F90
Source/Src_3d/Make.package
commit 5f71cc9a09422399709a22044b46648f975906ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 10:26:12 2016 -0400
a little cleaning
Source/Src_1d/Castro_1d.F90
commit 90449b734e49bcf91aec6649485e9078674f67d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 10:25:55 2016 -0400
first cut and syncing -2d
Source/Src_2d/CastroRad_2d.f90
Source/Src_2d/Castro_2d.F90
commit 6b76774e33b6e7aba2f1b274796f162fd3f1f503
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 29 09:38:53 2016 -0400
allow for cpp
Source/Src_2d/Castro_2d.F90
Source/Src_2d/Make.package
commit 107e5566b64c975603fed9a2494c36d957f36dda
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 22:55:03 2016 -0400
first_order_hydro moved
CHANGES
commit 889ae1ab539a50962437e86e92473b72d83445be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 22:53:35 2016 -0400
port radiation to ca_umdrv
Source/Src_1d/Castro_1d.F90
Source/Src_nd/flatten_nd.F90
commit 180d12b3bba3215b661459c45997cde91d42cfdd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 22:31:18 2016 -0400
move first_order_hydro from Radiation to Castro
Docs/runtime_parameters/runtime_parameters.tex
Exec/radiation_tests/RadBreakout/inputs.1d
Source/RAD_F.H
Source/Radiation.H
Source/Radiation.cpp
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/Castro_1d.F90
Source/Src_2d/CastroRad_2d.f90
Source/Src_3d/CastroRad_3d.f90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/radhydro_params.f90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 36a37f9ea18531608db7295350cf4cbc10630680
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 20:10:44 2016 -0400
fix some compilation problems from last cleanup
Source/Src_2d/RadHydro_2d.f90
Source/Src_3d/CastroRad_3d.f90
commit 1ed36cbccc1086c38da6296154f0bb5267cbc61f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 20:04:14 2016 -0400
remove ppflaten
Source/Src_1d/RadHydro_1d.f90
Source/Src_2d/RadHydro_2d.f90
Source/Src_3d/RadHydro_3d.f90
commit e017546187fe9f30c73bd496f001a2ebc17305ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 20:01:11 2016 -0400
move the radiation flatening and ppflaten into flattening_module
Source/Src_1d/CastroRad_1d.f90
Source/Src_2d/CastroRad_2d.f90
Source/Src_3d/CastroRad_3d.f90
Source/Src_nd/flatten_nd.F90
commit 3a8fc2ca448a8750ced901b9bdd5c63da3e48e27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 19:40:30 2016 -0400
move radiation flattening into this
Source/Src_nd/Make.package
Source/Src_nd/flatten_nd.F90
commit 082400fc9862012c85426b7038c6c11ce1c69458
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 19:00:23 2016 -0400
start of syncing the umdrv
need to generalize the flattening stuff first
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/Castro_1d.F90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Make.package
commit 89751e5ed438d1c490af602b88f8523482b6bb0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 14:59:03 2016 -0400
merge the blocks calling ca_umdrv for rad and hydro to reduce code replication
Source/Castro_hydro.cpp
commit 92ef734a7c5ff9021f180a5bbc617d95325fa895
Merge: cee448a7b 8090f1987
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 14:34:03 2016 -0400
Merge branch 'development' into unified_code
commit 8090f1987151d4a4be38ac891744519957ec4792
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 28 08:43:33 2016 -0400
fix non-RADIATION compilation
Source/Src_nd/advection_util_nd.F90
commit cee448a7b9d1f08f198000660811a8d176902558
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 22:05:47 2016 -0400
define NQ -- starting #47
Source/Castro.H
Source/Castro.cpp
commit 96eea9698cabcd769fac5b3d02148f563d758cf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 22:04:40 2016 -0400
fix a merge conflict
Source/Src_2d/CastroRad_2d.f90
commit 00de78f8c5af476ef0ef2ad819756dcbccc2665d
Merge: 4acb99653 ea10968ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 14:33:20 2016 -0400
Merge branch 'development' into unified_code
commit 4acb99653d5573ca2185324e59c2c3962bf9afd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 13:47:04 2016 -0400
move 1- and 2-d over to dimension-agnostic ctoprim
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/RadHydro_1d.f90
Source/Src_2d/CastroRad_2d.f90
Source/Src_2d/RadHydro_2d.f90
commit e2d88f8439b74b75825b6d304b9d5f76b30e8e8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 11:02:10 2016 -0400
remove ctoprim_rad
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/RadHydro_3d.f90
commit ec2301849e3df4b7e113a098ce044b1555cfb36d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 10:54:47 2016 -0400
QRADVAR is now a Castro class member
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/radhydro_params.f90
commit e43b15479f155722b339322b767c549cc029cafd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 10:23:26 2016 -0400
almost there -- need to write a function to pull QRADVAR into C++
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_3d/CastroRad_3d.f90
Source/Src_nd/advection_util_nd.F90
commit 297d833f5a5efdf7b822723f0322560892456db4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 27 09:57:14 2016 -0400
cons_to_prim is only needed with SDC
Source/Castro.H
Source/Castro.cpp
commit ea10968eafd89c6d63d311c5c17127a95bcce689
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 22:47:33 2016 -0400
fix the q_lo_3D and q_hi_3D
Source/Src_1d/CastroRad_1d.f90
Source/Src_2d/CastroRad_2d.f90
commit 21714124f5182468784a3fc22c51234d1599b097
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 22:30:28 2016 -0400
some work on getting the 3-d to compile with the agnostic ctoprim
need to address the ctoprim calls in Castro_sources
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/RadHydro_3d.f90
commit e652ef493385b7652038a1e997a4a2270c07d32d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 21:11:43 2016 -0400
fix interface -- Er and lambda come into ctoprim
Source/Src_nd/advection_util_nd.F90
commit 2d989a85fda7e6625025c879de1a23a43d375664
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 19:52:19 2016 -0400
make ctoprim work with radiation too
we should be able to sync radiation up with pure hydro for
ctoprim and srctoprim now
Source/Src_nd/advection_util_nd.F90
commit 4700274b79d7dfff546f8a208789595d206ba774
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 19:43:53 2016 -0400
bug fix -- we were computing QCSML incorrectly
Source/Src_nd/advection_util_nd.F90
commit cd664f4002a494c55f9a95e3d021b5024a32ca39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 19:32:27 2016 -0400
remove the courno stuff from ctoprim_rad and rely on the
dimension agnostic compute_cfl
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/RadHydro_1d.f90
Source/Src_2d/CastroRad_2d.f90
Source/Src_2d/RadHydro_2d.f90
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/RadHydro_3d.f90
commit f883a426567be54f016de569db14e73eb732cb58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 17:54:31 2016 -0400
accidentally commited a change to this
Exec/science/bwp-rad/inputs_3d
commit d3cdf3983afc15d39f01de9468d09ccd643251b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 17:29:21 2016 -0400
remove qaux, also fix 2-d internal energy
Source/Src_2d/RadHydro_2d.f90
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/RadHydro_3d.f90
commit 44060b2f496980133b06972237976f5b29e2c205
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 15:02:15 2016 -0400
use qaux
Source/Src_2d/CastroRad_2d.f90
Source/Src_2d/RadHydro_2d.f90
commit 2485ecf14268dc6e5d6039fc3da1881c12afa0cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 15:02:10 2016 -0400
fix flatn pass
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/RadHydro_1d.f90
commit 34b553d9fc045fd7d7c85f632120fdf84b11e575
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 14:40:00 2016 -0400
fix DPDR, DPDE, also sync the eint source up with pure hydro
Source/Src_1d/RadHydro_1d.f90
commit f5e26cc21a9ac9c706ecca948c0372fd99d997ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 14:15:02 2016 -0400
finish putting qaux throughout
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/RadHydro_1d.f90
commit 12dabdd747e806aa05161361d896555b4eb77afb
Merge: 85c80e7b6 13bade226
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 14:03:05 2016 -0400
Merge branch 'development' into unified_code
commit 13bade2269194a37db5438478b2ffc49d3a40c76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 14:00:21 2016 -0400
fix compute_cfl -- QC lives in qaux
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_nd/advection_util_nd.F90
commit 85c80e7b6f7b301993bc69f8a5df2962ed55fcee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 13:47:07 2016 -0400
work on qaux in 1-d
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/RadHydro_1d.f90
Source/Src_nd/advection_util_nd.F90
commit 9819b81226a96cb4aabbc2711431f000a6c53162
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 26 11:09:22 2016 -0400
Move old and new sources to their own methods
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_sources.cpp
commit 2e5c8a775f4e76ca45cd1d8e773467701a8f4334
Merge: b9fbd67f0 56d69cc8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 12:50:26 2016 -0400
Merge branch 'development' into unified_code
commit 56d69cc8cb4965c165a14e3814edba694f21f3e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 12:49:39 2016 -0400
fix QGAME
Source/Src_3d/RadHydro_3d.f90
commit b9fbd67f019d27b1e3b360bfb2cffd5c9d40bb9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 12:49:02 2016 -0400
move flattening out of ctoprim
Source/Src_2d/CastroRad_2d.f90
Source/Src_2d/RadHydro_2d.f90
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/RadHydro_3d.f90
commit 1245dc685dddaf5e51ec81ff1c3031b926433375
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 11:08:52 2016 -0400
move 1-d flattening out of ctoprim
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/RadHydro_1d.f90
Source/Src_nd/meth_params.F90
commit a1e02a77d22657b7f356d6186c0be9aa68496fc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 26 09:38:38 2016 -0400
add QGAMCG, QCG
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
commit 50d77013f303cd2c0f84f37a3d19286d1778e89c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 26 01:43:35 2016 -0400
Fix old refluxing again
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 7362e2706813eda157ecef29bcb808bbe130019c
Merge: ccd64e111 c7ad62e2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 25 23:52:21 2016 -0400
Merge branch 'development' into reflux
commit ccd64e1116556e23c98152868b7e7a15405b304c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 25 23:52:07 2016 -0400
Only define pres register in <3D
Source/Castro.cpp
commit 1c40cd5d095b2d396d3f01e6f4ba458d35fef636
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 25 22:30:50 2016 -0400
Move the diffusion MultiFabs into diffusion routines
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_sources.cpp
commit 5b1a46f999e2de4e2f9f749c5cc836eec5bfc926
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 25 22:07:40 2016 -0400
int --> real
Source/Castro.cpp
commit 90d70ebc7b4bc50edaa90791db17da9acea40d44
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 25 21:40:42 2016 -0400
Need to zero out temp fluxes to avoid NaNs
Source/Castro.cpp
commit c7ad62e2b5be185affb3dd8257a568dc36ee8a09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 25 18:21:25 2016 -0400
fix source term tracing -- it is always QVAR, even with radiation
Source/Src_3d/RadHydro_3d.f90
commit f9568eb58445bc0b06ac6f706d4fb715306132a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 25 12:19:42 2016 -0400
Fix number of components of rad_fluxes
Source/Castro_advance.cpp
commit fa845b5d2a775857d2ff7cfc8e7aef94ceb434e1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 23:58:39 2016 -0400
Fix some things for the old reflux method
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 939be4843dacde76536a1b17e6144b91ec33170b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 21:32:22 2016 -0400
Fix some missing std's
Source/Castro.cpp
commit e280bb6723d595d9e1cde337a67da3c5268eef5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 21:28:54 2016 -0400
const Rhs to make_radial_phi
Source/Gravity.H
Source/Gravity.cpp
commit fee447ea7ed6b54158b00ae80b79469e59c376e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 20:25:33 2016 -0400
Consistently set state data to zero if not using source
Source/Castro_gravity.cpp
Source/Castro_rotation.cpp
Source/Castro_sources.cpp
commit dc0722a7a62706ffe59ea3b7b0a310a804924eec
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 19:25:00 2016 -0400
Make the old refluxing strategy the default
Docs/runtime_parameters/runtime_parameters.tex
Source/_cpp_parameters
Source/castro_defaults.H
commit b537d8268bdf4cd1bfe9b6386828370385df2b75
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 19:22:50 2016 -0400
Copy the composite data back to phi_old
This was an oversight from the last commit.
Source/Castro_gravity.cpp
commit aecdf8806d4ced7bf93834ce39720496e1226e03
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 19:06:20 2016 -0400
Clean up and symmetrize the old/new level solves
Source/Castro_gravity.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 1d9bdc198dbdacc946eae811ecf4509fecb40c90
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 17:39:59 2016 -0400
Clean up a little
Source/Castro.cpp
commit a74b8e25ed8bef2519e81d002083ea28f7815cba
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 17:19:03 2016 -0400
For old method, reflux during advance
This ensures that the new-time source on the fine level uses
the latest possible information from the gravity solve.
Source/Castro.cpp
Source/Castro_advance.cpp
commit ec1e5daae41b2d6f2ffc247f5e83a27452664e64
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 16:48:52 2016 -0400
Do sphere renormalization in post_timestep
Exec/gravity_tests/uniform_cube_sphere/Prob.cpp
Exec/gravity_tests/uniform_cube_sphere/Prob_3d.f90
Exec/gravity_tests/uniform_cube_sphere/Problem.H
Exec/gravity_tests/uniform_cube_sphere/Problem.f90
Exec/gravity_tests/uniform_cube_sphere/Problem_F.H
commit 9d8a9c3ccda00fe312c78ed0aa6031f34b20efc0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 15:48:10 2016 -0400
Update uniform cube and allow refinement
Exec/gravity_tests/uniform_cube_sphere/inputs
Exec/gravity_tests/uniform_cube_sphere/probin
commit 21a0f5255b0bf55a4a59999f9cbd21ce438bbfd5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 15:35:47 2016 -0400
Always use all data when constructing BCs
Docs/runtime_parameters/runtime_parameters.tex
Source/Gravity.cpp
Source/_cpp_parameters
Source/gravity_defaults.H
Source/gravity_params.H
Source/gravity_queries.H
commit 102fb3934c8d4b72fbd0df204c9a3905eca13069
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 15:31:01 2016 -0400
Allow direct sum BCs on multiple levels
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
commit b924c0dac6b9578cfa1ebb4e7ca62dd7e813bfca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 23 12:50:54 2016 -0400
some index sorting fixes
Docs/CastroUserGuide.tex
Docs/Software/CastroSoftware.tex
commit 1685ff7323eed0fa8012a35d566a96c45064ec2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 05:37:18 2016 -0400
Fix the FluxRegister scaling for dphi
Source/Castro.cpp
commit 8f2cadfd0fca2482798460d9a87dc890f1b6077c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 05:06:53 2016 -0400
dphi should not be counted in boundary conditions
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
commit f267b81a85d80e3362f32f543697d3d4b2c6c77e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 23 03:02:48 2016 -0400
Fix various issues with the sync solve
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
commit e30d8d5e5f70b98576fcbc730e8602acebd73682
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 22:43:12 2016 -0400
Don't reflux if we have a coarse grid only
Source/Castro_advance.cpp
commit 20b8e362c5fe3ec9e94f66399993844d39ac0cac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 22 20:37:03 2016 -0400
add a note about the SingleGroupSolver
Docs/Radiation/CastroRadiation.tex
commit 8db7f84a5bc7a4b8e06c972d6ae2944bf5c85c95
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 19:28:07 2016 -0400
Fix GDPRES --> GDU
Source/Src_1d/RadHydro_1d.f90
commit a5aa0c742dba2c6b688cf6582da19300720fb711
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 18:56:56 2016 -0400
Fix Godunov array indexing
Source/Src_1d/RadHydro_1d.f90
commit 193a37c65577e481b29deb567322973ad2ec9593
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 18:32:10 2016 -0400
Scale by dt in radiation for pradial as well
Source/Src_1d/CastroRad_1d.f90
Source/Src_2d/CastroRad_2d.f90
commit fd354b6c478e398ebf88009cd7ae09bf03d2b511
Merge: fa8fe499e 96130793e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 18:31:14 2016 -0400
Merge branch 'development' into reflux
commit 96130793ec4a909bbc57201e3988b0b164cd18a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 18:30:47 2016 -0400
Sync up radiation with Godunov changes
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/RadHydro_1d.f90
Source/Src_2d/CastroRad_2d.f90
Source/Src_3d/CastroRad_3d.f90
commit fa8fe499ecd82e0385d8617a35c6c68c68bbb96f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 18:06:14 2016 -0400
Get rid of using std::...
Source/Castro.cpp
commit 7fedf62532e86108d03db7fe6b180b304b03f8f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 18:04:41 2016 -0400
Fix a few more recent bugs
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.cpp
commit 04f7f1b576976222c9d7e65b5005f3cce194650f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 16:02:05 2016 -0400
Only define P_radial for dim < 3
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 36b9e4d169b4b9ff14a348d335b8a75999bc803f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 15:17:29 2016 -0400
Remove a stray line that should have been gone
Source/Castro_advance.cpp
commit 6477f06a9ab7a255a1dd6047a2fe61e8a7e57c35
Merge: 06bbf9898 bc2832087
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 06:01:12 2016 -0400
Merge branch 'development' into reflux
commit bc28320879635035c5f2ba81113a8c1fd261c650
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 05:58:35 2016 -0400
Remove unused u_gdnv MultiFab
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_3d/Castro_3d.f90
commit 1e2aab01c9553e3faa5798e1d4753a06b79e0602
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 05:46:38 2016 -0400
Use the Godunov arrays in 1D
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/riemann_1d.F90
commit 06bbf989847a5a3f0f0bb069167154143d6582a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 05:20:29 2016 -0400
Fix some bugs to get radiation compiling
Source/Castro.cpp
Source/Castro_hydro.cpp
commit 62cc1da04b59797cb04764e73a09023c88aa6389
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 05:10:06 2016 -0400
Zero out flux registers before use
Source/Castro.cpp
commit 593132b27419cc8866aeb2b07682e5fd8c3ed125
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 04:57:01 2016 -0400
Fix clear statements
Source/Castro.cpp
commit caa6135896c0cfdd14821d180ff40a069e3d0161
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 04:30:42 2016 -0400
Clear internal borders before reflux
Source/Castro.cpp
commit cd9dd4be521f73dcf9cdb820e1fb21d3f1c45377
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 04:14:13 2016 -0400
Clean up a bit more
Source/Castro.cpp
Source/Castro_advance.cpp
commit de31b102928a18eff1ed48d21ee815f1809713fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 03:38:54 2016 -0400
Use PArray instead of Array for FluxRegister
Source/Castro.cpp
commit 641feacf7ce2dd9ac4ff32242894ced2783b30b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 03:35:28 2016 -0400
Get rid of obsolete phi_flux_reg
Source/Castro.H
Source/Castro.cpp
Source/Castro_gravity.cpp
Source/Diffusion.H
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
commit dc0967de31b04ef9615580cd6ecd4afd26e382db
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 03:21:31 2016 -0400
Allow old refluxing strategy to be used
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Gravity.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit f00517f60fd7fb1b7cb0d26ed0167ee485809a0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 01:30:49 2016 -0400
Update sources after reflux by default
Source/_cpp_parameters
commit fdce4ea8e74b22599e1cfa0199738a65df258493
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 00:50:28 2016 -0400
Update sources immediately after the reflux
Source/Castro.cpp
commit 825082dd2638dc41c719bf021ce1607fdaad7f0e
Merge: d2f43053f c69ac04b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 22 00:07:40 2016 -0400
Merge branch 'development' into reflux
commit d2f43053ff361c4b5f3d1c12f30649b6a286c3f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 21 23:37:45 2016 -0400
Move refluxes until after the hydro step on finest_level
Previously we would reflux in post_timestep after all levels finer
than the current level had proceeded. This had two related flaws.
First, the coarse timestep data was not updated as a result of
the fine grid timesteps until after the intermediate fine grid
steps had occurred, even though there was enough information at
the time to immediately update the state. This meant that in subsequent
interpolation steps when data was obtained from the coarse grid
to fill ghost zones or other data on the fine grid, we were not
using the most accurate version of the state available.
Second, the gravity sync solve at the end of the timestep was
also delayed relative to when the fluxes had actually occurred.
Now, with the gravity sync in particular, the source terms that we
calculated at the new time on the fine level were not correct.
This is more than just a re-statement of the first issue, because
previously we were attempting to correct for this with a sync source
applied after the sync solve had occurred. However, in general
with regridding it doesn't seem to be possible to calculate a
retroactive sync source that allows for the possibility that fine
grids may have appeared or disappeared over the course of the
coarse timestep, and even if you could do so, it would require
storage of the source terms you had applied as you went.
The drawback of this method is that it is more compute-intensive
because there's now one reflux and sync solve for every finest
level timestep. However, it is what is needed to ensure that
we have the most accurate value of the state data consistent
with the time integration strategy we use.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Castro_hydro.cpp
Source/Castro_sources.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_nd/gravity_sources_nd.F90
commit c69ac04b4bfa7b4745d1a61fa74be578110d5a8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 21:11:37 2016 -0400
some gravity documentation
Docs/Software/CastroSoftware.tex
commit 4ec7ed877db92a7fcb15f0eed00e9197a718f19d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 19:54:20 2016 -0400
update link + some cleaning
Docs/AMR/AMR.tex
commit 041a4572f4081310a45c6f708369b22d55f6120c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 21 18:57:44 2016 -0400
Update .gitignore for actual_network.f90
.gitignore
commit ccfc38f1cbff2c43cedc4bd334de669e2b7f7133
Merge: 7cebaf541 39c3d07db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 15:32:31 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 7cebaf541ca2156a1a0c56c29a58b1fef54454a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 15:32:12 2016 -0400
document running at NERSC
Docs/CastroUserGuide.tex
Docs/GNUmakefile
Docs/ManagingJobs/managingjobs.tex
commit 39c3d07dbc93af693b92eabab8b28abc89427ef6
Merge: ce66f66d8 dd438f2d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 12:07:33 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit ce66f66d85a9c4d4604565870f21a5e0ff676d9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 12:07:03 2016 -0700
update scripts
Util/job_scripts/edison/edison.xfer.slurm
commit dd438f2d8f5a08b416529dbe5371dcba6ed6b4cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 13:50:13 2016 -0400
fix diffusion compilation
Source/Castro.H
Source/Castro_diffusion.cpp
commit a152ba1c87cc35d5129dc67becea1f9520c1321d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 13:44:02 2016 -0400
remove level sets -- these were never fully implemented and are not
tested. The history lives on in git
.gitignore
Docs/CastroUserGuide.tex
Docs/LevelSet/LevelSet.tex
Docs/LevelSet/levelset.bib
Docs/Software/CastroSoftware.tex
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_levelset.cpp
Source/Make.package
Source/Src_1d/Make.package
Source/Src_2d/LevelSet_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/LevelSet_3d.f90
Source/Src_3d/Make.package
commit 36bd98e7840e9babe24a6a3afec2c91f21b044f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 10:23:03 2016 -0400
update changes
CHANGES
commit 0d6a74e010cb5b857142948b002623300597be84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 21 09:40:50 2016 -0400
remove tau -- this was not used nor tested anymore. It lives on it git's memory
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_react.cpp
commit 3dc78efc502cde2a19c56fee90cb56e39c942cf1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 22:33:02 2016 -0400
time-center species diffusion
Source/Castro_diffusion.cpp
commit 16b664e375d74678db9dd36afcb0ff9498167b8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 22:12:12 2016 -0400
fix notation
Docs/Gravity/CastroGravity.tex
commit e63c3ec135c736a93ef23785d0832c6d34c26d4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 21:17:39 2016 -0400
sort problems into categories
Docs/GettingStarted/CastroGettingStarted.tex
commit dc840ba4a4406b75fed285e381a047b71216d3e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 20:04:24 2016 -0400
new introduction chapter
Docs/CastroUserGuide.tex
Docs/GNUmakefile
Docs/Introduction/Introduction.tex
Docs/Preface/Preface.tex
Docs/Software/CastroSoftware.tex
commit b044c6cdc8cd0f0ed2807f5b5079f84efeb8b591
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Sep 20 12:37:49 2016 -0700
update due to change in BoxLib's PhysBCFunct
Source/Gravity.H
Source/Gravity.cpp
commit 91f9d7016918ba520d0e0c72a852461d1823eb6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 15:46:55 2016 -0400
clean up
Docs/CastroUserGuide.tex
Docs/FlowChart/FlowChart.tex
Docs/Inputs/CastroInputs.tex
Docs/Software/CastroSoftware.tex
commit da7c310be66f24dcf3ea725c43b3bc8b6e1ac3a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 13:31:23 2016 -0400
some tweaks
Docs/AMR/AMR.tex
Docs/Inputs/CastroInputs.tex
Docs/Software/CastroSoftware.tex
commit 8257a96dd8126858ed81ad48567568a7b58a0f4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 20 11:20:43 2016 -0400
Do final call to computeTemp before diagnostics call
Closes #14
Source/Castro.cpp
commit 9aa1f9c9b1fcc5a2b4d099d23315ffc8f217a0e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 11:15:16 2016 -0400
document problem-specific files
closes #20
CHANGES
Docs/CastroUserGuide.tex
Docs/Software/CastroSoftware.tex
commit 3aa27ac4dfdf4db942f9216882ea22eb74d1a123
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 10:42:32 2016 -0400
rename
Docs/CastroUserGuide.tex
Docs/GNUmakefile
commit 6079d343f3b884ba63adba26b2512aef0059d505
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 10:41:44 2016 -0400
rename
Docs/Verification/RT_ppm_type.eps
Docs/Verification/Verification.tex
Docs/Verification/radiating_source.eps
Docs/Verification/radiating_sphere.eps
Docs/Verification/sedov_cyl.eps
Docs/Verification/sedov_sph.eps
Docs/Verification/sod_3d.eps
Docs/Verification/sod_3d_ppm0.eps
Docs/Verification/test2_3d.eps
Docs/Verification/test3_3d.eps
Docs/Verification/test_suite_day.eps
Docs/Verification/test_suite_main.eps
Docs/Verification/verification.bib
commit 265e765e5bf96ce84b5b11602965ccec2bca9e01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 10:32:33 2016 -0400
typo
Docs/Software/CastroSoftware.tex
commit 996a7f6c97067cb62f77e83ba73f8616c85566ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 10:31:59 2016 -0400
index some problem setups
Docs/CastroVerification/Verification.tex
commit 1395c04079a2bccffe9f009aa982e60f77d882a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 10:28:27 2016 -0400
index as runtime parameter
Docs/FAQ/faq.tex
commit 8ef41bfd178e7635361b754e9fc7704cbbfcc8c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 20 10:26:06 2016 -0400
Add comment on how often dump_and_continue is checked
Docs/FAQ/faq.tex
commit c4e38a33a8d13cc154145f645384a4418cd0302c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 20 10:00:10 2016 -0400
add dump_and_continue et al. to the FAQ
Docs/FAQ/faq.tex
commit 74db2c1f442a136363135a06ea8a8c79e6263fb4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 23:18:28 2016 -0400
Must average down before gravity sync to isolate drho
Source/Castro.cpp
commit a9e4eb61939f2f828b053b295106169e54603431
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 21:38:10 2016 -0400
Permit re-computation of sources after reflux
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit dc18817462aa0293fcff9a5765a7581c7972c53d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Sep 19 14:44:10 2016 -0700
Radiation:clear_internal_borders has been moved to FluxRegister::ClearInternalBorders
Source/RadSolve.cpp
Source/Radiation.H
Source/Radiation.cpp
commit a21a679bb8bc3e7d68849a36ff10a2fb206a73ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 16:31:19 2016 -0400
If refluxing, keep the new_sources until end of timestep
Source/Castro.cpp
Source/Castro_advance.cpp
commit a12eae909a0e88e1c1f313cdb4732074b2cece2f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 16:29:10 2016 -0400
Reflux the hydro fluxes in post_timestep
Source/Castro.cpp
Source/Castro_advance.cpp
commit 193a967209a725aa573ce7e4241d2527a47628e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 19 16:16:56 2016 -0400
add note about FluxRegister
Docs/Software/CastroSoftware.tex
Docs/castrosymbols.tex
commit 2ea40ecbd14437cd71d5df5f9fbe2da43cba789a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 19 15:37:13 2016 -0400
fix namespace in indexing
Docs/CastroUserGuide.tex
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit c6f8a1bfdad949430faf6fe36c16d730acf53dc3
Merge: 18b04eed4 eb6f8d026
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 19 15:32:29 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 18b04eed47ee4f3cff57ac1b1ba184051c597fcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 19 15:32:25 2016 -0400
add some docs
Source/_cpp_parameters
commit eb6f8d0262b4d64b6362500ce7f4a9ef242f4040
Merge: c35beefeb 29af0726a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 14:40:58 2016 -0400
Merge branch 'development' into dmap
commit c35beefebf2d2cf8820a8b7fb18ea7e2cf216671
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 14:31:32 2016 -0400
Fix issues with the parallel copy of state data
Source/Castro_react.cpp
commit a1dbf2848eef6fe671d698672581d31c6ae6388a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 14:31:18 2016 -0400
Start with a plausible value for the reactions weighting
Source/Src_nd/React_nd.F90
commit 29af0726a56d72cd7897c939e78f113e4e6208c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 19 13:56:48 2016 -0400
deal with namespaces in the documentation
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit 9bed40f998c87d3e13e102b761434e08255c09ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 13:37:41 2016 -0400
Avoid a couple unnecessary copies
Source/Castro_react.cpp
commit 8263b54b136b6590528c5a7f6d320010b48eb729
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 11:19:11 2016 -0400
Don't try to access zones that don't exist
Source/Src_nd/React_nd.F90
commit 5c40d345557688ed6a7783f6e62f63f2b21af38d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 19 11:08:26 2016 -0400
Make sure every zone gets a weight
Source/Src_nd/React_nd.F90
commit 3c3990d325a641db2e7f78e36fb6f0e15e9851e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 20:23:15 2016 -0400
Clean up just a little
Source/Castro.H
Source/Gravity.cpp
commit 1ec3455aa3d7b52211de449dbef061f395126402
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 18:51:53 2016 -0400
update problem locations
Docs/CastroVerification/Verification.tex
Docs/GettingStarted/CastroGettingStarted.tex
Docs/ManagingJobs/managingjobs.tex
Docs/Radiation/CastroRadiation.tex
Docs/Software/CastroSoftware.tex
commit 568d747ab50e17f4da482a4470ef0c74ef3dee40
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 18:21:56 2016 -0400
Add test suite inputs for evrard_collapse
Exec/gravity_tests/evrard_collapse/inputs.test
Exec/gravity_tests/evrard_collapse/probin.test
commit 047095ee6b96a63a3e1eb4b542dd1c18e847aa84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 17:35:02 2016 -0400
problem reorg
CHANGES
commit ed036e6f887ec3738e9e6a45bd2289976745c4a1
Merge: 4677cd9bf f0fa059fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 17:31:56 2016 -0400
Merge branch 'development' into problem_org
commit f0fa059fb44d57de11551ed389aa77e7c5f69cb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 17:29:01 2016 -0400
formatting
CHANGES
commit b7943e538299981a758c690713d8583a94c07515
Merge: dde797b80 d4e29335f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 17:28:23 2016 -0400
Merge branch 'development' into runparams
commit d4e29335fd272cc90a9d9968d7689ff4b6f4082c
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sun Sep 18 14:13:26 2016 -0700
Change the print statements to correctly identify the file name of
the subroutine where the error occurs
Source/Src_nd/Castro_util.F90
Source/Src_nd/advection_util_nd.F90
commit 448d2ccc80d9648575af21a93059b7127dafd1c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 17:07:23 2016 -0400
Don't try to get ref_ratio on nonexistent levels
Source/Gravity.cpp
commit dde797b802523d2a29b185d41627c822050d9fa5
Merge: 71da63db9 cabba2216
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 15:22:19 2016 -0400
Merge branch 'development' into runparams
commit cabba22162d0f88fcfa9ac5170d8dcf0c381ca5e
Merge: dd3c82b91 37b14c530
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 15:20:28 2016 -0400
Merge branch 'development' into gravity_tolerance
commit dd3c82b910121ee511c1505ce5d99eae1402a6b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 15:18:13 2016 -0400
Rename test suite input parameters for tolerances
Exec/DustCollapse/inputs_2d_poisson_regtest
Exec/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/evrard_collapse/inputs
Exec/uniform_cube_sphere/inputs
commit e6f83ec1f5a3a37d93927b1cf0fbd381b2cea421
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 15:09:16 2016 -0400
Increase verbosity level for printing Ggravity
Source/Gravity.cpp
commit a16ecd9eba4d9910af3fc8ddfd479f53fdf6bfe6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 15:08:46 2016 -0400
Restore a relative tolerance option gravity.rel_tol
CHANGES
Docs/Gravity/CastroGravity.tex
Source/Gravity.H
Source/Gravity.cpp
commit 735df5c425d47c46e01028c71aa0229a1f1c7e77
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 14:37:51 2016 -0400
Allow abs_tol to be passed in as an array
CHANGES
Docs/Gravity/CastroGravity.tex
Source/Gravity.H
Source/Gravity.cpp
commit 693fa744bb3afc456177aeab8ea061a6674ff1cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 14:28:04 2016 -0400
Remove temp file
Source/.#Castro.cpp
commit fc01fc66fbce946e3cf39ae79a5bbe60741ab626
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 18 13:59:53 2016 -0400
Rename gravity.tol to gravity.abs_tol
Source/Gravity.H
Source/Gravity.cpp
commit 71da63db95281f98d698ac9db684b34ed3ae6195
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 12:22:27 2016 -0400
add note about change
CHANGES
commit 84ae47bc24d12db1ccc3ee3a96f5702202d63580
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 18 11:28:13 2016 -0400
add diffusion parameters
Source/Diffusion.H
Source/Diffusion.cpp
Source/Make.package
Source/_cpp_parameters
Source/diffusion_defaults.H
Source/diffusion_params.H
Source/diffusion_queries.H
commit c3d34400869a0234616cc48a5de99032f9424ac6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 22:19:30 2016 -0400
get_g_from_phi is now int, not logical
Source/Make.package
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit fb777f213a4fa082eab0bd6ef25ab3fd859cf74e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 22:08:37 2016 -0400
gravity is static
Source/Gravity.H
Source/Gravity.cpp
Source/_cpp_parameters
Source/gravity_params.H
commit 1f40572ae0b8899aad011d9ee78e3324c50d67bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 21:57:12 2016 -0400
need to set the C++ class in addition to the namespace
Source/Gravity.cpp
Source/_cpp_parameters
Source/gravity_defaults.H
Source/gravity_params.H
Source/gravity_queries.H
Source/parse_castro_params.py
commit e74321576e46c4904ec5f9420b69529b0ac90e61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 21:39:59 2016 -0400
clean
Source/parse_castro_params.py
commit 1eb9bfd9c50e9767a99dc2e3983b24e7dc5c2028
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 21:32:22 2016 -0400
get the namespace files produced
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/gravity_defaults.H
Source/gravity_params.H
Source/gravity_queries.H
Source/parse_castro_params.py
commit f21bf811fae0bf4ee4d909b899f84e8f6954c843
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 21:13:40 2016 -0400
allow for static or non-static class variables
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Gravity.cpp
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/parse_castro_params.py
commit 3f0a2d0d903226e7eb817c5c4f90616c2372ac00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 20:06:58 2016 -0400
more progress on getting the runtime parameters for gravity hooked in
we need to figure out how to deal with string parameters in Fortran
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/parse_castro_params.py
commit 8122c5d452cb475ca6255ea3d9e2ed75ef653790
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 18:57:33 2016 -0400
get all the gravity parameters moved -- still need to parse
this is start of work on #42
Source/Gravity.cpp
Source/_cpp_parameters
commit 66696011fba47fdf2f6203a2b8b9da2355293e3d
Merge: e57934298 37b14c530
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 18:25:46 2016 -0400
Merge branch 'development' into runparams
commit 37b14c5305182c0cb2ecaa68dda573d2d7bb35b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 18:25:20 2016 -0400
more grav documentation from slack
Docs/Gravity/CastroGravity.tex
commit e579342989c9303ad97a82e3e1b6715ef16217fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 18:25:12 2016 -0400
more params
Source/Gravity.cpp
Source/_cpp_parameters
commit 8f6ad114b8a9745d5d82aa433c8190cf0c0cc526
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 17:34:24 2016 -0400
Fix a stray bracket
Source/Gravity.cpp
commit 760cf8eb8409cc4f572fa7745934fb47aa8311e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 17:12:34 2016 -0400
Correct the absolute tolerance requirement in R-Z
Source/.#Castro.cpp
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.H
Source/Gravity.cpp
commit face0b5eb1e09ec9caffbe482a82afef9aaa4aa4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 16:01:04 2016 -0400
start of work on gravity parameters
Source/Gravity.cpp
Source/_cpp_parameters
commit 5b8a7950bf63b74926c62f44953feec2d5262e7c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 15:58:28 2016 -0400
Update test problem inputes for gravity tol
Exec/DustCollapse/inputs_2d_poisson_regtest
Exec/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/evrard_collapse/inputs
Exec/uniform_cube_sphere/inputs
commit c3c7208f6e28b607a7ceb09d8604cefb351951f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 15:49:07 2016 -0400
Update documentation for gravity tolerance changes
CHANGES
Docs/Gravity/CastroGravity.tex
commit a1c0c1cdb8249f30e3cc773768a151d71f128c9b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 15:48:41 2016 -0400
Warn also if the user tries to set delta_tol
Source/Gravity.cpp
commit 3e449981c160c399611b74e99757876773ac8ad7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 15:33:13 2016 -0400
On fine levels, loosen the absolute gravity tolerance
This reflects the idea that dx**2 gets smaller on fine levels,
so 1/dx**2 in the Laplacian operator gets larger in absolute terms.
Source/Gravity.cpp
commit 6f12b724f1ca363b033b5f83e1824a4d949f9ded
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 14:20:52 2016 -0400
Use only absolute tolerance in the Poisson multigrid solve
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.H
Source/Gravity.cpp
commit ab647f9458e548d89243c99f8ed32d6f88b7390c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 17 11:05:50 2016 -0400
Get diagnostics working for all density reset methods
Source/Src_nd/advection_util_nd.F90
commit aa3dbc3fe62253a41411ccfdd4f77d8089d95b40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 17 10:39:55 2016 -0400
we were handling the inflow boundary on the + faces incorrectly
closes #41
Source/Diffusion.cpp
commit 4677cd9bf3dfd451d6b2860aa4e97a349ceeba02
Merge: a0af87e28 c21a0aa78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 15 17:36:57 2016 -0400
Merge branch 'development' into problem_org
commit c21a0aa7887826f91e5ef87a64b16ce2ef3a12e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 15 15:18:49 2016 -0400
don't include FLD_limiter.F, but instead make it part of rad_util_module
Source/FLD_limiter.F
Source/Src_1d/RAD_1D.F90
Source/Src_2d/RAD_2D.F90
Source/Src_3d/RAD_3D.F90
Source/Src_nd/rad_util.f90
commit 6c94214587286ee72573e51b6d43ea4764e86983
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 22:44:10 2016 -0400
switch to using the ArrayLim.H macros instead of rolling our own here
note, this required switching to 1-based instead of 0-based lo/hi
Source/Src_1d/RAD_1D.F90
Source/Src_2d/HABEC_2D.F90
Source/Src_2d/RAD_2D.F90
Source/Src_3d/HABEC_3D.F90
Source/Src_3d/RAD_3D.F90
commit acf6b14ca8ef17a7d108639720d66e156595121b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 18:49:26 2016 -0400
time-centering diffusion
CHANGES
commit 24b9396c77d65c8f923b757afffd921e8f0112e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 18:48:27 2016 -0400
also time-center enthalphy diffusion
Source/Castro.H
Source/Castro_diffusion.cpp
commit 0e9e184d7ce45d4003e6d2a179ea27ed8db0a84b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 18:42:10 2016 -0400
confused is_old and is_new
Source/Castro_diffusion.cpp
commit 0f4ceda7685a759606124e82161747fcbfee02ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 18:38:22 2016 -0400
time-center diffusion. This addresses part of #22
still need to compare to the analytic solution
Source/Castro.H
Source/Castro_diffusion.cpp
commit db8911aed183c28ab6ede226ca63028aa9ea9cf1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 14 16:52:16 2016 -0400
QGAME is in q not qaux
Source/Src_nd/advection_util_nd.F90
commit 8d058a94a25847b90f08a1e38bb15707ed416896
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 14 16:04:34 2016 -0400
Move some data from q into a qaux auxiliary array
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Castro_setup.cpp
Source/Castro_sources.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 5a653a52340eeabd33a678e0024cafd5b1f55c89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 15:53:54 2016 -0400
move units into the software section
Docs/CastroUserGuide.tex
Docs/Equations/Equations.tex
Docs/GNUmakefile
Docs/Software/CastroSoftware.tex
Docs/UnitsAndConstants/CastroUnits.tex
Docs/castrosymbols.tex
commit a0af87e28988af1e75106639117ab46877fec472
Merge: 9359f31db 42c8cb15a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 10:51:44 2016 -0400
Merge branch 'development' into problem_org
commit 42c8cb15a0de35bbe5c2b6cc279328a7005e0800
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 10:50:17 2016 -0400
fix some indexing issues
Docs/Software/CastroSoftware.tex
commit c87e4fb673731eb77f22699b6f5b1d76f132500e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 10:48:00 2016 -0400
bc_fill is .F90
Docs/Software/CastroSoftware.tex
commit d23d4dd40fcae6a3c6e24973e83072f4e041c186
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 10:41:24 2016 -0400
clean up physical boundary condition section
Docs/Software/CastroSoftware.tex
commit 9eae147cc61c8a6dc3ac4723121658dc7bd105db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 14 09:40:09 2016 -0400
document grids
Docs/Software/CastroSoftware.tex
Docs/castrosymbols.tex
commit 97f0aad556ee1aef732a6181f6f0f17300c76883
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 20:33:18 2016 -0400
switch to bind(C)
Source/HABEC_F.H
Source/HypreABec.cpp
Source/HypreExtMultiABec.cpp
Source/HypreMultiABec.cpp
Source/RadSolve.cpp
Source/Src_1d/HABEC_1D.F90
Source/Src_2d/HABEC_2D.F90
Source/Src_3d/HABEC_3D.F90
commit 9359f31dbe9cfcfe3ce773c0bede3acbebc77ca6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 19:05:11 2016 -0400
move into categories
closes #32
Exec/gravity_tests/DustCollapse/GNUmakefile
Exec/gravity_tests/DustCollapse/Make.package
Exec/gravity_tests/DustCollapse/Prob_1d.f90
Exec/gravity_tests/DustCollapse/Prob_2d.f90
Exec/gravity_tests/DustCollapse/Prob_3d.f90
Exec/gravity_tests/DustCollapse/README
Exec/gravity_tests/DustCollapse/bc_fill_3d.F90
Exec/gravity_tests/DustCollapse/inputs_1d
Exec/gravity_tests/DustCollapse/inputs_2d_halfstar
Exec/gravity_tests/DustCollapse/inputs_2d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_2d_octant
Exec/gravity_tests/DustCollapse/inputs_2d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_fullstar
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/gravity_tests/DustCollapse/inputs_3d_octant
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest
Exec/gravity_tests/DustCollapse/inputs_3d_poisson_regtest_restart
Exec/gravity_tests/DustCollapse/make_1d_results
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Exec/gravity_tests/DustCollapse/make_2d_octant_results
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Exec/science/xrb_mixed/toy_xrb.hi_dens.hse.tanh.delta_12.000cm.dx_6.000cm.CNO
Exec/unit_tests/diffusion_test/GNUmakefile
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commit 48669aadf1b30bbfd2ad917ae278f6e92b9ec73d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 13 15:51:11 2016 -0400
Fix module include hidden in ifdef
Source/Src_nd/rotation_sources_nd.F90
commit 3acc3b7b722381534bf6010d003d13585c7fb5c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 13 15:19:42 2016 -0400
Remove unused Rotation.H
Source/Castro_advance.cpp
Source/Rotation.H
commit 6d17f33f2513b89e56b26196a1f1bf3d6256a2cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 15:07:24 2016 -0400
rmeove StateLayout.H -- get what we need from meth_params_module
Note: state() now uses 1-based indexing instead of 0-based indexing
Source/RAD_F.H
Source/Radiation.cpp
Source/Src_1d/RAD_1D.F90
Source/Src_2d/RAD_2D.F90
Source/Src_3d/RAD_3D.F90
Source/StateLayout.H
commit 4ae2052d62f8c2e5f6e342428ab791748170974d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 14:20:48 2016 -0400
call the actual kavg() function instead of relying on the preprocessor
Source/Src_1d/RAD_1D.F90
Source/Src_2d/RAD_2D.F90
Source/Src_3d/RAD_3D.F90
commit 0822fa02188fab2d0d11f2cf53e0657f742ba366
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 13:49:48 2016 -0400
fix implicit none
Source/Src_nd/kavg.F90
commit 236482bf640405e410a8daed44012d18fbc6babe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 13:45:37 2016 -0400
switch eddfac to new bind, but we don't seem to ever call this
Source/RAD_F.H
commit acc8814775a61fb7c0ad3efaaf8c970e773cc998
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 13:41:08 2016 -0400
switch to bind(C) interfaces, move kavg to it's on routine
Source/MGFLD.cpp
Source/RAD_F.H
Source/RadSolve.cpp
Source/Radiation.cpp
Source/Src_1d/RAD_1D.F90
Source/Src_2d/RAD_2D.F90
Source/Src_3d/RAD_3D.F90
Source/Src_nd/Make.package
Source/Src_nd/kavg.F90
commit d45b39bd9244877f97b2238a09a0c7b2b11f2446
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 09:40:27 2016 -0400
auto index runtime parameters
Docs/CastroUserGuide.tex
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit 3562d4bfddc5189c5e661f30f4b9a73c25bd928e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 09:23:31 2016 -0400
update issues
CHANGES
commit 4ef10f17a55896e8a7e1f7e10f831f9b5d6e5e23
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 13 09:18:25 2016 -0400
move the radiation documentation into the main users guide and update build info
closes #31
Docs/CastroUserGuide.tex
Docs/GNUmakefile
Docs/Radiation/CastroRadiation.tex
Docs/castrosymbols.tex
commit a4dde277a01fb0c8566619dff3f5e9af15b2a301
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 13 00:58:16 2016 -0400
Add the hybrid source term in the gravity sync
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/gravity_sources_nd.F90
commit a705542278372d49bc64001cfdc2acd7805c194b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 22:09:49 2016 -0400
switch to freeformat
Source/Src_1d/HABEC_1D.F
Source/Src_1d/HABEC_1D.F90
Source/Src_1d/Make.package
Source/Src_2d/HABEC_2D.F
Source/Src_2d/HABEC_2D.F90
Source/Src_2d/Make.package
Source/Src_3d/HABEC_3D.F
Source/Src_3d/HABEC_3D.F90
Source/Src_3d/Make.package
commit 0c98bdbb8b7ca29fe5f416ffeaa07f3889e8770e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 20:48:50 2016 -0400
move dimension-agnostic fortran
Source/Make.package
Source/Src_nd/Make.package
Source/Src_nd/RadDerive_nd.f90
Source/Src_nd/RadHydro_nd.f90
Source/Src_nd/Rad_nd.f90
Source/Src_nd/blackbody.f90
Source/Src_nd/filter.f90
Source/Src_nd/fluxlimiter.f90
Source/Src_nd/rad_params.f90
Source/Src_nd/rad_util.f90
Source/Src_nd/radhydro_params.f90
commit 04f82ebc71b2521e2c03602a4d718b66058dbb6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 20:41:40 2016 -0400
finish the switch to freeform
this contains a token pasting hack in the dims() preprocessing #define
we should eliminate this in terms of the explicit result
Source/FLD_limiter.F
Source/Src_1d/RAD_1D.F90
Source/Src_2d/Make.package
Source/Src_2d/RAD_2D.F90
Source/Src_3d/Make.package
Source/Src_3d/RAD_3D.F90
Source/StateLayout.H
commit f3fda15ea2b27abcf0f508e9b0b74188d6a489e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 19:50:34 2016 -0400
switch to freeform
Source/Src_3d/Make.package
Source/Src_3d/RAD_3D.F
Source/Src_3d/RAD_3D.F90
commit 4afd0822e8a783573c10a7f679168f305e0c959c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 19:44:19 2016 -0400
switch to freeform
Source/Src_2d/Make.package
Source/Src_2d/RAD_2D.F
Source/Src_2d/RAD_2D.F90
commit a0ed38b15eaaf7f97e6e85b5d9a41d25454adbab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 19:36:21 2016 -0400
switch to free-form
Source/Src_1d/Make.package
Source/Src_1d/RAD_1D.F
Source/Src_1d/RAD_1D.F90
commit 0ba2f4dc4da07ae16faf218f71b5d597b71518c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 18:15:11 2016 -0400
remove Using.H and explicitly use std::
Source/HypreABec.cpp
Source/HypreExtMultiABec.cpp
Source/HypreMultiABec.cpp
Source/MGFLD.cpp
Source/MGFLDRadSolver.cpp
Source/MGRadBndry.cpp
Source/RadBndry.cpp
Source/RadMultiGroup.cpp
Source/RadSolve.cpp
Source/Radiation.cpp
Source/SGFLD.cpp
Source/SGRadSolver.cpp
Source/Src_1d/DumpModel1d.cpp
Source/Using.H
Source/_interpbndry/RadBndryData.cpp
commit e9e2a2a47e0af7cf3d31d4544d45759ed26ff72d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 15:13:33 2016 -0400
some feedback from Max
Docs/Software/CastroSoftware.tex
commit 32fed6f55b9e890544362e262426bb840543f1c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 12:37:11 2016 -0400
a little cleaning
Docs/Software/CastroSoftware.tex
commit 88ec1781f42811584df14e21bb8945fb2b1a5919
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 12:16:31 2016 -0400
finish fillpatch documentation
Docs/Software/CastroSoftware.tex
Docs/castrosymbols.tex
commit eb613fc2bf053a7ed819b9a12d9b3da18a8e5105
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 12 12:13:19 2016 -0400
remove unneeded fpi.index()
Source/Castro.cpp
commit 46e44146d802cc595706df7dea7e954638a2a1ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 02:42:41 2016 -0400
Add a couple more hybrid syncs to guard against interpolation error
Source/Castro.cpp
Source/Castro_advance.cpp
commit 00ff4df7a39f4641ba2ce4787905be76ccab70dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 01:56:17 2016 -0400
Fill in some details about the rotation options
Docs/Rotation/CastroRotation.tex
commit bd229bc520fa6192049910ed7aed8936ce6f19f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 01:50:50 2016 -0400
Allow a rotation term to be disabled
Source/Src_nd/Rotation_nd.f90
commit 19d924aced4e0759b1f5fbd9e038324a1f1a968d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 01:50:02 2016 -0400
Fix implicit rotation update for inertial frame variables
Source/Src_nd/rotation_sources_nd.F90
commit 5e7f97768f0f145eeaca79ff4c84aa716c06d02c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 01:18:37 2016 -0400
Don't update energy in hybrid sync, it is now unnecessary
Source/Src_nd/hybrid_advection_nd.F90
commit 30f9c043fe458141e2092ac241cf355d55212ed8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 01:14:15 2016 -0400
Do a hybrid sync after the hydro + old sources update
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hybrid.cpp
commit 3459933684c8164e486064423ef05069432aa75d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 00:59:36 2016 -0400
Don't add rotation to hybrid momentum if not in rotating frame
Source/Src_nd/rotation_sources_nd.F90
commit 0f0969305ccc54961f39dfe63c0c2ed93f454053
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 12 00:58:23 2016 -0400
If state in rotating frame, subtract rotation in ctoprim
Source/Src_3d/riemann_3d.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
commit ce5952210390fa8aec13420fc9b012f7343672fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 19:45:19 2016 -0400
update changes
CHANGES
commit ace6f93c1575bbcb1ac723897b35b3a3023edf71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 19:43:54 2016 -0400
documentation of dimension agnostic problem setups and prob_params_module
closes #29
Docs/Software/CastroSoftware.tex
commit 2010b24b6f39f576a3c60dc613e9b17cd1e34674
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 19:11:32 2016 -0400
save current doc
Docs/Software/CastroSoftware.tex
commit 4a9120e7238872d326b2c80dc8f606b932d4f502
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 13:28:35 2016 -0400
some more Fortran modules
Docs/Software/CastroSoftware.tex
commit b4c05d5e4617798da8f59f1ff12ebe537fc9f9b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 12:41:58 2016 -0400
fix build
Docs/Software/CastroSoftware.tex
commit 822ba216b37ebad814f267788ab27b1fdf8811e6
Merge: 31e362116 82cec4af4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 10:13:17 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 31e3621167e5c51ca37d48894845d47951569a3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 11 10:13:10 2016 -0400
some cases for fillpatch
Docs/Software/CastroSoftware.tex
commit 82cec4af4e14491f288c88b23a7d2cc3c572bb3a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 11 00:48:29 2016 -0400
Fix some indexing issues in a recent commit
Source/Gravity.cpp
commit b59477183d5b14aef09a6c4ecea017549cef6b35
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Sep 10 19:13:19 2016 -0700
minor simplification and omp
Source/MGFLDRadSolver.cpp
commit d83cfc070574f710c7b858cc74d9144dd20ce562
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 20:07:26 2016 -0400
problem-specific files
Docs/Software/CastroSoftware.tex
commit b3942fde4b544953591d412a1afd40f961477852
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 14:47:19 2016 -0400
update changes
CHANGES
commit 21faa1c7db5bd1c084c7c717b25503194b81bb27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 14:42:11 2016 -0400
fix build
Source/Src_2d/Make.package
Source/Src_3d/Make.package
commit 36e366c5da4b62a9157cee615ecd089e34a13e8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 14:01:41 2016 -0400
radiation is merged
Docs/GettingStarted/CastroGettingStarted.tex
commit aac3d1b4de6e41da260207e9c8b077fabb6e85b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 13:59:12 2016 -0400
update to reflect radiation merge
README.md
commit fa74fd9ec1fb1ff3be5b4d49f1fc87a4bbd8612d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 13:48:15 2016 -0400
integrate radiation into the main Castro repo
closes #24
CHANGES
Exec/Make.Castro
Exec/Make.CastroRad
Exec/Make.Radiation
Exec/Rad2Tshock/GNUmakefile
Exec/RadBreakout/GNUmakefile
Exec/RadCoreCollapse/GNUmakefile
Exec/RadShestakovBolstad/GNUmakefile
Exec/RadSlope/GNUmakefile
Exec/RadSphere/GNUmakefile
Exec/RadSuOlson/GNUmakefile
Exec/RadSuOlsonMG/GNUmakefile
Exec/RadThermalWave/GNUmakefile
Exec/bwp-rad/GNUmakefile
commit ddc2a0fa866a4d38e227f22488358831b1b87977
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 12:49:57 2016 -0400
move opacity over to Castro for the rad merge
Microphysics/opacity/Readme
Microphysics/opacity/breakout/Make.package
Microphysics/opacity/breakout/opacity_table_module.f90
Microphysics/opacity/null/Make.package
Microphysics/opacity/null/opacity_table_module.f90
Microphysics/opacity/powerlaw-example/Make.package
Microphysics/opacity/powerlaw-example/opacity_table_module.f90
commit a3647d9121f7353db440f5d9204e174d0b3fbe47
Merge: 79c2e7975 63d4322c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:54:43 2016 -0400
Merge branch 'development' of /home/zingale/temp/CastroRadiation into unified_code
commit 63d4322c30daab5ba96aa1bba759c57c40612eae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:39:43 2016 -0400
prepare for merge
Source/Castro_radiation.cpp
Source/FLD_limiter.F
Source/HABEC_F.H
Source/HypreABec.H
Source/HypreABec.cpp
Source/HypreExtMultiABec.H
Source/HypreExtMultiABec.cpp
Source/HypreMultiABec.H
Source/HypreMultiABec.cpp
Source/LHH.H
Source/MGFLD.cpp
Source/MGFLDRadSolver.cpp
Source/MGRadBndry.H
Source/MGRadBndry.cpp
Source/Make.package
Source/NGBndry.H
Source/RAD_F.H
Source/RadBndry.H
Source/RadBndry.cpp
Source/RadDerive_nd.f90
Source/RadHydro_nd.f90
Source/RadMultiGroup.cpp
Source/RadPlotvar.cpp
Source/RadSolve.H
Source/RadSolve.cpp
Source/RadTypes.H
Source/Rad_nd.f90
Source/Radiation.H
Source/Radiation.cpp
Source/SGFLD.cpp
Source/SGRadSolver.cpp
Source/Src_1d/CastroRad_1d.f90
Source/Src_1d/DumpModel1d.H
Source/Src_1d/DumpModel1d.cpp
Source/Src_1d/HABEC_1D.F
Source/Src_1d/MGFLD_1d.f90
Source/Src_1d/MGFLDneut_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/RAD_1D.F
Source/Src_1d/RadBndry_1d.f90
Source/Src_1d/RadEOS_1d.f90
Source/Src_1d/RadHydro_1d.f90
Source/Src_1d/RadPlotvar_1d.f90
Source/Src_1d/filt_prim_1d.f90
Source/Src_1d/trace_ppm_rad_1d.f90
Source/Src_2d/CastroRad_2d.f90
Source/Src_2d/HABEC_2D.F
Source/Src_2d/MGFLD_2d.f90
Source/Src_2d/MGFLDneut_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/RAD_2D.F
Source/Src_2d/RadBndry_2d.f90
Source/Src_2d/RadEOS_2d.f90
Source/Src_2d/RadHydro_2d.f90
Source/Src_2d/RadPlotvar_2d.f90
Source/Src_2d/filt_prim_2d.f90
Source/Src_2d/trace_ppm_rad_2d.f90
Source/Src_3d/CastroRad_3d.f90
Source/Src_3d/HABEC_3D.F
Source/Src_3d/MGFLD_3d.f90
Source/Src_3d/MGFLDneut_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/RAD_3D.F
Source/Src_3d/RadBndry_3d.f90
Source/Src_3d/RadEOS_3d.f90
Source/Src_3d/RadHydro_3d.f90
Source/Src_3d/RadPlotvar_3d.f90
Source/Src_3d/filt_prim_3d.f90
Source/Src_3d/trace_ppm_rad_3d.f90
Source/StateLayout.H
Source/Using.H
Source/_interpbndry/DIMS.H
Source/_interpbndry/Make.package
Source/_interpbndry/RADINTERPBNDRYDATA_1D.F
Source/_interpbndry/RADINTERPBNDRYDATA_2D.F
Source/_interpbndry/RADINTERPBNDRYDATA_3D.F
Source/_interpbndry/RADINTERPBNDRYDATA_F.H
Source/_interpbndry/RadBndryData.H
Source/_interpbndry/RadBndryData.cpp
Source/_interpbndry/RadBoundCond.H
Source/_interpbndry/RadInterpBndryData.H
Source/_interpbndry/RadInterpBndryData.cpp
Source/blackbody.f90
Source/energy_diagnostics.cpp
Source/filter.f90
Source/fluxlimiter.f90
Source/rad_params.f90
Source/rad_util.f90
Source/radhydro_params.f90
commit 79c2e7975d88282a27d380f55d19f739dbf6a5ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:34:57 2016 -0400
clean up after the rad merge
Make.Castro
Make.Radiation
Rad2Tshock/Castro_error.cpp
Rad2Tshock/GNUmakefile
Rad2Tshock/Make.package
Rad2Tshock/Makefile.bc
Rad2Tshock/Prob_1d.f90
Rad2Tshock/Prob_2d.f90
Rad2Tshock/Prob_3d.f90
Rad2Tshock/Tools/bc.f90
Rad2Tshock/bc_fill_1d.F90
Rad2Tshock/bc_fill_2d.F90
Rad2Tshock/bc_fill_3d.F90
Rad2Tshock/inputs.M2
Rad2Tshock/inputs.M2.mg
Rad2Tshock/inputs.M2.test
Rad2Tshock/inputs.M2.test.multid
Rad2Tshock/inputs.M5
Rad2Tshock/inputs.M5.mg
Rad2Tshock/inputs.M5.mg.test
Rad2Tshock/inputs.M5.mg.test.multid
Rad2Tshock/probdata.f90
Rad2Tshock/probin.M2
Rad2Tshock/probin.M5
Rad2Tshock/python/LowrieEdwardsUnits.py
Rad2Tshock/python/RadShock.py
Rad2Tshock/python/initincgs.py
Rad2Tshock/python/paper-M2-mg.py
Rad2Tshock/python/paper-M2.py
Rad2Tshock/python/paper-M5-mg.py
Rad2Tshock/python/paper-M5.py
Rad2Tshock/python/phys.py
Rad2Tshock/python/read_gnu.py
RadBreakout/GNUmakefile
RadBreakout/Make.package
RadBreakout/Prob_1d.f90
RadBreakout/filt_prim_1d.f90
RadBreakout/inputs.1d
RadBreakout/model.input.87a.23
RadBreakout/model.input.bo
RadBreakout/model.input.envel
RadBreakout/probdata.f90
RadBreakout/probin.1d
RadBreakout/probin.1d.87a.23
RadCoreCollapse/Castro_error.cpp
RadCoreCollapse/GNUmakefile
RadCoreCollapse/Make.package
RadCoreCollapse/Prob_1d.f90
RadCoreCollapse/Prob_2d.f90
RadCoreCollapse/Prob_3d.f90
RadCoreCollapse/Tagging_nd.f90
RadCoreCollapse/bc_fill_2d.F90
RadCoreCollapse/bc_fill_3d.F90
RadCoreCollapse/filt_prim_1d.f90
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadCoreCollapse/modelInput
RadCoreCollapse/probdata.f90
RadCoreCollapse/probin.1d.mgfld
RadCoreCollapse/probin.2d.mgfld
RadCoreCollapse/probin.3d.mgfld
RadShestakovBolstad/GNUmakefile
RadShestakovBolstad/Make.package
RadShestakovBolstad/Prob_1d.f90
RadShestakovBolstad/inputs-Tf0.1
RadShestakovBolstad/inputs.Planck
RadShestakovBolstad/inputs.common
RadShestakovBolstad/probdata.f90
RadShestakovBolstad/probin.common
RadShestakovBolstad/python/initunits.py
RadShestakovBolstad/python/paper.py
RadShestakovBolstad/python/phys.py
RadShestakovBolstad/python/read_gnu.py
RadSlope/GNUmakefile
RadSlope/Make.package
RadSlope/Prob_1d.f90
RadSlope/inputs
RadSlope/probdata.f90
RadSlope/probin
RadSphere/GNUmakefile
RadSphere/Make.package
RadSphere/Prob_1d.f90
RadSphere/README
RadSphere/Tools/GNUmakefile
RadSphere/Tools/analytic.f90
RadSphere/Tools/fradsphere.f90
RadSphere/Tools/radbc.f90
RadSphere/inputs
RadSphere/probdata.f90
RadSphere/probin
RadSphere/python/RadGroup.py
RadSphere/python/paper.py
RadSphere/python/phys.py
RadSphere/testsuite_analysis/radsphere.py
RadSphere/testsuite_analysis/radsphere_analytic.out
RadSuOlson/GNUmakefile
RadSuOlson/Make.package
RadSuOlson/Prob_1d.f90
RadSuOlson/inputs
RadSuOlson/probdata.f90
RadSuOlson/probin
RadSuOlson/python/paper.py
RadSuOlsonMG/GNUmakefile
RadSuOlsonMG/Make.package
RadSuOlsonMG/Prob_1d.f90
RadSuOlsonMG/inputs.common
RadSuOlsonMG/probdata.f90
RadSuOlsonMG/probin.common
RadSuOlsonMG/python/initunits.py
RadSuOlsonMG/python/paper.py
RadSuOlsonMG/python/phys.py
RadSuOlsonMG/python/read_gnu.py
RadThermalWave/Castro_error.cpp
RadThermalWave/GNUmakefile
RadThermalWave/Make.package
RadThermalWave/Prob_1d.f90
RadThermalWave/Prob_2d.f90
RadThermalWave/Prob_3d.f90
RadThermalWave/Tagging_nd.f90
RadThermalWave/inputs.1d
RadThermalWave/inputs.1d.test
RadThermalWave/inputs.2d
RadThermalWave/inputs.2d.test
RadThermalWave/inputs.3d
RadThermalWave/inputs.3d.test
RadThermalWave/probdata.f90
RadThermalWave/probin.1d
RadThermalWave/probin.2d
RadThermalWave/probin.3d
bwp/GNUmakefile
bwp/Make.package
bwp/Prob_2d.f90
bwp/Prob_3d.f90
bwp/SolarLike_0.2M.hse.1280
bwp/inputs_2d
bwp/inputs_2d.test
bwp/inputs_3d
bwp/probdata.f90
bwp/probin
commit 613fbb61332883ba130330cff0f6d2c5d7956dc0
Merge: dac873de5 f11f8249a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:28:30 2016 -0400
Merge branch 'development' of /home/zingale/temp/CastroRadiation into unified_code
commit f11f8249ae8d9ae914de666ef69ec3c03b6555dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:22:07 2016 -0400
rename
Exec/bwp-rad/GNUmakefile
Exec/bwp-rad/Make.package
Exec/bwp-rad/Prob_2d.f90
Exec/bwp-rad/Prob_3d.f90
Exec/bwp-rad/SolarLike_0.2M.hse.1280
Exec/bwp-rad/inputs_2d
Exec/bwp-rad/inputs_2d.test
Exec/bwp-rad/inputs_3d
Exec/bwp-rad/probdata.f90
Exec/bwp-rad/probin
commit 0c18c548a2917fe2fce2624a16b93a2708b52077
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:17:51 2016 -0400
preparing for move
Exec/Make.CastroRad
Exec/Make.Radiation
Exec/Rad2Tshock/Castro_error.cpp
Exec/Rad2Tshock/GNUmakefile
Exec/Rad2Tshock/Make.package
Exec/Rad2Tshock/Makefile.bc
Exec/Rad2Tshock/Prob_1d.f90
Exec/Rad2Tshock/Prob_2d.f90
Exec/Rad2Tshock/Prob_3d.f90
Exec/Rad2Tshock/Tools/bc.f90
Exec/Rad2Tshock/bc_fill_1d.F90
Exec/Rad2Tshock/bc_fill_2d.F90
Exec/Rad2Tshock/bc_fill_3d.F90
Exec/Rad2Tshock/inputs.M2
Exec/Rad2Tshock/inputs.M2.mg
Exec/Rad2Tshock/inputs.M2.test
Exec/Rad2Tshock/inputs.M2.test.multid
Exec/Rad2Tshock/inputs.M5
Exec/Rad2Tshock/inputs.M5.mg
Exec/Rad2Tshock/inputs.M5.mg.test
Exec/Rad2Tshock/inputs.M5.mg.test.multid
Exec/Rad2Tshock/probdata.f90
Exec/Rad2Tshock/probin.M2
Exec/Rad2Tshock/probin.M5
Exec/Rad2Tshock/python/LowrieEdwardsUnits.py
Exec/Rad2Tshock/python/RadShock.py
Exec/Rad2Tshock/python/initincgs.py
Exec/Rad2Tshock/python/paper-M2-mg.py
Exec/Rad2Tshock/python/paper-M2.py
Exec/Rad2Tshock/python/paper-M5-mg.py
Exec/Rad2Tshock/python/paper-M5.py
Exec/Rad2Tshock/python/phys.py
Exec/Rad2Tshock/python/read_gnu.py
Exec/RadBreakout/GNUmakefile
Exec/RadBreakout/Make.package
Exec/RadBreakout/Prob_1d.f90
Exec/RadBreakout/filt_prim_1d.f90
Exec/RadBreakout/inputs.1d
Exec/RadBreakout/model.input.87a.23
Exec/RadBreakout/model.input.bo
Exec/RadBreakout/model.input.envel
Exec/RadBreakout/probdata.f90
Exec/RadBreakout/probin.1d
Exec/RadBreakout/probin.1d.87a.23
Exec/RadCoreCollapse/Castro_error.cpp
Exec/RadCoreCollapse/GNUmakefile
Exec/RadCoreCollapse/Make.package
Exec/RadCoreCollapse/Prob_1d.f90
Exec/RadCoreCollapse/Prob_2d.f90
Exec/RadCoreCollapse/Prob_3d.f90
Exec/RadCoreCollapse/Tagging_nd.f90
Exec/RadCoreCollapse/bc_fill_2d.F90
Exec/RadCoreCollapse/bc_fill_3d.F90
Exec/RadCoreCollapse/filt_prim_1d.f90
Exec/RadCoreCollapse/inputs.1d.mgfld
Exec/RadCoreCollapse/inputs.2d.mgfld
Exec/RadCoreCollapse/inputs.3d.mgfld
Exec/RadCoreCollapse/modelInput
Exec/RadCoreCollapse/probdata.f90
Exec/RadCoreCollapse/probin.1d.mgfld
Exec/RadCoreCollapse/probin.2d.mgfld
Exec/RadCoreCollapse/probin.3d.mgfld
Exec/RadShestakovBolstad/GNUmakefile
Exec/RadShestakovBolstad/Make.package
Exec/RadShestakovBolstad/Prob_1d.f90
Exec/RadShestakovBolstad/inputs-Tf0.1
Exec/RadShestakovBolstad/inputs.Planck
Exec/RadShestakovBolstad/inputs.common
Exec/RadShestakovBolstad/probdata.f90
Exec/RadShestakovBolstad/probin.common
Exec/RadShestakovBolstad/python/initunits.py
Exec/RadShestakovBolstad/python/paper.py
Exec/RadShestakovBolstad/python/phys.py
Exec/RadShestakovBolstad/python/read_gnu.py
Exec/RadSlope/GNUmakefile
Exec/RadSlope/Make.package
Exec/RadSlope/Prob_1d.f90
Exec/RadSlope/inputs
Exec/RadSlope/probdata.f90
Exec/RadSlope/probin
Exec/RadSphere/GNUmakefile
Exec/RadSphere/Make.package
Exec/RadSphere/Prob_1d.f90
Exec/RadSphere/README
Exec/RadSphere/Tools/GNUmakefile
Exec/RadSphere/Tools/analytic.f90
Exec/RadSphere/Tools/fradsphere.f90
Exec/RadSphere/Tools/radbc.f90
Exec/RadSphere/inputs
Exec/RadSphere/probdata.f90
Exec/RadSphere/probin
Exec/RadSphere/python/RadGroup.py
Exec/RadSphere/python/paper.py
Exec/RadSphere/python/phys.py
Exec/RadSphere/testsuite_analysis/radsphere.py
Exec/RadSphere/testsuite_analysis/radsphere_analytic.out
Exec/RadSuOlson/GNUmakefile
Exec/RadSuOlson/Make.package
Exec/RadSuOlson/Prob_1d.f90
Exec/RadSuOlson/inputs
Exec/RadSuOlson/probdata.f90
Exec/RadSuOlson/probin
Exec/RadSuOlson/python/paper.py
Exec/RadSuOlsonMG/GNUmakefile
Exec/RadSuOlsonMG/Make.package
Exec/RadSuOlsonMG/Prob_1d.f90
Exec/RadSuOlsonMG/inputs.common
Exec/RadSuOlsonMG/probdata.f90
Exec/RadSuOlsonMG/probin.common
Exec/RadSuOlsonMG/python/initunits.py
Exec/RadSuOlsonMG/python/paper.py
Exec/RadSuOlsonMG/python/phys.py
Exec/RadSuOlsonMG/python/read_gnu.py
Exec/RadThermalWave/Castro_error.cpp
Exec/RadThermalWave/GNUmakefile
Exec/RadThermalWave/Make.package
Exec/RadThermalWave/Prob_1d.f90
Exec/RadThermalWave/Prob_2d.f90
Exec/RadThermalWave/Prob_3d.f90
Exec/RadThermalWave/Tagging_nd.f90
Exec/RadThermalWave/inputs.1d
Exec/RadThermalWave/inputs.1d.test
Exec/RadThermalWave/inputs.2d
Exec/RadThermalWave/inputs.2d.test
Exec/RadThermalWave/inputs.3d
Exec/RadThermalWave/inputs.3d.test
Exec/RadThermalWave/probdata.f90
Exec/RadThermalWave/probin.1d
Exec/RadThermalWave/probin.2d
Exec/RadThermalWave/probin.3d
Exec/bwp/GNUmakefile
Exec/bwp/Make.package
Exec/bwp/Prob_2d.f90
Exec/bwp/Prob_3d.f90
Exec/bwp/SolarLike_0.2M.hse.1280
Exec/bwp/inputs_2d
Exec/bwp/inputs_2d.test
Exec/bwp/inputs_3d
Exec/bwp/probdata.f90
Exec/bwp/probin
commit dac873de501a84bf6e659c04ca96d40852f039f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 10 09:12:49 2016 -0400
a few fixes
Docs/Software/CastroSoftware.tex
commit dcc778c7c2592c6d89d4b5014d21e5869f5d7eb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 23:49:27 2016 -0400
some const corrections
Docs/Software/CastroSoftware.tex
commit a24989a5e9bb6561165dba73ff2e07afb144185a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 23:24:11 2016 -0400
finish the MFIter stuff
Docs/Software/CastroSoftware.tex
commit ed35803cdbebdca49c7caac32b6d01a2107791f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 22:39:51 2016 -0400
If not using centrifugal force, disable rotational potential
Source/Src_nd/Rotation_nd.f90
commit 74d834fca8067fc517da8352d66515e108f963fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 22:36:18 2016 -0400
a few more comments
Docs/Software/CastroSoftware.tex
commit 26b2b3949bb49954077f41d10a910b99d99647ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 22:12:50 2016 -0400
fuller example of working with Fortran
Docs/Software/CastroSoftware.tex
commit f005f9f0eca0670bc12b30040e315cb4dd44e30e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 16:36:16 2016 -0400
Set the weights to one in the reaction step
Source/Src_nd/React_nd.F90
commit 21aee01011d61be62e8eca69cb2bdcc6b32b2d3d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 16:01:55 2016 -0400
Use a temporary distributionmap in Strang reactions
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_nd/React_nd.F90
commit eb546bae31161f2af2c6d39cb1609b7a22f5b372
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 15:37:07 2016 -0400
remove the separate parallel stuff
Docs/CastroUserGuide.tex
Docs/GNUmakefile
Docs/Parallel/Parallel.tex
Docs/Software/domain-tile.eps
Docs/Software/domain.py
commit 9bf319427d24e197022caa01bde6723b315bdfcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 15:29:09 2016 -0400
more integration
Docs/Software/CastroSoftware.tex
commit eae3679e8c09ad71b9df0dcc44974769da276859
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 15:25:10 2016 -0400
Use c_light instead of hardcoding the value
Source/Src_nd/Gravity_nd.f90
commit f02c816a38ac8a1193b4d8d6eb83d6e223c88410
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 15:22:03 2016 -0400
minor fixes
Docs/Software/CastroSoftware.tex
commit ff326d8ad251dcb4028c6cde3275a22623f8cee2
Merge: 28ec193d6 5562bc42b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 15:21:21 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 28ec193d6a40c80a5f6284e636ed820663a8242e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 15:20:57 2016 -0400
some MFIter work
Docs/Software/CastroSoftware.tex
commit 5562bc42bd4b902df37d857fde6c572f995e3546
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 15:16:46 2016 -0400
Remove seemingly unused function
Source/Src_2d/Gravity_2d.f90
commit 9edb272d201ff258b7f1fe4610ac3218e28309fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 15:14:51 2016 -0400
Fix inconsistency in number of state components for GR
Source/Gravity.cpp
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit 78700cb80c3b7b24c9c1bcc5962aa05c3feeb14a
Merge: 45b348c9b 47fa591ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 14:15:41 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 45b348c9bf4a68e15a115bae1dbc36bbddaf0c9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 14:15:32 2016 -0400
a little more reorg
Docs/Parallel/Parallel.tex
Docs/Software/CastroSoftware.tex
commit 47fa591acea259ada4919530c011acfe1653227e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 9 14:08:31 2016 -0400
Fix the sign of phi in ca_integrate_phi
Source/Src_nd/Gravity_nd.f90
commit 52fde0a0245bee760c632bcac9565022d4c09180
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 12:57:39 2016 -0400
finish first pass at core data structures
Docs/Software/CastroSoftware.tex
Docs/castrosymbols.tex
commit 4f8a9cf2ce2dbb1d871c31c879beb2dbef347f34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 12:15:23 2016 -0400
update changes + start refering to the github issue where appropriate
CHANGES
commit 4e726c3ed6a766a0bd46e2ad7c880e6957a60d70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 12:06:48 2016 -0400
more architecture reorg
Docs/CastroUserGuide.tex
Docs/Software/CastroSoftware.tex
commit c660e21bb7f44a54e087e6aaf8b44d410309d173
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 10:52:39 2016 -0400
more statedata code
closes #23
Docs/CastroUserGuide.tex
Docs/Software/CastroSoftware.tex
commit 1bb7eb04eea04ffd263cedca76cdb20b18fac568
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 9 10:13:07 2016 -0400
a little more, some cribbing from the boxlib guide
Docs/CastroUserGuide.tex
Docs/Software/CastroSoftware.tex
Docs/castrosymbols.tex
commit 198c69d9ac554c2ad5fc8b625292dc99b56fc6f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 23:00:30 2016 -0400
change the strategy for buildInfo.cpp/.o
previously, buildInfo.cpp was written independently of the compilation
of it into buildInfo.o. Now the creation and compilation are part
of a single target/rule. The main consequence of this is that if
the build fails, then we always rebuild buildInfo.cpp. We have to
force this in a slightly hackish way: there is a phony target
.FORCE that is used to force the rebuild
Exec/Make.Castro
commit 0acede5b8a6f0e36f7c1a3ead088882bb93e2cbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 22:28:34 2016 -0400
a little cleaning
Docs/Software/CastroSoftware.tex
commit 92105dc789aff44f6a6c1e657b574b2eb1d8514f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 22:05:08 2016 -0400
a little more docing
Docs/Software/CastroSoftware.tex
commit 12bbb33c3c69aec1da73c0d953f11ff8ab98a52d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 21:18:00 2016 -0400
data structures are in the previous chapter
Docs/FlowChart/FlowChart.tex
commit d054ffe8232e1c5c738e740db82831cc5055e15c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 21:01:58 2016 -0400
save doc hacking midstream
Docs/CastroUserGuide.tex
Docs/Software/CastroSoftware.tex
Docs/Software/index_grid2.pdf
commit c6c9fe54f19667921a13486df4cdbff4a85ed3c4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 8 16:21:32 2016 -0400
Move use_custom_knapsack_weights to the parameter list
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.H
Source/Castro.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit a0e92a4d50107ef784af4b226ac3099194a5aaf0
Merge: af9ad3177 3073e704e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 8 16:14:19 2016 -0400
Merge branch 'development' into dmap
commit ce01f1eec3a313b810cc34a642275ae29b763186
Merge: 95c005742 3073e704e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 16:08:11 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 95c005742d74a9af38085f10a120727a230293a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 16:07:45 2016 -0400
this is the version from wdmerger, which fixes ghost cell issues
and the new class methods
Util/yt/vol-wd.py
commit 3073e704e43be35fdf3b4a75273600721442b9b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 8 14:55:36 2016 -0400
Floor value of (rho e) depends on runtime options
Source/Src_nd/advection_util_nd.F90
commit f098e3f90616a788e00362195b115e2b523b2b84
Merge: 3b5fb90e7 e54547c63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 14:13:12 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit e54547c630dd20253cd6d9c0d4a8c1251b0088c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 8 13:49:56 2016 -0400
Fix a comment
Source/Castro.cpp
commit 8fa48cd714a26721d4f5a39d150bc346cf3c757f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 8 13:39:16 2016 -0400
Deal with case where density/energy already violated the floor
Source/Src_nd/advection_util_nd.F90
commit 3b5fb90e7ccdcdbd4e9e2331f18ec3fce1236706
Merge: 1fdcf00d8 5ea0932cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 09:06:56 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 1fdcf00d8e30510d865aa85d374673b968688abf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 8 09:06:46 2016 -0400
update comments
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 5ea0932cbb4b539dbcc923e3c054399c5ab6ce4c
Merge: 55f966b3a 621495679
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 21:20:26 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 55f966b3acc41eabc830cc5f4002f289a266d0af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 21:20:07 2016 -0400
finish the overview of the single-level strang algorithm
Docs/FlowChart/FlowChart.tex
commit 6214956797d491e07b327e9b2d8bbd2e66c631fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 21:03:51 2016 -0400
Fix indexing issue for shock variable
Source/Src_2d/Castro_advection_2d.F90
commit 85816fd1f09fe2a6509ca088b7fd3fb22e263122
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 20:30:15 2016 -0400
some updates
Docs/needs_doc
commit 6e1ac6ed7aa419e94170b5cf46944d5fcb4a4c2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 20:20:02 2016 -0400
fix typo
Docs/CastroUserGuide.tex
commit 0f039747db3fde0c37ad2220ac5e1347d2ba1d57
Merge: e01198624 9c6203501
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 20:01:17 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit e01198624463b2e05d5693af5fe67e2f9d8970b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 20:01:08 2016 -0400
fix formatting
Docs/FlowChart/FlowChart.tex
Docs/Software/CastroSoftware.tex
commit 9c6203501bdeca36892dc820fc3e43b84e810062
Merge: ee84d2fe5 fa11b9bdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 20:00:41 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit ee84d2fe5fc4729be5b8be8da972333f0ec2da24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 20:00:33 2016 -0400
more updates
Docs/FlowChart/FlowChart.tex
commit fa11b9bdc23a65c177b43b66171ea84f6d7d4bed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 18:58:38 2016 -0400
add LAPACK back -- radiation needs it (inelastic scattering?)
Util/LAPACK/Make.package
Util/LAPACK/dgtsv.f
Util/LAPACK/xerbla.f
commit 9f96138e03f6d139f5e18bbf312ee2a1a9543197
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 7 13:25:22 2016 -0700
Remove unused "include_pressure"
Source/Src_1d/Castro_advection_1d.f90
commit ba39b26943c9caf469c5391923464b008c0f801c
Merge: a5e3ab130 c3c0a9cca
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 7 13:24:53 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit a5e3ab13054abac33115a554d1ec6f1682bdf823
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 7 13:24:35 2016 -0700
Remove unused theta* variables
Source/Src_1d/Castro_advection_1d.f90
commit c3c0a9ccaa7b43033e68432ea6fe2f950e55cd8e
Merge: 87ebc89fe 71c6cca98
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 16:20:14 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 87ebc89fe5fd52058d89174e8cd239bbf4d38487
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 16:20:03 2016 -0400
lots more flow charting
Docs/CastroUserGuide.tex
Docs/Diffusion/CastroDiffusion.tex
Docs/FlowChart/FlowChart.tex
Docs/Rotation/CastroRotation.tex
commit 71c6cca981b40d92e14234cd863f0f66b3edbcf1
Merge: 9eb41d80c 0810d466a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 7 13:19:26 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 9eb41d80c19e1d799f9f79af958066b017ec386d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 7 13:18:57 2016 -0700
Fix file name in error output.
Source/Src_3d/trace_3d.f90
commit 0810d466a1e458053151724e520609917198b27c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 16:17:40 2016 -0400
Fix inconsistencies in flux weightings by dA and dt
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.F90
commit 21bd48296991d0a1e85420d8ff7344353f20fd67
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 15:57:03 2016 -0400
Re-insert accidentally deleted update code in 1D consup
Source/Src_1d/Castro_advection_1d.f90
commit f6da83659bad07e23367d5bfa432226fecbf66f2
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 7 12:56:02 2016 -0700
Remove unused variables and correct file name in error statement.
Source/Src_2d/trace_2d.f90
commit 919a8e5d847dc13168e06cc48d98e5f047efc67a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 15:12:31 2016 -0400
Fix the calculation of the source term predictor
The evaluation of dS/dt is now correct, at least for the momentum
source terms. All other source terms are now ignored for the predictor,
since only the momentum source terms really matter in the hydro right now.
Closes #18
Source/Castro_advance.cpp
commit 225e5822f1170196dc1e495cd465705b19742ceb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 15:03:55 2016 -0400
Update the CHANGES file
CHANGES
commit b0acd59bb740480c48bacb3657d9f7ae11c8318c
Merge: 0a41fd262 2599ad0c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 15:00:44 2016 -0400
Merge branch 'development' into flux_limiting
commit 0a41fd26217f56bf189023c5e7bfdd7d6d91aca9
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 14:44:05 2016 -0400
Use the dimension agnostic density flux limiter in 1D
Source/Src_1d/Castro_advection_1d.f90
commit 9078b56b001ec069be5f8d30835acbdd5474a96f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 14:40:13 2016 -0400
Hook up 2D hydro to the density flux limiter
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
commit 2dfcb9b8686aeb892cd7ffd350eda422122d4421
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 14:39:35 2016 -0400
Move density flux limiter to dimension agnostic source
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/advection_util_nd.F90
commit 2599ad0c62f889576ada76c3123fd2d06e263ee2
Merge: fb43c7bf5 ff3f8725c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 14:20:16 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit fb43c7bf5fb484bdee04022d8e6201dc6373acb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 14:20:03 2016 -0400
better write out the sequence of updates in equation form
Docs/FlowChart/FlowChart.tex
commit ff3f8725c8f15eaa804244cdd5439afecbf884cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 14:06:36 2016 -0400
Fix some tiling-unsafe array zeroings
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/advection_util_nd.F90
commit 59920977c191794dfbba380816f92a84568bc7b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 13:50:02 2016 -0400
Use UEINT source term as primitive QREINT source term
Previously, we used the UEDEN source term and subtracted off the
kinetic energy contribution. This allowed gravity and other source
terms to affect the pressure and (rho e) updates.
Closes #19
Source/Src_nd/advection_util_nd.F90
commit 5aff497d93734e82bf572b499cdb1bb3da0eeebf
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 7 13:46:38 2016 -0400
Fix gravity tolerance bug for single level runs
If you had a single level and did not specify gravity.ml_tol or
gravity.sl_tol in the inputs, then the tolerance would have been
set to a nonsense value. This has been fixed, the default tolerance
is now used if you don't specify it.
Source/Gravity.cpp
commit 7c7341abe4dffdb1f5e7e5abeb8e5738701b2c53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 12:12:42 2016 -0400
no more VODE et al.
CHANGES
commit 84a012962e98392f017e80e6256ee14dbeef3e55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 12:11:20 2016 -0400
add a note about compiling fun
Util/exact_riemann/README
commit d607727e39f99f7f8882671af72cbbb5fc9ecc72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 12:09:40 2016 -0400
don't need copies of BLAS, VODE, or LAPACK -- Microphysics controls these now
Util/BLAS/GPackage.mak
Util/BLAS/Make.package
Util/BLAS/daxpy.f
Util/BLAS/dcopy.f
Util/BLAS/ddot.f
Util/BLAS/dscal.f
Util/BLAS/idamax.f
Util/LAPACK/Make.package
Util/LAPACK/dgtsv.f
Util/LAPACK/xerbla.f
Util/VODE/GPackage.mak
Util/VODE/Make.package
Util/VODE/dacopy.f
Util/VODE/dewset.f
Util/VODE/dgbfa.f
Util/VODE/dgbsl.f
Util/VODE/dgefa.f
Util/VODE/dgesl.f
Util/VODE/dumach.f
Util/VODE/dvhin.f
Util/VODE/dvindy.f
Util/VODE/dvjac.f
Util/VODE/dvjust.f
Util/VODE/dvnlsd.f
Util/VODE/dvnorm.f
Util/VODE/dvode.f
Util/VODE/dvset.f
Util/VODE/dvsol.f
Util/VODE/dvsrco.f
Util/VODE/dvstep.f
Util/VODE/iumach.f
Util/VODE/ixsav.f
Util/VODE/test/GNUmakefile
Util/VODE/test/tvode.f
Util/VODE/vode.H
Util/VODE/xerrwd.f
Util/VODE/xsetf.f
Util/VODE/xsetun.f
commit 53efc5c5265f2b7a8510c8493d4a93f08e0cccfe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 12:05:38 2016 -0400
get this compiling again
Util/exact_riemann/GNUmakefile
commit 9000eaaa7bb4c30aac3900cde50b751879325d6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 11:52:50 2016 -0400
fix name
Docs/Software/CastroSoftware.tex
commit 8f02733695524c89155b87b4d5eade16fe65eb96
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 6 22:35:49 2016 -0400
Limit on (rho e) violating the energy floor
Source/Src_3d/advection_util_3d.F90
commit 7611751cedce9eb621df07e52ee4902ba9927c70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 22:24:58 2016 -0400
move source routines to their own file
Source/Castro.cpp
Source/Castro_sources.cpp
Source/Make.package
commit 951d1d390f1f78800f8ec52b8cbf3ea000e0632f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 22:14:11 2016 -0400
a little indexing
Docs/Inputs/CastroInputs.tex
commit c115adfa54955fa8648a873b63c9591930b751ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 21:40:42 2016 -0400
ignore index stuff
.gitignore
commit 8d523f89c616c6756d7bfb28689585476cd59c9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 21:40:07 2016 -0400
add an index
Docs/CastroUserGuide.tex
Docs/GNUmakefile
commit 4a9ae73cda1ac3e711204243fd5c80c4aa3c3848
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 21:33:34 2016 -0400
finish first pass at the flow chart
Docs/Equations/Equations.tex
Docs/FlowChart/FlowChart.tex
Docs/Gravity/CastroGravity.tex
commit 7fcd5c89fdb718fbce6bbd813f503a42c753ee2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 6 20:25:04 2016 -0400
Limit the intermediate LF fluxes too
Source/Src_3d/advection_util_3d.F90
commit 964f7a51c9968380be35945325efe0390feb45db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 20:06:15 2016 -0400
more work on the flowchart
Docs/FlowChart/FlowChart.tex
commit 1eb9068c766b5659c0cf8cbb643452b9004c8067
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 6 17:50:43 2016 -0400
Update 3D density flux limiting to new scheme
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/advection_util_3d.F90
commit 05c854259ad7e296675df274a9d0d4ca963b11bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 16:07:35 2016 -0400
add some comments to clarify which data structures we are operating on
Source/Castro_advance.cpp
commit 44cef1e314c445651e710d4e48f4a60e33e710b4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Sep 6 13:00:40 2016 -0700
tidy
Radiation.cpp
commit 7060bea59dae1ee4efef22786f52c0dbe396b721
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 6 14:42:35 2016 -0400
Add a clean_state that takes old data
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 9b42a120c293d850ab9e444dff5abc6a7e2863c2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Sep 6 11:25:34 2016 -0700
reduce duplicated BoxArrays in Radiation ::restart
Radiation.cpp
commit 1511c18cbfd7dd647639e8c6322d1e2c8477812e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 6 13:56:56 2016 -0400
Fix another hybrid flux issue
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/hybrid_advection_nd.F90
commit c9cde7edd1bff4375f1fc9d7d49c0b58516fa5fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 13:35:07 2016 -0400
finish outlining the main driver
Docs/CastroUserGuide.tex
Docs/FlowChart/FlowChart.tex
commit 88def439fd487ba3e0c13b384d07fd083b174646
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 6 12:54:18 2016 -0400
Fix a flux issue with hybrid fluxes
Source/Src_nd/advection_util_nd.F90
commit 270deab69c1bec95cf51812230a8269c585b47c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 12:42:07 2016 -0400
fix formatting
Docs/FlowChart/FlowChart.tex
Docs/GNUmakefile
Docs/castrosymbols.tex
commit 9e83f0c9cb55e8e09ff15788a2e2286e510c7055
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 12:10:07 2016 -0400
outline the main driver
Docs/CastroUserGuide.tex
Docs/FlowChart/FlowChart.tex
Docs/castrosymbols.tex
commit 72574a628d2f01cd1b512522ba00776d90140da8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 12:00:09 2016 -0400
some more comments on arguments
Source/Castro_advance.cpp
commit 2ce905e073c808c2adb5f5e37717bbe5a320be77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 11:41:57 2016 -0400
add a comment
Source/Castro_advance.cpp
commit d5eba420d788683dd216b145429c08511bb99896
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 6 09:44:25 2016 -0400
a little cleaning
CITATION
commit 6be337476b091663d137512d0194f27295aa8f81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 22:44:39 2016 -0400
add a CITATION file
CITATION
commit d5998dff0050e7e88161289e10bbcb13c2c1328c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 5 22:14:59 2016 -0400
Fix the Noh problem setup
Exec/Noh/Prob_nd.F90
Exec/Noh/bc_fill_nd.F90
commit cd880bf92d9495b726852ccfd06f48aeba7c1e72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 21:07:11 2016 -0400
forgot to initialize dtau
Src_3d/trace_ppm_rad_3d.f90
commit 4f58d815a5ae2e1ef0050dccc5a7b78212c01fc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 20:17:39 2016 -0400
update to reflect recent changes
CHANGES
commit 8dc1921b454789f6400f1ba6668d3f6e5476a9c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 19:07:45 2016 -0400
some radiation sync cleaning
Source/Src_3d/trace_ppm_3d.f90
commit 440f03fedf60071740b7bf25f45bcc597171ced8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 19:07:20 2016 -0400
implement ppm_predict_gammae
Src_3d/RadHydro_3d.f90
Src_3d/trace_ppm_rad_3d.f90
commit f1edc2bdf8205aa0282bf0b3a8d0c6b5e348e339
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 5 17:59:27 2016 -0400
Enable a new version of the density flux limiter in 1D
This follows the scheme of Hu et al. (2013) in JCP, which drops the
flux to a first-order scheme that guarantees positivity of density.
We have modified it to enforce the stronger limitation that the
density must remain above the user-specified small_dens limit.
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
commit f6cadb3d22c8a8fd859a05ecd843e404ef0db2ed
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 5 17:57:47 2016 -0400
Add a routine to compute a cell-centered flux
Source/Src_nd/advection_util_nd.F90
commit db4e804224c06548b46ef9688b59ef5803063e3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 15:40:25 2016 -0400
fix the gamma
Src_2d/trace_ppm_rad_2d.f90
commit 731d017f136523849950110e934b02f91c3ca14b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 5 14:53:20 2016 -0400
Fix gamma for double rarefaction problem
Exec/Sod/probin-double-rarefaction
commit 82678e69264586196ecdf8a6fe1a2e39db3664ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 11:29:15 2016 -0400
a little cleaning
Source/Src_2d/trace_ppm_2d.f90
commit 7394b11fd74a3307b2f56884ac149d61a1558e93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 11:28:51 2016 -0400
fix compilation issue
Src_2d/trace_ppm_rad_2d.f90
commit 76572b56937395f8c75261f5ab6c69b581831985
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 11:25:02 2016 -0400
1.d0 -> ONE
Src_2d/trace_ppm_rad_2d.f90
commit ab26b90ad540a96c200ae03507a97b4d27a2d979
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 5 11:16:28 2016 -0400
first pass at gammae stuff
Src_2d/trace_ppm_rad_2d.f90
commit 430155e04824eb75ba2eef9aa8485a2c2664023c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 22:06:42 2016 -0400
cleaning for the rad merge
Source/Src_2d/trace_ppm_2d.f90
commit bac4d75134ae76b3ba64a3f58145fda680afa828
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 22:05:58 2016 -0400
cleaning
Src_1d/trace_ppm_rad_1d.f90
commit 6b01d3cdc96a7af205ca679d4e599bfc18e7958c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 22:05:34 2016 -0400
start of gammae stuff
Src_2d/RadHydro_2d.f90
Src_2d/trace_ppm_rad_2d.f90
commit 30ebde0ed776387ba12177d454a472582ea413eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 20:44:50 2016 -0400
fix typo
Docs/radiation_notes/rad.tex
commit f3e753d5706703c5ef408ebe7e2b3a2c4027bfbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 20:43:54 2016 -0400
update notes for gamma_e radiation case
Docs/radiation_notes/rad.tex
commit 8f90c27e46b93d3ad4298d2a4bad6a8c2674f925
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 19:45:11 2016 -0400
fix the radiation energy state
Src_1d/trace_ppm_rad_1d.f90
commit f7674c5fe43e05937b0acc51a7993ea08d6cab9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 18:32:15 2016 -0400
start implementing the gammae stuff
Src_1d/RadHydro_1d.f90
Src_1d/trace_ppm_rad_1d.f90
commit b3ed78d067a9f105a9f13666e18bafaf120427f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 4 18:06:34 2016 -0400
a little cleaning to sync for rad merge
Source/Src_1d/trace_ppm_1d.f90
commit adef2337a8ddc9d49c95b37f9b8b969beeb31587
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 3 14:15:35 2016 -0400
fix a big typo
Docs/radiation_notes/rad.tex
commit e0ead115458fa070c8a2a540c1b9efac6a7f2299
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 2 18:35:05 2016 -0400
Add another double rarefaction Sod problem
Exec/Sod/inputs-double-rarefaction
Exec/Sod/probin-double-rarefaction
commit 76c6b3be9c1a41cd75c2da4cf08dafa156ef81aa
Merge: b2b64fdfd 0f88bde79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 1 19:18:00 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b2b64fdfd1b799cf378df4775d1b0c9cbca0a7bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 1 19:17:46 2016 -0400
more detailed notes on pressure interface issues
Docs/radiation_notes/rad.tex
commit 0f88bde7941a4aa4dec79238acf02641fef8d794
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 1 15:43:25 2016 -0700
Don't need QFS or QFX
Source/Src_2d/trace_2d.f90
commit 612b4697579fa8c910bf57601404e6d44554ddc0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 1 15:26:14 2016 -0400
Remove obsolete inputs parameters
Exec/Detonation/inputs-det-x
Exec/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/Sod/inputs-slowshock-x
Exec/Sod_stellar/inputs-test1-helm
Exec/Sod_stellar/inputs-test1-helm.gammae
Exec/Sod_stellar/inputs-test2-helm
Exec/Sod_stellar/inputs-test3-helm
Exec/Sod_stellar/inputs-test4-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/Sod_stellar/runs/CW/inputs-test1-helm
Exec/Sod_stellar/runs/CW/inputs-test2-helm
Exec/Sod_stellar/runs/CW/inputs-test3-helm
Exec/Sod_stellar/runs/CW/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC/inputs-test1-helm
Exec/Sod_stellar/runs/MC/inputs-test2-helm
Exec/Sod_stellar/runs/MC/inputs-test3-helm
Exec/Sod_stellar/runs/MC/inputs-test4-helm
Exec/StarGrav/inputs_2d
Exec/StarGrav/inputs_2d.test
Exec/bwp/inputs_2d
Exec/convective_flame/inputs.2d.test
Exec/gresho_vortex/inputs.2d
commit beb2b530a4bba24757d50b5b248f20cbcd50eab1
Merge: 4354b09be a6cd4b477
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 1 13:16:59 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 4354b09be7ebaec655a7549a11e9e042f556b878
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 1 13:16:39 2016 -0400
add tag
CHANGES
commit a6cd4b4774ef2fa9b0b834e5bf0249745464d019
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 1 12:18:35 2016 -0400
Only print out a warning on IO proc
Source/Castro.cpp
commit c5a747b366f33ed3f1fc7c9c20b9b8bd2a9d77f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 31 21:50:39 2016 -0400
Clear out some trailing whitespace
Source/Castro.cpp
commit b8d363770223af9771d26ed4593bf91b762a4ea1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 31 21:37:00 2016 -0400
No need to create drho_and_drhoU if not syncing gravity
Source/Castro.cpp
commit 47b4c1ac37df4208160e8ca51468d779a7c4f4cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 31 21:27:33 2016 -0400
Throw an error if the user provides no inputs file
Source/main.cpp
commit 7ce86134e963974645aa666a2bf7b4ba72fcb8fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 30 23:29:39 2016 -0400
Interpolate grad(phi) when using gravity.max_solve_level
Source/Gravity.H
Source/Gravity.cpp
commit 30299b6dd1787f633bf04b20aba6252c16dbd346
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 30 21:41:35 2016 -0400
some notes on pressure interface state
Docs/radiation_notes/rad.tex
commit 1c907b672c8d3a199754082e5053645df9e5058e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 30 15:15:04 2016 -0400
Fix capitalization typo
Microphysics/networks/general_null/write_network.py
commit 6eb1a892ec42e04df991760c5305c36c9e9c5235
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 20:46:39 2016 -0400
sync left and right tau_s for ppm_predict_gammae
Source/Src_3d/trace_ppm_3d.f90
commit babbebc6de73d75618c128214e1f12ad7344c040
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 19:12:43 2016 -0400
fix plotting
Exec/symmetry/inputs.1d
Exec/symmetry/inputs.2d
Exec/symmetry/inputs.3d
Exec/symmetry/probin
commit f3be42ecae6ca480959bbe2e360035b9e72c51c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 19:05:18 2016 -0400
add a new problem for symmetry testing
Exec/symmetry/GNUmakefile
Exec/symmetry/Make.package
Exec/symmetry/Prob_1d.f90
Exec/symmetry/Prob_2d.f90
Exec/symmetry/Prob_3d.f90
Exec/symmetry/README
Exec/symmetry/inputs.1d
Exec/symmetry/inputs.2d
Exec/symmetry/inputs.3d
Exec/symmetry/probdata.f90
Exec/symmetry/probin
commit f133ed008301248a3911a3719dbfa17f1085d25d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 18:49:42 2016 -0400
fix dimensioning in 1-d and uninitialized UMZ in 2-d
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
commit 2749082e8f3914280256996de19a93482b82897b
Merge: 69692a1fb 84365b04e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 14:46:30 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 69692a1fbdd5c4fb673874ed872b38caf5210cef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 14:46:13 2016 -0400
symmetry fix for ppm_trace_gammae = 1
Source/Src_2d/trace_ppm_2d.f90
commit af9ad3177f718ec2f6b23a24007bf5193ebe3987
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 29 10:52:57 2016 -0700
add Knapsack_Weight_Type
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
commit df117ed4548f80e19850d7b30c574f70bbfca2bf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 29 10:52:14 2016 -0700
Make NUM_STATE_TYPE a static variable and rename it to num_state_type. This provides flexibility of adding optional StateData.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
commit 84365b04e1614dbb32feac54a0291a3416609c51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 29 09:58:15 2016 -0700
a Castro-specific version
Util/job_scripts/edison/process.xrb
commit 4206929398aa7bd5f660a5c2b19dc04d5f4c5d4a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 25 17:57:28 2016 -0700
use the new FAbArray::BuildMask function
Source/Castro.cpp
commit e8e88fdcc6bb58abd4fde85d25e8b21df38dfc54
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 25 17:29:43 2016 -0700
remove calls to BoxLib::fill_boundary because it is deprecated
Source/Castro.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_hydro.cpp
Source/Castro_levelset.cpp
Source/Castro_react.cpp
Source/Gravity.cpp
commit 003936025330b029d88d82b02c0cc904f0ad8f65
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 25 16:05:17 2016 -0700
start to use FillBoundary for periodic boundaries
MGFLD.cpp
MGFLDRadSolver.cpp
RadSolve.cpp
Radiation.cpp
commit f8ae5703b110a67c988e888947261b8be0c34153
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 25 15:45:32 2016 -0700
remove unnecessary fillperiodicboundary calls because they do not even ahve ghost cells
Source/Castro_diffusion.cpp
commit 0fa866fdfaefccf0e45e267a3510ee6687195df2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 25 11:05:54 2016 -0700
use FabArray::copy for periodic copy
Source/Gravity.cpp
commit e74aa82a6aeaa3caaf6b752f50ca3267fef80583
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 25 02:05:00 2016 -0400
Make temporary copy of state for enforce_min_density
Source/Castro.cpp
commit b4a275805b56b2e6f9b8c5abf7c58711be41c19b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 23 12:30:05 2016 -0400
Keep fluxes in addition to other sources
Source/Castro.cpp
Source/Castro_advance.cpp
commit 085fe1e5974e4261e287566d554948f0a4bdf6df
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 23 02:31:22 2016 -0400
Use tileboxes in enforce_min_density
Source/Castro.cpp
commit 4711296de248f6226be16034ccf0ab2a522ebcd6
Merge: c9eebe575 60ccf14ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 21 19:02:39 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit c9eebe575bd7224dfa716a2cd1a1a4804bb90079
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 21 19:02:33 2016 -0400
formatting
Source/Src_nd/advection_util_nd.F90
commit 60ccf14ea369a8d359a6b41afd1692b17cf6c463
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 21 15:14:28 2016 -0400
Report grid bounds on a density reset
Source/Src_nd/advection_util_nd.F90
commit 4bcd25683409bb8477c517a06aecfc0ab2266bdd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 20 21:36:37 2016 -0400
Fix some inconsistencies in aux variables
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.F90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Enthalpy_nd.f90
Source/Src_nd/advection_util_nd.F90
commit cf416773c2daad236b589e817d8f8ee4629f22b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 20 21:19:06 2016 -0400
Add a hook to override the eos_t before EOS call
Microphysics/EOS/Make.package
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_override.F90
commit 3f78a206f3c809a3fdaa71ecbcbfa1f8b2294275
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 20 20:59:56 2016 -0400
Add C bindings to ca_compute_avgpres
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_3d/GR_Gravity_3d.f90
commit c2e0c845faf143a9bcec15aed93316eb0a9ab2de
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 20 20:59:26 2016 -0400
Make 1D GR gravity consistent with 2D/3D
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/GR_Gravity_1d.f90
commit 1ac68e9e4109c88b516dfcfbc4f0bfca933e070c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 21:25:05 2016 -0400
remove some unused variables
Src_1d/RadHydro_1d.f90
Src_1d/trace_ppm_rad_1d.f90
Src_2d/trace_ppm_rad_2d.f90
Src_3d/RadHydro_3d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 0ea355850d0315e4c02c94c0d2631ea719e88ab9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 21:03:16 2016 -0400
define QGAME
Src_1d/RadHydro_1d.f90
Src_2d/RadHydro_2d.f90
Src_3d/RadHydro_3d.f90
commit d76e4c6fb757ad330154c5537ee5679bfa432bae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 19:52:49 2016 -0400
remove drhoe and alpha0e -- they are not actually used
Src_1d/trace_ppm_rad_1d.f90
Src_2d/trace_ppm_rad_2d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 0f619dec6e96be4859105ea0a80e5ecdfed24c69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 19:18:35 2016 -0400
comments
Src_1d/trace_ppm_rad_1d.f90
commit 91f69d722d2672c6f6284b20b817204acf31f341
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 13:33:01 2016 -0400
update CHANGES to reflect 1-d ppm_predict_gammae
CHANGES
Source/Src_2d/trace_ppm_2d.f90
commit 91c32227d892994bf2333699335b74187ed11846
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 13:32:21 2016 -0400
update
Source/Src_1d/TODO
commit b47f84cef7abdd8b02105822a756ace72284fde5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 13:32:08 2016 -0400
add ppm_predict_gammae
Source/Src_1d/trace_ppm_1d.f90
commit dcbf472ff2f58ce0fef8357d8c99802a28974a40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 19 12:51:39 2016 -0400
update parameter changes
CHANGES
commit 78c8b57097434c8a5648c4dd183b87183fd35610
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 23:37:54 2016 -0400
a little cleaning
Src_1d/trace_ppm_rad_1d.f90
Src_2d/trace_ppm_rad_2d.f90
Src_3d/trace_ppm_rad_3d.f90
commit cb84da0a504352e5759204ed2c2c72723f4a95e2
Merge: ae35e3a7c 0c555f663
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 23:07:48 2016 -0400
Merge branch 'development' into hydro-cleaning
commit 0c555f663027e98dade1c9a7b79c06b744a085f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 23:05:17 2016 -0400
reenable gammae
Exec/Sedov/inputs.2d.cyl_in_cartcoords.gammae
commit 6ab05e1d708feef6205333af681206c0c8fa0222
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 22:56:01 2016 -0400
need a separate probin to set gamma
Exec/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/Sedov/probin.2d.cyl_in_cartcoords.gammae
commit ae35e3a7c00d18fa291109c6a56ae3acd0e4a8cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:59:49 2016 -0400
remove ppm_tau_in_tracing
Exec/Sod_stellar/trace_ppm_2d.f90
commit b3baab5baa6202917b1ba1645e60020769685885
Merge: 2b762210e 870d7ceeb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:39:52 2016 -0400
Merge branch 'development' into hydro-cleaning
commit 870d7ceeb5779bc85193476a9fcc590583000bd9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:39:29 2016 -0400
enable gammae
Exec/Sod_stellar/inputs-test1-helm.gammae
commit cd16ca8f3037bd0ce3d7af196c0c624e81ef5da8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:34:21 2016 -0400
remove redundant probin
Exec/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/Sedov/probin.2d.cyl_in_cartcoords.tau
commit 01d8e9ec52e4d55f55bcf85f4bf77436c0f4d746
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:33:07 2016 -0400
remove unused parameters and add gammae with tau to prep for tau removal
Exec/Sedov/inputs.2d.cyl_in_cartcoords.gammae
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
commit abdbd7d0883aa457eacadabee7f0aa82ae310587
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:16:50 2016 -0400
remove ppm_tau_in_tracing
Src_1d/trace_ppm_rad_1d.f90
Src_2d/trace_ppm_rad_2d.f90
commit 2b762210e400ce4229d29ba8eae062d9706bf96a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:08:23 2016 -0400
remove ppm_tau_in_tracing
Source/Castro.cpp
Source/Src_1d/TODO
Source/Src_3d/trace_ppm_3d.f90
commit 7c88ca33b35fde04c041cb4c7758ffeef4045b8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 21:08:01 2016 -0400
these are no longer used -- the F90 parmparse takes over
Source/castro_call_set_meth.H
Source/castro_set_meth.H
commit 8e988b81d9d7822a314249d3d46efffb53e48609
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 20:54:59 2016 -0400
remove ppm_tau_in_tracing
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 5203c55524007a59aee68b286f9d256c5227ff2a
Merge: c45a490c7 6e0ae31f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 20:51:45 2016 -0400
Merge branch 'hydro-cleaning' of ssh://github.com/BoxLib-Codes/Castro into hydro-cleaning
commit c45a490c7c398bbe1d7fa0007f0d517cd0d026ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 20:51:36 2016 -0400
remove ppm_tau_in_tracing
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 6e0ae31f3ac4a7f3368f972d21c9eb37df7ddff5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 20:34:36 2016 -0400
removed the wrong reference state for -z face
Source/Src_3d/trace_ppm_3d.f90
commit 30f123c5bd4994fc4effe91354f4df3fb2fa9c3d
Merge: 565a462ea 1e073126b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 19:29:53 2016 -0400
Merge branch 'hydro-cleaning' of ssh://github.com/BoxLib-Codes/Castro into hydro-cleaning
commit 565a462ea877009beae35da5986135e23e8b2d1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 19:29:46 2016 -0400
some tau_in_tracing work
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 1e073126b411555094fe25f7a6b6f03a20b7877f
Merge: 651f8e333 c3e5ff335
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 19:29:18 2016 -0400
Merge branch 'hydro-cleaning' of ssh://github.com/BoxLib-Codes/Castro into hydro-cleaning
commit 651f8e333609625d267ae959d316a1a51d77c532
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 19:29:09 2016 -0400
a little more cleaning
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/trace_ppm_3d.f90
commit c3e5ff3352ed8a77ad96208e549682a37f11d47b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 19:20:41 2016 -0400
update parameters
Docs/Equations/Equations.tex
commit 66e843be44729eaf340ef0db0ce59ac23eb621fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 18:32:45 2016 -0400
add note about removed reference state
Docs/runtime_parameters/rp_intro.tex
commit f592860ac186d7b2ff38b0e7a05b2258a7394095
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 18:27:09 2016 -0400
rmeove ppm_reference parameters
bwp/inputs_2d
bwp/inputs_2d.test
commit 1fdb1e9097eef76743b0456f6f2193bac92ffae7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 18:08:49 2016 -0400
fix compilation
Source/Castro.cpp
commit 0ece396788edc77b6421c04e5c2a10f8e27d0727
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 18:01:54 2016 -0400
no more ppm_reference_edge_value or ppm_reference
Src_1d/trace_ppm_rad_1d.f90
Src_2d/trace_ppm_rad_2d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 58b9258c5f81c490f5f243c86bbd4eb0e183e7bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 17:50:28 2016 -0400
no more ppm_reference or ppm_reference_edge_values
Exec/Sod_stellar/trace_ppm_2d.f90
commit 3663114bc1c454060a5420f304ab101fd231e456
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 16:34:41 2016 -0400
clean up the prediction -- we always use ppm_reference = 1 and
ppm_reference_edge_limit = 1, so we removed them as options
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 213f4ffc53463141084551c7be4b37a2720229aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 16:21:36 2016 -0400
remove ppm_reference and ppm_reference_edge_limit
Exec/Detonation/inputs-det-x
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/Sod/inputs-slowshock-x
Exec/Sod/inputs-test1-helm
Exec/Sod/inputs-test2-helm
Exec/Sod/inputs-test3-helm
Exec/Sod_stellar/inputs-test1-helm
Exec/Sod_stellar/inputs-test1-helm-y
Exec/Sod_stellar/inputs-test1-helm-z
Exec/Sod_stellar/inputs-test1-helm.tau
Exec/Sod_stellar/inputs-test2-helm
Exec/Sod_stellar/inputs-test3-helm
Exec/Sod_stellar/inputs-test4-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/Sod_stellar/runs/CW/inputs-test1-helm
Exec/Sod_stellar/runs/CW/inputs-test2-helm
Exec/Sod_stellar/runs/CW/inputs-test3-helm
Exec/Sod_stellar/runs/CW/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC/inputs-test1-helm
Exec/Sod_stellar/runs/MC/inputs-test2-helm
Exec/Sod_stellar/runs/MC/inputs-test3-helm
Exec/Sod_stellar/runs/MC/inputs-test4-helm
Exec/StarGrav/inputs_2d
Exec/StarGrav/inputs_2d.test
Exec/bwp/inputs_2d
Exec/convective_flame/inputs.2d.test
Exec/double_bubble/inputs_2d.single
Exec/double_bubble/inputs_2d.single.equal
Exec/flame_wave/inputs_2d
Exec/gresho_vortex/inputs.2d
Exec/reacting_bubble/inputs_2d
Exec/reacting_bubble/inputs_2d_test
Exec/test_convect/inputs_2d
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 87a2f78e60c5640f6a7e78d595e09197c5259832
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 18 12:15:24 2016 -0400
fix runtime parameter docs
Docs/CastroUserGuide.tex
Docs/runtime_parameters/rp_intro.tex
commit 0168701801bf49293faefdf3e4b75488a8ad03b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 20:05:48 2016 -0400
fix compilation error
Src_2d/trace_ppm_rad_2d.f90
commit a4b464ecd8f1379ba97176f5ee1cf265f7e66bd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 17:03:03 2016 -0400
more syncing with hydro
Src_2d/trace_ppm_rad_2d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 1ab703ac7555b081c0d354df5a8337b36d0b2543
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 17:02:41 2016 -0400
more syncing with rad
Source/Src_3d/trace_ppm_3d.f90
commit 793bad549092ae05ec6d884f50ced0cfedd91d2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 16:21:23 2016 -0400
a little more cleaning
Source/Src_2d/trace_ppm_2d.f90
commit 6a51628fd101d0642c525f1b7ab15cb2b1033f55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 14:40:00 2016 -0400
more cleaning and syncing
Source/Src_2d/trace_ppm_2d.f90
commit f0fc3af06b50d74214b3a3177312dc848981baa0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 14:02:29 2016 -0400
more syncing
Src_1d/trace_ppm_rad_1d.f90
commit bfa5ea1c7c9aaea769a7c10d73a4a06a0658dc8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 14:02:04 2016 -0400
more syncing
Source/Src_1d/trace_ppm_1d.f90
commit d2879fdd5a97d0ae70763dd2a9d4d2fa4e856f99
Merge: 105e2cbd2 bdbf65018
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 13:35:53 2016 -0400
Merge branch 'development' into hydro-cleaning
commit 105e2cbd2c48158410e9e5fe6c838423a4216463
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 17 13:34:34 2016 -0400
more cleaning progress
Source/Src_1d/trace_ppm_1d.f90
commit bdbf65018085804f40249917424a768096570e20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 22:00:12 2016 -0400
syncing with the radiation version
Source/Src_3d/trace_ppm_3d.f90
commit eca494507cb10e8c08cbb454855aa16061bca996
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 21:31:20 2016 -0400
more syncing with the rad version
Source/Src_2d/trace_ppm_2d.f90
commit b871d4dddf2a49d361ddec29ccd889e9bd734bf3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 21:10:44 2016 -0400
rename the alphas to be consistent with rad hydro -- this cleans up the diffs
Source/Src_1d/trace_ppm_1d.f90
commit a7508f6f7fb2d68e417ee3f0ffd245e62bff0e7f
Merge: 3dcc5874d a8ccebdb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 20:19:11 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit a8ccebdb7982da3c5434d1eef854f3f1b244eb92
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Aug 16 15:54:28 2016 -0700
add function declarations for a number of problem_post_*
Source/Castro.cpp
Source/Problem.H
commit 3dcc5874d9c0739cce8ae5120d5f83919f41a70b
Merge: c0e833eeb 0872e3031
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 18:53:33 2016 -0400
Merge branch 'development' into hydro-cleaning
commit 0872e3031de9430f5959629c429b56ef803e88c1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Aug 16 14:20:37 2016 -0700
more fixes for USE_GR
Source/Src_2d/GR_Gravity_2d.f90
commit 5514ed42127a821ecf8ed3e2ce4598bb9cb974e8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Aug 16 14:12:33 2016 -0700
fix some typos in USE_GR
Source/Gravity.cpp
commit c0e833eeb6c92fff576faf1bb90326facc243ee1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 16:20:11 2016 -0400
sync up with the main versoin
Exec/Sod_stellar/trace_ppm_2d.f90
commit 2c8489484568155ca0feda5b458023cfdbf8222b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 16:01:05 2016 -0400
fix game_ref on +y face
Source/Src_2d/trace_ppm_2d.f90
commit 1adc40809582259f56f9f45b0d5916f7bca4d073
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 13:46:12 2016 -0400
remove checkpoint_version entirely
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit ff0a979b0befe18903b4d83ba0ca62e4b1310f83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 13:40:09 2016 -0400
update parameters
Docs/runtime_parameters/runtime_parameters.tex
commit 93c2e35f8b8382b14fecbc5652fd03c68995c719
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 13:38:27 2016 -0400
more checkpoint_version and do_reflux into _cpp_parameters
Source/Castro.H
Source/Castro.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 400fd01465e7a3c28e6b19b6801f754fbd25a9bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 13:24:31 2016 -0400
also note the separate flux register used for axisymmetric pressure
Docs/AMR/AMR.tex
commit 1745c8a24b05e03fe98ba17855cd3942d56deac3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 13:20:58 2016 -0400
document do_reflux and gravity.no_sync
Docs/AMR/AMR.tex
commit e98557340dbcf4f349c63181064c15d3a0806c76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 13:08:21 2016 -0400
sync with the pure hydro version
Src_3d/RadHydro_3d.f90
Src_3d/trace_ppm_rad_3d.f90
commit d03e333592e0ce944681c24cdd8e40d7b10f736b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 12:50:11 2016 -0400
sync with rad version
Source/Src_3d/trace_ppm_3d.f90
commit d257a8faa958bf5c20ee7a78a13c7d166289a215
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 11:41:44 2016 -0400
sync up with the pure hydro version
Src_2d/trace_ppm_rad_2d.f90
commit 9bfdaac07245c72e1149c2217309cc02695ea91c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 11:38:38 2016 -0400
sync with the rad version
Source/Src_2d/trace_ppm_2d.f90
commit 3b42acebad30e90e0e1cbdc87cd2b2ca8b0a75dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 10:59:30 2016 -0400
sync up with the pure hydro verison.
no answers should change
Src_1d/RadHydro_1d.f90
Src_1d/trace_ppm_rad_1d.f90
commit a2ddcb2c2d6290c7cc02afd1559a25db8a180b0b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 10:51:14 2016 -0400
some syncing with radiation to help with a merge.
No answers should change.
Source/Src_1d/trace_ppm_1d.f90
commit 3353e28cddad89170cc3c303d9bf626e726353fe
Merge: 7a174c291 221193b02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 10:01:51 2016 -0400
Merge branch 'development' into hydro-cleaning
commit 87b71c3a054e264513b936129b99e32f75572068
Merge: 9cab69726 880910e51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 09:57:47 2016 -0400
Merge branch 'development' into hydro-cleaning
commit 880910e51bc2d109c21222eda44ef372b1939d87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 09:56:59 2016 -0400
add intro
Docs/runtime_parameters/rp_intro.tex
commit 221193b02dd3395dfa0dc9eec5800ad278e69228
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 16 09:53:55 2016 -0400
fix compilation error
Src_2d/RadHydro_2d.f90
commit 7a174c2911487d5ae0cdcb7de6fbe45027fe820f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 23:31:39 2016 -0400
remove ppm_flatten_before_integrals
Src_1d/trace_ppm_rad_1d.f90
Src_2d/trace_ppm_rad_2d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 9cab697268997714919de16db1ca7e77a95c4f98
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 23:19:04 2016 -0400
remove ppm_flatten_before_integrals
Source/Src_3d/ppm_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 44e2cd9525a562685ee4d3785eaa64f4c2537e70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 23:05:47 2016 -0400
remove ppm_flatten_before_integrals
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 7d6f54dbc09b39c71e7a91c5670273eda56c378e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 22:54:06 2016 -0400
remove ppm_flatten_before_integrals -- note this also adds flattening to ppm_type = 2
Source/Src_1d/ppm_1d.f90
Source/Src_1d/trace_ppm_1d.f90
commit 22b1f535d549b1a407dd9c198cb4e3a87194f839
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 22:45:26 2016 -0400
remove ppm_flatten_before_integrals
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 508828c7cf9c3bac594b138e9de7d549feb55694
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 22:43:19 2016 -0400
rmeove ppm_flatten_before_integrals
Exec/Detonation/inputs-det-x
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/Sod/inputs-slowshock-x
Exec/Sod_stellar/inputs-test1-helm
Exec/Sod_stellar/inputs-test1-helm.tau
Exec/Sod_stellar/inputs-test2-helm
Exec/Sod_stellar/inputs-test3-helm
Exec/Sod_stellar/inputs-test4-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/Sod_stellar/runs/CW/inputs-test1-helm
Exec/Sod_stellar/runs/CW/inputs-test2-helm
Exec/Sod_stellar/runs/CW/inputs-test3-helm
Exec/Sod_stellar/runs/CW/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC/inputs-test1-helm
Exec/Sod_stellar/runs/MC/inputs-test2-helm
Exec/Sod_stellar/runs/MC/inputs-test3-helm
Exec/Sod_stellar/runs/MC/inputs-test4-helm
Exec/StarGrav/inputs_2d
Exec/StarGrav/inputs_2d.test
Exec/bwp/inputs_2d
Exec/convective_flame/inputs.2d.test
Exec/gresho_vortex/inputs.2d
Exec/reacting_bubble/inputs_2d_test
Exec/test_convect/inputs_2d
commit b23e0e98f0dd0b89a31bf976091b6c38bf425d0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 22:37:42 2016 -0400
new section
Docs/CastroUserGuide.tex
Docs/GNUmakefile
Docs/runtime_parameters/rp_intro.tex
Docs/runtime_parameters/runtime_parameters.tex
commit 5381ab01d3e50ebae4a5543e171ad6498c25535e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 22:14:40 2016 -0400
actually trace the sources...
Source/Src_1d/trace_ppm_1d.f90
commit 9df7986aee01b1a0dfc9c70eb0c946f257bf8515
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 20:46:29 2016 -0400
update
CHANGES
commit 973bf3b5245aace0145189ef27f5832018f73c50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 20:43:33 2016 -0400
update TODO
Source/Src_1d/TODO
commit e503accdef5b89eec1070787b95111eb352f966f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 20:43:04 2016 -0400
add source tracing and fix flattening
Source/Src_1d/trace_ppm_1d.f90
commit 129546d5b6dfae72a6ace42b2996119d6deeb6f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 20:01:40 2016 -0400
fix indententation
Source/Src_1d/trace_1d.f90
commit 04312fac7c0d52c4eff9f1decd413423498b711f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 11:22:23 2016 -0400
fix ilo,ilo -> ilo,ihi
Src_1d/trace_ppm_rad_1d.f90
commit 35eeaffcc8df4144ee50174119ee368057a1e378
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 10:50:51 2016 -0400
QU: -> QU
Src_1d/trace_ppm_rad_1d.f90
commit da23d9ffaa548dfb97cd943d89c86d064ac9f13c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 15 10:04:38 2016 -0400
we were not dimensioning srcQ correctly
regardless of radhydro, it is always QVAR, not QRADVAR
Src_2d/RadHydro_2d.f90
commit 9ee369430f9cc05acd62369bd01294a4833bad28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 14 12:10:21 2016 -0400
if we do ppm_type = 0, then drop back to ppm_trace_sources = 0
we use parmparse to reset it so the F90 queries know about the change
Source/Castro.cpp
commit becba4b983c7e1168c6eafb4fc7d41575433d01c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 14 03:07:06 2016 -0400
If keeping source terms, wait until level 0 to clear
Source/Castro.cpp
commit fed1ce7e5d40e3eb81005851c179a8d85037f4fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 13 23:26:34 2016 -0400
Only use fine-level data for multipole on multilevel solve
Source/Gravity.H
Source/Gravity.cpp
commit fb8051083a130f7a7160e8f5dad1611cc6b4a14e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 13 22:53:32 2016 -0400
Fix some bugs in the multilevel multipole solve
Source/Gravity.cpp
commit 8b8604446cc6efcb2f08997bd3ccf1a89abb39e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 20:15:06 2016 -0400
add a comment
Src_3d/trace_ppm_rad_3d.f90
commit 36f9d3d1bd2c9b11b89d2e5eff5d1d597a8ab5ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 19:53:42 2016 -0400
make ppm_trace_sources = 1 the default
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
commit 912fd0e723a4e6553df5705644e26b50f535df78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 18:06:45 2016 -0400
fix rhoe_ref
Src_3d/trace_ppm_rad_3d.f90
commit 8b0484ac68e784f20c2f1a6183bf99e0a1bcc3a5
Merge: c996d6a45 f0afbe6be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 17:50:13 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit c996d6a45fba67dccea2c5fb89de2f9f8ef1a8eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 17:49:46 2016 -0400
note about 3-d radiation
CHANGES
commit f0afbe6be5794c3209b6664211c814c2df2f05a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 17:31:23 2016 -0400
ppm_trace_sources works with radiation now
Source/Castro.cpp
commit 2ccf18a97b92b61cf54a4521d8e51426850e5706
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 17:16:37 2016 -0400
sync up with the pure hydro version. In particular, this
implemented reference states (already was done in 1- and 2-d)
and source term tracing
Src_3d/RadHydro_3d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 9ea9d6a2431eccf2c7da1654f2df9edd64970be2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 21:33:12 2016 -0400
add a section on the point mass based on Slack conversation with
Max and Austin
Docs/Gravity/CastroGravity.tex
commit 163c8ceff9c4db5a34a9de4389b7e151da02ad56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 21:06:42 2016 -0400
change the default of point_mass_fix_solution to 0
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
commit ab4614c0347f340b7157b21b5f114ba1beeafa26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 20:47:49 2016 -0400
add allow_negative_energy
CHANGES
commit 07c87472ac7f2f2591814ded99e46b532961d761
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 12 20:45:21 2016 -0400
Update F90 version of point_mass if it changes
Source/Castro_F.H
Source/Castro_pointmass.cpp
Source/Src_nd/Castro_nd.F90
commit e83e2d7276bbda63030061a67d048d7bec002a71
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 12 20:35:16 2016 -0400
Make some source term arguments optional
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 8047ba89796d78eacc8227c630f74d5bda254b81
Merge: 07b101f01 3997e5ef2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 15:09:37 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 07b101f0187e38ab116e1abd37c1d5da23d902e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 15:09:09 2016 -0400
change allow_negative_energy default to 0 -- this is a safer
default. If you really know what you are doing, you can reset
it to 1
Docs/runtime_parameters/runtime_parameters.tex
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
commit 3997e5ef2eac899fcba839b97f728bad31cd8cec
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 12 14:47:03 2016 -0400
Expanded temperature/density range
Exec/test_react/probin
commit 6e848e2fb4d285caddd5d16067bd7f12af8cd1fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 12 14:28:34 2016 -0400
Use the make_radial_gravity routine in 1D
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Gravity_1d.f90
commit db38b93d0f72a4a61bab5460eb99b6bd356837d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 10 17:56:08 2016 -0400
Add some Fab_allocate arguments
Source/Castro_advance.cpp
commit afc705e2c5483c9e7317edbbd50485f9fad161d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 10 17:30:09 2016 -0400
Update rotation references to fluxes
Source/Castro_rotation.cpp
commit 2f9bc14dc532c3ea719d43cf3e3de1d32d5b51d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 21:17:30 2016 -0400
add note about axisymmetric fix
CHANGES
commit 213e3003702a4a3b15d85f9963d5650293a41a9d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 8 18:10:08 2016 -0700
forgot to uncomment pres_reg Reflux
Source/Castro.cpp
commit 281963f5603cebfb730650a5f407e35dc4c027b3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 8 17:30:31 2016 -0700
pressure reflux in curvilinear coordinated
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Castro_io.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
commit d24c220332145a2316594095530e45ca71978a79
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 8 18:01:34 2016 -0700
pressure reflux in curvilinear coordinates
Src_1d/CastroRad_1d.f90
Src_1d/RadHydro_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
commit 3738d9796f2987f78306eb13adbfe1a7435efe50
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 18:51:13 2016 -0400
Give dPdr a value so that we aren't testing on nonsense value
Microphysics/EOS/gamma_law/gamma_law.F90
commit c88501ea5fe321e6462b772afac62d3381cbb1db
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 8 15:17:19 2016 -0700
remove FluxRegister*
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
commit ad51050f7b52ea1442473a60fd55fe3c09943b08
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 8 15:07:20 2016 -0700
remove a number of MultiFab*
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_hydro.cpp
Source/Castro_react.cpp
Source/Castro_rotation.cpp
Source/Castro_sponge.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 4cc09959266399267267e7e019162306605fe008
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 8 14:16:01 2016 -0700
remove raw pointer fine_mask
Source/Castro.H
Source/Castro.cpp
Source/Gravity.cpp
Source/sum_utils.cpp
commit 314937a5ffc9c249ec67b643d6536c7d72aeff96
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 15:55:56 2016 -0400
Clean up Sborder after advance is done
Source/Castro_advance.cpp
commit a68a7badf2bd555fb8c9382ebb73100ade54e68f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 14:35:37 2016 -0400
Optionally retain source terms until end of post_timestep
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.cpp
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit eecb60a7be74c676d447d4acdc5b4ba661220f37
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 13:55:41 2016 -0400
Only update sponge parameters if doing sponge
Source/Castro_sponge.cpp
commit 5c35970e07582f235541bf12ed930f24b3df4562
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 12:52:44 2016 -0400
Optionally time-center the sponge source term
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro_sponge.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 7357dcacdb2028debb83ecb0d44d0073d4822b0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 11:52:47 2016 -0400
Allow sponge to vary on range other than [0, 1].
Source/Src_nd/Castro_nd.F90
Source/Src_nd/sponge_nd.F90
commit d6cf676683ab4989c2d3d76e3a6b7e7858dd5c20
Merge: aa5020845 cdc1717ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 11:16:51 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit aa50208454a3ad6122ee478e259359de24df68e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 11:16:41 2016 -0400
add support for n_rhs, n_jac
Microphysics/networks/burn_type.F90
Microphysics/networks/sdc_type.F90
commit cdc1717ad46b3a49cc1342966b07c237134f969b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 8 10:22:39 2016 -0400
Preprocessed file needs to be .F90
Microphysics/EOS/gamma_law/Make.package
Microphysics/EOS/gamma_law/gamma_law.F90
commit f70aebeba0f028321303487a54998c72f7aa9c6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 09:43:17 2016 -0400
reremove species derivatives
Microphysics/networks/burn_type.F90
commit badaf689bd1652a86199b02e416fcc1ed59bde75
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 7 14:15:18 2016 -0400
Update some source term comments
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/rotation_sources_nd.F90
commit 0eccdbba5576782ad1065a7e35b507197f10f855
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 7 01:49:08 2016 -0400
Clean up white space
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/advection_util_3d.F90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trans_3d.F90
commit 7e1b10301196dca2af8662c47ccdd252cea850d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 7 00:49:41 2016 -0400
Move the species flux normalization after the AV in 1D/2D
Fixes #4
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.F90
commit 92edd05930b7d8736f948d1d3e834922a5cbb8b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 7 00:22:26 2016 -0400
Fix another undefined variable issue
Source/Castro.cpp
commit 5ab6c5cfbbab698887f7763bb9b4ec59f586aee0
Merge: 2cc20947f b3b6acba8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 7 00:11:15 2016 -0400
Merge branch 'development' into oac_reactions
commit 2cc20947f03752d88a6d38d94d42da00dc7f18e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 21:24:45 2016 -0400
Quiet unused variable warnings
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Derive_nd.f90
commit 4853a9de3cd9fe448933bbb72e3177a8fd19255e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 21:24:24 2016 -0400
Fix an undefined variable problem
Source/Castro.cpp
commit c90275fb2e61e28f08d256ddc35d1f178f99fd15
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 19:59:21 2016 -0400
Remove smallt/smalld from eos_t
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.f90
commit cdc835b0b6a8a077201860c4aaa73ef577fa1f5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 19:36:23 2016 -0400
Include missing module reference
Microphysics/networks/general_null/actual_rhs.f90
commit b2a385d91716ae04aff1ca44355a6b0ba0cfbd7e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 17:03:52 2016 -0400
Move some test_react parameters to the extern module
Exec/test_react/GNUmakefile
Exec/test_react/_parameters
Exec/test_react/probin
Exec/test_react/testburn.f90
commit 69319619b2b5c4ec93f9a9f9a8df5ff033fe724d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 17:03:24 2016 -0400
Allow extern_core to be set by the problem
Exec/Make.Castro
commit e5e1f701c95584219be2178f8669b7982158cba7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 16:02:34 2016 -0400
Add missing endif
Microphysics/EOS/eos.F90
commit ecbcac3ecc92006491e0d9a6021558ffecb088c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 14:44:49 2016 -0400
Remove shock from burn_t
Microphysics/networks/burn_type.F90
Microphysics/networks/burner.F90
Source/Src_nd/React_nd.F90
commit bf8660d0ed2f6053e61b55611309d73f88419094
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 14:27:12 2016 -0400
Do not initialize the burn_t
Microphysics/networks/burn_type.F90
commit f336ea12cf44355981e2cb05e3a409dc298401b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 14:22:31 2016 -0400
Reorganize subroutines
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.f90
commit b3b6acba88aaa6f21a7ebdc9548594aad759b3c2
Merge: 834ac3594 95e6b21b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 6 13:47:11 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 834ac359476d389f6fe2c27fcd32f3a26f9c4a8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 6 13:46:58 2016 -0400
add note from slack
Docs/notes.txt
commit d0c17d51141b6277e4df3cbda0d71e96b6b5a247
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 13:36:45 2016 -0400
Do not explicitly check inputs for validity
Microphysics/EOS/eos.F90
commit 5f0afeb476daa2db74c99ab856b6914c462b2de9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 13:07:04 2016 -0400
Make EOS resetting mandatory
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.f90
Microphysics/networks/burn_type.F90
Source/Src_2d/trans_2d.F90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/timestep.F90
commit 204de2fc925f8e7049ccb12b44bc46ab39f022b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 12:48:11 2016 -0400
Avoid bl_error in ACC mode for gamma_law
Microphysics/EOS/gamma_law/gamma_law.f90
commit 84a8e1e84de4c935af5a300d82550db4064d958f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 12:47:47 2016 -0400
Make consistent the validity checking in EOS
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.f90
commit 19a1c7869ccf25d66e1586d81d4993618c7a2074
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 12:23:16 2016 -0400
Split up EOS checking and resetting
Microphysics/EOS/eos.F90
commit 5a992f1668e152428c9ee29ab8c039c0b20ccbed
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 11:48:04 2016 -0400
Add a clean_state routine to the EOS
Microphysics/EOS/eos_type.f90
commit b6342ebd85689259088157a786ed76dfa08ddb84
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 11:34:01 2016 -0400
Simplify: get rid of smallt/smalld in EOS
Microphysics/EOS/eos.F90
Microphysics/EOS/eos_type.f90
Source/Src_nd/Castro_nd.F90
commit 95e6b21b2fed65dcae8d41e9f5c93ffd456b4078
Merge: 4db6226e3 1392dc487
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 5 19:12:41 2016 -0400
Merge branch 'development' into riemann-cleaning
commit 1392dc487dc45e2ad6ea78c01870c05a2070f2ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 5 19:12:29 2016 -0400
formatting
CHANGES
commit 94deff9cf912a1b2a7ecf4cfdb586f35a3f90044
Merge: cb6ca1eac ad1f4c36f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 18:38:41 2016 -0400
Merge branch 'development' into oac_reactions
commit ad1f4c36f9cf3a876a1147455933816712cc0435
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 18:30:25 2016 -0400
Add some changes
CHANGES
commit 1c64916c0d71f2abfbe7e282c38cb6f8bf0a93fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 18:23:18 2016 -0400
Flip the sign on the gravitational potential
Docs/AMR/AMR.tex
Docs/FlowChart/FlowChart.tex
Docs/Gravity/CastroGravity.tex
Source/Castro_gravity.cpp
Source/Gravity.cpp
Source/Src_1d/Gravity_1d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/pointmass_nd.f90
commit 68f4c2ccd1d34316710e3959bc60dd3758dc9c0e
Merge: 0a2eabd94 2e340c3f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 14:04:11 2016 -0400
Merge branch 'development' into SDC
commit 841cda4fe531efa5815f62b036e7beae45db49c6
Merge: 7455329d1 9138d2f33
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 14:00:29 2016 -0400
Merge branch 'development' into SDC
commit 4db6226e32372cfca96c836cd5799a191f470b2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 5 12:33:30 2016 -0400
move the pstar bisection fallback into riemann_util
Source/Src_2d/riemann_2d.F90
Source/Src_nd/riemann_util.f90
commit 7455329d1b3dc0c341c859eecf39c70897a280ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 11:45:02 2016 -0400
Remove unused variables
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
commit a7aa92996061e83d019d92f61660a7d5cd0c8419
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 11:43:55 2016 -0400
Clean up the diffusion code
Source/Castro.H
Source/Castro_diffusion.cpp
commit d967876afdd0292d2d494cb804b3be08b5b7c84a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 5 11:08:45 2016 -0400
Rename a data log
Exec/toy_flame/inputs.1d
Exec/toy_flame/inputs.1d.testsuite
commit 0a2eabd9499a9b7195b859473b77ac488bbab234
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 4 22:46:48 2016 -0700
moved inelastic scattering code from Castro to here and reworked a little
Castro_radiation.cpp
MGFLD.cpp
RAD_F.H
Rad_nd.f90
Radiation.H
commit 6f7477031dfcd472d13f7ec7cceec025970d8cf1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 4 22:34:26 2016 -0700
move inelastic scattering out of the main Castro
Source/Castro_hydro.cpp
commit b3300244ccd4fabed573e60f72960762b760ecf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 4 21:57:53 2016 -0400
this does a more robust bisection
Source/Src_2d/riemann_2d.F90
commit 9138d2f33fc75ce9456e6c2497bffefb45eaf817
Merge: 74cf9d325 5cf3915bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 4 21:43:52 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 74cf9d325a6d0ee022f3a3d070f253c4dbbfd4ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 4 21:43:27 2016 -0400
this seems to run fine with the CG solver -- the trick is
to use the gamma_e prediction it seems
Exec/bwp/inputs_2d
commit b84195e94db3ffbe493b6a486eae1a7e6ffcfcbb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 21:09:05 2016 -0400
Initialize radiation energy if not doing hydro
Source/Castro_advance.cpp
commit 2e340c3f22f26c947fa39dd325ea1005fc85a57f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 20:18:45 2016 -0400
Revert commits that should have been in a topic branch
This reverts commit 2f959ff9563459487a6e0ab5f600fd77472ea2f7.
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit ef5b2b86fd630919d656120909f0d6686a592e6d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 04:27:07 2016 -0400
Don't duplicate enforce_min_density/normalize_species
Src_1d/CastroRad_1d.f90
Src_2d/CastroRad_2d.f90
Src_3d/CastroRad_3d.f90
commit 12881c1a0a45c1eb0353458a25b253c038b7aaae
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 04:08:33 2016 -0400
Update consup_rad to not overwrite old sources
Src_1d/RadHydro_1d.f90
Src_2d/RadHydro_2d.f90
Src_3d/RadHydro_3d.f90
commit 1507945b55a42f565f2265e82839432cc3cf5843
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 4 16:44:20 2016 -0700
fix new bugs
Src_2d/RadHydro_2d.f90
Src_3d/RadHydro_3d.f90
commit 5f0c247c393d5a767ebdcefecd38edb185688ad0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 19:39:22 2016 -0400
Remove obsolete assertion
Source/Castro.cpp
commit d8b7a8ea58606de286ddfc4be065ca99c003ba2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 15:44:36 2016 -0400
fill_boundary on hydro sources for backward compatibility
Source/Castro_hydro.cpp
commit 9b7fbce653111ee93a61eb1499e5432361b4088d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 15:41:38 2016 -0400
Revert to old handling of source terms in ghost zones
Source/Castro_gravity.cpp
Source/Castro_hydro.cpp
Source/Castro_rotation.cpp
commit 5cf3915bcf961e22c01ad834ce2468d79351ba71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 4 11:57:53 2016 -0400
CG solver cleaning: mostly renaming for consistency, but some additional checks too
Source/Src_2d/riemann_2d.F90
commit a096730b7bb7e8ec0eaa39facce3d5b0f6ade2df
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 05:07:37 2016 -0400
Do new-time source terms without ghost zones, for now
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_rotation.cpp
Source/Castro_sponge.cpp
commit dbb2336ed4cb3921eeed480fa86bf4dee866f680
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 04:27:07 2016 -0400
Don't duplicate enforce_min_density/normalize_species
Src_2d/CastroRad_2d.f90
Src_3d/CastroRad_3d.f90
commit 00f840e0b5c79ae822983e1a24d2fb7fe3817e37
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 04:08:33 2016 -0400
Update consup_rad to not overwrite old sources
Src_2d/RadHydro_2d.f90
Src_3d/RadHydro_3d.f90
commit 7f690baa0b00a8426652a5cae851bd58ce4aa0b5
Merge: 9b7dc67be f8fc638e1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 01:35:42 2016 -0400
Merge branch 'development' into SDC
commit 9b7dc67befbe969ffa183f6bf7849fadb00fce04
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 01:35:27 2016 -0400
Fix radiation compile failure
Source/Castro_hydro.cpp
commit 086bc1cd86f7cd1848bbb99e1706f99ea45b2eda
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 01:01:02 2016 -0400
Fix bug for 1D diffusion
Source/Castro_diffusion.cpp
commit 614f21119a5b169149d609fba26b12573f2b96ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 4 00:25:07 2016 -0400
Fix typo
Source/Src_2d/Castro_advection_2d.F90
commit f8fc638e1c6cd9d69174dbad8960cbf64315adea
Merge: ef4e4cc87 b65f86269
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 23:14:34 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit ef4e4cc87db303662d6197c6a359d606bf07a759
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 22:45:49 2016 -0400
add riemann_test_zone
CHANGES
commit b65f86269ff027222864aec4770ed2dc05a06f55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 22:42:24 2016 -0400
this is a case that fails from BWP
Exec/riemann_test_zone/inputs.2d
Exec/riemann_test_zone/probin
commit a2ed9026a66ba169991ac117242d9af6e05fc871
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 22:13:09 2016 -0400
this is a simple fake setup that just calls the riemanncg solver
given a left and right state (via probin). This can be used to
diagnose Riemann convergence failues by initializing this problem
with the output from the riemann solver from non-convergence
Exec/riemann_test_zone/GNUmakefile
Exec/riemann_test_zone/Make.package
Exec/riemann_test_zone/Prob_2d.f90
Exec/riemann_test_zone/README
Exec/riemann_test_zone/inputs.2d
Exec/riemann_test_zone/probdata.f90
Exec/riemann_test_zone/probin
commit 87678eff0fd1ba1a6818399e27ddc61d25bb0b8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 21:51:58 2016 -0400
make riemanncg public for unit testing
Source/Src_2d/riemann_2d.F90
commit b92155de09dfcd442cf1eca573283a78e3051412
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 21:19:56 2016 -0400
output more info if we fail to converge
Source/Src_2d/riemann_2d.F90
commit a688e21ac536e15b3b7b1274b60b301152c905b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 3 16:14:53 2016 -0400
Fix some ghost zone logic
Source/Castro.cpp
commit d11994168a91acd32267887ea7776966c8f4f91d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 3 12:40:38 2016 -0400
new sponge based on density
Exec/bwp/probin.dens_sponge
commit 7099810424d3e2a31c209f790c8780815a940357
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 2 19:51:28 2016 -0400
Permit state data to have ghost zones
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_setup.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit d7626d9e8b7e716a40bff2fc50e174b1c7d9c0ad
Merge: a211ddec6 bacb7f009
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 2 19:07:38 2016 -0400
Merge branch 'development' into SDC
commit bacb7f009214ce97b90f3b1ed21d9a211e4ed919
Merge: b0bd4f85d ae93d74c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Aug 2 15:21:18 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b0bd4f85d3529d1a82630efce4f34a874e538d0b
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Aug 2 15:20:58 2016 -0700
Latest version of inputs
Exec/Vortices_LWAcoustics/inputs.2d
commit 620129ed4cce2eb6ef2df6bc751f6715bfea9c94
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Aug 2 15:20:39 2016 -0700
Cleaned up for easier readability
Exec/Vortices_LWAcoustics/Prob_2d.f90
commit ae93d74c53d988addd61d58b65e90b1d35a550fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 2 18:19:51 2016 -0400
make castro.cg_blend = 2 the default. This has no effect unless
you select castro.riemann_solver = 1
CHANGES
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
commit 2d328fd661fb0495b3a79468a680e2e194f95d03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 2 11:32:04 2016 -0400
note some other parameters to document
Docs/Equations/Equations.tex
commit 66194e64f2086f2aee4cfd1e2bbcef520083a341
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 2 11:06:04 2016 -0400
typo
Docs/Equations/Equations.tex
commit d4888bc06ad779d680a8617954860b6eaed71690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 2 11:02:20 2016 -0400
document cg_blend
Docs/Equations/Equations.tex
commit d33e08242e8b842395e028766c2f571b43551d17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 2 10:09:39 2016 -0400
PGI doesn't like 0-sized arrays. Set nrates = num_rate_groups = 1
Microphysics/networks/general_null/network.template
commit 5bca502cb0db2b33308ba0e48a815223f80ce221
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 15:55:32 2016 -0400
doc stuff to steal from Max's thesis
Docs/needs_doc
commit d0c83b42e874be13d1dbedf81a5a79eae9d7cfe4
Merge: efb8bcd99 d1fbcce17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 15:54:34 2016 -0400
Merge branch 'development-next' of ssh://github.com/BoxLib-Codes/Castro into development-next
commit efb8bcd99b69f6e4ef8d081a5a6ebf0ac0e4134a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 15:42:05 2016 -0400
steal density reset stuff from Max's thesis
Docs/needs_doc
commit d1fbcce17e8151da11a1256487993f6243192a2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 10:17:38 2016 -0400
add justification for our sign convention
Docs/Gravity/CastroGravity.tex
commit 03c6b468d4f88b7200b4d3a5b04881d2d583e733
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 09:43:51 2016 -0400
more grav doc
Docs/Gravity/CastroGravity.tex
commit 23983eb173986dcb00323a36269a0f36327e5f3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 20:33:57 2016 -0400
more cleaning
Docs/Gravity/CastroGravity.tex
commit 082ecc7e8a924d2468d55bb045859b0184cce2cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 19:22:18 2016 -0400
more clean-ups
Docs/Rotation/CastroRotation.tex
Docs/refs.bib
commit dade70ed115968a61efb4001f8d0246e0778f2c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 18:32:15 2016 -0400
a little cleaning of the rotation docs
Docs/Rotation/CastroRotation.tex
commit 54f91a4911c157a288ff9f31d808eee065ce52ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 18:14:17 2016 -0400
note about timestep limiter
Docs/Diffusion/CastroDiffusion.tex
commit 4cac872494fdbec798628be692c27a0176ba027c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 17:29:18 2016 -0400
a little doc
Source/parse_castro_params.py
commit 4fc23392f480748d62b136e1dbed46a9d2310dd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 16:36:04 2016 -0400
start the next list of changes
CHANGES
commit c13d9cd0d76c78fde5f6c22c73b7fec03fa3f4c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 31 16:26:03 2016 -0400
gravity and rotation source type updates:
now we do grav_source_type and rot_source_type = 4 by default
-- these is a conservative formulation for the energy equation
that incorporates the source as a flux in the energy equation.
See Katz et al. 2016 for details.
We also do implicit_rotation_update = 1 by default -- this does
a slightly better coupling of the Coriolis force in the momentum
equation by doing an implicit velocity update
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
commit a211ddec6df9aa61810307848190fc475788263c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 31 01:11:07 2016 -0400
Don't update density/momentum after SDC burn
Source/Src_nd/React_nd.F90
commit 0d84deb2f93008bdcc3889af6c27aefd1888697d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 31 01:10:54 2016 -0400
Rearrange state variables for SDC
Microphysics/networks/sdc_type.F90
commit d58c826c90fb7882249d898aecbbf4b61c11d8cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 21:05:44 2016 -0400
use grav_source_type = 4
Exec/bwp/inputs_2d
commit 0e1d3df1b244747187c44cd1346b2befdee9f2e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 19:03:06 2016 -0400
updates
Exec/Detonation/inputs-det-x
commit b1e067bf2132313b1d669b43df8ba6448cd0ee18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 19:01:56 2016 -0400
git funniness
Exec/bwp/inputs_2d
commit 9116940408582cf8fd092846f2ac7d866b508873
Merge: fccbf347d 8ab7cfa79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 18:55:53 2016 -0400
Merge branch 'development' into development-next
commit 8ab7cfa79629f95c2f5e447591d86d82561bd5b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 18:50:36 2016 -0400
lower ambient density model from Lupe
Exec/bwp/SolarLike_0.2M.hse.1280
commit 02be821cf98d5ad3e212d3304116263e80d3260b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 30 16:20:40 2016 -0400
Store SDC sources in state data
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
commit fccbf347d3d37ee3000d27ffed68d4f81193ab5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 15:59:59 2016 -0400
set do_constant_volume_burn = T, up the levels for refinement
Exec/Detonation/probin-det-x
commit 4c7e2fed7bb510961fa6731239f61320b331c809
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 30 15:11:40 2016 -0400
BS integrator, better PPM params
Exec/Detonation/GNUmakefile
Exec/Detonation/inputs-det-x
commit 66bffee9b2d39fa3787395be42317b3acc2eae93
Merge: 545e028c2 99976e32d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 12:23:36 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 545e028c278663152b4427988a62840bf9b03db8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 12:23:23 2016 -0400
problem_post_init needs doc
Docs/needs_doc
commit 99976e32d3c3ef2854e878e26b477206559c5bfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 11:39:46 2016 -0400
more info about changes
CHANGES
Exec/Make.Castro
commit f7cf06395fc48c0fdb93c5647b8fd5e9a1e1d707
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 06:10:12 2016 -0400
Fix bug in last commit
Source/Gravity.cpp
commit 57e4bd39fda87ff2a47d42df54323c7e222558cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 05:45:33 2016 -0400
Update state between new-time source term evaluations
This reverts to the original Castro behavior, but now we have an option
to evaluate all source terms at the same time using update_state_between_sources = 0.
Docs/runtime_parameters/runtime_parameters.tex
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit d616c0b91e9a9d66ae85b97b9c589825bda4bd34
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 05:33:39 2016 -0400
Add source terms to hydro / dSdt automatically
This introduces small changes because for some of the forces we
were adding them to the hydro using add_force_to_sources rather than
the more generic form we use now where each source term completely
specifies its effect on the NUM_STATE components.
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_hydro.cpp
Source/Castro_rotation.cpp
Source/Castro_sponge.cpp
commit 91f1a2b20f99c82547bb08b69304484efa3c6d36
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 05:08:05 2016 -0400
Include the sponge in the hydro sources
Source/Castro_sponge.cpp
commit a3cee849064d8ee6a7a4c2b4f21d10681e5d126b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 05:04:31 2016 -0400
Replace adds with saxpy's
Source/Castro.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_hybrid.cpp
commit 4e0d299b22010de8a1c1883b7f4ff63e5df238ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 04:59:15 2016 -0400
Construct sources one by one
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_hydro.cpp
Source/Castro_rotation.cpp
Source/Castro_sponge.cpp
commit 34b47826ad69c3308dd5715766a82a176ebf36c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 04:38:14 2016 -0400
Wrap in an SDC ifdef
Source/Castro.cpp
commit 190466550a88010a76bcc9a6d9fbaa2d94b23fda
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 29 04:12:50 2016 -0400
Re-order the source terms for backward compatibility
Source/Castro.H
Source/Castro.cpp
commit a91595f1383901dfe5e22eecb989814641d6590c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 28 18:37:00 2016 -0400
Allow multipole BC to use fine levels
Source/Gravity.H
Source/Gravity.cpp
commit 20b7bf080efe2e52b37b116d8facc295eb12b387
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 28 02:13:42 2016 -0400
Get SDC MultiFabs working on a restart
Source/Castro.cpp
Source/Castro_hydro.cpp
Source/Castro_io.cpp
commit 1c1888ad1013355fe982e37acb64cce37572b605
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 28 01:12:38 2016 -0400
Fix an error message
Source/Castro.cpp
commit 5f813958347f62c61e639305075e41676b01bfa7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 28 00:53:46 2016 -0400
Be more consistent in cleaning the state
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit a3b5e4a91e60e1df5ad585f3510e4de4fa604eaa
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 28 00:53:08 2016 -0400
Improve error message in ctoprim
Source/Src_nd/advection_util_nd.F90
commit f429f2c2c8e9775804657501beed4b134f1dacc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 20:15:39 2016 -0400
Do the minimum density enforce before the renormalization
This helps in case the density resets create an inconsistent set of species
Source/Castro_advance.cpp
commit 281514d208fd4f21171318e7d6100ee70eb1dce0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 20:06:36 2016 -0400
Fix some runtime output in reactions
Source/Castro_react.cpp
commit 19e04e4786db985375cf4c3182c97f0aaf0c4873
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 19:01:55 2016 -0400
Check for NaN's after each SDC iteration
Source/Castro_advance.cpp
commit 58e1086a48af5d36fe5279475fdbbe00e5e88c1f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 18:44:41 2016 -0400
Add EOS hooks to get maxtemp/maxdens
Microphysics/EOS/eos.f90
commit 71d7753ae8e06326603a8b29d500c8a6f994c219
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 17:38:03 2016 -0400
Don't delete hydro_source after hydro update
Source/Castro.cpp
commit f5569db2b7bfb5efb07b9c39ecf2ff62348db782
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 17:37:47 2016 -0400
Add a comment
Source/Castro_advance.cpp
commit 9d8bc717e946334d3765f6c61b36d2c943f861d3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 16:20:31 2016 -0400
Fix diffusion memory leak
Source/Castro_advance.cpp
commit 6c1a95c6e1c1c560c72012053414eeae2bdb42ad
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 14:39:43 2016 -0400
Don't multiply old/new by 0.5 in SDC
Source/Castro.cpp
commit 4ef43157c2c781d0f7d301bb5536c116094f179b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 14:29:01 2016 -0400
Don't do source_term_predictor in SDC
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 3367fd8bc70bed598565be839bb0ad8688cf74e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 14:28:33 2016 -0400
Avoid use of BL_TO_FORTRAN
Source/Castro_F.H
Source/Castro_react.cpp
commit e29f3afd777f58e166c9b5e79075468d7d00a377
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 01:30:26 2016 -0400
Fix argument list in Castro_1d/Castro_2d
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
commit 67214c2f4d750c7e03a70c9237440253985843aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 01:00:08 2016 -0400
Fix some conditional logic
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit fb9c403d8506be8e4b326e3080f9fe8c526ee053
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 27 00:38:06 2016 -0400
Check in a first attempt at the SDC burn
Docs/runtime_parameters/runtime_parameters.tex
Exec/Make.Castro
Microphysics/networks/Make.package
Microphysics/networks/burner.F90
Microphysics/networks/general_null/Make.package
Microphysics/networks/sdc_type.F90
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
Source/Src_nd/React_nd.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 8cb54340906a634f0badf0dfa431400f47a03d20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 11:20:50 2016 -0400
add info about make file_locations
Docs/FAQ/faq.tex
commit 964cd24119f369bb7407f334e7bd507338fd167a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 09:30:40 2016 -0400
Insert machinery for SDC iterations
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 31588560011b055f3dd6280f3e4c246a2df1fef9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 09:06:43 2016 -0400
Do not delete/recreate source MFs for SDC
This is a temporary fix to make SDC work on a single level
Source/Castro.cpp
Source/Castro_advance.cpp
commit a54285cb44a687267fdb67094d2b38ced9e73504
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 09:05:00 2016 -0400
For SDC, time-center the sources to the hydro
Source/Castro.cpp
commit 9e9a9cca17427cc433356be29503532f49d6d0dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 08:32:18 2016 -0400
Add reactive source term to the hydro
Source/Castro.cpp
Source/Castro_hydro.cpp
commit a030603707545e2049a011e0e4aa35dd23f574c5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 08:22:02 2016 -0400
Use MF saxpy instead of FAB saxpy
Source/Castro.cpp
commit bdba7cd097f8f648887ce9051a549887a3a59a51
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 08:17:37 2016 -0400
Move ctoprim/srctoprim up to C++
Source/Castro_F.H
Source/Castro_hydro.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
commit af28b6fcd5dff45f43800ca4035d9ae8bc4ee5e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 07:35:52 2016 -0400
Move react_src to Castro
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 815c2ce345c50e32bfbd40ebc7c1b64825aaa14a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 07:28:09 2016 -0400
Write an algorithm for getting the reactive source term
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 8115cfb71fa26495bbcf25aa32d9c6d85c02a182
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 06:01:37 2016 -0400
Create a do_sdc parameter
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit a84932f8a4cf561ae16dd589cf6da3bae8280bca
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 05:50:38 2016 -0400
Add routine to convert conservative MF to primitive
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.F90
commit 5ee69b41813505f4738c511faf0bc089b0d29234
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 05:50:21 2016 -0400
Fix C bindings
Source/Src_nd/advection_util_nd.F90
commit dc209f2a9b5e749c3a758b6f07804d3a769a2e97
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 05:27:55 2016 -0400
Reorganize a little
Source/Castro.cpp
Source/Castro_diffusion.cpp
Source/Castro_levelset.cpp
Source/Make.package
commit 4029a29c1e5dd55f243e6ffbc91cb2cb4d5596fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 05:11:22 2016 -0400
Rename function for consistency
Source/Castro.H
Source/CastroParticles.cpp
Source/Castro_advance.cpp
commit 4a5a8a1c4c4729f28a7789f9ba8c9cf2e3aebedf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 05:08:24 2016 -0400
Convert source to primitive in separate subroutine
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_nd/advection_util_nd.F90
commit dc625735935e399534ba7d1dcde6ddf2f5ee7a21
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 04:45:17 2016 -0400
Make ctoprim dimension agnostic
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/advection_util_nd.F90
commit cf6424c6765d4960c65cfea7df5ebca7829317c7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 04:33:50 2016 -0400
Remove ngp from ctoprim argument list
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
commit 2b3b1f27451234fd6e8bd602cd9cf034bbdb5d2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 04:23:55 2016 -0400
Move some quantities into QVAR
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 3ab135a56fba50f2e8899806a2ce9e69b028cb49
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 03:36:41 2016 -0400
Don't pass flatn to ctoprim
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
commit c89d74849190582d1b272844408938d11ce10b82
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 03:17:53 2016 -0400
Use eos_t % reset instead of explicit reset
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.F90
commit c45e7b5f82c0bdfd3a195686ca5f2c3eb31470ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 03:10:57 2016 -0400
Move flattening to main hydro routine
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
commit 100488478bd9c6c9adec9d15496eb92182a53ff6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 02:43:09 2016 -0400
Move CFL computation to new subroutine
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/advection_util_nd.F90
commit b00e82b793a4aad543f1ba29b3196696606fd7ef
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 01:36:37 2016 -0400
Remove some unused variables
Source/Src_nd/advection_util_nd.F90
commit df39a6b9ac09616f11ad5c5f812465b9303a9bf3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 01:36:06 2016 -0400
Always enforce against neg dens after interpolating
Source/Castro.cpp
commit 9760d3e7bbdbc45633fc5faae51d6a9cb7b772e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 01:29:25 2016 -0400
Move the application of the hydro source up
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit e65d0effda0f11dec869bc9612cf1278fec0210d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 25 00:42:01 2016 -0400
Move enforce_minimum_density to its own routine
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit a0947772b49376bf10fb864d3b104b7376180e9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 23:35:17 2016 -0400
Move normalize_species call out of hydro
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
commit 14f8aed192cbff267a71d49a7ba928e7a45ac004
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 23:33:14 2016 -0400
Rename enforce_nonnegative_species -> normalize_species
Source/Castro.H
Source/Castro.cpp
commit 0539d2ff5c156516c8e659845c703897aac04e17
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 22:39:26 2016 -0400
Simplify even further
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hydro.cpp
Source/Castro_react.cpp
Source/Make.package
commit 3c68df7b1df97e00095bc4a4672a738200cb98f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 22:24:29 2016 -0400
Create init/finalize for advance_hydro
Source/Castro.H
Source/Castro_advance.cpp
commit d870ca69bfc0b8bbecf40ca57d228c8718b5838c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 21:58:36 2016 -0400
Fix the location of some MF initializations
Source/Castro_advance.cpp
commit d4630aa788c66a3b9ddfc6b530f8e7c9dc8f1255
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 17:26:51 2016 -0400
Move the retry functionality to a new function
Source/Castro.H
Source/Castro_advance.cpp
commit 0f64a01c90db8ee8a4a789a2d27f8f0a418a5725
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 17:26:41 2016 -0400
Fix hybrid momentum bugs
Source/Castro.cpp
Source/Castro_hybrid.cpp
commit 809d5d78ea8eb6c92464febcdbe4b8e236d0010c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 17:08:24 2016 -0400
Create advance initialize/finalize operations
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 3caf241f762903dc7171b3e9fe3a5df71a1ee081
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 16:58:45 2016 -0400
Make u_gdnv an Array
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit a6f22f1fea2d8b1cbaf0f276a12a7c94c3da9ef7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 16:51:21 2016 -0400
Move inits/deletes up to advance
Source/Castro_advance.cpp
commit a3a3a84e52d291c49c571572eed628da2d5b78db
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 16:45:47 2016 -0400
Move hydro_source to Castro
Source/Castro.H
Source/Castro_advance.cpp
commit e0ef9ef6130f96ad792752ed6da0d758a723d5b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 16:41:36 2016 -0400
Move fluxes to Castro
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Castro_rotation.cpp
commit 52dd313b051dd249f575e9c0c0333539fd298993
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 06:00:19 2016 -0400
Move Sborder to Castro
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_rotation.cpp
commit b7dec4326d43256ee4c6fd9b705ab28ace4d778f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 05:43:16 2016 -0400
Move old_sources/new_sources to Castro
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_rotation.cpp
Source/Castro_sponge.cpp
commit 86daae99b3e0bdb02e336fc583d5913c97d22c12
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 05:21:14 2016 -0400
Remove obsolete error message
Source/Castro_advance.cpp
commit 6c704812ad04ec5dad31b3a2031fb58c2a762af3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 05:20:16 2016 -0400
Remove unused box
Source/Castro.cpp
commit df0bd95ed9772358a35bee3d7ef4e2e7013c2426
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 05:18:53 2016 -0400
Remove advance_no_hydro
Source/Castro.H
Source/Castro_advance.cpp
commit f93828108da237ab014c0ecf2e68113bd865653d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 05:15:17 2016 -0400
Move sources_for_hydro to be Castro member
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_rotation.cpp
commit 15b0eddaa0e78a620fca37c0756a76f524c27838
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 05:04:30 2016 -0400
Move initialization steps into new routines
Source/Castro.H
Source/Castro_advance.cpp
commit 3b368591fedc759ccfe03a2ffd2015122e668fcf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 04:54:11 2016 -0400
Make tau_diff a Castro component
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_react.cpp
commit ae44a58961968c02a9510bb29837f0c66ec0157e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 04:39:15 2016 -0400
Group the new-time source term construction/application
This changes the order of operations a bit; in particular, we used to
apply the source terms one by one and then for most of them do a
computeTemp call in between, so that the order in which we applied
the various source terms mattered. Now every new-time source term
only sees the state updated by the hydro, so it is order-independent.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 1c0a21944e0c4f14eb1b362de5f6b165c7de6a44
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 04:14:59 2016 -0400
Move NaN checking to a function
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 6ebfd4881cdfdfdb0192fc27052434f7a83820c5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 04:11:34 2016 -0400
Move the hydro update itself to a separate function
Source/Castro.H
Source/Castro_advance.cpp
commit 6e27b35e7679d8ef70cc9afd03ee88264a17f6d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 03:51:05 2016 -0400
Move diffusion terms to be Castro components
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
commit b3ff83396e8b7d364c7386eec60609c9d1d72ffd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 03:40:55 2016 -0400
Group all old-time sources together
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 2da4c5218ec94c2ca48d6719c1465540831b65fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 03:24:03 2016 -0400
Initialize the source arrays all in one place
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_external.cpp
Source/Castro_gravity.cpp
Source/Castro_hybrid.cpp
Source/Castro_rotation.cpp
Source/Castro_sponge.cpp
commit 3962ec1e89e4da41d9a986d811032aabf5a2e846
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 03:18:40 2016 -0400
Apply the old-time source terms before hydro update
Source/Castro_advance.cpp
commit aa1b06e301f768dd5f7289a6768b74c27116ddb2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 03:11:05 2016 -0400
Move the S_new copy to be earlier
Source/Castro_advance.cpp
commit e666866f708c05e15971c15e7a9b8ec02c8f2558
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 03:00:34 2016 -0400
Write a function for expanding Sborder
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 57f134deba47bf46cbfe5e3ba56d3f3845eeff21
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 02:40:19 2016 -0400
Enforce positive species for Sborder not S_old
Source/Castro.cpp
Source/Castro_advance.cpp
commit 4cc0920f15e8397231de31cc85ed48d1259bead7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 02:32:22 2016 -0400
Move particle update to its own routine
Source/Castro.H
Source/CastroParticles.cpp
Source/Castro_advance.cpp
commit 200122f692c519af30a8b309074c627f55a2f83f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 02:21:45 2016 -0400
Move the pointmass code to a new routine
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_pointmass.cpp
Source/Make.package
commit 9c66228aa8b18c3169fdc5811897840b8449e836
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 02:21:06 2016 -0400
Fix incorrect variable name
Source/Src_nd/sponge_nd.F90
commit b4642e8020df2c5271dc9dac45ed5a97e400d0c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 02:20:56 2016 -0400
Remove unused variables
Source/Src_nd/timestep.F90
commit 99bbb9aff167c287e1f9b8c8b7230de0aaa3bf86
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 01:07:19 2016 -0400
Move the sponge to the source formalism
Source/Castro.H
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_sponge.cpp
Source/Make.package
Source/Src_nd/sponge_nd.F90
commit 8d872466866023336490f60fe3c545348dc2e3f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 00:30:48 2016 -0400
Clean up some alignment and scoping
Source/Castro_advance.cpp
commit 3c240be6fb717ee575b9232ac217108180abe283
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 24 00:11:02 2016 -0400
Create new functions for diffusion
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
commit 515af684bc09acfc7dd2260cfe5316fc85fa4dd8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 23:38:58 2016 -0400
Strip out SGS code
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/sum_integrated_quantities.cpp
commit 124866acf2a7798173e0f2046c183dddf0832838
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 23:24:19 2016 -0400
Move the hybrid sources to new functions
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_hybrid.cpp
Source/Make.package
commit 12e991c6160650a7e584ff307b9c6a96858b0c4b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 23:23:57 2016 -0400
Fix some bugs in external source term
Source/Castro_external.cpp
commit ca10a8a313e85edf10be4999211bb39309d6c1fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 22:51:03 2016 -0400
Fix holdover bugs in grav/rot sources
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/rotation_sources_nd.F90
commit 23aa0fedb06846557d092e8cf2243a439fd6dbfb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 22:04:12 2016 -0400
Fix typo in hybrid advection
Source/Src_nd/hybrid_advection_nd.F90
commit 04cbdcf03ba2b4210c47a03593c2d3745f054630
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 21:53:19 2016 -0400
Move external source terms to new function
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_external.cpp
Source/Make.package
commit f18e342d2c4158c3200472d3f2dcef6153b6d277
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 20:56:43 2016 -0400
New function to apply source to state
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 26c305f13691cc684d5de49852fddd60c49604ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 20:43:50 2016 -0400
Move rotation source construction to new function
Source/Castro.H
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
Source/Src_nd/rotation_sources_nd.F90
commit 8283abd7d4391c2a8710b492cce0b2175656664f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 20:43:21 2016 -0400
Fix issues with diagnostic sums
Source/Castro_gravity.cpp
commit 712b245c5eb5c7c973910db3e9daa77e1b684bb0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 19:40:23 2016 -0400
Move gravity source construction to new function
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Src_nd/gravity_sources_nd.F90
commit 63182088bf1da1e4854c4a867504f46d803a7a48
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 18:48:19 2016 -0400
Construct rotation in new functions
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
commit fea43e6eb68ec4b87d529374e1fdb6e0608a0adf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 18:29:17 2016 -0400
Clean up whitespace
Source/Castro_advance.cpp
commit e600e852c19f430e954f2f4b7bea3fd72f72c8d3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 17:57:59 2016 -0400
Move the filling of phi/grav to new functions
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_gravity.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Make.package
commit 0ed805f31f69caa194f7e03bf3e7d1b1ca463e5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 16:22:56 2016 -0400
Move the sources enum to the header
Source/Castro.H
Source/Castro_advance.cpp
commit 886a2706e012e10020f69b9995971be7782daeae
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 11:00:35 2016 -0400
react_half_dt --> react_state
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 049a44d409e93ac26ca6097e38db9e989c990fc9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 10:43:30 2016 -0400
Do new hybrid sources in PArray
Source/Castro_advance.cpp
commit 1af38794fc00ebc48175c95bd9e425d1828fbbb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 10:38:12 2016 -0400
Move the gravity source to the PArray
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/gravity_sources_nd.F90
commit 9a8b9229a0312048b1ae25b82e62e3a29a124ab1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 10:00:28 2016 -0400
Do the copy from old to new state before hydro call
This allows new data to be written by hydro call
Source/Castro_advance.cpp
commit 0e54476791abf4eaf91cee059d80507726ef9df6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 09:58:33 2016 -0400
Move the rotation source to the PArray
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/rotation_sources_nd.F90
commit 70ddbefefc5930f0f0af42ee998eedf974677186
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 08:52:28 2016 -0400
Begin to PArray manage the source terms
Source/Castro_advance.cpp
commit 4ff52b6ab65ec487dd5b7bbfcab0b016f31625b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 08:02:34 2016 -0400
Move the application of the hydro update to C++
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
commit ed26baa123b18648077bdd1fc6ede92992fce3c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 07:08:05 2016 -0400
Construct an explicit array with the hydro update
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/hybrid_advection_nd.F90
commit bff25890c3cf026212b248882a1a8c9de7f3f8fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 05:37:04 2016 -0400
Move enforce_minimum_density to C++
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_3d/Castro_3d.f90
commit b99130ea6ae7937730a0dc7fc6de6d3601c2b317
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 23 05:02:24 2016 -0400
Move ca_normalize_species to C++
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_3d/Castro_3d.f90
commit 51bebbd9bf26765241972d107c3d8a5e1eaeda1a
Merge: f910a60c0 5c1526abf
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Fri Jul 22 11:50:54 2016 -0700
Merge branch 'development' of https://github.com/BoxLib-Codes/Castro into development
commit f910a60c0751a746de8fea50fd8f0b64b524883a
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Fri Jul 22 11:45:37 2016 -0700
Adding bwp to study the Hydro evolution of the companion
Exec/bwp/GNUmakefile
Exec/bwp/Make.package
Exec/bwp/Prob_2d.f90
Exec/bwp/SolarLike_0.2M.hse.1280
Exec/bwp/inputs_2d
Exec/bwp/probdata.f90
Exec/bwp/probin
commit 5c1526abff4b0bbd4df6c57babd0d6cc800fe118
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 16:17:32 2016 -0400
add normalize_abundances_burn
Microphysics/networks/burn_type.f90
commit a0c2a6fbd708af2dbb3aed9504bf62126ba27667
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 15:44:36 2016 -0400
no need for enthalpy in burn_t
Microphysics/networks/burn_type.f90
commit 5ba4be6991102b6680d2f4a175fbc6f14780ff9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 17 12:09:38 2016 -0400
turn on the shock variable for this test
Exec/oddeven/GNUmakefile
commit baf6040997452875b87ce30164c329a8a055ae82
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 17 12:07:28 2016 -0400
More fixes for shock variable
Source/Src_2d/Castro_advection_2d.F90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/Castro_nd.F90
commit d725252d235b63d95476d601c8f83507fed27e40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 17 11:36:46 2016 -0400
pass USHK through
Source/Src_2d/Castro_advection_2d.F90
commit dd6490c70f8510d6f636f7cf27e26aabc31223be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 17 11:23:58 2016 -0400
need to actually allocate storage for USHK
Source/Src_nd/Castro_nd.F90
commit e0a4a924380948e47445e5f28626068883ae50bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 18:44:07 2016 -0400
more cleaning
Docs/runtime_parameters/rp.py
commit ecc60b94438f497775181c2365dfb77c7f9fceb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 18:32:31 2016 -0400
some cleaning
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit a954ea290e6f8dd91d17cc861422d505130b38a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 16 02:56:53 2016 -0400
Don't pull in VODE/BLAS if reacting
Exec/Make.Castro
commit e4951433bf368b06bebb865f96165134ef89a13c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 10:22:10 2016 -0400
add update_unevolved_species
Microphysics/networks/general_null/actual_rhs.f90
commit cb6ca1eac3b061cd9d781ab4cac0ec0d1f31d1f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 10:14:18 2016 -0400
add update_unevolved_species
Microphysics/networks/general_null/actual_rhs.f90
commit b9b91f2d96b0582e41a1e0411309ef7f8c242f0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 14 09:51:01 2016 -0400
Allow prescribed phi in PrescribedGrav
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_nd/Make.package
Source/Src_nd/prescribe_phi_nd.F90
commit 466970dcd75e0adc506f40b2feb11f1828caec24
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 14 07:52:04 2016 -0400
Fix logic for PrescribedGrav and allow in 1D
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Src_nd/prescribe_grav_nd.f90
commit c949ca1fcb02d8d7ba4da516f27a9a9343d22e4b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 14 07:47:44 2016 -0400
Update references to Docs in gitignore
.gitignore
commit 12e8fa67fe6b90b3abb33139f96a5cefa07d4995
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 23:13:34 2016 -0400
add note about MICROPHYSICS_HOME
Docs/GettingStarted/CastroGettingStarted.tex
commit a78510e422c8bdac18a05a77ea276b009ae9bec3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 11:17:04 2016 -0400
Microphysics/eos is now Microphysics/EOS
Exec/Make.Castro
commit b8779559733d18a20d5a0a81c28f16d499d81a6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 11:08:27 2016 -0400
add a warning that these files are automagically generated
Source/Src_nd/meth_params.F90
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/parse_castro_params.py
commit 862de4f6f9a3ef42f12c3ab865b0899bb4132a1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 6 16:30:19 2016 -0400
Add OpenACC routine declarations
Microphysics/EOS/eos.F90
commit 0c791f29a79d8c36f8e6f73a7b9809a482ee9463
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 6 16:29:47 2016 -0400
Fix a bug from the merge
Source/Src_nd/React_nd.F90
commit d24271240f98bb12bf458f0664e6af9b6c954c42
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 6 16:15:51 2016 -0400
Update the OpenACC declarations
Source/Src_nd/meth_params.F90
commit 059ea861f77b1878661116dc4fced41ac28e3b05
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 6 16:05:20 2016 -0400
CASTRO_DIR -> CASTRO_HOME
Exec/test_react/GNUmakefile
commit 694564c889d62221f193ed2c923713ae1395d9a7
Merge: a2b1aaf9f 71319c5f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 6 16:04:17 2016 -0400
Merge branch 'development' into oac_reactions
commit 71319c5f170d8f8e6bc49f3b1097eedf83953b57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 6 10:46:37 2016 -0400
fix the warnings -- they were referring to 3-d versions of the source
Source/Src_nd/Castro_util.F90
Source/Src_nd/advection_util_nd.F90
commit f76537b1409ef37b8a77ad1747fa8ffb173250bd
Merge: 432d2864d e724bc5b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 21:06:35 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/CastroRadiation into development
commit 432d2864d27e0d33376afef1c1d4d204b36d14ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 21:00:59 2016 -0400
test suite version
bwp/inputs_2d.test
commit f683a0928632f5857b0c68955636e9dfc95d830f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 20:47:10 2016 -0400
fix uninitialized variable
We were computing update_factor before we computed sponge_factor.
But sponge_factor needs to be computed on a zone-by-zone basis.
Source/Src_nd/sponge_nd.F90
commit e40aa691c36f9fd517df5a0d4ab078013fc76596
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 5 13:08:34 2016 -0400
Replace a divide with a multiply
Source/Src_nd/rotation_sources_nd.F90
commit 71c92312188f47532c5387a324d23f0816f0c80e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 5 13:07:56 2016 -0400
Fix a holdover bug in the domegadt terms
Source/Src_nd/rotation_sources_nd.F90
commit 2698a03fa6e6f277f08cabddd00c32a113d3986e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 12:53:51 2016 -0400
keep a history
CHANGES
commit 89790506762ab6dcf33154f517a57dbb260f31d5
Merge: 2c26c9466 6bd017e37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 12:53:09 2016 -0400
Merge branch 'development-next' into development
commit 2c26c9466ecc495bb64dcdb7840f6109731ec22f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 12:52:51 2016 -0400
update version
CHANGES
commit d1940ef05cf5028a99275dfc86106732b18f90ad
Merge: dfb1556ef 584653957
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 12:15:50 2016 -0400
Merge branch 'master' into development
commit 6bd017e37470916f0ad9c540a47d0fa0f777fc89
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 4 11:48:51 2016 -0400
Make the PLM reconstruction order a parameter
Docs/runtime_parameters/runtime_parameters.tex
Source/Src_1d/trace_1d.f90
Source/Src_2d/trace_2d.f90
Source/Src_3d/slope_3d.f90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 828d0048ebc5d4c04f7eccabf925bb57473ef944
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 3 13:38:55 2016 -0400
Enable an explicit version of the sponge update
Activate it with castro.sponge_implicit == 0
CHANGES
Docs/runtime_parameters/runtime_parameters.tex
Source/Src_nd/meth_params.F90
Source/Src_nd/sponge_nd.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 1af59181bc8e9ffb3452669dd79e4bb8ce5e87f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 3 13:26:29 2016 -0400
Add hybrid momentum source to the sponge
CHANGES
Source/Src_nd/Make.package
Source/Src_nd/sponge_nd.F90
commit c4272c4ba592c735b38159c89045a866cb43acba
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 2 19:09:21 2016 -0400
Avoid possibility of undefined value
Microphysics/EOS/eos.f90
commit a342615d146261ce47be02a605730218aa9d1c51
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 2 02:43:37 2016 -0400
Clean up unused variables
Source/Src_nd/React_nd.F90
commit 5c17fe420ea60cfb2686ea119ec4997b59377a0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 2 02:09:53 2016 -0400
Add a check_inputs option to the eos_t
Microphysics/EOS/eos.f90
Microphysics/EOS/eos_type.f90
commit dfb1556ef29358e7eab56fcbdf3721273402714b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 17:54:48 2016 -0400
update docs
Docs/runtime_parameters/runtime_parameters.tex
commit c4eb2299e4d3e7519316517bbde754b38663ca7c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 30 21:57:27 2016 -0400
Print out Microphysics git hash at runtime
Source/Castro_setup.cpp
commit 6910c08748f090487ee3f311e484b122cf9fc3e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 30 10:00:28 2016 -0400
update changes to note the reset behavior with ghost cells nows
CHANGES
commit bc37b7e9d8549ea5792f082771a2dd7aabc5d672
Merge: f2aaf0cbe d628dc83d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 29 20:43:38 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f2aaf0cbe99e81d9d99486019346d1245aff6461
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 29 20:43:25 2016 -0400
shorten the test problem -- it takes too long
Exec/reacting_bubble/inputs_2d_test
commit d628dc83d2fcf567063cfb3f4441e42070c79024
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 29 04:12:20 2016 -0400
Pass in dx and cs explicitly rather than t_sound
Microphysics/networks/burn_type.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/timestep.F90
commit fd835a6276c7cf235b78b95a1707768e122cce9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 28 23:39:58 2016 -0400
Add sound-crossing time to burn_t
Microphysics/networks/burn_type.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/timestep.F90
commit 9c31b8c83427d685eb56094fccddf5e3780a69e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 28 18:27:13 2016 -0400
Save some work if we're masking a burn zone
Source/Src_nd/React_nd.F90
commit bb9959d2d94ea68d33381c7003011a89174b30bf
Merge: 6c872c8e1 a13836272
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 14:06:48 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 6c872c8e1e5b9003303c2e2dbfebc9af83eaba71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 14:05:25 2016 -0400
CASTRO_DIR -> CASTRO_HOME
Docs/GettingStarted/CastroGettingStarted.tex
commit e724bc5b2cadf3594d1ec3acd0362481628225fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:50:26 2016 -0400
CASTRO_DIR -> CASTRO_HOME;
MICROPHYSICS_DIR -> MICROPHYSICS_HOME
Make.Castro
bwp/GNUmakefile
commit a13836272879a991437c8ae3d576c1725878c665
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:45:20 2016 -0400
update environment variables
CHANGES
commit 726dc75b8f39bc5aa2d65e65b511a708cf844e4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:42:26 2016 -0400
decouple this from Castro/Microphysics and instead use MICROPHYSICS_HOME
essentially this solver now has no Castro dependencies. It only lives
in Castro/ since it is a Riemann solver, but it uses the F90 build
system instead of the Castro build system.
Util/exact_riemann/GNUmakefile
commit 57798ff09bcdda273d6524fea906bfb0f98bbd96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:31:31 2016 -0400
CASTRO_DIR -> CASTRO_HOME
Docs/GettingStarted/CastroGettingStarted.tex
Exec/Detonation/GNUmakefile
Exec/DustCollapse/GNUmakefile
Exec/HCBubble/GNUmakefile
Exec/KH/GNUmakefile
Exec/Make.Castro
Exec/Noh/GNUmakefile
Exec/RT/GNUmakefile
Exec/RT_particles/GNUmakefile
Exec/Sedov/GNUmakefile
Exec/Sod/GNUmakefile
Exec/Sod_stellar/GNUmakefile
Exec/StarGrav/GNUmakefile
Exec/Vortices_LWAcoustics/GNUmakefile
Exec/convective_flame/GNUmakefile
Exec/diffusion_test/GNUmakefile
Exec/double_bubble/GNUmakefile
Exec/evrard_collapse/GNUmakefile
Exec/flame_wave/GNUmakefile
Exec/gamma_law_bubble/GNUmakefile
Exec/gresho_vortex/GNUmakefile
Exec/hydrostatic_adjust/GNUmakefile
Exec/oddeven/GNUmakefile
Exec/reacting_bubble/GNUmakefile
Exec/rotating_torus/GNUmakefile
Exec/test_convect/GNUmakefile
Exec/toy_convect/GNUmakefile
Exec/toy_flame/GNUmakefile
Exec/uniform_cube_sphere/GNUmakefile
Exec/xrb_mixed/GNUmakefile
Microphysics/networks/general_null/Make.package
Util/scripts/get_castro_date.sh
commit 0aa09f6286d2dc8121178987bcb3dbc368003ed5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:31:05 2016 -0400
some updates to reflect the parmparse changes
Util/exact_riemann/GNUmakefile
commit dd8af6ab1f9c4f9d2bf9b6a434ffbb61883febf3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 11:09:32 2016 -0400
fix use_colglaz check
Radiation.cpp
commit e9c56f9c3261aaad354f773c98b6a14d1a8afc56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 09:43:18 2016 -0400
need to initialize vol in scope
Source/Castro_advance.cpp
commit 9beade6351cc8ef1de6cfca7955d065913406c82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 09:42:52 2016 -0400
fix interface to enforce_minimum_density
Src_1d/CastroRad_1d.f90
Src_2d/CastroRad_2d.f90
Src_3d/CastroRad_3d.f90
commit a886e9e742edc8a8c2a9f9f97462083fc5f5adb2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 21:11:37 2016 -0400
Do proper volume weighting in runtime diagnostics
Closes #3
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/sponge_nd.f90
commit 72b83ecab4b0d9e9997318d53ffa75441d3a57d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 18:35:53 2016 -0400
Avoid a potentially unnecessary operation
Source/Src_nd/sponge_nd.f90
commit f54fd48afbcf7e968d87a65ce12a74e236e40bc3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 16:37:07 2016 -0400
Add the component with NaNs to the abort message
Source/Castro_advance.cpp
commit a2b1aaf9faa260d0ab434df38c7d84db982b8998
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 16:37:07 2016 -0400
Add the component with NaNs to the abort message
Source/Castro_advance.cpp
commit b72e60d79ef6531dfd944d85df4bc450bc8b7740
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 27 13:30:36 2016 -0400
use_colglaz -> riemann_solver
Exec/Sod_stellar/inputs-test1-helm
Exec/Sod_stellar/inputs-test1-helm-y
Exec/Sod_stellar/inputs-test1-helm-z
Exec/Sod_stellar/inputs-test1-helm.tau
Exec/Sod_stellar/inputs-test2-helm
Exec/Sod_stellar/inputs-test3-helm
Exec/Sod_stellar/inputs-test4-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/Sod_stellar/runs/CW/inputs-test1-helm
Exec/Sod_stellar/runs/CW/inputs-test2-helm
Exec/Sod_stellar/runs/CW/inputs-test3-helm
Exec/Sod_stellar/runs/CW/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC/inputs-test1-helm
Exec/Sod_stellar/runs/MC/inputs-test2-helm
Exec/Sod_stellar/runs/MC/inputs-test3-helm
Exec/Sod_stellar/runs/MC/inputs-test4-helm
commit 0269858dc205594f4a9fc57cc42517c484fbebcb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 27 13:19:17 2016 -0400
abort if use_colglaz is set -- riemann_solver = 1 is the new alternative
Source/Castro.cpp
Source/Src_2d/riemann_2d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
Source/castro_defaults.H
commit 1b6ec7fa460c2147ddacd582356cd6b5ce33610e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 12:55:29 2016 -0400
Reproduce parameter overrides from C++
Source/Src_nd/Castro_nd.F90
commit 26aed0bf980c0457ffa452450104512ba5f6e7ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 27 10:50:49 2016 -0400
update README with development model
README.md
commit 00f15c01d852aa0abfe863460a2ad069791406b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 02:11:26 2016 -0400
Fix incorrect reading of double precision parameters
Source/Src_nd/meth_params.F90
Source/parse_castro_params.py
commit 17fad1205d68e3c44cdb14a4612aa8c8c15e6f03
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 27 01:07:29 2016 -0400
Fix floating point typo
Source/Src_nd/Castro_nd.F90
commit 9dd82cda19f846575e568b10c531c80132f942ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 26 23:57:22 2016 -0400
Make dual_energy_update_E_from_e an integer
Source/Src_nd/Castro_util.F90
Source/Src_nd/meth_params.F90
Source/_cpp_parameters
commit dbeb64cf9115b08e2aa4d45f4ad87e271b320273
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 26 20:36:42 2016 -0400
Don't ifdef the parameter defaults
Source/Src_nd/meth_params.F90
Source/parse_castro_params.py
commit f44bb6c4920703d2e231db6649885062968bc76c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 26 13:03:15 2016 -0400
Give F90 parameters the correct default values
Source/Src_nd/meth_params.F90
Source/parse_castro_params.py
commit f32865cbede6792bd3d7faa2e849830d27caa8e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 26 13:02:55 2016 -0400
Properly ifdef a rotation operation
Source/Src_nd/Castro_nd.F90
commit 258c9d599e654edf7d9bdca3fa8fd375d1e872fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 22:39:24 2016 -0400
Create an inputs file for test_react
Exec/test_react/inputs
Exec/test_react/testburn.f90
commit 0d40ea70abf6be4eaa3202fcb3c1cd6e31f7a9d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 22:38:47 2016 -0400
Copy in the mask in react_state
Source/Src_nd/React_nd.F90
commit 899d82ee959aa3904b538a7a5722f48addfab53a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 22:20:52 2016 -0400
Restore some accelerator device updates
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
commit 6401f3ccb1f16ace8a7ea74cbcad7072caaacde6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 21:55:41 2016 -0400
Uninitialize some more variables
Microphysics/networks/burn_type.F90
commit fa9fb07ae76776f199fddd495c41b58d6717d765
Merge: 3988e2326 7ee3c534a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 21:43:16 2016 -0400
Merge branch 'development' into oac_reactions
commit 7ee3c534a94ddff41d521426bac4ef89d4eb2f63
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 21:42:12 2016 -0400
Make the parmparse module be PGI-compliant
Source/Src_nd/parmparse_mod.f90
commit 3988e2326641498b5c8f5705c85075ede63868ed
Merge: 6f445735a 7deeb3cf6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 21:31:35 2016 -0400
Merge branch 'development' into oac_reactions
commit 7deeb3cf600e2479f0ab3be707919264965c73f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 20:23:12 2016 -0400
Have meth_params_module read in C++ parameters directly
This removes the previous dependence on the C++ ParmParse querying
by having the queries occur in the meth_params_module. Thus
the results shouldn't change, but this cleans up the interfaces a bit
and means that we can read in the Castro parameters from the inputs file
without needing to go through the Castro::variableSetUp() routine.
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Make.package
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Make.package
Source/Src_nd/castro_meth_params.template
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/set_castro_params.f90
Source/mk_params.sh
Source/parse_castro_params.py
commit 95688e98c3f43eb5474d15d63d96667feffd1bd7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 20:19:31 2016 -0400
Add a version of the F90 ParmParse module
Source/Src_nd/parmparse_fi.cpp
Source/Src_nd/parmparse_mod.f90
Source/Src_nd/string_mod.f90
commit a4720c48f049613f207d5561157ba1d75c51c1ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 15:58:09 2016 -0400
better initial value for the indices -- this is ghost cell safe
Microphysics/networks/burn_type.f90
commit 180cb8a6d902e2b6fcce00fdc22b3940c261188f
Merge: c255baec6 b0d0a0423
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 13:24:19 2016 -0400
Merge branch 'development' into sdc_diag
commit b0d0a0423bc223eba4adae7858acc503a6b4fbc7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 21:11:24 2016 -0700
mask: no need to do box intersection stuff if no ghost cells.
Source/Castro.cpp
commit e83312fc9e72a39dd442b89dbc4085160ded717d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 23 21:51:40 2016 -0400
Fill ghost zones for reactions step rather than burn directly
Source/Castro.H
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
Source/Src_nd/React_nd.F90
commit 70feb623369b95e05ba7736405d5a8fa8c20a62f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 18:10:53 2016 -0700
removed unused variable
Source/Castro.cpp
commit 72ef3f89dcee51b4ffba1477af51927b1de7b4e0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 18:07:54 2016 -0700
try again to fix bug in interior boundary mask
Source/Castro.cpp
commit f9c713469a19cbddbee2cdea0ee1fa8d5a4a3336
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 18:06:06 2016 -0700
fix bug in interior boundary mask
Source/Castro.cpp
commit ad649e5fac7d080e9a9aeae74fb5c55b04362ec1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 13:44:20 2016 -0700
RVO
Source/Castro.cpp
commit d11997d8a288d09d20b6f6ce70331c6f7e594f1c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 13:29:14 2016 -0700
interior mask: 1 means cells to burn and 0 means not
Source/Castro.H
Source/Castro.cpp
commit 05a530846e1ca2e5b1cb5e0c426645ee1ca08e03
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 23 13:21:06 2016 -0700
interior boundary mask
Source/Castro.H
Source/Castro.cpp
commit c255baec6410ec026230b9f25716f13305c571dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 15:33:54 2016 -0400
do the strang fix in the actual hydro part
Source/Castro_advance.cpp
commit 66782d9f56209607c5aedec567e96df7cebae014
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 15:16:06 2016 -0400
strang correct the time into second half
Source/Castro_advance.cpp
commit f5e2a8a7c0615f4c8f8fe7920b3a86c52acdf2c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 14:46:15 2016 -0400
exclude ghost cells
Source/Src_nd/React_nd.F90
commit dd957b3f606bc04272e27c4a22f75fde43706415
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 13:20:48 2016 -0400
store time
Microphysics/networks/burn_type.f90
commit ce17540d3b890c899740618b7c5ca5b97791304a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 12:14:53 2016 -0400
set i,j,k
Source/Src_nd/React_nd.F90
commit d933ce18508097de5dd63f50747d2fe7bfa44279
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 12:13:13 2016 -0400
have burn_t know i,j,k
Microphysics/networks/burn_type.f90
commit 61b38d866fa845aa3bdf350ea2f2d3838e497257
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:42:18 2016 -0400
update info on convert checkpoint
Docs/ConvertCheckpoint/ConvertCheckpoint.tex
Docs/Software/CastroSoftware.tex
commit 61804ab2bce1695adc30c1fe3af95ad87d5ea1b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:38:08 2016 -0400
note new locations
CHANGES
commit d2f97035cf2beeeaac060f31bf36e5eaf04d710e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:37:13 2016 -0400
move to a more sensible location
Util/ConvertCheckpoint/Embiggen.cpp
Util/ConvertCheckpoint/GNUmakefile
Util/ConvertCheckpoint/Make.package
Util/ConvertCheckpoint/README
Util/ConvertCheckpoint/probinit.f90
commit 549d68c68d9e1f5bea7c5e18eb97d15d020d1fcb
Merge: f17547139 cfc4b3678
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:20:16 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f17547139e32938351c7b41458e6652f88893a47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:19:57 2016 -0400
update Users Guide location
Exec/convective_flame/probin
README.md
commit cfc4b367868987f4c664c41667a93a46081e8db7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:16:36 2016 -0400
update paths
Docs/ManagingJobs/managingjobs.tex
Docs/Software/CastroSoftware.tex
commit 8b51ef468bacb91e88b6a4ca861639b40b2a95e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:08:50 2016 -0400
temp file
Docs/CastroUserGuide.out
commit b09e3631ed1c894e0d5ffdbb9c602bfd9fcceeec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:08:26 2016 -0400
rename for consistency
Docs/AMR/AMR.tex
Docs/CastroUserGuide.out
Docs/CastroUserGuide.tex
Docs/CastroVerification/RT_ppm_type.eps
Docs/CastroVerification/Verification.tex
Docs/CastroVerification/radiating_source.eps
Docs/CastroVerification/radiating_sphere.eps
Docs/CastroVerification/sedov_cyl.eps
Docs/CastroVerification/sedov_sph.eps
Docs/CastroVerification/sod_3d.eps
Docs/CastroVerification/sod_3d_ppm0.eps
Docs/CastroVerification/test2_3d.eps
Docs/CastroVerification/test3_3d.eps
Docs/CastroVerification/test_suite_day.eps
Docs/CastroVerification/test_suite_main.eps
Docs/CastroVerification/verification.bib
Docs/ConvertCheckpoint/ConvertCheckpoint.tex
Docs/ConvertCheckpoint/grown_center_2.eps
Docs/ConvertCheckpoint/grown_center_3.eps
Docs/ConvertCheckpoint/grown_corner_2.eps
Docs/ConvertCheckpoint/grown_corner_3.eps
Docs/ConvertCheckpoint/orig_center.eps
Docs/ConvertCheckpoint/orig_corner.eps
Docs/Diffusion/CastroDiffusion.tex
Docs/EOSNetwork/EOSNetwork.tex
Docs/Equations/Equations.tex
Docs/FAQ/faq.tex
Docs/FlowChart/FlowChart.tex
Docs/GNUmakefile
Docs/GettingStarted/CastroGettingStarted.tex
Docs/Gravity/CastroGravity.tex
Docs/Gravity/gr.bib
Docs/Inputs/CastroInputs.tex
Docs/Introduction/CastroIntroduction.tex
Docs/LevelSet/LevelSet.tex
Docs/LevelSet/levelset.bib
Docs/MAESTRO_restart/MAESTRO_restart.tex
Docs/ManagingJobs/managingjobs.tex
Docs/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
Docs/ManagingJobs/scaling/wdmerger/titan_041516/README
Docs/ManagingJobs/scaling/wdmerger/titan_041516/one_level_omp4.txt
Docs/ManagingJobs/scaling/wdmerger/titan_041516/three_level_omp4.txt
Docs/ManagingJobs/scaling/wdmerger/titan_041516/three_level_omp8.txt
Docs/ManagingJobs/scaling/wdmerger/titan_041516/two_level_omp4.txt
Docs/Parallel/Parallel.tex
Docs/Parallel/domain-tile.eps
Docs/Parallel/domain.py
Docs/Particles/Particles.tex
Docs/Rotation/CastroRotation.tex
Docs/Scaling/ScalingTest.pdf
Docs/Scaling/Sod_scaling.pdf
Docs/Scaling/scaling_jaguarpf.pdf
Docs/Software/CastroSoftware.tex
Docs/Software/tiling.tex
Docs/UnitsAndConstants/CastroUnits.tex
Docs/Visualization/CastroVisualization.tex
Docs/Visualization/LineQueryPlot_0_t_magvel.eps
Docs/Visualization/LineQueryPlot_0_t_magvel.png
Docs/Visualization/OffAxisProjection_density.eps
Docs/Visualization/OffAxisProjection_density.png
Docs/Visualization/Profile2D_1_Density_magvel_kineng.eps
Docs/Visualization/Profile2D_1_Density_magvel_kineng.png
Docs/Visualization/Slice_z_pressure.eps
Docs/Visualization/Slice_z_pressure.png
Docs/Visualization/isocontours.eps
Docs/Visualization/isocontours.png
Docs/Visualization/volume.eps
Docs/Visualization/volume.png
Docs/Visualization/yt_images.tar.gz
Docs/needs_doc
Docs/notes.txt
Docs/refs.bib
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit 53d1b04cd54774f102787b4164293dd4e66f4bdc
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 20 21:24:03 2016 -0400
Define omega vector in the right place
Source/Src_nd/Rotation_nd.f90
commit 564b608e8f5decc74835d66b9ef32ddfb6bf7e0a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 20 19:24:03 2016 -0400
Respect dimension agnosticity of enforce_minimum_density
Source/Castro.cpp
Source/Castro_advance.cpp
commit f1ae41c2c9bd608f36ae510808eae735027bac41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 20 12:12:32 2016 -0400
add another data point
UsersGuide/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
commit 8627114bb5af8133fc7de9fb952684afc4cc8420
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 19 19:49:50 2016 -0400
Fix an incorrect calculation of domhi_level
Source/Castro.cpp
commit b728cd63355192309c957d4654966f079b66d6cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 19 13:57:21 2016 -0400
Update the CHANGES file with recent commit information
CHANGES
commit 7a2a84f5d538f4b774b0f9dc6da6d3f89111cf67
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 19 02:58:45 2016 -0400
Revert unintended change to module variable iorder
This was introduced in commit f2145187a0b554371f53572bfe1a9a6b1e912487.
Source/Src_nd/Castro_nd.F90
commit 6d130f8485687957e28751229784a934c1b9c481
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 18 17:15:26 2016 -0400
Fix a restart issue
Also, improve the output when a run is stopped by okToContinue()
Source/Castro.H
Source/Castro.cpp
Source/main.cpp
commit b6cfa482517d94a6bcffd5051c5e334e036f69a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 16 20:29:38 2016 -0400
Add a hook for a problem post_restart routine.
Source/Castro.cpp
commit 7e3c2f16fe83eb56cf9370e42cf818b25b28b269
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 16 19:14:11 2016 -0400
Create a flag that allows Castro to tell BoxLib to stop the run
The signalStopJob flag, if true, will set okToContinue() to false,
telling BoxLib to stop at the end of this step and write a checkpoint.
It starts the run as false and can be triggered using the stopJob() function.
This works in addition to the existing functionality that discontinues
the run if the timestep gets smaller than dt_cutoff.
Source/Castro.H
Source/Castro.cpp
commit 356bac16951f5373321433257caa41fdb6445673
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 16 13:22:21 2016 -0400
Sync up with enforce_minimum_density changes
Src_1d/CastroRad_1d.f90
Src_1d/RadHydro_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit 72d2e5c889136f2aeed09ec452ab6e3d5fe36ba3
Merge: cd0d8d00d 15e8b66fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 16 07:21:30 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit cd0d8d00dd5c2eca4f487dfab804444c8283bb4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 16 07:21:06 2016 -0700
a little reorg -- no need for constant_conductivity parameter
Microphysics/conductivity/constant_opacity/Make.package
Microphysics/conductivity/constant_opacity/_parameters
Microphysics/conductivity/constant_opacity/constant_conductive_opacity.f90
commit 15e8b66fa67825430e07d83c19b8968a9b048a1b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 16 00:37:45 2016 -0400
Add new options for resetting a negative density
One new option uses the average of all adjacent zones; the other
resets to the original zone density before the hydro update.
Source/Src_nd/advection_util_nd.F90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 750d01f972717039306b93f11a5cbff0433c6837
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 15 23:32:14 2016 -0400
Make the enforce_minimum_density routine dimension agnostic
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/Castro_util.F90
Source/Src_nd/Make.package
Source/Src_nd/advection_util_nd.F90
commit 607e2bba8fc27b5626825df2b9faabe69907bc0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 15 21:07:10 2016 -0400
Add an option to limit fluxes so that rho > small_dens
The new option is castro.limit_fluxes_on_small_dens. By setting it to 1,
a new piece of code is called after the fluxes are constructed that checks
if the sum of the fluxes leaving that zone would cause the density to
drop below the small_dens limit. If so, it limits those fluxes (and only
those fluxes, not the fluxes that would increase the density) such that
the resulting density is above the limit. This is intended to provide an
outlet that permits the avoidance of enforce_minimum_density (though the
latter is still used even when this option is on). It is not currently
fully conservative, though, since there can be differences in fluxes
constructed at box edges.
At present it is only implemented in 3D.
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 2efee6ca33f3bf790f87eb423eea3b8be4462386
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 20:23:14 2016 -0400
Move some user-facing files from .f90 to .F90
This allows them to be preprocessed. These are mostly dimension
agnostic files and so most existing code will be unaffected.
Exec/KH/Prob_nd.F90
Exec/Noh/Prob_nd.F90
Exec/rotating_torus/Prob_nd.F90
Exec/rotating_torus/problem_tagging_nd.F90
Source/Src_nd/Make.package
Source/Src_nd/Prob_nd.F90
Source/Src_nd/Rotation_frequency.F90
Source/Src_nd/ext_src_nd.F90
Source/Src_nd/problem_tagging_nd.F90
commit 849e74cfa32d13638adbf094ab38197632f5c269
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 04:12:17 2016 -0400
Pass blocking_factor to Fortran
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_nd.F90
Source/Src_nd/prob_params.f90
commit f2145187a0b554371f53572bfe1a9a6b1e912487
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 03:39:39 2016 -0400
Pass n_error_buf and ref_ratio to Fortran
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_nd.F90
Source/Src_nd/prob_params.f90
commit 9c26f8c2a30b3010892926a3370c9ac8fc99fb84
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 01:55:45 2016 -0400
Disable Coriolis forcing when appropriate
Source/Src_nd/rotation_sources_nd.F90
commit 3cd3747e67230e4d73bdef34c3a5f9591be6d150
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 00:18:51 2016 -0400
Fix logic for when to create the rotation matrix
Source/Src_nd/rotation_sources_nd.F90
commit 04fdf2b5675f088a61db3ca3b43b45d2a63285e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 13 18:31:19 2016 -0400
Add notes on LANL systems courtesy of Platon
UsersGuide/ManagingJobs/managingjobs.tex
commit 9aa98f312bb974ed14c0462397e0d9a673bc06af
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 12 15:41:34 2016 -0400
Protect against (rho E) < 0 in reset_internal_e
Source/Src_nd/Castro_util.f90
commit 7e7cad8b22de9a0c66711881310c4272a6888373
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 12 13:51:30 2016 -0400
Update KE when we do the hybrid sync
Source/Src_nd/hybrid_advection_nd.F90
commit f54725c92130cbe54009b75350e7a4b3c3c5aa2e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 12 13:46:20 2016 -0400
Restrict to a single hybrid sync in post_timestep
Source/Castro.cpp
commit 6b2ff7c4d4efad473fb8930bbb14f423e91fb068
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 12 13:37:51 2016 -0400
Update AMR module info in post_timestep
Source/Castro.cpp
commit d5295860c64b676da82c5978cb8ef82fc04d003d
Merge: 975b63f98 a0b7ba821
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 11 20:37:10 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 975b63f98de795aaa9daac451c2bbab5378c67c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 11 20:36:14 2016 -0400
more sensiible default for eos_gamma
eos_gamma is now explictly 5/3. Previously it was 0 and reset
to 5/3 in the init. This is clearer
Microphysics/EOS/gamma_law/_parameters
Microphysics/EOS/gamma_law/gamma_law.f90
commit a0b7ba821b9b5e75b03da9001f0cf1fd6278efa3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 11 17:55:16 2016 -0400
update the params
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 85559db4e62abc8a1faa38346c072fb3bfea9ec7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 11 16:36:37 2016 -0400
1.e-30 -> 1.d-30
Microphysics/networks/_parameters
commit 7e98fb8b66c7ccebac147c8aeaece8fc0f84b3f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 11 00:04:52 2016 -0400
Add a rotating reference frame using inertial frame variables
Enable it with castro.state_in_rotating_frame = 0.
Source/Src_3d/riemann_3d.F90
Source/Src_nd/Make.package
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/hybrid_advection_nd.F90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit debf4718bad8795e6fda55e7707f2a6f7a40912c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 22:10:19 2016 -0400
Print out old density after a neg dens reset
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/advection_util_3d.F90
commit b8158aa988c992537d8b5eb28aca946ff296feeb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 20:46:14 2016 -0400
Fix indexing bug in gravity sync source
The component of the sync src that was being added to Eden
was not the energy component of the source but the Xmom component.
This has been around at least since the initial git commit in 2012.
The indexing is correct in Nyx, however.
Source/Castro.cpp
commit 41808ed6c38199c1b77f3ed9ecd41967adbc201c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 20:45:36 2016 -0400
Sync hybrid momentum after gravity sync
Source/Castro.cpp
commit 5eb13f9ac118934f9af7935c01dab90fbf98cf51
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 20:41:31 2016 -0400
Update the hybrid momentum in the gravity sync
Source/Castro.cpp
commit 2c79de735320fd359a550f704f712c90dc7dc7e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 20:39:08 2016 -0400
Update for change to small_x
Source/Src_nd/timestep.F90
commit 59e7940bbea96d0234ec429dfefd293045dca966
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 10 20:02:20 2016 -0400
clean up and make this work with python 3
this closes issue #2
Microphysics/networks/general_null/write_network.py
commit 8e407947c08e1d484f770a4c76e66ba6c66381fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 10 15:22:07 2016 -0400
small_x now belongs to the network
Microphysics/EOS/eos_type.f90
Microphysics/networks/_parameters
Source/Src_nd/Castro_util.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit 5db51c58677771c38012ee75792c693126efd378
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 10 09:01:07 2016 -0700
slurm job chaining
Util/job_scripts/edison/chainslurm.sh
commit 80b72b9e5effba28c39b269248d756b1e2d99670
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 10 11:49:09 2016 -0400
Sync up with hybrid momenta after a reflux
Source/Castro.cpp
commit 38d342108b03372f35d415558cd444bf56b67074
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 9 16:25:59 2016 -0400
Disable the minimum density check for piecewise constant
Source/Castro_advance.cpp
commit a139f58157f757937c789b3dac878e27b0771106
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 9 15:59:12 2016 -0400
Enable piecewise-constant interpolation onto fine grids
Use the new parameter castro.state_interp_order == 0 to access it.
Default is 1, the existing linear interpolation scheme.
Source/Castro_setup.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit f5f034819814c268a3751e2ca2884bbf196f0b3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 14:32:04 2016 -0400
add PFMG #s
UsersGuide/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
commit 04e1dc588502bcf8c66e8978d32148e3bf53323e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 13:42:35 2016 -0400
fix typo
UsersGuide/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
commit 9fb39b76a223b5586c3613ab7ba6ac075d26e83b
Merge: 448cea78e a7052bab1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 13:42:09 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 448cea78e9f2b4dd7798c5475ee97cb302cb0d0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 13:41:56 2016 -0400
a bit more about hypre at NERSC
UsersGuide/ManagingJobs/managingjobs.tex
commit a7052bab12cad45d682e81f5e9fc29712c323b00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 10:10:39 2016 -0700
add radsolver info
UsersGuide/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
commit 7fe3294de58e39a03a053ea31ca67f2313cf308f
Merge: 3d11013c3 7a65ab47e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 10:08:38 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 3d11013c34d1be4e5251652f7461338752787843
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 10:07:51 2016 -0700
some prelim castro radiation BWP scaling #s
UsersGuide/ManagingJobs/scaling/bwp/edison_20160609/scaling.txt
commit c4c6b74606fd8905bd3a4b030d5c322afc77415b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 10:01:56 2016 -0700
an example with open mp
Util/job_scripts/edison/edison.MPI.OMP.slurm
commit ddfc5e4ce54d7469883a26a6c5c2fd757124cef3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 09:44:14 2016 -0700
better gridding
bwp/inputs_3d
commit 7a65ab47ec9d9aac4fbd16586a2cd9d077af1dbb
Merge: 82f177e26 596c52587
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 11:54:33 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 82f177e26f720575ab7b7926860cd59d4530363c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 11:54:19 2016 -0400
use the new build stuff
Source/Castro_io.cpp
commit 59932b02ed25ad50fc1b16575f624ea33cb08a40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 11:53:54 2016 -0400
forgot to commit the hooks for opacity and conductivty to buildInfo
Exec/Make.Castro
commit 7b9c0f48eb4f3840c2665706fb7d0b5362829425
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 9 11:53:13 2016 -0400
add a note about Hypre at NERSC
UsersGuide/ManagingJobs/managingjobs.tex
commit 596c52587e55957d6ea416812ad5e6a35d67efe5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 9 10:50:51 2016 -0400
Enable verbosity in the new enforce_minimum_density call
Source/Castro_advance.cpp
commit c51316210a0a2657dd0f17097ae9fcb8aa23a853
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 8 16:25:41 2016 -0400
Check the fillpatch'd state data for negative densities
For now, only when lin_limit_state_interp == 1
Source/Castro_advance.cpp
commit 8adf6e05e63d2fa5d9e1280edccfa313faf73831
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Wed Jun 8 15:46:33 2016 -0400
3d version of bwp setup
bwp/Prob_3d.f90
bwp/inputs_3d
commit 9c0d8dab571a0f1fea928bd108a33c32a747a45b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 8 15:17:31 2016 -0400
fix index bug
rad_util.f90
commit 288ef86c192ab84937582110750a9c3f56084b95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 8 14:28:53 2016 -0400
a bit more clean-up on the total pressure and passive stuff
Src_1d/RadHydro_1d.f90
Src_2d/RadHydro_2d.f90
Src_3d/RadHydro_3d.f90
commit 14007376efdcb0c8cc1bdda44b6c76e39b06eeb8
Merge: 848219b73 f88db7b2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 8 14:01:32 2016 -0400
Merge branch 'development' into radmerge
commit 848219b7361e9bc85daaefaaa948f96b38968a62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 8 14:01:23 2016 -0400
start of rad merge
Source/Src_2d/trace_ppm_2d.f90
commit 5d892bb5205195e77840f8343ad339015ace7840
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 8 13:46:24 2016 -0400
add a rad_util_module to compute some common radiation expressions
this will allow us to easily reconstruct the radiation pressure
in a merged tracing routine
Make.package
Src_2d/RadHydro_2d.f90
Src_2d/trace_ppm_rad_2d.f90
rad_util.f90
commit d0c0ce8c24fed8831b364d1006cbb24aa32980e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 7 14:28:39 2016 -0400
this file is not needed
bwp/WD_rhoc_2.e9_M_1.1.hse.2560
commit 6f445735a476dca1b614335d8b142c198aaba88d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 13:59:12 2016 -0400
Initialize RHS in test_react
Exec/test_react/testburn.f90
commit f88db7b2c9cb120992d7b477b7b86c703ef72450
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 7 13:20:04 2016 -0400
consolodate the job_info stuff for the regular and small plotfiles
Source/Castro.H
Source/Castro_io.cpp
commit c26afff3df63e905addcc9af2dd5e1294a5f0ab3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 12:56:02 2016 -0400
Restore the acc declare create in the EOS
EOS/eos_type.f90
commit f8060d5d516e1bf5c96d806e5184dc2acfd8f5ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 7 12:53:00 2016 -0400
AstroDev -> Microphysics
Source/Castro_io.cpp
commit 471d4b4eb8fd8a6e2af69a03fb29b0027760a12c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 7 12:51:27 2016 -0400
AstroDev -> Microphysics
also remove the obsolete USE_TRACING stuff
Exec/Make.Castro
commit 42c647d6ec7751e9e87736c10ec3651931557050
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 7 12:29:25 2016 -0400
hook CastroRadiation into buildInfo, so we get the hash in job_info
Make.Castro
commit 0135ff555242311b6be701a7a5626db47edfa177
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 6 21:41:13 2016 -0400
add the bit Max discovered about python and swapping to the Cray compilers
UsersGuide/ManagingJobs/managingjobs.tex
commit d7ad37ae8335c73042a67234f16f094eb41a0835
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 6 13:12:34 2016 -0400
Fix call to get new data, not old data
Source/Gravity.cpp
commit 96bf2bcb05e722eb6778150c6158d11eb533c194
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 6 12:39:21 2016 -0400
a little more detail about running at NERSC`
UsersGuide/CastroUserGuide.tex
UsersGuide/GNUmakefile
UsersGuide/ManagingJobs/managingjobs.tex
commit 32d456f2742428a634de3477ed077affeb1c2c7b
Merge: 50c604393 321515296
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 6 07:34:39 2016 -0700
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 50c6043934c6b1c5afe0a2b78c737209511665d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 6 07:18:39 2016 -0700
enable diffusion, taller box
Exec/flame_wave/GNUmakefile
Exec/flame_wave/inputs_2d
commit 321515296a9424531b6311b6db33376a8617ad03
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 18:01:21 2016 -0400
Restore an integer that radiation needs
Source/Src_3d/trans_3d.F90
commit 7d8fb2824d34b0b130c199fcd6f263eb0ecb0951
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 17:52:39 2016 -0400
start a changes file for releases
CHANGES
commit 4251538c62f6cd1446dce9eafe6f027d1431de57
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 17:05:54 2016 -0400
Fix a bug introduced in a recent commit
Source/Gravity.cpp
commit eba6b2c142c01a0b95da604b45c56b64d94a1f57
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 16:21:02 2016 -0400
Pull in a network subroutine
Exec/toy_flame/Prob_1d.f90
commit c7db0b8e74028701a72dd16990f3ca9b27702d03
Merge: df1b5ba2c a384961ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 16:07:23 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit df1b5ba2ca90f8892c8bde99f22196cf27ef910c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 16:07:08 2016 -0400
need to define CASTRO_DIR
Exec/flame_wave/GNUmakefile
commit a384961cee24496895b72ce8e6456bc9a5687d38
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 14:28:59 2016 -0400
Use Sborder for source term since it has ghost cells
Source/Castro_advance.cpp
commit 72fd521310dcd831b52406e9bdb2792b48e48bc3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 14:28:46 2016 -0400
Reverse an assertion
Source/Castro.cpp
commit caab2b9189a3d57097702eebc67b436b4dee57ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 13:50:11 2016 -0400
Eliminate unused variables
Source/Castro_advance.cpp
Source/Gravity.cpp
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/trans_3d.F90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/hybrid_advection_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/sponge_nd.f90
commit 372c81a31ded7ce2bdcb612b6baaa9ef32ca1ab7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 13:43:11 2016 -0400
need mempool module in ctoprim_rad
Src_3d/RadHydro_3d.f90
commit f2ff5907bf684594e2b40e42e49e14007d479b85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 13:00:22 2016 -0400
update network location
Exec/DustCollapse/GNUmakefile
Exec/HCBubble/GNUmakefile
Exec/KH/GNUmakefile
Exec/Noh/GNUmakefile
Exec/RT/GNUmakefile
Exec/RT_particles/GNUmakefile
Exec/Sod/GNUmakefile
Exec/Vortices_LWAcoustics/GNUmakefile
Exec/diffusion_test/GNUmakefile
Exec/evrard_collapse/GNUmakefile
Exec/gamma_law_bubble/GNUmakefile
Exec/gresho_vortex/GNUmakefile
Exec/oddeven/GNUmakefile
Exec/uniform_cube_sphere/GNUmakefile
commit 5514afa0d5e9d5ca31bd04a5f3d72a82aab2ba2d
Merge: 7444af830 384728c4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 12:55:45 2016 -0400
Merge branch 'development' into microphysics_move
commit 384728c4d893ab861457765035c86108bfb54f14
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 5 12:26:42 2016 -0400
Explicitly hook in network to gamma_law
EOS/gamma_law/gamma_law.f90
commit 7444af8304c08b3bd4f7a5768fa5bc0812c810ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 12:15:52 2016 -0400
reorganization attempt...
Exec/Make.Castro
Exec/Sedov/GNUmakefile
Exec/double_bubble/GNUmakefile
Microphysics/EOS/Make.package
Microphysics/EOS/README
Microphysics/EOS/_parameters
Microphysics/EOS/eos.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/constant/Make.package
Microphysics/conductivity/constant/_parameters
Microphysics/conductivity/constant/constant_conductivity.f90
Microphysics/conductivity/constant/constant_viscosity.f90
Microphysics/conductivity/constant_opacity/Make.package
Microphysics/conductivity/constant_opacity/_parameters
Microphysics/conductivity/constant_opacity/constant_conductivity.f90
Microphysics/conductivity/constant_opacity/constant_viscosity.f90
Microphysics/networks/Make.package
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
commit 13f631dad1bbf5b326d2827c8b44018a936beb3c
Merge: 8f23ec584 3b3239013
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 19:33:56 2016 -0400
Merge branch 'development' into oac_reactions
commit 3b323901365ff60fb942f61447c1ac9dc7639c7f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 19:32:34 2016 -0400
Only need RHS when doing burning
Source/Src_nd/Castro_nd.F90
commit 781738b28c43e179d21b7d79464f716b15d4cc95
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 16:43:14 2016 -0400
Consolidate eos_data variables into eos_type_module
EOS/Make.package
EOS/eos.f90
EOS/eos_data.f90
EOS/eos_type.f90
EOS/gamma_law/gamma_law.f90
Exec/hydrostatic_adjust/Prob_1d.f90
Exec/hydrostatic_adjust/extra_derives.f90
Util/exact_riemann/GNUmakefile
commit 8f23ec58422bfc5129a52060e4497730d56497c8
Merge: ba3442242 f4fe08901
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 15:24:29 2016 -0400
Merge branch 'development' into oac_reactions
commit f4fe08901f3d9e1f0c4245175a3a900df338e646
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 15:20:23 2016 -0400
Add an RHS initialization routine
Networks/general_null/actual_rhs.f90
Source/Src_nd/Castro_nd.F90
commit ba3442242575b99b1842fe66cc9c2a937f584695
Merge: 1c1000f25 3b16f6eb4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 14:41:22 2016 -0400
Merge branch 'development' into oac_reactions
commit 3b16f6eb4ba26a938f4155d92a915e780d7ee15f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 14:37:23 2016 -0400
Remove actual_network_data and actual_burner_data
Networks/burn_type.f90
Networks/general_null/Make.package
Networks/general_null/actual_burner_data.f90
Networks/general_null/actual_network_data.f90
Networks/general_null/network.template
commit 1c1000f25b25eac99d07b933f9ca25bafe0f3294
Merge: 5d25949fc 9866d37b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 01:07:51 2016 -0400
Merge branch 'development' into oac_reactions
commit 9866d37b2d011986c220d5efc87e8b7f54be6065
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 00:01:44 2016 -0400
Add a missing pressure term to the hybrid momenta
Source/Src_nd/hybrid_advection_nd.f90
commit 5d25949fc167b7280fbd69700db10029992b4aa1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 22:17:10 2016 -0400
add a comment
Source/Src_nd/hybrid_advection_nd.f90
commit 31432a8e97564f80cb3803be96119c726b7ce3a7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 3 15:06:52 2016 -0400
Quiet some unused variable warnings
Source/Castro.cpp
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/slope_1d.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/sponge_nd.f90
Source/Src_nd/timestep.F90
commit bca6f7608994e17a9df0825e764e9c07320515a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 14:30:11 2016 -0400
start consolidating all of the compiler and scaling stuff into a
single chapter. This matches what we do with Maestro
UsersGuide/CastroUserGuide.tex
UsersGuide/GNUmakefile
UsersGuide/ManagingJobs/managingjobs.tex
UsersGuide/Scaling/Scaling.tex
UsersGuide/Scaling/ScalingTest.eps
UsersGuide/Scaling/Sod_scaling.eps
UsersGuide/Scaling/scaling_jaguarpf.eps
UsersGuide/Suggestions/Suggestions.tex
commit a7501aefa2978a8191b8d462cdfc03bd5b8f76cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 14:01:35 2016 -0400
start an archive of Castro job scripts to mirror Maestro's
Util/job_scripts/edison/edison.MPI.slurm
commit 71f5e80080b49cdb8801834483854b5d33b07d58
Merge: fd66a7ad7 e0a2f9efa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 12:20:12 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit fd66a7ad7cbf1baef7a5b76caa637697acf90b9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 12:20:04 2016 -0400
a little tweaking
Exec/flame_wave/inputs_2d
commit e0a2f9efaf90d3e85b9c53552e9ec9643d1d505c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 3 10:24:38 2016 -0400
PGI needs named C bindings in a module
Exec/flame_wave/bc_fill_2d.F90
commit 014dd77f25b769b0df97dd6e26c7805478fb2ad8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 20:38:05 2016 -0400
a more sensible perturbation
Exec/flame_wave/probin
commit fb36d83f08da64d4d56703fd74397f63133d214c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 20:36:04 2016 -0400
some cleaning
Exec/flame_wave/Prob_2d.f90
commit 6e66aebca753a274ffbb958c5e4a869a9b82d1f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 20:31:02 2016 -0400
fix the namelist stuff
Exec/flame_wave/Prob_2d.f90
Exec/flame_wave/probdata.f90
Exec/flame_wave/probin
commit d3e4a68035766bb0d32541a03937cd61c49ad4fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 20:22:57 2016 -0400
remove some stray variables
Exec/flame_wave/Prob_2d.f90
commit 19d767669541af32b767fcf60257618cb1c6de58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 20:18:21 2016 -0400
turn on refinement, fix blocking factor, smaller domain width
Exec/flame_wave/inputs_2d
commit 38b7c97e75616bd405d3ec079c4be7c609085901
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 20:18:03 2016 -0400
remove some debugging output
Exec/flame_wave/Prob_2d.f90
commit 0b265fc7e319727ad65524aa99177ccea2f2ffd5
Merge: 81cd7ab41 db22a04f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 19:55:56 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 81cd7ab41a1581cb36db37bcf3215c9e8cb4c77e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 2 19:55:18 2016 -0400
update the initial model
this model was generated by toy_atm in MAESTRO using
_params.xrb.flame_wave.2H
Exec/flame_wave/flame_wave.hse
Exec/flame_wave/flame_wave.hse.tanh.delta_12.000cm.dx_10.000cm
Exec/flame_wave/probin
commit db22a04f5266fa95d9c4feb00d81397d8a8c3172
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 09:47:25 2016 -0400
Rename sources -> hydro_sources for clarity
Source/Castro_advance.cpp
commit 1f9e0c1ac7b2c1cbb2b2368722bdd293099d5c55
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 09:43:23 2016 -0400
Remove reliance on add_ext_src for hybrid hydro source
Source/Castro_advance.cpp
commit 7c613d14aab591abdb20b3b7876644385eaafc9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 00:51:36 2016 -0400
Zero out arrays to avoid potential NaNs
Source/Src_nd/gravity_sources_nd.F90
commit faf7a8908ebf7c566006ace4e1957cf250b72589
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 00:24:31 2016 -0400
Free diffusion source terms from reliance on add_ext_src
The diffusion source terms are now handled with their own MultiFabs
in a way that is analogous to how the ext_src_old and ext_src_new
are handled. The subtlety comes with the numerous calls to computeTemp
that are sprinkled throughout Castro_advance.cpp. These can change
behavior significantly if not done in the same order. We therefore
insert a computeTemp call at the beginning of the new-time diffusion
source term update, which was happening before if we had add_ext_src
== 1 (which was necessary to do diffusion properly).
Though note that at present the new-time diffusion source terms are
equivalent to the old ones, so in practice the computeTemp call was
the only difference.
Fixes #1
Source/Castro_advance.cpp
commit b617353774f4efbc6e17a8f63ac4e8b04c6cc93b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 2 00:01:30 2016 -0400
Fix the same diagnostic bug in 1D and 2D
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.F90
commit 898512619cd8507c5d462baf802df84418252712
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 1 23:55:52 2016 -0400
Fix two bugs in the grid loss tracking diagnostics
1) We were not calculating the angular momentum with respect to center
2) The z-angular momentum had a bug in one of the loops
Source/Src_3d/Castro_advection_3d.F90
commit b226298974791aea5a0ff1fe057d0878bfa6a1ca
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jun 1 20:50:50 2016 -0700
remove unused variables
Source/Castro.H
commit c2b01996b6d636230af3544f9f59642b5108d999
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Jun 1 20:32:16 2016 -0700
Need to initialize species diffusion term to zero before we compute it.
Source/Castro.cpp
commit a9062f56f9806efa5c6e6b2e5a245057c5e33ba3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 1 14:11:06 2016 -0400
bigger box, more levels
the big fix here though is that we now set the Rosseland mean
opacity, and we multiply the Kramer's form of the opacity by
another factor of rho to get it in 1/cm units
bwp/inputs_2d
commit ef0b24fe0100d02d10e81d5b5016d89c92324ff4
Merge: 9c87eff6b 4338c0f03
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Wed Jun 1 13:38:00 2016 -0400
Merge branch 'development' of https://github.com/BoxLib-Codes/CastroRadiation into development
commit 9c87eff6bda74a443f96a290347edf0102251c1d
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Wed Jun 1 13:36:12 2016 -0400
Initial model modified
bwp/GNUmakefile
bwp/SolarLike_0.2M.hse.1280
bwp/inputs_2d
bwp/probin
commit c40ae13ff925253beaac982a44f6f0963278ce24
Merge: 364286cf5 96dad5fc2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 1 09:41:17 2016 -0400
Merge branch 'development' into oac_reactions
commit 96dad5fc21a150491936f8ac3fc822be46878dc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 1 09:40:57 2016 -0400
Fix typo
Networks/general_null/actual_network_data.f90
commit a6cd07bbd911e81c1c92a35ff1a1fe137555bb86
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 15:14:30 2016 -0400
Move nrates from burner to network data
commit 364286cf5df41dc9ba656f54a70efc3f688b2175
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 17:48:33 2016 -0400
Re-enable some derived type initializations
EOS/eos_type.f90
Networks/burn_type.F90
commit 8bda46678b521f3cd58d81d20f346e0da523e787
Merge: 6b85a1148 cf67f82d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 15:25:26 2016 -0400
Merge branch 'development' into oac_reactions
commit cf67f82d80b850d054563d22b80e22ca67410713
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 15:14:30 2016 -0400
Move nrates from burner to network data
Networks/burn_type.f90
Networks/general_null/actual_burner_data.f90
Networks/general_null/actual_network_data.f90
commit 6b85a11480d36e7b812cd7d8692d53fa26010180
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 23:04:33 2016 -0400
Preprocess out aux vars from burn_t if naux == 0
Networks/Make.package
Networks/burn_type.F90
Source/Src_nd/React_nd.F90
Source/Src_nd/timestep.F90
commit d75a1c5ccb804f73aa27e94766cd08adbe4a73cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 29 21:53:01 2016 -0400
reset the plot frequency to a longer value
Exec/reacting_bubble/inputs_2d_test
commit 98cfa3f72dd84a11dc04fca49433a51430d784dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 29 21:24:00 2016 -0400
add Backtrace
.gitignore
commit 06288636ead8a85359a3cdc092385d5f14d56599
Merge: 696c66323 2d1a13869
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 19:35:47 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 696c66323153f1ed899a2c46fb3f69ba4846fa87
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 15:05:31 2016 -0400
Do the EOS call at the end of the burn here
Networks/burn_type.f90
Source/Src_nd/React_nd.F90
commit 2d1a138691e0f1a07630e9882559e829c2cdbaaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 29 19:29:18 2016 -0400
this file is extraneous
Exec/reacting_bubble/inputs_2d.test
commit 3a9c267883ebe66e70b477aeecb4c0c4351c46e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 29 15:51:28 2016 -0400
rename inputs file + new defaults
use ppm_type = 1 + some nice ppm options
clean up the hse BCs
add tagging
Exec/reacting_bubble/bc_fill_2d.F90
Exec/reacting_bubble/inputs_2d
Exec/reacting_bubble/inputs_2d_test
Exec/reacting_bubble/probin
commit 523d136dfaf30fd4229159d5b172bfde049857c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 15:05:31 2016 -0400
Do the EOS call at the end of the burn here
Networks/burn_type.f90
Source/Src_nd/React_nd.F90
commit 6fac074e4e2e29884e0e654babcd6726b8c02fe0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 29 13:32:59 2016 -0400
cfl 0.9 -> 0.8
Exec/reacting_bubble/inputs_2d_smalldomain
commit ea612286d37ded9fed52b82982b42c527b56bed3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 28 19:00:32 2016 -0400
hook in the versioning
Exec/Make.Castro
commit 091613136f3b685ea7edc3b468b44f2df876828d
Merge: 2d4678678 1ce30ab2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 28 14:57:56 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 2d467867810781a95cef5517b5efd5d992201a2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 28 14:57:40 2016 -0400
add versions of the compiler to job_info
Source/Castro_io.cpp
commit 1ce30ab2bcf001cb740de1e43e6a00620c13c8bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 27 18:14:56 2016 -0400
a little cleaning
Exec/flame_wave/GNUmakefile
commit 67a457d33538f8cf7dcbf1aaf46335fd59c512a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 27 17:02:21 2016 -0400
this is the flame wave problem that looks at a burning front spreading
through the XRB atmosphere. This was started with Luke
Exec/flame_wave/GNUmakefile
Exec/flame_wave/Make.package
Exec/flame_wave/Prob_2d.f90
Exec/flame_wave/README.md
Exec/flame_wave/bc_fill_2d.F90
Exec/flame_wave/flame_wave.hse
Exec/flame_wave/hse_check.py
Exec/flame_wave/inputs_2d
Exec/flame_wave/probdata.f90
Exec/flame_wave/probin
Exec/flame_wave/problem_tagging_2d.f90
commit e19033f107d299407bd1eaf2b4cf867845542250
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 22:27:00 2016 -0400
Insert a hook for doing a device update of probin parameters
Source/extern_probin.template
commit 1d6133bc8ef3ff5c8b2866d85ee3524bb2113c29
Merge: 14bf2a84f 70c7bfa55
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 10:48:57 2016 -0400
Merge branch 'development' into oac_reactions
commit 70c7bfa55a9710b525783bf5bbee4bfec85eaa8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 10:48:39 2016 -0400
Fix eos input variable
Networks/burn_type.f90
commit 14bf2a84fd040964c18db1bca55c6c932f3297ef
Merge: 738ea9a3f 7893b399c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:53:43 2016 -0400
Merge branch 'development' into oac_reactions
commit 7893b399c92b7258bb87617188522b9ff2a2f20f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:53:31 2016 -0400
Add option for EOS call at end of burn
Networks/burn_type.f90
commit b016ec194c2788575ab327cd3c6b7051f3745ab3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 22:13:59 2016 -0400
networks :)
UsersGuide/needs_doc
commit 738ea9a3f96ee9ef4651eff8c5c224d72bc44466
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 22 16:29:32 2016 -0400
Add various updates to the test_react problem
Exec/test_react/probin
Exec/test_react/testburn.f90
commit ec1723ceebbd12d9ae6070623d09fe07b80d4c43
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 22 04:29:26 2016 -0400
Fix some PGI OpenACC issues in react_state
Source/Src_nd/React_nd.F90
commit 3e3323b505508746c75fe366f1bb6037f6111d32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 22 00:58:04 2016 -0400
make aprox13 the default
Exec/test_react/GNUmakefile
commit 2ec6257a1a16cf8df203b9ba31c227ade2fcdc2e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 19 19:44:32 2016 -0400
Eliminate two unused variable warnings
Source/Castro_advance.cpp
Source/sum_integrated_quantities.cpp
commit b589ce9935c34d0f59bd7b365f06140274ea160e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue May 10 10:45:57 2016 -0700
fix clear_internal_borders in case of periodic boundaries
Radiation.H
Radiation.cpp
commit 4338c0f030ea0bc604901db7f905de8062b7c987
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon May 9 21:52:01 2016 -0700
revert 040c8ea33
Rad2Tshock/inputs.M2.test.multid
Rad2Tshock/inputs.M5.mg.test.multid
commit 6af2dd62c1db44a9db1bed876f9bdbe4494b3d16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 9 19:15:51 2016 -0400
change the hypre solver. From Weiqun:
The multi-D Rad2TShock tests have periodic boundaries in the directions
parallel to the shock surface. The y and z velocities are supposed to be
zero. With 103 or 1003, we do get perfect zero. But with SMG and PFMG,
these velocity grow out of control. I don't know whether that is a
problem of hypre's algorithm or our hydro or we did not set up periodic
boundary correctly in our radiation code interacting with hypre. The
periodic case was never really used.
Rad2Tshock/inputs.M2.test.multid
Rad2Tshock/inputs.M5.mg.test.multid
commit f9ff77fbc251a236692028900539288d61ad1c83
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 8 14:43:51 2016 -0400
Write out separate copy statements to appease Cray
Source/Src_nd/React_nd.F90
commit faf2a7548b1d8fb6f0b81756dedc76bdb9b3967a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 8 10:57:36 2016 -0400
Insert changes needed to get test_react running well
Exec/test_react/testburn.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/meth_params.f90
commit 5d913edda209ff850741ba9a23d5ec418ae88a35
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri May 6 22:45:13 2016 -0700
fix a bug: get_center is a fortran function that takes 3D array.
Source/Gravity.cpp
commit 7697beb49e4a964e491679e8e6f38dccdf89cdde
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 15:11:05 2016 -0400
Unset probin variables since they're not used anyway
Exec/test_react/probin
commit 10dbc4a77fdba7fb28e5fe606a5e461eaa184c7b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 15:10:17 2016 -0400
Update device data for parameters in test_react
Exec/test_react/testburn.f90
commit 8528fbe686c2c20cf873a26fa7617c0fae4ef977
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 03:48:37 2016 -0400
Add a test_react problem similar to that from MAESTRO
Exec/test_react/GNUmakefile
Exec/test_react/main.cpp
Exec/test_react/probin
Exec/test_react/testburn.f90
commit c10356a097e40978f74a381d2358aedfa2c0461f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 02:25:18 2016 -0400
Fix incorrect variable declaration
Source/Src_3d/Prob_3d.f90
commit 67b1a8de58d30af5810a4fd7816da413b4fabc3d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 01:16:24 2016 -0400
Run the script and add the OpenACC sections
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
commit 811fc7cf728490ed21b4570fdb707a50aa759e94
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 01:15:35 2016 -0400
Add OpenACC declaration block to the parm parse script
Source/parse_castro_params.py
commit c3dc4ebb045da0c2deea07066f4624ee66216068
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 01:14:41 2016 -0400
Update a parameter in the header file
Source/castro_defaults.H
commit c2933e82cf92173a30f4069c35999c5afb84cc68
Merge: 0fbee55f9 b98382f28
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 15:18:39 2016 -0400
Merge branch 'development' into oac_reactions
commit b98382f286fb99ce5e9672d7372ef8f159bd4c22
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 15:10:29 2016 -0400
Insert smallt and smalld into the EOS type
EOS/eos.f90
EOS/eos_type.f90
commit 0fbee55f984879b0f1c126e2bb348fb5376a1362
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 13:05:23 2016 -0400
Fix some PGI errors by writing out some implied loops
Source/Src_nd/React_nd.F90
commit 3d8aa5808a374feb121a4251786de1a3f7699bab
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 04:55:50 2016 -0400
Parallelize the react_state loop for the GPUs
Source/Src_nd/React_nd.F90
commit 2314717a3945c4d4fd11652c7c1e8663b5b08a08
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 04:54:21 2016 -0400
OpenACCify the burner interface and derived type
Like the EOS type, we've commented out the initialization of the
derived type members as a temporary fix.
Networks/Make.package
Networks/burn_type.f90
Networks/burner.F90
commit 7d1c5bf324b41e6edf55c3438928426ad05115d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 04:52:19 2016 -0400
OpenACCify the EOS interface and derived type
At present, PGI is not happy with initializing the derived type
members with our testing number. So this is disabled for now,
but this must be resolved in the future.
EOS/Make.package
EOS/eos.F90
EOS/eos_data.f90
EOS/eos_type.f90
commit 97c6609b1c9cef258f0da8374b6dad9db7d9af4d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 04:48:37 2016 -0400
Define a macro when we're using OpenACC
Exec/Make.Castro
commit eb2ca3588306d079dfd583ff2db6754731dd5180
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 21:20:17 2016 -0400
Copy the CastroHeader file in a checkpoint embiggening
ConvertCheckpoint/Embiggen.cpp
commit cb8a62c23aa4c7453ec7ccbbab78bf28298a5b27
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon May 2 17:42:19 2016 -0700
Fix bug in post_grown_restart -- only shows up if you Embiggen to create
a new checkpoint file then restart with grow_factor > 1.
Source/Castro.cpp
commit 870231dd809f8c015483105b1ea0b974ac16d365
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 2 16:39:30 2016 -0400
Insert a missing subtraction of center
Source/Src_nd/hybrid_advection_nd.f90
commit 4812adb31f5fc566bfac18603d8736de0d4b2899
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 26 15:33:37 2016 -0400
Mention castro.use_retry in the docs
UsersGuide/FlowChart/FlowChart.tex
commit 5e9639c487055b194bb49f7c69633447848cc8b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 22 11:05:24 2016 -0400
Add a have_rates logical to burn_t
Networks/burn_type.f90
commit 34e5de1e86221661415bbd3e37060440113f9425
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 21 15:52:42 2016 -0400
more needs doc
UsersGuide/needs_doc
commit caf7597f5facd00e25e0e3ea197dbd6c2ad37e83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 21 15:46:28 2016 -0400
get this compiling in 1-d
ConvertCheckpoint/Make.package
commit 4aaede48da976177e6a8758e0dcc32e6759df57a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 21 09:47:59 2016 -0400
Add variables for specific heat prediction to burn_t
Networks/burn_type.f90
commit 5b1db4cfca2b79b01f879d7b2e4986f668950e37
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 20 13:30:14 2016 -0400
If we did a reset, no need to call EOS twice
EOS/eos.f90
commit a5765b9cec9da9770f2342a33032e9a64bf56da5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 20 12:44:28 2016 -0400
we need T in the EOS state in order to have a good initial guess for
root finding on the EOS
We also need to catch cases where we try to come in with a negative e
and instead use (rho, small_temp)
Source/Src_nd/Diffusion_nd.f90
commit c51e9b844b1ebe3d8a4fa92a14be21ab482d7f86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 20 12:08:39 2016 -0400
add a comment on dg
Source/Src_nd/prob_params.f90
commit 5abc7776317f4f01c92832d0d4f75608124c8933
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 20 11:42:02 2016 -0400
Add raw scaling data for Titan runs of wdmerger, 04/16
UsersGuide/ManagingJobs/scaling/wdmerger/titan_041516/README
UsersGuide/ManagingJobs/scaling/wdmerger/titan_041516/one_level_omp4.txt
UsersGuide/ManagingJobs/scaling/wdmerger/titan_041516/three_level_omp4.txt
UsersGuide/ManagingJobs/scaling/wdmerger/titan_041516/three_level_omp8.txt
UsersGuide/ManagingJobs/scaling/wdmerger/titan_041516/two_level_omp4.txt
commit 5846539576c256ae6f577392bea61197215c54ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 8 01:13:48 2016 -0400
Avoid trying to allocate an already-allocated array
Source/Src_nd/Castro_nd.F90
commit 821c982f6fd3790946cc873ceb26a6417e0c48c4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 18 09:51:43 2016 -0400
Some more things that need documentation
UsersGuide/needs_doc
commit 8ddcb9e921e2867d1bcaee02e708a28befed265a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 17 15:58:03 2016 -0400
Define an EOS input to use during a burn
Networks/burn_type.f90
commit cd2879e252be66237b4ca122921d9e762470742e
Merge: 74a391dba a6f5ddc95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 17 12:16:20 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 74a391dba7e95007c5b659759ae4e98c0b5be65b
Merge: e4222e246 e4c5a4ec1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 17 12:15:36 2016 -0400
Merge branch 'development' into new_defaults
commit a6f5ddc95281b528828c7167055605e9aaed7475
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 17 12:14:34 2016 -0400
Loosen restriction on when we calculate dhdX
In principle there is no reason dpdr needs to be greater than zero,
it just needs to be non-zero for the division to make sense.
EOS/eos_type.f90
commit e4c5a4ec1005954379a176016e68f34d45a16340
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 17 11:50:24 2016 -0400
Reverse the convention for dual_energy_eta3 so that it is consistent with the hydro variables
Source/Src_nd/React_nd.F90
Source/_cpp_parameters
UsersGuide/Equations/Equations.tex
UsersGuide/runtime_parameters/runtime_parameters.tex
commit d695e8d12a2f152c96900a184e387da6b21b0994
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 17 11:45:28 2016 -0400
Add documentation about the flags for the internal energy variable
UsersGuide/Equations/Equations.tex
UsersGuide/refs.bib
commit e4222e2466c20dfa1566515246cd55884ca0b078
Merge: 19309ab66 bc298188e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 17 10:01:39 2016 -0400
Merge branch 'development' into new_defaults
commit bc298188e72f872c16668e49c8ea2849c8384df8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 16 23:13:09 2016 -0400
Add comment explaining use of Fortran parallel_IOProcessor()
EOS/eos.f90
commit 19309ab661fcbb7d2da9aab274b4e21c3f6f0f91
Merge: 0d70b1c23 19865b8ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 22:23:40 2016 -0400
Merge branch 'development' into new_defaults
commit 19865b8efc55107660dcca4f47545df0ca6e7247
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 22:22:35 2016 -0400
fix a comment
Source/_cpp_parameters
commit 36959215ec78c8f869482f24f97d19259d983294
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 19:43:54 2016 -0400
more things in need of doc
UsersGuide/needs_doc
commit 95f8dd8b94176c5db04e9bcb30428ee401d941e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 18:31:51 2016 -0400
what needs better docs?
UsersGuide/needs_doc
commit 0d70b1c23997736b710b1bb64cc3cb6ea8d521d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 14 19:16:48 2016 -0400
update defaults
Source/castro_defaults.H
commit 49910184de672f2c8ac48ea11c4480c7a3ae6890
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 14 19:16:10 2016 -0400
can't do reference_eigenvectors just yet...
Source/_cpp_parameters
commit dba559fbae26152e1203bfe288d75b60460a3bbc
Merge: 0d2658770 3029b7b70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 14 18:59:34 2016 -0400
Merge branch 'development' into new_defaults
commit 04e256f8945ca6cb9cd2e20998c7cf2f973a86ca
Author: Jasmine Garani <jgarani@bender.astro.sunysb.edu>
Date: Thu Apr 14 15:00:54 2016 -0400
add a tagging routine
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probdata.f90
Exec/convective_flame/problem_tagging_2d.f90
commit 2aa33c85636d70fa23374ad0686f086db9d99ad6
Merge: d8ee89e64 bafa28316
Author: Jasmine Garani <jgarani@bender.astro.sunysb.edu>
Date: Thu Apr 14 14:46:05 2016 -0400
Merge branch 'development' of https://github.com/BoxLib-Codes/Castro into development
commit d8ee89e641ab4a95c13f13971118382ad3a8fbb8
Author: Jasmine Garani <jgarani@bender.astro.sunysb.edu>
Date: Thu Apr 14 14:45:34 2016 -0400
make the diffusion cutoff higher -- this reduces the Mach
number above the atmosphere
Exec/convective_flame/inputs.2d.test
commit bafa2831685e9391daa814378c9502a92a1181a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 14 11:59:47 2016 -0400
Add a parameter that controls state data interpolation limiting
Source/Castro_setup.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 817897a6854fc4fad0931c32104f9840e19dd157
Merge: 2e32915a7 6d8c0a44b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 14 09:17:10 2016 -0400
Merge branch 'master' into development
commit 45a9105bf82cbef8e59c687fb44621bd8cfbb74b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 12 20:50:38 2016 -0400
add a note that gamma is wrong for verification
Exec/Sedov/README
commit 02c6308f7eea5e09f03254b3326f958f3be5fdf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 12 15:07:25 2016 -0400
this runs, but the opacity is not right yet
bwp/inputs_2d
commit 2376032fb8a2ff6b72b0c28b616a6cb3c77856da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 12 15:01:12 2016 -0400
put in a radiation field (but it is commented out for now)
bwp/Prob_2d.f90
commit 6bf26bec60ad9d87dd0374f7e47bc9c40a067e55
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Tue Apr 12 14:31:42 2016 -0400
start of the BWP problem
bwp/GNUmakefile
bwp/Make.package
bwp/Prob_2d.f90
bwp/WD_rhoc_2.e9_M_1.1.hse.2560
bwp/inputs_2d
bwp/probdata.f90
bwp/probin
commit bbc6752be23c453dd42d294b45523af032b7b945
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 12 09:08:13 2016 -0400
remove hook of exact_riemann in the GNUmakefile
we were not using exact_riemann at all, and the probin changes there
cause this to now fail.
Exec/Sod_stellar/GNUmakefile
commit 45dcf2673e0bb09ade77fd1cc14c9e0e6e0966fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 12 00:07:41 2016 -0400
Updated inputs for stellarcollapse
Util/exact_riemann/inputs.stellarcollapse
commit 9b2518a556426e1648253675a7d693173fe4d8aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 12 00:07:07 2016 -0400
Parameterize the max number of iterations to find the star state
Util/exact_riemann/_parameters
Util/exact_riemann/riemann_star_state.f90
commit d8af12f8afe6eafd3ccdab8e83f92dd1f52c4254
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 12 00:03:08 2016 -0400
Allow the initial temperature guess to the EOS to be a runtime parameter
Util/exact_riemann/_parameters
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit e58e930b35f2c30f7270420fe3a1868ce200fef1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 11 23:52:36 2016 -0400
Check in a sample problem for the stellarcollapse EOS
Util/exact_riemann/inputs.stellarcollapse
commit 0a88f9a36d8da2d72d19886320be222fc823801d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 11 23:04:52 2016 -0400
Add compilation support for the stellarcollapse EOS
Util/exact_riemann/GNUmakefile
commit a0f42483f5c4e8ae2d599b93ff7b242f5a722d36
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 11 16:51:21 2016 -0400
Have general_null define nspec_evolve for consistency's sake
Networks/general_null/network.template
commit 9cb57b3f4788bb1c5c3f6b3c3c59f630dc5a897b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 11 16:46:21 2016 -0400
Define the number of equations in burn_t with nspec_evolve number of species components, not nspec.
Networks/burn_type.f90
commit ad796d39f0e0442f727fb5f2e0d3628aa230c204
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 11 09:21:04 2016 -0400
Sync up the exact_riemann utility with the current Microphysics structure
Util/exact_riemann/GNUmakefile
Util/exact_riemann/exact_riemann.f90
commit c7ace56c914531f00d308a131d0db610df4d6bab
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 11 09:07:00 2016 -0400
Have the EOS rely on the Fortran parallel_IOProcessor() function, not the C++ one
EOS/eos.f90
commit 3029b7b70641653fc2be73976517468d9341fddc
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 8 01:49:34 2016 -0400
Don't zero out the reactions data on a restart; that was a holdover from when it was not stored in the checkpoint.
Source/Castro.cpp
commit e06529fa6afea810b6d505986eeee5e520b25139
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 8 01:44:46 2016 -0400
Another typo
Source/Castro_io.cpp
commit b4bd7cee40c201457d2822496be2e502431fbad7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 8 01:42:50 2016 -0400
Fix typos
Source/Castro_io.cpp
commit 8b239b6cc4c8a580885186d924bd46a6d4e26e90
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 8 01:13:48 2016 -0400
Avoid trying to allocate an already-allocated array
Source/Src_nd/Castro_nd.F90
commit fe8fa886d8c521c34e236bd391884d0eed3c8051
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 7 01:10:12 2016 -0400
Scale the cell volume inside the multipole gravity the same way we scale the position.
Source/Src_nd/Gravity_nd.f90
commit 189ef4f3a01b1f5cbbfdce9987c644e750dd7107
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 6 23:20:04 2016 -0400
Resolve some outstanding issues with how 2D axisymmetric was being treated in the multipole gravity.
Source/Src_nd/Gravity_nd.f90
commit 3d9067430bd6bcf3ceba6ff1a56ef4e25b822f88
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 5 12:11:14 2016 -0400
Add a sanity check: CFL must be between 0 and 1.
Source/Castro.cpp
commit 88ca670e0b361ae59db6425e4f7f5c9b8b5b3df3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 5 12:06:28 2016 -0400
Add a comment about the CFL factor in diffusion
Source/Castro.cpp
commit fc2b5c21b38c4a0f717c1a2adbf812bd7f52af85
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 5 12:05:12 2016 -0400
If we were limited by max_dt, this was still getting hit with a factor of CFL. This is now fixed.
Source/Castro.cpp
commit 7e857d962e468de06486c39a0d3f220b3bd0b1dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 4 12:59:58 2016 -0400
Fix an indexing issue in the multipole gravity
Source/Src_nd/Gravity_nd.f90
commit 0d2658770a3c202197608901cd858c26f9ecc3b3
Merge: 261c6f6b7 3ae12e399
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 3 21:50:32 2016 -0400
Merge branch 'development' into new_defaults
commit 3ae12e3994e94a504d28cde8b1edc523e0a6bab7
Author: jbb <jbbell@lbl.gov>
Date: Sun Apr 3 13:09:05 2016 -0700
fix for enthalpy diffusion
Source/Castro.cpp
Source/Src_nd/Diffusion_nd.f90
commit 63e7559ecd00f1952d02e2f07ac1a1c3319d7982
Author: jbb <jbbell@lbl.gov>
Date: Sat Apr 2 21:08:36 2016 -0700
We need to compute the enthalpy on one ghost cell as well as the interior
in order to copmute the gradient of it later.
Source/Src_nd/Enthalpy_nd.f90
commit d126f03ff8dc5fd7922cd29fc19de0707f6b9617
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Apr 2 12:24:03 2016 -0700
Remove unused variables.
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_1d/riemann_1d.F90
Source/Src_1d/trace_1d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/advection_util_2d.f90
Source/Src_nd/Enthalpy_nd.f90
commit b60e407e5ef7f20f3cc66f472112a7104c5c7ca7
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Apr 2 12:14:54 2016 -0700
Quiet the warnings of unused variables when REACTIONS is not true.
Source/Src_nd/timestep.F90
commit dd6c46cff8589be98cd060ac031f57a551bdfe3a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Apr 2 12:07:42 2016 -0700
Make a separate timestep routine if we are diffusing enthalpy instead of
temperature.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/timestep.F90
commit f7ae4983a34adead9a813adf15bf3df73a01809a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 1 16:27:46 2016 -0400
Forgot to wrap a statement for only 2D/3D
Source/Gravity.cpp
commit 261c6f6b7504e473444050f146c7222eb383cae7
Merge: d91f22bca 760008f74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 31 19:39:36 2016 -0400
Merge branch 'development' into new_defaults
commit 760008f7423e5058763f11c8460c31529c0d3fc9
Merge: 8caa1aa51 6e13ad520
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 31 19:35:37 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 8caa1aa51d35cfd241d1968bb2ca452e37821f7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 31 19:34:54 2016 -0400
remove the check on ppm_flatten_before_integrals and ppm_type --
the message was wrong actually, and it really doesn't affect
ppm_type = 0, since that is linear, so it's a non-issue.
Source/Castro.cpp
commit 6e13ad520b89d288a6a98a87ef0f1c57f37ff479
Author: Jasmine Garani <jgarani@bender.astro.sunysb.edu>
Date: Thu Mar 31 14:48:01 2016 -0400
higher temperautre cutoff
Exec/convective_flame/inputs.2d.test
commit 80208f9c69588c6e3c7b3095fb148a97ec3a4128
Author: Jasmine Garani <jgarani@bender.astro.sunysb.edu>
Date: Thu Mar 31 14:46:22 2016 -0400
fix spelling
Source/_cpp_parameters
commit d91f22bcaffc7aa44ec81422d11abebf7c1c3743
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 31 14:12:26 2016 -0400
trace_sources doesn't work for ppm_type = 1 nor radiation, so disable it
Source/_cpp_parameters
Source/castro_defaults.H
commit 4d0ed009d02017fa877f4edef1d72b64ec7d07db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 31 13:47:35 2016 -0400
new hydro defaults to be tested
Source/_cpp_parameters
Source/castro_defaults.H
commit 52712a46103c899c85b15ff79fe8e4560dd445b7
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Mar 31 08:37:53 2016 -0700
The EOS needs to be gamma_law_general, not gamma_law, because we
need the EOS to return cv.
Exec/diffusion_test/GNUmakefile
commit 3de470e5f7e7f97fd673d23e4e3caca3cb1fa9e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 31 09:57:06 2016 -0400
Reduce some redundancy in the multipole gravity, and calculate some pre-factors at initialization
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_nd/Gravity_nd.f90
commit 08684d67b5a0faed3f96705b9d556b35911a67b1
Merge: 84ec52132 eee436e8c
Author: Luke Nolan <ltrnolan@gmail.com>
Date: Wed Mar 30 09:35:31 2016 -0700
Merge branch 'development' of https://github.com/BoxLib-Codes/Castro into development
commit 84ec52132a692e1fa7299e69a08d6375a2620c05
Author: Luke Nolan <ltrnolan@gmail.com>
Date: Wed Mar 30 09:35:08 2016 -0700
add a constant opacity
Conductivity/constant_opacity/Make.package
Conductivity/constant_opacity/_parameters
Conductivity/constant_opacity/constant_conductivity.f90
Conductivity/constant_opacity/constant_viscosity.f90
commit eee436e8c15d9029a4700f3a324a2873015b35fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 30 10:06:49 2016 -0400
Print out more information when a thermo variable is nonsense in the EOS
EOS/eos.f90
commit e1a53b7f8d30508ccb9f94dd8c7b5a8cd5e3fb7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Mar 30 06:51:43 2016 -0700
Oops -- only include Enthalpy_nd.f90 if DIFFUSION is TRUE.
Source/Src_nd/Make.package
commit 178eeeec7de545903579ad1afa09317f79c1fbb8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 15:42:37 2016 -0700
Add the ability to compute the energy source term in terms of enthalpy instead of
in terms of temperature.
Exec/diffusion_test/GNUmakefile
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Enthalpy_nd.f90
Source/Src_nd/Make.package
commit 68e6ffde0a1c7984ca2a5111dd4a9db32d56a42b
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 14:05:30 2016 -0700
Fix an oops from the last commit.
Source/Src_nd/timestep.F90
commit 419fcc61411ca5bffc644f08528698f633716399
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 14:05:04 2016 -0700
Quiet the compiler observations.
Source/Src_nd/timestep.F90
commit 55eae575156509b0f83f3d8a630c0d4eb4f51769
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 14:03:23 2016 -0700
Remove more unused variables.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_nd/Tagging_nd.f90
commit 6d37ea46c2c4880cbe40643c01f1b9d09688dccd
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 13:58:39 2016 -0700
Remove unused variables.
Source/Src_nd/Diffusion_nd.f90
commit e0480ef9994af66371a77129af54b0914ae97eaf
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 13:55:58 2016 -0700
Just some cleanup to get rid of unused variables and fix the comments in the tagging routine.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Tagging_nd.f90
commit b049e99a77fe8232e18385de7b826918bd1c0fe5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Mar 29 13:45:37 2016 -0700
Rename kappa --> bulk_visc in ca_fill_secnd_visc_coeff
Source/Src_nd/Diffusion_nd.f90
commit c8407928f25a412b5444ccc1c5c0207b9c8be7b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 29 14:13:23 2016 -0400
don't know how this got here
Networks/general_null/actual_network.f90.test
commit d19e9a2633c2bd059292b76330094b715179dff3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 29 13:51:36 2016 -0400
we don't need eos_type_module
Networks/general_null/actual_burner.f90
commit 5d7410612372a2a2c2bbc2567b1112cb26caa51d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 23 11:38:13 2016 -0400
Fix intent on the diagnostic quantities in 3D; they should be inout, not out.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/advection_util_3d.F90
commit 9c332d6a9dda1d4ce1d72659db5bb21ead1215d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 23 11:34:17 2016 -0400
Enable the multipole BCs for Poisson gravity to be useable in 2D. In order to maintain backwards compatibility, the existing monopole solver will continue to be used if gravity.max_multipole_order = 0, with the multipole BCs activated only for higher values.
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
Source/Src_nd/Gravity_nd.f90
commit 23a62ba369f2c187149c842b4e7d3432dc826702
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 22 07:46:51 2016 -0400
1) Add a new makefile variable USE_SHOCK_VAR and a corresponding preprocessor macro SHOCK_VAR. If enabled, we append a new variable Shock to the state type, which is indexed by USHK in Fortran. Note that at present, this is only calculated in multi-d. 2) At the beginning of each hydro advance, we fill that variable with the output of the shock() subroutine that determines if we are inside a hydrodynamic shock. 3) Add to the burn_t a new logical parameter shock, and inside ca_react_state, make it correspond to the value of USHK if it is defined. 4) Define a new parameter castro.disable_shock_burning. If turned on by setting to 1, then we do not burn in zones for whom the shock parameter is true.
Exec/Make.Castro
Networks/burn_type.f90
Networks/burner.f90
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.F90
Source/Src_2d/Make.package
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/React_nd.F90
Source/Src_nd/meth_params.f90
Source/Src_nd/meth_params.template
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit 3edc7ec588681fade70f02bec2c160a006c3121d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 21 16:25:25 2016 -0400
add shock detection for r-z
Source/Src_2d/riemann_2d.F90
commit 694d1ad0ac9fade8ab944253f3f339eb206dc59d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 21 13:11:57 2016 -0400
Remove commented unused code
Source/Castro.cpp
commit ecb357603c3c6ff3dcc9343a829604aa802bd525
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 20 05:51:16 2016 -0400
Fix the sign on the angular momentum flux in the hybrid terms. Also, do the pressure terms for the radial momentum equation using the n+1/2 Godnuv state instead of doing it using predictor-corrector. The former is a bit better behaved numerically and doesn't require additional EOS calls.
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/hybrid_advection_nd.f90
commit 5295ca9611273bb79dc9e82a3a090ae26d3ebecc
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 18 02:32:39 2016 -0400
Add a reactfill to hydrostatic adjust
Exec/hydrostatic_adjust/bc_fill_1d.F90
commit 856085db908a7e32e13d9f06993ee3500f9372e6
Merge: 2821ab331 5d234f08e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 17 08:22:02 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 5d234f08eb76d8bb4b810d9d4401314f8f7529b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 17 01:54:01 2016 -0400
Switch over hydrostatic_adjust to use the Castro model_parser_module rather than rolling its own model reader. This permits it to be used with other networks.
Exec/hydrostatic_adjust/GNUmakefile
Exec/hydrostatic_adjust/Prob_1d.f90
Exec/hydrostatic_adjust/probdata.f90
commit e0ae7c8d510060ff1e66428e4d1a638b6a4ea64c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 17 00:51:57 2016 -0400
Fix a variable conflict with the networks
Exec/hydrostatic_adjust/ext_src_1d.f90
commit 2821ab331a8c6ff5e56cb6f36555ab845bd93d1b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 16 11:47:07 2016 -0400
Add parameters that allow the various contributions to the rotation to be disabled.
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit eaf9af62c7d0fba6499afc62e7f564c41c179d1c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 15 12:39:06 2016 -0400
Make error message more informative
EOS/eos.f90
commit 9571639057c624041af240a28f2cebfd80552516
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 14 16:58:28 2016 -0400
Fix output for wall-time
Source/main.cpp
commit b333f8e0413090914e04b85822856cdf0ba72ba1
Merge: 312c6f578 8d1cc8a81
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 13 05:21:24 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 8d1cc8a81aa1a193fcb501a9ad68abccb6e17278
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 12 15:55:48 2016 -0500
add "Castro" to the first heading to make it easy to tell what's happened
Source/Castro_io.cpp
commit 8a9827c5bba778b5c27a8af335fedb5162085baf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 12 15:53:55 2016 -0500
Add a new parameter castro.track_grid_losses. If enabled, we explicitly track the hydrodynamical fluxes of material at domain boundaries and sum them up over the course of the simulation. (At present, we don't account for source terms.) This is done separately at each level, but no attempt is currently made to account for refluxing, so it will not be reliable if you have refined grids that touch domain boundaries. This will persist over restarts, but currently only for the losses on level 0.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/Castro_util.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit ec36e63e0e36e014be083b16cc6969567a80afdd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 12 15:42:59 2016 -0500
Fix the output in the case where we do a density reset and we're resetting to small_dens rather than a neighboring zone.
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/advection_util_3d.F90
commit bb937447923a707e084093e7fac2e8aa974dcd19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 12 15:02:13 2016 -0500
a sample yt volume-rendering script
Util/yt/vol-wd.py
commit 312c6f578a1354625c0f5a034182c6253e898443
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 11 23:07:55 2016 -0500
Fix the sign on the rotational potential
Source/Src_nd/Rotation_nd.f90
commit e7d83ce266419aaaea71af610383426cb5937f43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 10 11:45:14 2016 -0500
add some comments
EOS/eos_data.f90
commit 5290f434f09cc49e541d6b4fcd040740c724e6ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 10 09:30:01 2016 -0500
fix some clone info
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 62ce66513595389f54521890a73169b24e04ffae
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 9 20:23:32 2016 -0500
Fix a reduce in the wrong place
Source/Castro_advance.cpp
commit 0564ee8d4877c91a0910a8fc2bb93ecb621d18fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 8 10:54:49 2016 -0500
Make the retries on negative density resets optional through the use of a parameter that controls the target density change threshold on these retries.
Source/Castro_advance.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit ccc4b7fabcbe118e91b6ab19649ab1bea2dfefc7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 6 12:09:29 2016 -0500
Allow minimum/maximum densities for reactions, analogous to the temperature controls.
Networks/burner.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 80610d7eef98ead4c1a8a076ae02fcb63e57c91f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 5 02:48:03 2016 +0000
Fix a formatting issue
Source/_cpp_parameters
commit c9bb7d234d5cca0f0c8462017c75d473456eaa52
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 5 02:47:43 2016 +0000
Add the python warning about Mira as well
UsersGuide/Suggestions/Suggestions.tex
commit 3b3824ed64fb7f94134718f3a0b5d7cb8c307573
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 4 00:51:57 2016 -0500
Fix identification of Coriolis and centrifugal terms
Source/Src_nd/Rotation_nd.f90
commit 1b9dea675c21e89ed5493dce16ee63e2338ed6b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 4 00:40:21 2016 -0500
Rather than use OMP critical on Fortran flush, just move all calls to the flush outside of OpenMP regions.
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/Castro_util.f90
Source/Src_nd/io.f90
commit 616049de44cb561f585ac2e4b05187bbe3921989
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 3 17:10:37 2016 -0800
remove vector always because they are dangerous
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.F90
commit 7e33d75605d6b272b292d435b938dfc07054d809
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 3 17:08:23 2016 -0800
add omp critical for flush
Source/Src_nd/io.f90
commit 2a004d51ab541c73e45b85e8beb01e48ab190e64
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 3 02:46:47 2016 -0500
Slightly generalize the implicit rotation update by using the rotational_acceleration routine to add all but the new-time Coriolis force. This also fixes a bug in how we computed the centrifugal force for the corrector.
Source/Src_nd/rotation_sources_nd.F90
commit b5ed30a61c507a99acfba5d76da4e1dcf3996dfb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 3 02:46:00 2016 -0500
Allow the individual components of the rotational forcing to be turned off.
Source/Src_nd/Rotation_nd.f90
commit 5f4cff994c634d707b0f0b801af13938cd8bb82d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 1 15:12:05 2016 -0800
explicitly construct std::string for the happiness of Intel compiler
Source/Castro_setup.cpp
commit 21a08e999ffb3ea10f20d787f1ac7c8308d3b7db
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 1 14:43:27 2016 -0800
suggestion about Edison and Cori
UsersGuide/Suggestions/Suggestions.tex
commit 1f7cdabc8cb737b193d599ded0571adfb4c2c2c4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 1 14:29:34 2016 -0800
fix latex by adding backslash in front of underscore
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 010c5761ca51da46da57713feaaa1276661f0543
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 29 12:20:03 2016 -0500
Remove accidentally added temp file
Source/Src_3d/.#Castro_advection_3d.F90
commit eed15ce988851fde51640cd17186d8a9dec1c35d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 28 18:34:32 2016 -0500
Add a parameter allow_small_energy. If set to 0, then the internal energy variable will not be allowed to go below the energy corresponding to small_temp at that zone's density. In particular, if it does go below, we reset it to an energy consistent with UTEMP.
Source/Src_3d/.#Castro_advection_3d.F90
Source/Src_nd/Castro_util.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 1fb0cf6b2370b1739e6721d97c15e7f4ed856a31
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 28 16:59:04 2016 -0500
Add some comments to the parameters file
Source/_cpp_parameters
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 96856a7fd67a04c52554a4a531cf821c8e37ae38
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 28 16:49:05 2016 -0500
If we reset the internal energy, only update the total energy with the daded energy difference if dual_energy_update_E_from_e is true.
Source/Src_nd/Castro_util.f90
commit 9e7eec4b0f0a032e1dde40e248b051997425c90b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 27 00:47:15 2016 -0500
Remove a debugging print statement
Source/Src_2d/Castro_advection_2d.f90
commit 47c6b2205a375481ac0ddafd780c6bdacd031d50
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 27 00:41:09 2016 -0500
Only enable hybrid momentum for 3D simulations.
Exec/Make.Castro
commit ba9f59d389c01082acad96a2f5bba87f12922a39
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 26 00:04:41 2016 -0500
The existing subcycling strategy on a retry was dangerous because sometimes it would allow for a very short last subcycle timestep, and things can go wrong if we take a very short timestep. So, when we do a retry, instead attempt to make every subcycled timestep equal in length.
Source/Castro_advance.cpp
commit e48e2da974e851eb7deb2920250646f82d6640a1
Merge: cee4c4629 0c084864f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 23 18:57:36 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit cee4c4629c7085d1c66b55d1777eb8472bf275ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 23 18:57:27 2016 -0500
turn on plotfiles
Exec/StarGrav/inputs_1d
commit 0c084864fcc647ecbff8ffde79de0de763d81a5b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 18:55:26 2016 -0500
We want to add the source term to the hybrid momentum always
Source/Castro_advance.cpp
commit 646dc7251f09a8f995bd375f207a66b39c4b70ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 18:51:02 2016 -0500
Fix the addition of the source terms to the hybrid momenta
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/hybrid_advection_nd.f90
commit 00c142b3cd1e52efd36eb193758ca1f22949662f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 02:51:15 2016 -0500
Sync up treatment in advance_hydro and advance_nohydro
Source/Castro_advance.cpp
commit a3a132bcf6bfa6062dd1fb2eec561b9ed64f3532
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 02:29:43 2016 -0500
Wrap a code section in ifdef's
Source/Castro_advance.cpp
commit 035cfbd973baa6e35a0dd64e28e8086f3ddb9850
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 01:35:23 2016 -0500
OMP some loops that were recently added
Source/Castro.cpp
Source/Castro_advance.cpp
commit 980ce63445d663ca311abd10593e738ee4e9a67c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 01:28:11 2016 -0500
Simplify the hybrid hydrodynamics even further. We still evolve the hybrid momenta in parallel with the linear momenta. Now, if hybrid_hydro .eq. 1, the only additional change is that at the end of Castro::advance_hydro, we do a sync so that the linear momenta are overwritten to be consistent with the hybrid momenta. This is much easier than trying to keep them in sync every time we add a source term to the state, and shouldn't make much of a difference in terms of accuracy.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_advection_3d.F90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/hybrid_advection_nd.f90
Source/Src_nd/rotation_sources_nd.F90
commit 043bb41050db492a17b6c7fe3c3b95d18423e0ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 00:43:23 2016 -0500
Fix the same comment issue for the rotation source term
Source/Src_nd/rotation_sources_nd.F90
commit a773e035c855b192cfb1a3c250817c874ebd6391
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 23 00:39:45 2016 -0500
Make a comment clearer. Also, fix some alignment issues.
Source/Src_nd/gravity_sources_nd.F90
commit e7ecaaf796070c12fef311aac76d3618887299cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 22 09:01:14 2016 -0500
Use const ints again in an array declaration
Source/sum_integrated_quantities.cpp
commit 423e56423e31c8c8b1a41c51bd871aea8c72dd18
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 23:46:35 2016 -0500
Add an implicit_rotation_update parameter (disabled by default) so that all rotation versions can use the implicit rotation solve for the Coriolis force. We disable it when hybrid_hydro .eq. 1 though because the Coriolis force automatically drops out for the hybrid momentum update.
Source/Src_nd/meth_params.f90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit c673419cea5ebab81e41020bbeab8333a1f671c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 21:48:42 2016 -0500
Compute the fluxes for the hybrid momenta inside the Riemann solver like all the other fluxes are computed.
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/hybrid_advection_nd.f90
commit 01986a867cabe9024be5949898b1637124f25644
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 13:11:55 2016 -0500
No negative energies in the rotating torus problem
Exec/rotating_torus/inputs_3d
Exec/rotating_torus/inputs_3d.test
commit ad503a49a6ceb65590456012756bfa5d2c6b9eeb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 13:09:53 2016 -0500
Guard against negative internal energy
Source/Src_nd/hybrid_advection_nd.f90
commit 05707f64f4e50f87ef9efe0604c7e7c336962a8e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 13:01:44 2016 -0500
Treat the source term for the hybrid radial momentum as an external source term that we do predictor-corrector on
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/hybrid_advection_nd.f90
commit 7148ebf3976ae1e3e7085e9b5a14b59158495c1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 20 23:30:59 2016 -0500
Updates for the rotating torus problem
Exec/rotating_torus/GNUmakefile
Exec/rotating_torus/inputs_3d
Exec/rotating_torus/inputs_3d.test
commit fd9ecbc3f13e7f12511a517f925096519068c8ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 20 23:27:44 2016 -0500
Revised strategy for hybrid advection. We define a preprocessor variable HYBRID_MOMENTUM; if this is enabled in the makefile with USE_HYBRID_MOMENTUM=TRUE, then we get three additional momenta added to the State_Type, corresponding to a radial momentum, an angular momentum, and a linear momentum perpendicular to both. These are updated in the same place that we update the normal momenta. Then if we set hybrid_hydro == 1, each time we update the hybrid momenta, we also overwrite the normal momenta to be consistent with them. This should ensure that the updates for angular momentum and the perpendicular momentum are conservative.
Exec/Make.Castro
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_3d/Castro_advection_3d.F90
Source/Src_3d/Make.package
Source/Src_3d/advection_util_3d.F90
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Make.package
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/hybrid_advection_nd.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/meth_params.template
Source/Src_nd/rotation_sources_nd.F90
Source/sum_integrated_quantities.cpp
commit f2b7bc2f34678821c8cf58e3c9b0a1a1f76270bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 20 12:43:03 2016 -0500
Account for special boundaries in the hybrid advection calculation
Source/Src_nd/hybrid_advection_nd.f90
commit cd1a9053e4874865c9618ab04420fd2b8b1028c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 19 15:00:28 2016 -0500
Add an option to disable the correction of the density near the gravitational point-mass.
Source/Castro_advance.cpp
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit cd7bcf26193c6ae3b58d230468a78d1b87c28da3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 19 01:33:09 2016 -0500
When we print out diagnostics from the hydro, also print out the mass added.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 779ee6329cb44bf0d839c353eb463829aebeb4ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 23:13:24 2016 -0500
Add a note about the issue with Python on Titan
UsersGuide/Suggestions/Suggestions.tex
commit 5a2310f4d47f0d81185ca0427e2a7447c0cb792a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 16:45:53 2016 -0500
Fix default value of small_x
Source/_cpp_parameters
Source/castro_defaults.H
commit 5fa864037b16489fc7f233a2a52b7e4be4f940a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 00:54:01 2016 -0500
Print out not just which retry subcycle we're on but how many total there are
Source/Castro_advance.cpp
commit 3127cefb124266ba5a34cf68832103484be2cd70
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 22:05:51 2016 -0500
When we do a retry for a negative density reset, allow the density to change by 10% per timestep; 1% was too restrictive.
Source/Castro_advance.cpp
commit 9feef08b7ddcd1f19beda387313f17eb0ff23bbc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 22:02:50 2016 -0500
Also use flush_output inside reset_internal_energy
Source/Src_nd/Castro_util.f90
commit e281553976857d6af6613c662d186f65d97e910f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 21:59:32 2016 -0500
Use the flush_output routine at the end of enforce_minimum_density so that we always know at the time it happens that densities were reset.
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/advection_util_3d.f90
commit bcb4a506125c2c72140db5fa5bf3bcc8bd6a594e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 21:58:55 2016 -0500
Add a Fortran subroutine, flush_output(), that forces the stdout buffer to be flushed.
Source/Src_nd/Make.package
Source/Src_nd/io.f90
commit 90fc745d342be9dfacb7aeec05b6aac04c2a4e73
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 12:57:34 2016 -0500
Take the smallx parameter from the network module and turn it into a Castro parameter, castro.small_x, which defaults to 1.d-30.
EOS/eos_type.f90
Networks/network.f90
Source/Src_nd/Castro_util.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 4bfd8df79085845db9cf5fa133f549b8ac87e839
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 12:33:27 2016 -0500
Dimension agnostic ca_compute_avgstate
Source/Castro.cpp
Source/Castro_F.H
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Castro_util.f90
commit 6a65995968ad76731768b63e4a03023c52de287d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 11:45:10 2016 -0500
Dimension agnostic moving center routines
Source/Castro.cpp
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Castro_util_2d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_nd/Castro_util.f90
commit 479632163c1699445df57993ed642c65945d542d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 10:54:21 2016 -0500
Dimension agnostic ca_check_initial_species
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Castro_util_1d.f90
Source/Src_2d/Castro_util_2d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_nd/Castro_util.f90
commit a6a0d3864c849f24e2e05eed2cc1a480acaf2d70
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 16 16:46:40 2016 -0500
On a make print-%, delete buildInfo.cpp at the end.
Exec/Make.Castro
commit ef121160c082c47870a52749e91edb9e56dbedcd
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 16 11:09:55 2016 -0500
Also need to increase size of history array
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
commit 093e9359f2b13ae889b42d5b091ac27fd4033b6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 16 11:09:47 2016 -0500
Update comment
Source/_cpp_parameters
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 2f48e0b54b9b05f2d64beaa2c19fab98b582563a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 16 11:00:28 2016 -0500
Bisection root finding is slow -- give it 2 * cg_maxiter iterations to find a solution.
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
commit 6b41e8e020fbae887f28f407edd974b62dff5cc0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 15 18:04:37 2016 -0500
label the binds
Exec/xrb_mixed/bc_fill_2d.F90
Exec/xrb_mixed/problem_tagging_2d.f90
commit 0d8c89ab774e7de205abbd8aec44119c1b0b8b51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 15 18:02:30 2016 -0500
label the binds
Exec/toy_convect/bc_fill_2d.F90
Exec/toy_convect/problem_tagging_2d.f90
commit e5e80a4b42825ae187c970e82ff88fbf55c93866
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 15 14:00:43 2016 -0500
Pick a more reasonable value for smallx.
Networks/network.f90
commit 8056d0424bececbed96c8d86ec558c8fe0b7a2b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 15 14:00:08 2016 -0500
We shouldn't be coming into the timestep estimation with zeroed mass fractions, but in case we do, protect against that.
Source/Src_nd/timestep.F90
commit 8bf2ee388bcd781ba1becf3c769100a6dd46d8c6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 10:40:39 2016 -0500
Update the EOS/Network section of the user's guide
UsersGuide/CastroUserGuide.tex
UsersGuide/EOSNetwork/EOSNetwork.tex
commit a06398ceebc14f137b415b1c0ad4e3cfd093f052
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 10:23:42 2016 -0500
Fix LaTeX issue
Source/_cpp_parameters
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 6bff9f6a63aea988f6fb2929ac84d62430c4807f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 10:12:13 2016 -0500
Add an integer parameter cg_blend that determines what we do when the secant iterations of the Colella and Glaz riemann solver fail to converge to a consistent star state. The default is cg_blend == 0 and preserves existing behavior, which is to print out the iterations and signal a crash. For cg_blend == 1, we do not crash but instead revert to the original guess for pstar and continue. For cg_blend == 2, we perform another cg_maxiter iterations using a bisection root find. The bounds are provided by the secant iterations. This was motivated by the observation that in cases where the secant method failed to converge, it was oscillating around the correct solution.
Source/Src_1d/riemann_1d.F90
Source/Src_2d/riemann_2d.F90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 1a47afa9275a8ad6b3804eb8aa71b5b10fde2bd2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 00:05:22 2016 -0500
Zero out the srcQ array before filling it; this guards against accessing nonsense data.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 0f83b54a4b40921695ac49eef211d533e7d95501
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 23:18:03 2016 -0500
Update the C++ interface to enforce_minimum_density
Source/Castro.cpp
Source/Castro_F.H
commit ebca7fafa1345675bc0cee951f5450bfbe41b038
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 21:22:04 2016 -0500
Add some explanatory comments about the checkpoint version numbering to Castro_io.cpp, and also make the current version number a variable up top for clarity.
Source/Castro_io.cpp
commit af9a9ef4e37c4e56b83f87a93dbfb136b8623f5c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 20:18:42 2016 -0500
Rewrite the state-saving/restoring part of the retry code so that we are actually generating a new StateData object and filling it with the new StateData member functions.
Source/Castro_advance.cpp
commit 2e32915a7c35b326b6674384ef7ad394465c65db
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 19:42:48 2016 -0500
Update interfaces for species normalization
Src_1d/CastroRad_1d.f90
Src_1d/RadHydro_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit 83392625f1e1ffced3c472dca84f42d98d4e1873
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 19:14:51 2016 -0500
Fix scoping of a multifab sum
Source/Castro_react.cpp
commit cdbd7f02db48c9376b99abe8cea5b2304d56c2f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 18:37:44 2016 -0500
1. Remove the normalize_species parameter; species and species fluxes are now renormalized by default at the end of the hydro update. This was happening anyway inside EOS/burner calls. 2. Condense ca_enforce_nonnegative_species and normalize_new_species into a single subroutine, ca_normalize_species, that both ensures the species are between zero and one and then renormalizes them so they sum to unity. This is the same approach as inside the EOS. 3. Make this routine dimension agnostic and move it to Castro_util_nd.f90.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/advection_util_3d.f90
Source/Src_nd/Castro_util.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 8ceaad06817c05a47c539a29205c357e4200429d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 18:35:03 2016 -0500
fix bind for pgi
Exec/double_bubble/bc_fill_2d.F90
commit 2a71f1b02d36611acf33d5dfd0c30a4b2331e1e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 18:33:24 2016 -0500
fix binds for PGI
Exec/convective_flame/bc_fill_2d.F90
Exec/convective_flame/bc_fill_3d.F90
commit de5e3638f0a9ad627bbe82ea7126b6cb99138ffc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 13 16:00:38 2016 -0500
If we generate energy during a burn, print it out if we're verbose
Source/Castro_react.cpp
commit a768f35058946746d35e5c842439950706c2e40f
Merge: 2691d8371 f86ce5502
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:37:03 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 2691d8371d4953786603d68a9b3479a7a5793a1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:36:14 2016 -0500
missed a bind
Source/Src_1d/Gravity_1d.f90
commit f86ce550262a02f0831ce5ee86d1efb4cba967e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:07:27 2016 -0500
label the binds to make PGI happy
Exec/reacting_bubble/bc_fill_2d.F90
Exec/reacting_bubble/problem_derive_nd.f90
commit cbbdcca6762996660f7f35de47645f5408213a3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:05:17 2016 -0500
label the binds to make pgi happy
Exec/hydrostatic_adjust/bc_fill_1d.F90
Exec/hydrostatic_adjust/extra_derives.f90
commit 4badb6faf340d7e1921ab275dfb787a47b2d401a
Merge: 8fb6ea6dc c174c37f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:03:42 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/CastroRadiation into development
commit 8fb6ea6dc1a72c630a068f403635590bd4005d7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:03:06 2016 -0500
label the bind to make pgi happy
RadThermalWave/Tagging_nd.f90
commit 9a616b28076ef4cc23d17b4ddbf9055e8e9bc2bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 14:01:36 2016 -0500
label the binds to make pgi happy
Rad2Tshock/bc_fill_1d.F90
Rad2Tshock/bc_fill_2d.F90
Rad2Tshock/bc_fill_3d.F90
commit f6787dcc0303e40e6a43f02c9ad0f46085c80731
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 13 09:56:55 2016 -0500
label the bind(C)
Networks/burner.f90
commit 174e34b8ba005417ec2545157098f951627f1d10
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 12 18:37:27 2016 -0500
Add Reactions_Type data to checkpoint. Increment checkpoint version number to 4. Backwards compatibility should be maintained.
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
commit 0fe14af0d5ae979847c8e35394c4bb8f248d679e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 12 11:02:05 2016 -0500
fix line lenghts
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/bc_fill_1d.F90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_2d/bc_fill_2d.F90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/advection_util_3d.f90
Source/Src_3d/bc_fill_3d.F90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Castro_util.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/pointmass_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/problem_tagging_nd.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/sponge_nd.f90
Source/Src_nd/timestep.F90
commit 04398e6f0464b09b8c45d5405442bf5816e61e55
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 12 10:41:45 2016 -0500
Avoid a potential overflow situation
Source/Src_nd/timestep.F90
commit 49356d4a53a037c61eab91aeb105f382b28e17f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 12 10:38:26 2016 -0500
add name argument to bind(C) to shutup PGI
Exec/Sedov/bc_fill_1d.F90
Exec/Sedov/bc_fill_2d.F90
Exec/Sedov/bc_fill_3d.F90
commit 7b299ff67a381d4e7667ec9d4537249e9513efbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 12 10:37:52 2016 -0500
add name argument to bind(C) to shut up PGI
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_1d/bc_fill_1d.F90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_2d/bc_fill_2d.F90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/advection_util_3d.f90
Source/Src_3d/bc_fill_3d.F90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Castro_sums_nd.f90
Source/Src_nd/Castro_util.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/React_nd.F90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/pointmass_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/problem_tagging_nd.f90
Source/Src_nd/rotation_sources_nd.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/sponge_nd.f90
Source/Src_nd/timestep.F90
Source/Src_nd/update_sponge_params.f90
commit 89418262880db7a6159e352c5c03e663d46cf8e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 11 23:26:50 2016 -0500
Update the visualization docs to reflect the fact that as of yt version 3.0, the hierarchy no longer exists and its associated routines were moved to the datasets themselves, while the field information was moved to the index.
UsersGuide/Visualization/CastroVisualization.tex
commit a2503d937abe82e1991a597a864b8a1e6a97be24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 11 20:23:06 2016 -0500
add some notes about branches
UsersGuide/GettingStarted/CastroGettingStarted.tex
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 9163ccbecd80ab473e05233d1f9f60a5bc04488b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 11 20:22:56 2016 -0500
gix latex issue
Source/_cpp_parameters
commit b61f8c5107253eedfbb18f5fa3940078a82f77bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 11 20:13:15 2016 -0500
some notes that need to be generalized for the docs
UsersGuide/notes.txt
commit 6f5ae5d9ab23dcd3441a1edcd734d65ed7226a4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 10 22:35:02 2016 -0500
Add a dtnuc_mode parameter that controls how we estimate the de/dt and dX/dt used for burning timestep limiting. Version 1 is the existing method that calls the burner's RHS. Version 2 is the old method that uses the second-half of the burning in the last timestep. Version 3 uses both burning stages in the last timestep. Version 4 uses the total internal energy change, including the hydro update. Also, give the limiter parameters themselves more accurate names, dtnuc_e and dtnuc_X.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 6802bdba1b63c397a3ee37006a2d8e720117c5a6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 10 11:40:02 2016 -0500
Update interface for enforce_minimum_density change
Src_1d/CastroRad_1d.f90
Src_2d/CastroRad_2d.f90
Src_3d/CastroRad_3d.f90
commit f85116e9f294e5cee62eaa89f26acad04f653a58
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 10 00:28:15 2016 -0500
Don't print react_half_dt walltime if we're not doing reactions
Source/Castro_react.cpp
commit 18cf42d76cae6ef0a659f51deb5b6f6d408dc109
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 10 00:27:51 2016 -0500
The use_retry option will now automatically handle the case of resets from negative densities. If it detects that such a reset occurred, we trigger a retry with maximum timestep set so that (to first order) the density in the affected zones does not change more than 1% per timestep.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/advection_util_3d.f90
commit 14643a8e03f88cc51edb7cd55c1b96d45242be04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 19:34:02 2016 -0500
updated instructions on backtrace
UsersGuide/FAQ/faq.tex
commit 22fd58d8b1532d286523c15cba39cb77317d6296
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 13:37:59 2016 -0500
fix shock detection
Source/Src_2d/riemann_2d.F90
commit c174c37f79f460c6884bfef05504d0496a4e2dc8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 13:23:06 2016 -0500
for high groups, the denominator of the Planck function can overflow
IEEE precision -- just zero out the energy density there.
Also, we had pi = 4.14... instead of 3.14... :)
RadSphere/Prob_1d.f90
commit 877d485e1179870cbd48235f3099234329350469
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 12:47:40 2016 -0500
silence NaNs when we are constructing the shock jump check with U = 0,
also compute the interface value of gammae with HLLC, even though
it should never really be trusted, since the transverse stuff plays
with this (and it will be used if we decide to predict gammae)
Source/Src_3d/riemann_3d.F90
commit 3dba724067f8144f9eaf2189ba6238dedf05e8c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 12:20:35 2016 -0500
even though we don't deal with fluxes of T, we need to initialize
the HLLC state for T to 0 just to make things happy
Source/Src_nd/riemann_util.f90
commit adbc74406edd05e3a7915834cd595168768ed2b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 11:20:30 2016 -0500
don't multiply uninitialized ghost cells
Src_3d/RadHydro_3d.f90
commit b9a77ee98b554c1ce5f265fc5dbf0dcf15fe76ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 11:14:26 2016 -0500
don't multiply uninitialized ghost cells
Src_2d/RadHydro_2d.f90
commit 0d05986ea1fb81cf2de28ea291e0a5e90f1c676c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 11:05:40 2016 -0500
fix a Backtrace issue -- there was no real bug, but we can no longer
just multiply two arrays together a la Fortran, because the ghost cells
aren't all used, and therefore NaNy.
Src_1d/RadHydro_1d.f90
commit c4a9de7bcd0c810787951714780b9a83ed751514
Merge: e5ce07e87 65b31acb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 9 10:50:47 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 65b31acb423fcd6c733b654fcd94c34d50671cc3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 9 03:21:23 2016 -0500
Add a sum_per option that is the amount of simulation time that goes by before we do a call to the diagnostic runtime global sums. Compatible with the existing sum_interval option. It is to sum_interval what amr.plot_per is to amr.plot_int. Only enabled if you set castro.sum_per > 0.0 in the inputs file.
Source/Castro.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 56bedf5d508704747ddcc340b4f56d9fd78a0738
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 9 00:15:21 2016 -0500
Add the CFL criterion to the retry stability check
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_set_meth.H
commit ed2fba810b3005f0f42c9d60acd542128d6b6316
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 8 23:47:12 2016 -0500
The time level swapping for the retry still wasn't right.
Source/Castro_advance.cpp
commit 8075f8cd7478da22c43757c3a0ae359fd65e22e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 8 20:26:15 2016 -0500
Wrap gravity statements in ifdefs
Source/Castro_advance.cpp
commit 1e002d469e99fa4756a826c4a349d4a04770074e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 8 20:22:34 2016 -0500
The last bug broke the time level swapping for the retries -- this is fixed now
Source/Castro_advance.cpp
commit 6c8e411f82995001480b3cba1c18627691d8ccdd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 8 15:25:25 2016 -0500
Simplify and centralize the swapTimeLevels calls in Castro_advance.cpp. This also fixes a bug in the use_retry option.
Source/Castro_advance.cpp
commit a1d777bf5eb3fd15097b0b168cc28dae2eb76056
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 7 15:08:09 2016 -0500
Fix bug in the retry dt variables
Source/Castro_advance.cpp
commit 27563d2b93d29d74c441e1c7a1cf2db9871f0c8f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 6 22:19:40 2016 -0500
Fix fluxregister bug from recent commit
Source/Castro_advance.cpp
commit dad5132f1d403ac0adede4033b8c6b18c14db3f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 6 20:30:46 2016 -0500
Make verbose output a little more consistent
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 7e418604136f2154aea0e3989728ae0e67bf389f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 6 19:01:13 2016 -0500
Add a new option: castro.use_retry. This solves the following problem: we have some stability criteria which are expressed as timestep constraints. Sometimes an advance can result in a state that violates the stability criterion, even if the initial timestep was limited so as to satisfy them, based on the information available at the beginning of the coarse timestep. If this occurs often enough during a simulation errors may creep up. If use_retry == 1, we check whether the stability criteria were violated during a level advance. If so, we generate a new, smaller timestep that satisfies the criteria, and then we perform subcycled advances using this smaller timestep until we reach the original target time. Since this occurs entirely on a single level, it does not directly affect the AMR scheme. Note that this method requires making a copy of all of the state data, which can effectively double the code's memory requirements.
Source/Castro.H
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 94650a9bd1e686e3fba8c116c7352bda95638a8c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 21:28:17 2016 -0500
Revert "Add a routine that specifies, for a given derived field, whether we fail to meet the tagging criteria necessary to do a tagging check (e.g. level > max_denerr_lev). If so, skip the tagging step for that field. This saves us from doing unnecessary MultiFab derives."
This turned out to be infeasible as written because we cannot distinguish between normal tagging through ca_*error and tagging through laplac_error or custom tagging on a given field.
This reverts commit 089fc999c964200cfe37e5d02dc0172ae8c2ce8c.
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_nd/Tagging_nd.f90
commit 8bfe442c2052238e91c6087538c57b858c86f9e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 21:16:39 2016 -0500
Re-fix indexing bug
Source/Src_nd/timestep.F90
commit 2967c0545125c6977700d863b046178ffcae9eb9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 21:02:49 2016 -0500
Fix indexing bug
Source/Src_nd/timestep.F90
commit 2dc43551c18b361a1417820faaac6f785efa59cf
Merge: d6d7d4b32 e5ab16409
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 11:01:55 2016 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit d6d7d4b32fabcdb512531e29e5c006784bcbbbe7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 11:01:41 2016 -0500
Add a burner_initialized variable that is analogous to the network_initialized variable.
Networks/burner.f90
commit 26530dfc6cd6a11279e252a1772e8194f8dd0443
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 10:58:53 2016 -0500
Add a function ok_to_burn that evaluates the criteria that determine whether we call the burner or not.
Networks/burner.f90
Source/Src_nd/timestep.F90
commit 44c78737ce109ba6eb863fec56080aef85aa692b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 10:51:54 2016 -0500
Add a new burning timestep limiter that does for changes in species what the existing limiter did for changes in energy. We limit the timestep so that the relative change in any zone of any mass fraction is less than castro.dsnuc.
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit e5ab164094c70ae52ac3658f3baff250aff09711
Merge: 45a83749c ee621cfe2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 5 10:34:00 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 45a83749c383846e0c7a950fe07958a7f7cea1c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 5 10:33:52 2016 -0500
start of a FAQ:
UsersGuide/CastroUserGuide.tex
UsersGuide/FAQ/faq.tex
UsersGuide/GNUmakefile
commit ee621cfe2146c72e5bf849f20a782b8be3131e3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 10:33:11 2016 -0500
Modify the burning timestep limiter. Instead of using de/dt as computed in the last timestep, we instead do an RHS call to the burner. This gives a more accurate estimation of the current rate of change of internal energy.
Source/Src_nd/timestep.F90
commit 9f95cf57b61bcb5baceacb39675c174252a30627
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 01:56:26 2016 -0500
Add an actual_rhs_module to general_null, for consistency
Networks/general_null/Make.package
Networks/general_null/actual_rhs.f90
commit 86c0360d9c0de8a2e6e1296f935ba74f8af6a400
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 5 01:45:59 2016 -0500
Add some more fields to the burn_t type so that it can be more directly used in the network integration
Networks/burn_type.f90
commit 089fc999c964200cfe37e5d02dc0172ae8c2ce8c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 4 18:11:24 2016 -0500
Add a routine that specifies, for a given derived field, whether we fail to meet the tagging criteria necessary to do a tagging check (e.g. level > max_denerr_lev). If so, skip the tagging step for that field. This saves us from doing unnecessary MultiFab derives.
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_nd/Tagging_nd.f90
commit 165f58651ca72c4110fb5ca31290c519653cb7cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 4 18:08:47 2016 -0500
Move some tagging parameters into the correct namelist
Exec/Detonation/probin-det-x
commit 8950f4c95fb004121806533ec2201eee614f0ce1
Merge: a3eb5e7a8 4121f96a9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 4 15:49:54 2016 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit 23d677cd9c3a7729d1d43b88cf380c8f34643730
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 15:43:20 2016 -0500
remove unused variable
Src_3d/CastroRad_3d.f90
commit e5ce07e87cb076f840a2f5db26869e31b829078a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 15:42:10 2016 -0500
remove unused variables
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trace_3d.f90
commit 4121f96a94f3d0258f528c4a0ab0f341d92422e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 15:38:48 2016 -0500
remove unused variablew
Source/Src_nd/flatten_nd.f90
commit bdf89539b2be894c381970bbcfad3f0b0d2ad912
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 15:36:18 2016 -0500
remove unused variable
EOS/eos_type.f90
commit a3eb5e7a8eaf20215f997bfebcf410f5d3194eef
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 4 15:11:43 2016 -0500
Add a new parameter max_solve_level to the Gravity class. For all AMR levels above this level, we do not explicitly solve for the potential and the gravitational acceleration, but instead we interpolate from coarser levels. Note that at present this is not yet implemented for the sync solve.
Source/Gravity.H
Source/Gravity.cpp
UsersGuide/Gravity/CastroGravity.tex
commit a95703cd4cc51cd2f2c193da2ee67f3ea114f829
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 13:54:40 2016 -0500
fix a missing block of radiation code
Source/Src_3d/trans_3d.F90
commit ac21d8974793a46c55556344675400dd2ae644b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 12:49:34 2016 -0500
no longer needed -- merged with Castro
Src_3d/trans_rad_3d.f90
commit 8aca80b52c949985bf41635db01f0a73ac0239e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 12:49:20 2016 -0500
use the merged transverse stuff
Src_3d/Make.package
Src_3d/RadHydro_3d.f90
commit 6d98fdccf8b4772b27ebddf6ada86bdba73aaec2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 12:48:46 2016 -0500
update to finish the radiation merge
Source/Src_3d/trans_3d.F90
commit f9fb27a7bb1031600ede6ec500171353466caf9f
Merge: 50a9765d2 8f7c2c64e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 10:23:29 2016 -0500
Merge branch 'development' into radmerge
commit 8f7c2c64e1499d1018654b4df58c64c52e1de8cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 12:46:54 2016 -0500
fix the treatment of the pressure term in the momentum equation.
Castro now includes the pressure term in the momentum flux if
we are in a Cartesian direction. So we were adding it a second
time in Cartesian coordinates (in both directions). But also,
we were always adding it with area factors, so even long ago,
it was not right. This should be better now.
Source/Src_2d/trans_2d.F90
commit ecbaec893d42aa4317e07c54a04403028f271bd8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 3 08:58:10 2016 -0500
Despite the last change, we still need to call read_params before extern_init.
Source/Castro_setup.cpp
commit 50a9765d2c359937b219f47f49130a4e95ee645c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 22:07:09 2016 -0500
more merging work
Source/Src_3d/trans_3d.F90
commit 572c0b69da231f6833b4ffcb94c1734cc42c2676
Merge: 853e9c89d 701e9c64d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 21:35:16 2016 -0500
Merge branch 'development' into radmerge
commit 701e9c64d557ed11ad21a8b28c315fe6116ed5aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 2 19:22:08 2016 -0500
Sometimes the network/burner depend on values in the extern_probin_module, so initialize that before we do network_init and burner_init.
Source/Castro_setup.cpp
commit 853e9c89d990ed4a637d66b7f4678dbabc68b169
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 18:12:02 2016 -0500
some work on merging radiaiton in
Source/Src_3d/Make.package
Source/Src_3d/trans_3d.F90
commit e5890e682d211ddd4671f8139bd766d4d4697511
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 12:52:17 2016 -0500
merge the transverse stuff into the main castro version
Src_2d/Make.package
Src_2d/RadHydro_2d.f90
Src_2d/trans_rad_2d.f90
commit 075be69ebe09745305ad86f961b5e055fa6f203f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 12:49:23 2016 -0500
fix compilation with rad
Source/Src_2d/trans_2d.F90
commit 25d69e9a98944d4fa992fd3f4cecb8568e2401e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 12:45:49 2016 -0500
fix compilation
Source/Src_2d/Make.package
Source/Src_2d/trans_2d.F90
commit aaa5b695cc3104be71125522d98bdf3799ba76e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 12:34:13 2016 -0500
radiation merged version
Source/Src_2d/Make.package
Source/Src_2d/trans_2d.F90
commit 62c0e17cbc44b9a90eff7b24492b32189ae0847a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 11:07:15 2016 -0500
no source tracing with radiation
Source/Castro.cpp
commit 9312490ee5718598542df7ae24f949c008dd195f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 2 09:08:26 2016 -0500
add note about Palette
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 84986e34ffc9609c1b0773b2d5f0fb6621a98504
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 1 22:14:51 2016 -0500
add intents
Source/Src_3d/Castro_3d.f90
commit f6226a6b31b5683bef7509fbc4cbce417f990600
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 1 21:25:13 2016 -0500
add intents
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.F90
commit 1c4585564dcb5c297f8ac91abe5da7f803014777
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 17:04:22 2016 -0500
Add gravity.ml_tol and gravity.delta_tol to the user's guide
UsersGuide/Gravity/CastroGravity.tex
commit 656ab3333e7629171c1b4c220a5bf845dd31a7f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 16:57:10 2016 -0500
The burner interface now uses the new burn_t derived type, instead of the eos_t derived type.
Networks/burner.f90
Networks/general_null/actual_burner.f90
Source/Src_nd/React_nd.F90
commit f8d2af68726942595b2c42cf13639ced18756b9a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 16:55:23 2016 -0500
Add a burn_t which is similar in nature and scope to the eos_t. It contains several state variables as well as some other data unique to burning, such as reaction rates. The associated module contains routines to go back and forth from an eos_t to a burn_t.
Networks/Make.package
Networks/burn_type.f90
commit 317472cf1dc1af34b4c6e9420d49ecd9c4fccc83
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 15:52:18 2016 -0500
Also add an anticipatory empty actual_network_data module
Networks/general_null/Make.package
Networks/general_null/actual_network_data.f90
commit cc6d6b47f1b96070f1eda1ca538305af9a6a1523
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 14:22:12 2016 -0500
Add an empty actual_burner_data module -- this is in anticipation of some changes to Microphysics
Networks/general_null/Make.package
Networks/general_null/actual_burner_data.f90
commit fcb990fa1be9b25db0853fd9238ee4dd78044b0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 14:20:51 2016 -0500
Update names to match the Microphysics conventions
Networks/general_null/Make.package
Networks/general_null/actual_burner.f90
Networks/general_null/actual_network.f90.test
commit 9172fa9bb8045318ee5b1f835e8ef87331b960b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 1 13:31:41 2016 -0500
Print out react_half_dt walltime if verbose == 1, not verbose > 1. This makes it more consistent with what we do for gravity.
Source/Castro_react.cpp
commit 9678f4bfd4689e344e3711ed917e5d7962d87762
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 31 23:37:07 2016 -0500
For the gravity solve use the tolerance on the fine level not the tolerance on the coarse level, since usually the fine level will be less restrictive than the coarse level.
Source/Gravity.cpp
commit fb1402e2c1aaa6c100959cd2dc5c230b4fc6b670
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 31 18:47:33 2016 -0500
Accessed an extra illegal value of ml_tol/delta_tol
Source/Gravity.cpp
commit 4460f663b945dc2a67c57e8ccb2d0c86f48cb2ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 31 18:35:52 2016 -0500
add intents + a comment for CMA
Source/Src_3d/advection_util_3d.f90
commit ce0a83912bf2be8fa55b792c174ece0ea883d63e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 31 18:13:10 2016 -0500
add intents to the arguments
Source/Src_3d/trace_ppm_3d.f90
commit a28faa9b257a63e0efa3777bf3c4a2c699e0a853
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 31 14:39:45 2016 -0500
still add the pressure source if we do reset_state. Also, make the
small_pres check more inclusive
Source/Src_3d/trans_3d.f90
commit 9fb23521dbd1ccec01583f83015afc129802792a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 31 12:17:22 2016 -0500
add small_pres protection
Source/Src_2d/trace_2d.f90
commit a1f7e419d0d2a7f7277edfda88701d2d1865ae9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 31 12:04:29 2016 -0500
add small_pres protection
Source/Src_3d/trace_3d.f90
commit 4926a910ac9732f7beaec0f5e1df8e270da3bdba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 31 11:53:03 2016 -0500
switch to the Saltzmann / Colella 1990 version of the piecewise linear
hydro. This defines a reference state that the characteristic tracing
is done against. This brings the 3-d solver in line with changes I
made to 2-d over a year ago.
Source/Src_3d/trace_3d.f90
commit 859ec6331e3b07ab90c56ebe43bca3111392d745
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 31 02:11:00 2016 -0500
Allow the user to set gravity.ml_tol and gravity.delta_tol as arrays of values in the inputs file. If ml_tol has multiple values, it must have enough to fill all possible levels; otherwise if it only has one, that will be used on all levels. As before, gravity.sl_tol will be used only on a single level calculation, and still remains a single-value parameter.
Source/Gravity.H
Source/Gravity.cpp
commit 7f78386818ad8924b5866f52855f2fca4a7093b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 30 20:29:06 2016 -0500
remove unused variable
Source/Src_3d/trace_3d.f90
commit 64f6e49b8def5bcc0cf1ba5de9714eb0574ddbd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 30 18:42:07 2016 -0500
fix the transverse_reset_density stuff -- if we reset things, we shouldn't
be adding the transverse stuff to pressure or rho e either
Source/Src_2d/trans_2d.f90
commit fe14a99a33eb4a1ff44d61963306179311e187b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 30 17:23:08 2016 -0500
fix how transverse_reset_density is done -- previously, we were not resetting
the (rho e) or p states -- now we do. Note: we still need to deal with
the passive quantities.
Source/Src_3d/trans_3d.f90
commit 5fe5464c1ec21263cdcbe7ce0411b0f44217474b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 30 13:16:36 2016 -0500
extract all of the resetting of the rhoe stuff into a subroutine.
THis simplifies a lot, and also fixed a bug where the reset was being
done on an entire vector instead of just a single interface
Source/Src_3d/trans_3d.f90
commit 5dd3875d8355e90b1c52e902f0c8c362e940f31a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 30 11:32:41 2016 -0500
add small_pres and small_dens protection to the reference states,
also add small_pres protection in 1-d to the final interface state
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/trace_ppm_3d.f90
commit ea0e1cc3bd5e280e38f4746ebd602480bbe3c4ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 15:32:09 2016 -0500
clarify the setting of BOXLIB_HOME based on feedback
UsersGuide/CastroUserGuide.tex
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 52b549b29594e9a82877a3fad02fc4c460551c44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 10:51:34 2016 -0500
finish putting the godunov state all throughout
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit 7e3b49735f11889ea77a35f29321417329d39328
Merge: a05d95224 d8de4e547
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 09:54:35 2016 -0500
Merge branch 'development' into radmerge
commit d8de4e5476ef828e973ba5a92c9430f20a48b328
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 09:32:30 2016 -0500
no need to use tagging_params_module
RadThermalWave/Tagging_nd.f90
commit bdd9b91defceaaf282d50a9006c91744e31617d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 09:31:12 2016 -0500
fix the same Riemann bug in 1-d -- 3 for 3 ...
Source/Src_1d/riemann_1d.F90
commit a05d952247e1b9e515fea4d87ba141f6c94d6dfb
Merge: eca9af67e 5406edbc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 09:23:22 2016 -0500
Merge branch 'development' into radmerge
commit 5406edbc36d7b15272ea0c4dbea5d747bb6bbd20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 29 09:23:07 2016 -0500
sync with master
RadThermalWave/Tagging_nd.f90
commit 68fa1253ed6c19ff38acf39afef7f840472170d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 22:31:15 2016 -0500
more interface fixes
Src_3d/RadHydro_3d.f90
commit d9549223ee16ca30d7e5bc15b0db9b8e5a86c967
Merge: 850488ae7 69e6fc907
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 22:30:34 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 850488ae752d110fd5025857eba00b73fc817d4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 22:30:06 2016 -0500
use new bl_allocate interface
Source/Src_3d/Castro_advection_3d.f90
commit 69e6fc9075976b1dd39f38cdc75801d886b6f710
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 22:06:41 2016 -0500
fix the same variable problem as in 2-d
Source/Src_3d/riemann_3d.F90
commit 6d6bc9bdbab6bd93820d5cd5ac1484772b860ed8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 22:03:00 2016 -0500
add comments
Source/Src_nd/Tagging_nd.f90
commit eca9af67e87ddae3461290169ec1575a620d20a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 22:02:41 2016 -0500
sync with the recent Tagging changes
RadThermalWave/Tagging_nd.f90
commit 8ddbcf472354061dc239f4f9c90867c06f9ca34e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 21:54:56 2016 -0500
styling for better diffing
Source/Src_3d/Castro_3d.f90
commit ac40e4a184e7a6ce2d97b94ef9715ff5cc1dde77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 21:54:22 2016 -0500
use the godunov indices
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit b2ab2f89ee00fed5b30a1325e500cd67fc72cbb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 19:14:28 2016 -0500
remove empty ifdefs
Source/Src_2d/riemann_2d.F90
commit 6a5886582ea8e2bf4b719958e2e626a0d74ea4b0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 28 15:36:12 2016 -0800
uninitialized variable was used
Source/Src_2d/riemann_2d.F90
commit f97eef51e5bd0ccd55d7ae350921ec999f2cbc91
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 28 18:24:44 2016 -0500
We don't need a separate module to store the tagging parameters anymore.
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/tagging_params.f90
commit ad10a8054a41154ba0faeceeefbb61695a760855
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 28 18:12:31 2016 -0500
Trying to get at the sound-crossing time nuclear burning instability doesn't work via the timestep. Instead we've converted it into an AMR tagging criterion: if the sound-crossing time is not smaller (by some factor dxnuc) than the energy-injection timescale, tag that zone for refinement, effectively making the sound-crossing time smaller.
Source/Castro_error.cpp
Source/Castro_error_F.H
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit a5508b59060736efec39cb9c0713add56a73f8c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 16:32:22 2016 -0500
finish the synxing
Src_3d/trans_rad_3d.f90
commit b82736cf08ccf46a136427b5676cf81c79a52d85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 28 14:53:15 2016 -0500
almost done with the transverse sync
Src_3d/trans_rad_3d.f90
commit 8274d9cb84ddae0bb9c376a403447b8a6be35b83
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 28 13:08:23 2016 -0500
Avoid a potential roundoff issue in a comparison
Source/Src_nd/timestep.F90
commit 621f32493fd144071ca1c0af358d9394cf1bdc7c
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Jan 27 13:43:16 2016 -0800
Need to define CrseDen when creating the viscous terms as well.
Source/Castro.cpp
commit 7cbf6a3da372fbb298a6fb9c873573d2d4195691
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Jan 27 13:39:04 2016 -0800
Need to define CrseDen in Castro::getSpecDiffusionTerm
Source/Castro.cpp
commit 828cd4b4295fdde66862e5a7bb2ebdb31969dd46
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 26 15:51:30 2016 -0500
Fix spelling
Source/_cpp_parameters
commit 10bc1228817f867ce3f4c9a50e96a082143e5f08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 26 15:05:18 2016 -0500
update more transverse stuff to be in sync with the main version
Src_3d/trans_rad_3d.f90
commit ed1a1d9fe5d206d1e62fd5bf5b0ef49e796b578c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 26 10:37:51 2016 -0500
more syncing
Src_3d/trans_rad_3d.f90
commit 0fd09e4bed9d7c934d51c398350aeb575f6fb7d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 26 10:18:53 2016 -0500
remove wrong comments
Source/Src_3d/trans_3d.f90
commit f3125bd1d4d907afb7e2b276c1d71296dd2f2b1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 26 08:27:50 2016 -0500
refix the enforce_min_dens stuff -- something got out of sync
Src_1d/CastroRad_1d.f90
commit 6179cac63bab60b2b5175d488a7470913ccfb1c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 20:54:34 2016 -0500
fix compilation
Src_3d/trans_rad_3d.f90
commit 8b5ae310712e982f681709c7d4b0db98152a8477
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 20:50:16 2016 -0500
remove some comments
Source/Src_3d/trans_3d.f90
commit a0831d3e80e8fe7f38927fd3c546463dca95ab96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 20:49:14 2016 -0500
more work on syncing
Src_3d/trans_rad_3d.f90
commit 2fd562483c9f59abf05b89658e4fe1eea27836f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 14:32:28 2016 -0500
some syncing with Castro/ -- now we use the passive maps to make
the passive updates simpler
Src_3d/trans_rad_3d.f90
commit 38b4d2b54a60d3bdbeb2a1d64341a431201f0b59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 14:32:00 2016 -0500
some styling to make the diff with CastroRadiation easier
Source/Src_3d/trans_3d.f90
commit dedfe8e3c443d7015fa0772dd5dd893e36ebe87b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 25 12:07:51 2016 -0500
Update user's guide instructions for downloading BoxLib
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 14f860dac86dbaeb84652ec3d792d89aa6fa0e7e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 25 10:08:33 2016 -0500
Update module reference
Exec/rotating_torus/Prob_nd.f90
commit 935329ac42e0dcc6ea11bbea8f8a4e90e4b5dbb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 25 09:14:27 2016 -0500
fix the pass
Src_1d/CastroRad_1d.f90
commit 7b50ed8193e3d4a6218976e7c9cf6921a8cec428
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 24 21:53:02 2016 -0500
Break out the get_omega and get_domegadt routines into their own file, Rotation_frequency.f90. This allows the user to set custom rotation frequency profiles without directly affecting the hydro.
Source/Src_nd/Make.package
Source/Src_nd/Rotation_frequency.f90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit f7b60e1c6d58026c8854c73485d71f4a504e55c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 24 21:16:34 2016 -0500
Fix error message
Source/Src_nd/Rotation_nd.f90
commit 57d4cc283ab4bb035cd67e5f419702002abd6153
Merge: 4ba60797e 002b365f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 19:40:55 2016 -0500
Merge branch 'development' into radmerge
commit 4ba60797e6bfe961a66dbdf9954a39f4fe2d209c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 19:29:55 2016 -0500
fix compilation
Src_2d/trans_rad_2d.f90
commit d0255b5490c81a616cf8b1ccab6e8787916fa146
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 19:15:36 2016 -0500
sync up with the pure hydro version. This does 2 fixes:
-- we now don't write to states that don't exist
-- we fix the divergence for the axisymmetric coordinate in the p update
Src_2d/trans_rad_2d.f90
commit 4e8f4c8a8a5565db324bb89de9de85e3c96633e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 17:05:25 2016 -0500
remove an obsolete comment
Source/Src_2d/trans_2d.f90
commit 002b365f0f508f0bf2eb7e2dfb4186a2e45edb46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 24 14:06:29 2016 -0500
update to reflect enforce_minimum_density changes
Src_2d/CastroRad_2d.f90
commit cd4d17fc53817db7b74964cde357c9bc08b8fde0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 24 12:34:46 2016 -0500
Use arrays for bounds in enforce_minimum_density in 1D/2D
Source/Src_1d/Castro_1d.f90
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/advection_util_2d.f90
commit f2d98d075d9e4111fcde28a285008c201022f7f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 24 10:42:20 2016 -0500
Fix the interfacing between C++ and Fortran for enforce_minimum_density
Source/Castro.cpp
Source/Castro_F.H
commit 5b38e2fe8eba5d95fc3af320d72881c4cf39a17f
Merge: 524aa9604 2c8e0e50d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 21:52:10 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/CastroRadiation into development
commit 524aa9604c097ec074d6f33d7ecf00c473958279
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 21:52:04 2016 -0500
indenting
Src_3d/CastroRad_3d.f90
commit c78a3df86a5da7ac2453a460771ae39b73c1a433
Merge: 06b4105cc b5e406996
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 20:43:22 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 06b4105ccdf3660bf9ae2e7a9838512f345dee07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 20:42:51 2016 -0500
fix compilation
Source/Src_3d/riemann_3d.F90
commit b5e406996d559ea835bc454576523d9365c4e2f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 23 20:36:18 2016 -0500
We need to do the check for small density *after* the avgDown(), not before it
Source/Castro.cpp
commit 2c8e0e50dd178401f4d29b8f5c91d7c1be24c31c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 19:24:01 2016 -0500
styling
Src_3d/CastroRad_3d.f90
commit f82fb8c240cc082f289ed8d97ce382422b37e4d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 19:15:09 2016 -0500
use the Godunov interface throughout the hydro
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
commit 92c88290231d4f8019a355557c591d86b450afaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 18:50:18 2016 -0500
first cut at simplifying interfaces using Godunov state
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
commit f0fb63b514d72414c38efc9d3f5499a5ecee7db0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 18:49:30 2016 -0500
remove unused variables
Source/Src_2d/Castro_advection_2d.f90
commit 5a40b4eda60a88e823da4a1974f5a1887dca9c65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 18:19:29 2016 -0500
forgot to fill ugdx, ugdy -- curiously, this didn't affect any test results...
Source/Src_2d/Castro_2d.f90
commit 59d36a90e275e5af47c28a70689f88e4e8273f1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 17:45:51 2016 -0500
styling
Src_2d/CastroRad_2d.f90
commit ed4588876ea82a7ada428f9af59b178509bb7922
Merge: c97b3083b b43d07a9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 17:32:19 2016 -0500
Merge branch 'radmerge' into development
commit 7f062d3137625682a0e7d36fa12c85066bd1b9bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 17:27:50 2016 -0500
turn back on the deallocates
Src_2d/RadHydro_2d.f90
commit b43d07a9ae807d77728ddb77f8895f352be8cde0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 16:54:03 2016 -0500
use the godunov indices to simplify the pass
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
commit cbb1d59bbd5272c70d7120cb3775b19f126e4cac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 16:53:52 2016 -0500
use new bl_allocate interface
Source/Src_3d/Castro_3d.f90
commit 225692c9bd893151e89b2b78d4ee4887bccfee3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 15:57:18 2016 -0500
fix indenting so this is easier to read.
Source/Castro_setup.cpp
commit c97b3083bb55ab66c967a9cdc6cf48997fe7c51f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 15:33:36 2016 -0500
remove unnecessary dq
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/trace_ppm_1d.f90
commit 615feafffab6d2f9c91abdf075cd7b847a3a7fb1
Merge: 20ee354c7 0d07fa59a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 15:07:23 2016 -0500
Merge branch 'development' into radmerge
commit 478b4d7afc6d65586d934b6912aa38a5cc833af8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 14:46:37 2016 -0500
fix name clashing
Src_2d/RadHydro_2d.f90
Src_2d/trans_rad_2d.f90
commit aa90c7c9ca776c12dc0cb8f98dcddca0a767a94d
Merge: 0b329c40f 5f913f4f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 14:25:54 2016 -0500
Merge branch 'development' into radmerge
commit 0d07fa59a23e8022bf4ac14e873a2522a82f668f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 14:16:18 2016 -0500
add a multid version for the test suite -- we only go 10 steps.
We violate a CFL condition on a finer level if we go much further.
Rad2Tshock/inputs.M5.mg.test
Rad2Tshock/inputs.M5.mg.test.multid
commit 5f913f4f69125e7120075436b85f062bf81b858d
Merge: 89ebe13d4 48c17601b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 13:28:48 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit e1fd584c39a567ba03b4bfb9f1067399db3f1c7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 13:23:16 2016 -0500
make this multid
Rad2Tshock/inputs.M2.mg
commit 20ee354c7f4243ab892979a9b8dafcabc46cf73a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 13:22:07 2016 -0500
this seems to work now with the consolodation of the Godunov
states to the Riemann solver
Rad2Tshock/inputs.M2.mg
commit e6bfdebebb397a3e3c33a11da57fcda62bd459f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 13:22:07 2016 -0500
this seems to work now with the consolodation of the Godunov
states to the Riemann solver
Src_2d/RadHydro_2d.f90
commit 48c17601b4acbd71d8b01d1b6efecba0f07adb37
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 22 23:24:46 2016 -0500
Add C bindings to enforce_minimum_density, then add a call to it after a reflux has been performed. This is done because it is possible for a reflux to generate a density less than small_dens.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/advection_util_3d.f90
commit 0b329c40fcdaa0a2440991cb85b084b658cfc218
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 21:31:28 2016 -0500
fix gamcg
Source/Src_2d/riemann_2d.F90
commit 8f320318b4c11bae49e04df83101f41e3d01cf34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 21:30:52 2016 -0500
almost done -- need to pass out the radiation quantities still
Src_2d/Make.package
Src_2d/RadHydro_2d.f90
Src_2d/trans_rad_2d.f90
commit 64c790c150304c47cbf19a132239b4986752632f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 18:01:21 2016 -0500
finish the clean-up of the pure hydro
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trans_2d.f90
commit fa8d65ff7248045fd6e29eff1594f8d943b909af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 15:54:11 2016 -0500
a bit of cleaning
Source/Src_3d/riemann_3d.F90
commit 30a6d02d646d5b0d8dd5927e8e33b6e2f18f2458
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 15:52:46 2016 -0500
work on syncing 2-d up with 3-d for the godunov state
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/TODO
Source/Src_2d/riemann_2d.F90
Source/Src_2d/trans_2d.f90
commit ec3473098316e601c5a282aa5e361e5488f96ac0
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jan 22 12:52:36 2016 -0800
Included the information that if you want to increase this problem to max_level = 3,
you need to relax the dualenergy_eta2 value from 1.e-4 to 1.e-3 otherwise (rho*e) goes nuts
Exec/DustCollapse/inputs_2d_poisson_regtest
commit 0ca41492d0177712a9a4fc9051dd42e3ac295bf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 13:39:01 2016 -0500
use bl_allocate() -- this now diffs pretty cleanly with the main Castro
version of umeth3d, so perhaps they should be merged soon
Src_3d/RadHydro_3d.f90
commit 89ebe13d4c9e94454d937637f584802bda055c3b
Merge: 25c431902 719167108
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 12:43:53 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 25c431902229f2dda49c42a4312b1b551e720903
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 12:43:45 2016 -0500
some tweaks to sync with radiation
Source/Src_3d/Castro_advection_3d.f90
commit 71916710898bf15be64130cff45b039a0dbe9619
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 10:55:02 2016 -0500
use the new vectorized interface to bl_allocate()
Source/Src_3d/Castro_advection_3d.f90
commit 89c1c7886dc8b276f86d88541c602f2cb54bf5ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 21:50:10 2016 -0500
accidentally turned on hydro at some point
RadSphere/inputs
commit c7c3d327d0d2b5f4668fb6474694ef221728e74b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 18:07:00 2016 -0500
this seems to work now
Src_3d/RadHydro_3d.f90
commit 51f4a7eb250e9f4471fc7aade1dc269d4d7220c9
Merge: 75e958c90 6567d51a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 16:20:45 2016 -0500
Merge branch 'development' into radmerge
commit 11f12022c772a8dda6109b9d7cc7e328bb178afa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 14:36:49 2016 -0500
switch over to the godunov indices, GDPRES,. ..
Src_3d/trans_rad_3d.f90
commit 6567d51a2c122c58e6bb62103a83fb365054cbb2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 21 11:01:50 2016 -0800
no need to fill ghost cells of grad_phi because we will call fillpatch on grav_vector later; cleanup
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit 5c26e1702c1ea06890b69e320d9a8d1aae26c645
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 13:51:44 2016 -0500
interfaces done
Src_3d/RadHydro_3d.f90
Src_3d/trans_rad_3d.f90
commit 75e958c907525eba829c6b7594f8b654c5b5a531
Merge: 9565802de d91738347
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 12:53:04 2016 -0500
Merge branch 'development' into radmerge
commit d9173834753c35b0b98cd14936a788d29e647f87
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 21 03:14:10 2016 -0500
Fix the expression for the new burning timestep limiter
Source/Src_nd/timestep.F90
Source/_cpp_parameters
UsersGuide/runtime_parameters/runtime_parameters.tex
commit a642ab40e2133b589a5da16ec29e9994a8639ee1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 21 02:33:12 2016 -0500
Add a second burning timestep limiter based on Kushnir and Katz (2013). This limits the timestep so that the nuclear energy injection rate does not become faster than the sound-crossing time.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/Src_nd/timestep.F90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 2e272c7fcc2296d6e59b7dc494a978f8c9b764f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 21 01:18:52 2016 -0500
Add Godunov indices to the meth_params.template so they don't get overwritten when we update the inputs parameters
Source/Src_nd/meth_params.template
commit b6c2d8b6db877c924728a0358c6c8bed26842965
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 20 23:39:38 2016 -0500
We don't protect against the density going less than small_dens in the trans_* routines. So, disable the new EOS check_small parameter so that the EOS doesn't call an error if we give it a small density in those routines.
Source/Src_2d/trans_2d.f90
Source/Src_3d/trans_3d.f90
commit 432f5d14a8a510afc19895c455c3520ed4ca332e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 20 23:38:39 2016 -0500
Add a check_small logical parameter to the EOS data type. It defaults to true, and so when we call the generic EOS wrapper we engage in the existing behavior of checking whether rho and T are less than small_dens and small_temp, respectively. If set to false, we don't check that.
EOS/eos.f90
EOS/eos_type.f90
commit c4ad7cf310b2ad402cc4ef20081f4be3b217a83e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 21:38:34 2016 -0500
more work on cleaning up interfaces
Src_3d/RadHydro_3d.f90
Src_3d/trans_rad_3d.f90
commit 6d12f804d7cebb51fbfc143502218392d71b67b2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 20 17:29:38 2016 -0800
no need to fillpatch z-direction grav_vector in 2D
Source/Gravity.cpp
commit eb79cf51a9ec970db41f39dcb4be7d56efd77c42
Merge: d1a388b8c 15d031fe6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 19:55:56 2016 -0500
Merge branch 'development' into radmerge
commit 0e9ac244a60cffa1c6e1affc92b5ee6d03c7ef25
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Jan 20 16:48:02 2016 -0800
These two changes appear to resolve the issue of phi having NaNs in the ghost cells for a 3-level problem.
Source/Castro.cpp
Source/Gravity.cpp
commit 15d031fe6605ecbe6b32adbe3c59cd852896bba1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 18:26:16 2016 -0500
a little more steps
Rad2Tshock/inputs.M2.test.multid
commit a4708b0ba6e03757095d8933f020175f76320eea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 18:08:43 2016 -0500
fix periodic
Rad2Tshock/inputs.M2.test
Rad2Tshock/inputs.M2.test.multid
commit 716c459ebe7e6051091c7043c77dbf12caa86b33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 18:03:13 2016 -0500
add a mulit-d variant that has less steps, for the testsuite
Rad2Tshock/inputs.M2.test
Rad2Tshock/inputs.M2.test.multid
commit 81fbf23abcc36ec303187d2c80043a2096400094
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Jan 20 13:07:09 2016 -0800
Need to call get_new_data(Gravity_Type) at level k inside the loop over k in Castro::post_init
Source/Castro.cpp
commit d1a388b8c591ea1f1ebea7cbaa2c1827863e1844
Merge: 088ac0978 0cd27f15e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 15:58:08 2016 -0500
Merge branch 'development' into radmerge
commit eeb0721a33c30adddd322089c7cfb5d7d64b217e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 20 15:24:10 2016 -0500
get_new_grav_vector was changed so that it doesn't automatically fill the state data, need to fix post_init and post_grown_restart to account for this. Now the plotfile at t=0 will have non-zero gravity data.
Source/Castro.cpp
commit 0cd27f15e518543a7a96f759d0a1c2d3ccfc4172
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 15:05:18 2016 -0500
add 3-d version
Rad2Tshock/Prob_3d.f90
Rad2Tshock/bc_fill_3d.F90
commit e58dc2c9e6940f8ee1d6bae70073ca0f20d9d92d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Jan 20 11:32:43 2016 -0800
Call the sanity_check on the levels in a multilevel solve as well as from the single-level old solve for phi.
Source/Gravity.cpp
commit be9cbac7b6f2631f61f2c2d7ff5ee2ab857a3e49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 14:29:07 2016 -0500
add a 2-d version -- this is still along the x-direction, but can test the
2-d solver
Rad2Tshock/Prob_1d.f90
Rad2Tshock/Prob_2d.f90
Rad2Tshock/bc_fill_2d.F90
Rad2Tshock/inputs.M2
commit 88415f50f65f6988c311c4d0fe861af741f34ef5
Merge: 172e2a5ea 49bedffb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 13:04:32 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/CastroRadiation into development
commit 172e2a5ea81bfd4d47df2ac7ad612bb67dc70965
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 13:04:14 2016 -0500
some cleaning before making 2- and 3-d versions
Rad2Tshock/Prob_1d.f90
Rad2Tshock/probdata.f90
commit 49bedffb7289b81e10a2c1e407683d17883e6422
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 10:50:50 2016 -0500
get a testsuite script that will plot the radiation energy vs. group
compared to the analytic solution
RadSphere/Tools/fradsphere.f90
RadSphere/testsuite_analysis/radsphere.py
RadSphere/testsuite_analysis/radsphere_analytic.out
commit f1fcb626298f61406aa8bf24841d08c5e6c2a083
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 10:26:05 2016 -0500
accept the plotfile as the first required argument, instead of -p
RadSphere/Tools/fradsphere.f90
commit fe28333eec386d6f41731244f5c87de8d2568d0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 21:16:28 2016 -0500
make trans module stuff public
Src_3d/RadHydro_3d.f90
Src_3d/trans_rad_3d.f90
commit 088ac097851945e4f7b886af08499960f68dd2e1
Merge: a9e841033 564a0721c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 21:11:13 2016 -0500
Merge branch 'development' into radmerge
commit 9565802dede3fca3c4fe1f8bf4c3e324570561ba
Merge: 1d01f93f9 0819498da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 21:10:17 2016 -0500
Merge branch 'development' into radmerge
commit 0819498da426160fe4b0a6f388b6bad8d5130a97
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 19 17:00:07 2016 -0800
remove deprecated parameter from inputs
Exec/DustCollapse/inputs_2d_monopole_regtest
Exec/DustCollapse/inputs_3d_monopole_regtest
Exec/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/DustCollapse/inputs_3d_poisson_regtest
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/Sedov/inputs.3d.sph.testsuite
Exec/Sod/inputs-sod-rt1
Exec/Sod/inputs-sod-rt2
Exec/Sod/inputs-sod-rt3
commit cc367c7457d43f679c7fa736b2ec7db690193b4b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 19 16:56:39 2016 -0800
Do multi-level for the DustCollapse 2D Poisson regression test
Exec/DustCollapse/inputs_2d_poisson_regtest
commit fb0b73edbb639e0c8f6df7afd157cca490c3872f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Jan 19 16:22:57 2016 -0800
Initialize the phi arrays with zero because ghost cells outside symmetric boundary conditions don't
actually get filled since they will only get multiplied by 0 in the apply stencil operations. But sometimes
0 times NaN is still NaN so we initialize them with 0 now.
Source/Castro.cpp
Source/Castro_advance.cpp
commit 564a0721c5b49ccc7f24ba420f305d935ec54314
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 19:21:04 2016 -0500
reduce the number of steps for a more reasonable test
Rad2Tshock/inputs.M5.mg.test
commit ee02bd1965cdaab5e91d74ae5aff12e6b2bd1f16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 19:08:22 2016 -0500
an inputs for the test suite
Rad2Tshock/inputs.M5.mg.test
commit 1e2f46cb3ed4b022c7a7d415375145a09775ca44
Merge: ecd444e77 bbb741529
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 18:38:51 2016 -0500
Merge branch 'development' into radmerge
commit a9e841033775abd73b2057633fcfd5e9193c59ba
Merge: 6382ae78d 9db5ee411
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 18:38:51 2016 -0500
Merge branch 'development' into radmerge
commit 6d8c0a44b27f60a0b7f938e0059c0b470fd8a29c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 19 14:41:24 2016 -0800
fixed a bug I introduced in Sept 2015: did not set dBdt correctly
blackbody.f90
commit 9db5ee4112f3c24a616960786c84ee8f95adf09d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 19 14:41:45 2016 -0800
tweak M2 test
Rad2Tshock/inputs.M2.mg
commit bbb7415295ce717dabcffa5c9e7a7485bbce51a1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 19 14:41:24 2016 -0800
fixed a bug I introduced in Sept 2015: did not set dBdt correctly
blackbody.f90
commit ecd444e77cca270980daea344d679b13f49d68ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 14:52:51 2016 -0500
some trans work
Src_3d/Make.package
Src_3d/RadHydro_3d.f90
Src_3d/trans_rad_3d.f90
commit e89b0b8fb17efe07f4de4e21373fbf8adac8f696
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 19 10:43:38 2016 -0800
need to initialize Godunov indices in post_restart
Source/Castro.cpp
commit 7032c24fce6acc2e04f2696739693f5654520c96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 11:20:39 2016 -0500
much more progress -- just need to update the trans routines and we are in business...
Src_3d/RadHydro_3d.f90
commit 6382ae78de56bfeacd5ce0475d3088188379399e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 10:46:05 2016 -0500
Merge branch 'development' into radmerge
RadSphere/inputs
commit 93b63655b121de94051efbbce5d9df39ba19a117
Merge: 83a840f47 3efdf7b9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 10:46:05 2016 -0500
Merge branch 'development' into radmerge
commit 3efdf7b9be85b7374b024142479467583b1ad321
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 19 10:39:07 2016 -0500
fix the indexing and make it consistent with the pure hydro
branch. We were going into the PPM stuff with the wrong
array bounds.
Src_3d/RadHydro_3d.f90
commit 83a840f472ca0a2037f06a80d60300169d550b17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 21:02:38 2016 -0500
more progress on getting the array stuff in
Src_3d/RadHydro_3d.f90
Src_3d/trace_ppm_rad_3d.f90
commit b05097107ac3531fed895008c26c5c930dfe8917
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 20:03:04 2016 -0500
more progress on using the array indices
Src_3d/RadHydro_3d.f90
commit 1d01f93f9616c0c8546024f92dd8c3dca0982fa8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 18:40:20 2016 -0500
get this compiling for radiation
Source/Src_3d/riemann_3d.F90
commit a3facfa087321f477a06daa58374b60945fa25e3
Merge: 4c3fd29d6 789291750
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 18:07:50 2016 -0500
Merge branch 'development' into radmerge
commit a10e772c8baac25bb81c8138d14d44a24803f814
Merge: 4d2b1561c 1ef085178
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 18:07:21 2016 -0500
Merge branch 'development' into radmerge
commit 78929175086b34f370511d9f369e0e7074a358bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 17:12:51 2016 -0500
the Godunov state indices are now set in a new routine, init_godunov_indices
(or the _rad variant). This allows us to know how many radiation groups
are required to pass information around
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit 1ef085178b0dfab02d99186824a8c8e8acd825fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 17:12:17 2016 -0500
add an initialization function for hte Godunov state indices
Rad_nd.f90
commit 26542fb509569ea419bc3dd79bc28e33df60a990
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 18 12:42:12 2016 -0800
skip timestamping particles if there is no particle on that level
Source/CastroParticles.cpp
commit 4d2b1561c0ac52c281137f1f225eaf83a47d6536
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 15:13:03 2016 -0500
more progress...
Src_3d/RadHydro_3d.f90
commit 4c3fd29d6b16439cc6171754dec54e61faac8c8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 15:11:13 2016 -0500
more cleanup of the Riemann solver for radiation -- now it works
off of the single qint array
Source/Src_3d/riemann_3d.F90
commit 70199ce05dcb7c49b77b33fc3260b977eae13f8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 20:22:29 2016 -0500
add some more problem descriptions. Some problems are not documented
yet -- someone else knows them better.
Exec/README
commit e2a764be62cf7dc97ea0ff058fda21492371fa76
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 16 20:01:06 2016 -0500
Same for toy_convect
Exec/toy_convect/problem_tagging_2d.f90
Exec/toy_convect/problem_tagging_nd.f90
commit db9d7c6721a744cd7764d84d2b39e6e88c9cd6b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 16 19:56:19 2016 -0500
xrb_mixed is not a dimension agnostic problem, so it should have a dimension specific problem tagging routine
Exec/xrb_mixed/problem_tagging_2d.f90
Exec/xrb_mixed/problem_tagging_nd.f90
commit 11e1d2f073bbf742e3a1aa622c699a09a6fef337
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 19:35:22 2016 -0500
need to bind(C)
Exec/xrb_mixed/problem_tagging_nd.f90
commit 0edb5da57b54d60f4ad661d1b42388d699f5e552
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 19:35:00 2016 -0500
need to bind(C)
Exec/toy_convect/problem_tagging_nd.f90
commit 2634c6cd54aa40c0d19d0f2fe875a0f7ea2a574a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 19:34:30 2016 -0500
need to bind(C)
Exec/rotating_torus/problem_tagging_nd.f90
commit 5bcb3de82b04f0f1fb14e57656c260d656d2ca42
Merge: 6c04587b8 733ba1212
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 19:11:23 2016 -0500
Merge branch 'radmerge' into development
commit 6c04587b894c760aab83bcf9c7637e1e756e936d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 16 19:10:24 2016 -0500
Inputs file for test suite
Exec/rotating_torus/inputs_3d.test
commit 733ba12125aca5bb8149135fdc2424aa6ac968bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 18:42:46 2016 -0500
propagate the new godunov indexing into the trans routines
Source/Src_3d/trans_3d.f90
commit 082cd283421a603581ab126096e593b5fe657b19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 18:04:42 2016 -0500
fix indexing
Source/Src_3d/riemann_3d.F90
commit 571daf076c4b20306c1ebe6b940111b14c9c8174
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 17:59:13 2016 -0500
more work on the new gdnv stuff -- this still does not work for
some reason. Something with a pressure index is messed up somewhere...
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/hybrid_advection_nd.f90
commit 7900697cd344060c88e1feafe906ef6fab2f1305
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 17:35:09 2016 -0500
this changes how we pass back the Godunov state on the interfaces
(not the fluxes). Previously, we changed things to have an array
q() of dim NVAR to hold the state, but this wastes a lot of memory.
Now we define a NGDNV and keys, GDRHO, GDU, GDV, GDW, GDPRES, GDGAME
to index.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit fc35c0d4e858dba686126bb122fe3749246b5e64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 16:01:59 2016 -0500
lots of work syncing back up with the main Castro -- need to address
the interface to cmpflx there before continuing
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit e075a7dd1294a26b2462abfd200be0ce3936f06d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 14 01:53:21 2016 -0500
Add some burning parameters to the XRB problem to keep it as close to the old behavior as possible
Exec/xrb_mixed/probin
commit f19f55ca53a21b90a1d5d0de85b648914ef41076
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 13 15:43:05 2016 -0500
Rather than updating the Castro makefile each time there's new things in Microphysics, we're just going to include the make packages in that repo and do any updates there.
Exec/Make.Castro
commit d2587619bce129e7356c1b11674a971c8fe33cfc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 13 13:17:51 2016 -0500
For KH problem 4 we should be halving the sinusoidal perturbation frequency not the delta-y parameter
Exec/KH/Prob_nd.f90
Exec/KH/README
commit 9437e50117fc7a8b567191bffd7cfa98a942e350
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 13 11:32:40 2016 -0500
Need to define center for the KH problem
Exec/KH/inputs.2d
commit b557fbfc95118be88ea3d1602fb9c4a0d256fbd2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 12 12:57:11 2016 -0800
In post_regrid, only when the level is the base level, we need to call Redistribute().
Source/Castro.cpp
commit 7b8d237a53bd5ed744bb706167da132ec6519205
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 12 12:55:37 2016 -0800
change max_level for RT_particles
Exec/RT_particles/inputs_2d
commit 2e7746d7ba5f1fe413f492ed65c37947c80876a3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 12 12:31:34 2016 -0800
tracer particles
Exec/RT_particles/README
Exec/RT_particles/amrvis.defaults
Exec/RT_particles/inputs_2d
Exec/RT_particles/particle_file
Source/Castro.H
Source/Castro.cpp
Source/CastroParticles.cpp
Source/Castro_advance.cpp
Source/Castro_error_F.H
Source/Castro_io.cpp
Source/Castro_setup.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 1beac9e1aacf6292fb1e68678c8d91618fafe48e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 11 16:34:30 2016 -0500
Initialize all EOS derived type values to the same (large, negative) number. This should make debugging easier in case uninitialized values are being used.
EOS/eos_type.f90
commit 23d552d7600b8f9e277a4173acb73e0c89f3a8c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 11 16:10:15 2016 -0500
No need to compile screening and reaction rates if we're not using reactions
Exec/Make.Castro
commit a7dd0de4406b48f2ddd261c7bfe7a42f9de11e6c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 11 14:49:22 2016 -0500
Add the new Microphysics rates directory to the Makefile
Exec/Make.Castro
commit fdd518399ed9145169a664a9274b9f7d261d6f06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 16:00:13 2016 -0500
update the Makefiles to account for some reorg
Src_1d/Make.package
Src_2d/Make.package
Src_3d/Make.package
commit 78c8d3bd486b72761b7080c34eb95d1875964c4e
Merge: afc2a91da 21452b4b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 14:58:53 2016 -0500
Merge branch 'development' into radmerge
commit f175b1794eec7de9f9cb3a6d2ccad7343c10ff66
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 10 12:10:03 2016 -0500
Have problem 4 be a revised version of McNally et al.'s problem with a transition that is twice as wide. The Lecoanet et al. problem is now numbered 5.
Exec/KH/Prob_nd.f90
Exec/KH/README
Exec/KH/inputs.2d.p5
Exec/KH/probin.p5
commit 33296a5f4ce8661dc0f4a4586395cb07a6384601
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 9 22:08:49 2016 -0500
Add a burner initialization call.
Networks/burner.f90
Networks/general_null/general_null_burner.f90
Source/Castro_F.H
Source/Castro_setup.cpp
commit fbf1b1193c0aafacc51f2422daace33903cef62f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 7 19:56:39 2016 -0500
remove this todo file
Source/TODO.RUNPARAMS
commit a77e401c109dd3f37f47e155e9def19e32954896
Merge: db019cb85 4dd36bde0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 19:39:52 2016 -0500
Merge branch 'development' into c_binding
commit db019cb85b84ef761abdeccc46e393784489f5a7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 19:39:37 2016 -0500
Somehow a bunch of changes to gravity_sources_nd.f90 got overwritten; this has now been fixed.
Source/Src_nd/gravity_sources_nd.f90
commit 384258cef1630c9985ef23c46d1604bd849b4d82
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 19:01:04 2016 -0500
We don't use this file anymore either
Source/Src_nd/EstDt_nd.f90
commit 392ef55396bc5b84836cd8f7d1b86ef82a6abbce
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 17:57:44 2016 -0500
Remove unused routines
Source/Src_nd/enforce_consistent_e_nd.f90
Source/Src_nd/reset_internal_energy_nd.f90
commit 3c7e019c2ca265197fe66ded52513dd8cb37b8d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 12:21:11 2016 -0500
C binding updates for BC fill routines
Rad2Tshock/bc_fill_1d.F90
Rad2Tshock/bc_fill_1d.f90
RadCoreCollapse/bc_fill_2d.F90
RadCoreCollapse/bc_fill_3d.F90
commit 06a33481ed7c6af36c810ba344cb03f2a21ff79a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 12:12:49 2016 -0500
filcc_nd needs to be .F90
Source/Src_nd/Make.package
Source/Src_nd/filcc_nd.F90
commit 4dd36bde0fdc34e1185f902190649fc54f7f836b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 11:30:45 2016 -0500
We had some arrays in 1D and 2D that were being allocated but not being deallocated.
Source/Src_1d/riemann_1d.F90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/riemann_2d.F90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 65cde7de0c03c87e70853f29c67429225ba9c7db
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 09:29:12 2016 -0500
We reverted problem_checkpoint/restart C bindings
Exec/toy_flame/Problem_F.H
commit 536c59fbb791276f9ec83aac1048d6d567caae43
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 09:17:55 2016 -0500
C binding for raderror
Source/Castro_error_F.H
Source/Src_nd/Tagging_nd.f90
commit c0ffc0b747e51023e26971aa673c7d4dec256262
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 7 09:08:22 2016 -0500
Revert C bindings for ext_src_*d for now
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/ext_src_1d.f90
Source/Src_2d/ext_src_2d.f90
Source/Src_3d/ext_src_3d.f90
Source/Src_nd/ext_src_nd.f90
commit 21452b4b7c7c2058b40206ad4a9fc67598c3f15c
Merge: eb4020230 4fba9edec
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 22:11:49 2016 -0500
Merge branch 'development' into c_binding
commit b508950dbdf061b8382b0cca3cb0dbf05f1050e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 22:11:44 2016 -0500
More C bindings, plus dimension agnostic derive routines
RadCoreCollapse/Tagging_nd.f90
RadThermalWave/Tagging_nd.f90
commit eb40202304a379e3ebef769facfa5e55f3664d44
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 22:11:44 2016 -0500
More C bindings, plus dimension agnostic derive routines
Make.package
RAD_F.H
RadDerive_nd.f90
Rad_nd.f90
Radiation.cpp
Src_1d/CastroRad_1d.f90
Src_1d/Make.package
Src_1d/RadDerive_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/Make.package
Src_2d/RadDerive_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/Make.package
commit 537f5c92b4059770c996bb83a30b67953d503d96
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 22:11:24 2016 -0500
Forgot a bind(C)
Source/Src_2d/bc_fill_2d.F90
commit e347d621a56e2c107c8987c38a5dbfc6066974ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 22:11:16 2016 -0500
ca_derertot is defined in CastroRadiation, shouldn't duplicate here
Source/Derive_F.H
commit bfb3f2edc929924011c6c82369592c9ad09a6bfb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 20:22:07 2016 -0500
F90 -> f90 for files that don't need to be preprocessed
Exec/DustCollapse/update_sponge_params.f90
Exec/reacting_bubble/problem_derive_nd.f90
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/ext_src_2d.f90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Castro_sums_nd.f90
Source/Src_nd/Castro_util.f90
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/amrinfo.f90
Source/Src_nd/ext_src_nd.f90
Source/Src_nd/filcc_nd.f90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/hybrid_advection_nd.f90
Source/Src_nd/math.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/prob_params.f90
Source/Src_nd/problem_derive_nd.f90
Source/Src_nd/problem_tagging_nd.f90
Source/Src_nd/rotation_sources_nd.f90
Source/Src_nd/sponge_nd.f90
Source/Src_nd/update_sponge_params.f90
Source/parse_castro_params.py
commit af013cf5b03c7f0304dea60d955289a6c5501c23
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 11:59:05 2016 -0500
Update Noh test BC routines with C bindings
Exec/Noh/bc_fill_nd.F90
Exec/Noh/bc_fill_nd.f90
commit e65c2e35956af9593ee7e1f353f288f2d05b237a
Merge: 8aad1ebde 552dbdeb9
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 11:51:16 2016 -0500
Merge branch 'development' into c_binding
commit 07d08e0bf8407ff89148613c46fdecfccb1832ae
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 6 11:48:07 2016 -0500
More C binding updates for radiation tests
Rad2Tshock/Castro_error.cpp
RadCoreCollapse/Castro_error.cpp
RadThermalWave/Castro_error.cpp
commit 552dbdeb9e364fa82c0208cbdff53bfa57d4ed82
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 16:50:06 2016 -0500
Typo in comment
Source/Src_nd/bc_fill_nd.f90
commit d976b2909d69a8474671e73a7dab94f9e3b75887
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 16:49:55 2016 -0500
Add the Noh (1987) hydrodynamic shock test, as described by the 2008 Athena paper.
Exec/Noh/GNUmakefile
Exec/Noh/Make.package
Exec/Noh/Prob_nd.f90
Exec/Noh/bc_fill_nd.f90
Exec/Noh/inputs_3d
Exec/Noh/probin
commit 7d980d024f9b63e9efd385cecfa5f1a84f0939f8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 5 13:36:11 2016 -0800
use the new BoxLib Geometry::PeriodicCopy function
Source/Gravity.cpp
commit 8aad1ebde01662f32dfa37fe8640260d86f8633b
Merge: 752784a57 540d50720
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 15:36:00 2016 -0500
Merge branch 'development' into c_binding
commit 540d50720cb7528ea4ae9d884a9eac6d232aac69
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 15:35:49 2016 -0500
Fix typo
Source/Src_1d/Castro_advection_1d.f90
commit 4655ae02126ec8c4d6b4890ada45851c95743875
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 15:30:57 2016 -0500
Remove unused variables
Source/Src_3d/Castro_advection_3d.f90
commit 752784a578b64153e0894bd444a14e76295b9a4f
Merge: 29c5652c5 fdc4c2dbb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 15:27:46 2016 -0500
Merge branch 'development' into c_binding
commit fdc4c2dbb2d26fd055a3e238e6180401d6d2023e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 5 14:29:28 2016 -0500
Only sum up the energy/momentum changes in the hydro if verbose == 1.
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit ea4d7df1377b2943270f6e62982496e4dcb2b582
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 5 13:27:13 2016 -0500
new model file with better resolution
Exec/convective_flame/convective_flame.hse.tanh.delta_0.040cm.dx_0.050cm
commit 6f06b84695d77c85d765a8e1ad10e41be12c0aee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 5 10:28:09 2016 -0500
no longer need the vpath hack -- it's in boxlib directly now
Exec/Make.Castro
commit 9751ffbb4fc1c0a55a435d9b565868cc3b45b6ea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 4 17:42:08 2016 -0800
When averaging the fine grad phi onto to coarse, we must take into account that fine boxes might touch periodic boundaries. In that case, we need to periodically shift the fine boxes and average down the shifted boxes too.
Source/Gravity.cpp
commit 29c3bd898050a531aa3378072c119dc7c7125bec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 4 18:43:50 2016 -0500
better parameters
Exec/Detonation/inputs-det-x.test
commit 09c70afd5de9e55b7d7c99562a49da7fa4754060
Merge: b71291fbb 1f51d6ef0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 4 18:12:28 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b71291fbbfd078c1c058878a9db93deb5d7d5e2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 4 18:10:25 2016 -0500
test suite version
Exec/Detonation/inputs-det-x.test
commit 1f51d6ef0bfccabcf249d9d9548246ee192742dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 4 16:48:34 2016 -0500
fix a stray &
Source/Src_nd/set_castro_params.f90
Source/parse_castro_params.py
commit d1083a4869ecbb1da658b8f543ddd5abc9849c37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 4 11:35:10 2016 -0500
add to the .f90 vpath for the new preprocessing behavior
Exec/Make.Castro
commit d6ae3c7ca457899219998898dacb5bec2d2a68be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 3 09:57:16 2016 -0500
fix the velocity initialization
Exec/gresho_vortex/Prob_2d.f90
commit 20942951bed7b1efb97436739def68f678a4b9f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 30 02:44:43 2015 -0500
Add a passively advected variable to the KH test, and for problem 4 add a dye variable as described by Lecoanet et al.
Exec/KH/GNUmakefile
Exec/KH/Prob_nd.f90
commit 505c337c54cae829a15fdb00965d32d84ec1d26c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 30 01:57:31 2015 -0500
Inputs and probin files for the new KH problem
Exec/KH/inputs.2d.p4
Exec/KH/probin.p4
commit 6f68ed85f427566b058c5cf1b8450161a1e54263
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 30 01:46:44 2015 -0500
Make it easier for the user to set up passively advected variables by examining if the NUM_ADV variable has been defined. If so, we use that many copies of passively advected variables. Use it (say for a single advected variable) by adding the following line to your makefile: DEFINES += -DNUM_ADV=1
Source/Castro_setup.cpp
commit 017053acb5a7dfeee9188e01b4f97876b3d5ad74
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 30 01:38:51 2015 -0500
Add a fourth Kelvin-Helmholtz problem, corresponding to that presented by Lecoanet et al. 2016.
Exec/KH/GNUmakefile
Exec/KH/Prob_2d.f90
Exec/KH/Prob_nd.f90
commit 90f3a8d19f49e6aa172c47e359efc8b69fa562e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 27 07:39:26 2015 -0500
Add a parameter castro.max_dt which sets the maximum possible timestep.
Source/Castro.cpp
Source/Src_nd/meth_params.F90
Source/Src_nd/meth_params.template
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit 08b0bf5bb6d56b620da1387556a14788ab20f543
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 17:35:40 2015 -0500
Change date output format
Source/main.cpp
commit 399a1f418a7c46af74ae42aa980ee7b33f64cba7
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 17:21:44 2015 -0500
If we have a burning-limited timestep, print it out separately, and indicate in the estTimeStep output line what is limiting the final timestep.
Source/Castro.cpp
commit e415a11a5078db813ce7d365cf279478c511c0b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 02:46:18 2015 -0500
Update the documentation on amr.check_per and amr.plot_per.
UsersGuide/Inputs/CastroInputs.tex
commit 4fba9edec46ecb1f9fa37656d3ea4565baa49757
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 22 16:11:51 2015 -0500
Sync up with some indexing changes in Castro 3D hydro
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit 45a9583b18b4f05f1d22815d4ca2ebbb66fe1ed7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 22 15:44:26 2015 -0500
Fix typo
Source/Src_3d/riemann_3d.F90
commit e07cadd4a9ad3234ca6041b57b7a039779325af1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 23:54:03 2015 -0500
Avoid a divide-by-zero for dim < 3.
Source/Src_nd/Castro_util.F90
commit 4fdfffc6293eaa420bdb215ec9e609e97c10ab35
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 15:37:59 2015 -0500
Change the order of a subtraction to cut down on roundoff error
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit b12691618d0a50bd0bb5aa91e2e32caf976579a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 14:31:11 2015 -0500
We had already defined the old source terms, no need to recompute them
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit 0bdaded0a60a5d6d2a2b8bfc79364083ff61908a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 12:33:42 2015 -0500
Revert addition of dx to reset_internal_e.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/reset_internal_energy_nd.f90
commit 3a340bee5e03311110465ac20edc77ede352d4cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 12:29:52 2015 -0500
Revert some changes to derkineng that caused roundoff level differences
Source/Src_nd/Derive_nd.f90
commit 3d2c4b01e7f5e8d78359b5bf945dd8d98a8433fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 01:09:01 2015 -0500
Reverse the order of the coupled momentum update for rotation; apply all the other terms before solving the implicit system.
Source/Src_nd/rotation_sources_nd.f90
commit 302d2c2ff06bb2d605e958e82ad3f440be01d119
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 20 23:04:31 2015 -0500
Write a separate subroutine for adding a momentum source term to the hybrid momentum.
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/hybrid_advection_nd.F90
Source/Src_nd/rotation_sources_nd.f90
commit e014026df60fec50a63ef6f738f90e117969375a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 20 21:22:05 2015 -0500
Move the hybrid update to a separate subroutine
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/hybrid_advection_nd.F90
commit d9b047e9728306e22450ac646339fdbeacf6baeb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 20 20:16:58 2015 -0500
Cut down on indexing difficulties by using 3D arrays in the 3D hydro, rather than passing individual components
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/advection_util_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/slope_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit ef17eee09633c800cc4151bc1282de7008109217
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 20 01:07:34 2015 -0500
Create edge-based primitive arrays to pass around, instead of working with many separate arrays for each primitive variable.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.F90
Source/Src_3d/trans_3d.f90
commit dc77a0b8ad4d6f8e4827157295fc53592d7aa37b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 21:27:15 2015 -0500
Deallocate temporary arrays
Source/Src_3d/Castro_3d.f90
commit 362134cc527586f26c13561a42675594f6e46af7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 20:16:42 2015 -0500
Forgot to make locations relative to center
Source/Src_3d/Castro_advection_3d.f90
commit fbe81986159771dece356ecb6c7192134d1a9aa2
Merge: 4b336ca1d 1a14ba683
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 20:16:22 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 1a14ba683c061b09de4fbdf31d4063455bf0f6aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 17:03:41 2015 -0500
Fix the application of the gravity sync source -- on refined levels, multiply the source by dt / 2 where the dt is the timestep on the base level whose reflux is generating the sync source. Previously we used dt / 2 on the fine level, but this misses the contribution of the gravity sync to the previous fine grid timesteps.
Source/Castro.cpp
commit 2cfb47a4d072ea683e8a15db3100b59d6510128e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 16:53:55 2015 -0500
Add the same predictor energy change for gravity/rotation using source_type == 4 that we do for the other options. Then completely remove this predictor when we do the correct time-level n+1/2 update. This shouldn't change results at present, but does make the method more consistent.
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit 4b336ca1d13ce1c344c8cc564cc969cd70820e9c
Merge: b9a46a605 279d4bc49
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 13:59:18 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 279d4bc49a3f4800d4d581b2fffeb3bbe935ecbf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 13:38:15 2015 -0500
In time_center_source_terms, undo the multiplication by dt/2 after applying the sources, since we're adding them to the source terms array for the predictor.
Source/Castro.cpp
commit b9a46a6057832c609f625cb481e8d939f75f3f82
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 01:35:15 2015 -0500
Add module
Source/Src_nd/hybrid_advection_nd.F90
commit 612496f7af65397acfbaa24e07ba90f9577aa7ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 00:14:00 2015 -0500
Get the momentum update for rotation consistent with the hybrid advection scheme -- except rot_source_type == 4.
Source/Src_nd/rotation_sources_nd.f90
commit d524ee0fb8cf86418309e0780aa2183a7740fe6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 00:13:40 2015 -0500
Minor touchup
Exec/rotating_torus/Prob_nd.f90
commit 34c03e46ff69f85e6c265536362143ac32a34879
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 21:45:51 2015 -0500
If we're doing external gravity, then the total energy has a contribution from rho * phi, not 0.5 * rho * phi.
Source/sum_integrated_quantities.cpp
commit ebe1803eddcec7e37aad5916036dfa76efd2cb30
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 21:24:31 2015 -0500
Move the hybrid advection stuff to its own module, and time-center the radial momentum source term by using a time-averaged value of rho and angular momentum.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/Castro_util.F90
Source/Src_nd/Make.package
Source/Src_nd/gravity_sources_nd.f90
commit cd07c8f39b473680f1cb4a8596ef6657fd3a2147
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 20:27:30 2015 -0500
Create a three-vector that is parallel to the rotation axis
Source/Src_nd/Castro_nd.F90
Source/Src_nd/meth_params.F90
commit fba8317b174280642257cc0e0ba8bdafd446a0cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 20:27:12 2015 -0500
Send the parsed params to Fortran before the manual ones
Source/Castro_setup.cpp
commit 29f7a1311148a4a0a6c42a7863326900f6a32f59
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 19:47:09 2015 -0500
Write functions to convert back and forth from linear to hybrid momentum.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/Castro_util.F90
Source/Src_nd/gravity_sources_nd.f90
commit 53964bd693724171522ffafe6906528eebb2ca05
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 18:46:15 2015 -0500
Cut down on memory usage
Source/Src_3d/Castro_advection_3d.f90
commit 1a2feae75cd1ccc048d6b8386c31ecd77d03d0fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 17:40:02 2015 -0500
For hybrid advection, calculate the gravity update to angular momentum and only then convert back to linear momenta. This helps with conservation.
Source/Src_nd/gravity_sources_nd.f90
commit 9fcf14c5926ea00260b67ede00b0419077e734de
Merge: 8b83f8587 0c8430ea4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 17:14:37 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 0c8430ea4f02b31406223e6650e7938298f46d37
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 16:58:56 2015 -0500
Add angular momentum to list of integral quantities
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_nd/Derive_nd.f90
Source/sum_integrated_quantities.cpp
commit 25eed965c6f641cb8248b426063ae743ecfbc375
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 04:12:38 2015 -0500
f90 -> F90 for some files so we can run them through the preprocessor
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Make.package
Source/Src_nd/meth_params.F90
Source/Src_nd/prob_params.F90
Source/TODO.RUNPARAMS
Source/parse_castro_params.py
commit a2fc87863f8a2cdf9857daf72aec5a3ab186fffe
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 17 02:37:04 2015 -0500
Simple function that converts a grid coordinate to the nearest cell-centered zone index on the current level.
Source/Src_nd/Castro_util.F90
commit 4727424964adc7f1977607d4b9f8a4189721a517
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 16 00:14:02 2015 -0500
Remove hook to ca_rotate, that no longer exists.
Source/Castro_F.H
commit ce86be17967e3ca61053557157293b816cc63bca
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 13:33:11 2015 -0500
Calculate phi in addition to g for the point-mass gravity.
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_nd/pointmass_nd.f90
commit 62bf62d8bea8cce23213e18d01fd80c021c0b59c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 12:08:19 2015 -0500
Updated rotating torus inputs, including allow_negative_energy = 1. In the polytrope EOS the energy isn't in the EOS so it shouldn't matter.
Exec/rotating_torus/inputs_3d
commit 5fc6e01cdfca8b80e7480b3d0a38ce76e8d5d3bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 12:07:41 2015 -0500
In the EOS, only complain about e < 0 if allow_negative_energy == 0.
EOS/eos.f90
commit 593d76f316f2b6d481937b2debc50d1af86cc878
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 01:30:19 2015 -0500
Add the rotating torus problem of Papaloizou and Pringle (1984). This problem exercises the rotation, point-mass gravity, and polytrope EOS modules, and is written in dimension-agnostic fashion, though it is meant to be a 3D test.
Exec/rotating_torus/GNUmakefile
Exec/rotating_torus/Make.package
Exec/rotating_torus/Prob_nd.f90
Exec/rotating_torus/inputs_3d
Exec/rotating_torus/probdata.f90
Exec/rotating_torus/probin
Exec/rotating_torus/problem_tagging_nd.f90
commit 263a67ac1e5e28a2ed7f090e9c78fb0656257cb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 01:28:03 2015 -0500
The dual energy criterion for determining the dynamical internal energy was incorrectly being applied in reverse.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 52a0c7b899b64129f7e7c1d90396104e0ac0cc26
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 01:00:11 2015 -0500
Update the AMR level before we tag for a regrid
Source/Castro.cpp
commit 5fc4f7604d92a941c097b5f0d6d220185357dbf9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 15 00:14:21 2015 -0500
Dimension agnostic point-mass routines
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Make.package
Source/Src_1d/pointmass_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/pointmass_2d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/pointmass_nd.f90
commit 24cdd9bd660f5ef89025756a8ea52ea7120d0eb3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 14 23:56:58 2015 -0500
Use S_old in the pointmass compute_delta_mass routine, rather than Sborder. For some reason things go wrong when using the latter but not the former, though I don't understand why. But since S_old and Sborder are equivalent with respect to density, it should be fine.
Source/Castro_advance.cpp
commit 23cceefbf19559f06b2ead7c568926a4b8cb7b7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 14 21:11:07 2015 -0500
Fix indexing bug in pointmass
Source/Src_3d/pointmass_3d.f90
commit ab1a2c9bbf81ed46e7f7acaa5043dd232114ea5c
Merge: 877ccb393 ebfe292a9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 14 16:25:39 2015 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit 877ccb393b31e0b56ed95aa0e92e8a45c605edfe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 14 16:25:19 2015 -0500
Move the point_mass parameter to be handled by the param parser script.
Source/Castro.H
Source/Castro.cpp
Source/Castro_setup.cpp
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit f354c7a82302e3b8c5c052ced6e373feeaba3c38
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 14 16:22:16 2015 -0500
Fix missing module reference
Source/Src_3d/pointmass_3d.f90
commit 29c5652c5de209005ca79ba0dc454e158ea73df4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 14 00:06:25 2015 -0500
Derive function for radiation energy
Source/Derive_F.H
commit f7c4202cfd2df2e7b480c1c1daa3cc99114aa13c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 23:51:19 2015 -0500
C bindings for a few stragglers
Source/Castro.cpp
Source/Castro_F.H
commit 68979c32019542501959ab200134e87660eece0a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 23:45:23 2015 -0500
C bindings for the rest of the stuff in Castro_advance
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/pointmass_3d.f90
commit fb4d8e4d5d7b6e3181f64d3fab95df631c917e5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 23:25:42 2015 -0500
C bindings for problem_checkpoint/problem_restart.
Exec/test_convect/Problem_F.H
Exec/toy_flame/Problem_F.H
Source/Castro_io.cpp
Source/Problem_F.H
Source/Src_nd/Problem.f90
commit 0c8302c89211aa1cfc4e0b0f2b81ad12f9cc0ec3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 22:41:03 2015 -0500
No usage of get_omb remains
Source/Castro_F.H
commit 2229125130f50ac75dbffd9056859333bd1bf12c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 22:38:41 2015 -0500
C bindings for the Castro parameters
Source/Src_nd/set_castro_params.f90
Source/castro_call_set_meth.H
Source/castro_set_meth.H
Source/parse_castro_params.py
commit dc958e88fd5dda42f0accbdadc86066011cf87a6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 22:28:26 2015 -0500
We never call FILCC from C++
Source/Castro_F.H
commit 957adabb7d5af4ab04bbe12951df8195e0247294
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 22:27:08 2015 -0500
C bindings for the tagging stuff
Source/Castro.cpp
Source/Castro_error.cpp
Source/Castro_error_F.H
Source/Src_1d/Make.package
Source/Src_1d/problem_tagging_1d.F90
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/problem_tagging_2d.F90
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/problem_tagging_3d.F90
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/Tagging_nd.f90
Source/Src_nd/problem_tagging_nd.F90
Source/Src_nd/problem_tagging_nd.f90
commit bd3a39f5c6e2f23fca8671bc2bf14fa04f4d1a31
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 22:11:19 2015 -0500
C bindings for the BC fill routines
Exec/DustCollapse/bc_fill_3d.F90
Exec/DustCollapse/bc_fill_3d.f90
Exec/RT_particles/bc_fill_2d.F90
Exec/RT_particles/bc_fill_2d.f90
Exec/Sedov/bc_fill_1d.F90
Exec/Sedov/bc_fill_1d.f90
Exec/Sedov/bc_fill_2d.F90
Exec/Sedov/bc_fill_2d.f90
Exec/Sedov/bc_fill_3d.F90
Exec/Sedov/bc_fill_3d.f90
Exec/convective_flame/bc_fill_2d.F90
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/bc_fill_3d.F90
Exec/convective_flame/bc_fill_3d.f90
Exec/double_bubble/bc_fill_2d.F90
Exec/double_bubble/bc_fill_2d.f90
Exec/gamma_law_bubble/bc_fill_2d.F90
Exec/gamma_law_bubble/bc_fill_2d.f90
Exec/hydrostatic_adjust/bc_fill_1d.F90
Exec/hydrostatic_adjust/bc_fill_1d.f90
Exec/reacting_bubble/bc_fill_2d.F90
Exec/reacting_bubble/bc_fill_2d.f90
Exec/test_convect/Problem_F.H
Exec/test_convect/bc_fill_2d.F90
Exec/test_convect/bc_fill_2d.f90
Exec/toy_convect/bc_fill_2d.F90
Exec/toy_convect/bc_fill_2d.f90
Exec/xrb_mixed/bc_fill_2d.F90
Exec/xrb_mixed/bc_fill_2d.f90
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_1d/Make.package
Source/Src_1d/bc_fill_1d.F90
Source/Src_1d/bc_fill_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/bc_fill_2d.F90
Source/Src_2d/bc_fill_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/bc_fill_3d.F90
Source/Src_3d/bc_fill_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/bc_fill_nd.F90
Source/Src_nd/bc_fill_nd.f90
commit 1bf61fad331d796fb4ab8ec21d914f023d127954
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 19:45:17 2015 -0500
C bindings for reactions and external source terms
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_1d/Make.package
Source/Src_1d/ext_src_1d.F90
Source/Src_1d/ext_src_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/ext_src_2d.F90
Source/Src_2d/ext_src_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/ext_src_3d.F90
Source/Src_3d/ext_src_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/React_nd.F90
Source/Src_nd/React_nd.f90
Source/Src_nd/ext_src_nd.F90
Source/Src_nd/ext_src_nd.f90
commit a08f40e4b47d7b7e5afcfc82ce2a614072a5de2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 19:30:07 2015 -0500
C bindings for Castro_nd and Castro_util_*d
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
Source/Gravity.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_util_1d.F90
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_util_2d.F90
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_util_3d.F90
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Castro_nd.F90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Make.package
commit 57e128618eb284cbfc931117e29ede2d3ebdf082
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 18:50:23 2015 -0500
C bindings for the diagnostic sum functions.
Source/Castro_F.H
Source/Gravity.cpp
Source/Src_nd/Castro_sums_nd.F90
Source/Src_nd/Castro_sums_nd.f90
Source/Src_nd/Make.package
Source/sum_utils.cpp
commit 2ecc1ad9fb0117f249b46621309addf32256b1ae
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 18:40:23 2015 -0500
Move compute_temp, enforce_consistent_e, and reset_internal_e to Castro_util.F90
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_util.F90
Source/Src_nd/Make.package
Source/Src_nd/compute_temp_nd.f90
Source/Src_nd/enforce_consistent_e_nd.f90
Source/Src_nd/reset_internal_energy_nd.f90
commit b438d0fc275b1eebefe3de5d49d3e48aab892f26
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 18:33:21 2015 -0500
More sponge fixes
Exec/DustCollapse/update_sponge_params.F90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/sponge_params.F90
commit 57ee64b15ec160e8343a6907c690d3735c7fd7a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 18:20:26 2015 -0500
C bindings for derive routines, plus more f90 -> F90
Exec/gamma_law_bubble/Derive_F.H
Exec/gamma_law_bubble/Problem_Derive_F.H
Exec/gamma_law_bubble/Problem_Derives.H
Exec/gamma_law_bubble/extra_derives_2d.f90
Exec/hydrostatic_adjust/Problem_Derive.H
Exec/hydrostatic_adjust/Problem_Derive_F.H
Exec/hydrostatic_adjust/extra_derives.f90
Exec/reacting_bubble/Problem_Derive_F.H
Exec/reacting_bubble/Problem_Derives.H
Exec/reacting_bubble/problem_derive_nd.F90
Exec/toy_flame/Prob.cpp
Exec/toy_flame/Problem.f90
Exec/toy_flame/Problem_F.H
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_nd/Derive_nd.F90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Gravity_nd.F90
Source/Src_nd/Make.package
Source/Src_nd/Rotation_nd.F90
Source/Src_nd/gravity_sources_nd.F90
Source/Src_nd/prescribe_grav_nd.F90
Source/Src_nd/problem_derive_nd.F90
Source/Src_nd/rotation_sources_nd.F90
Source/Src_nd/update_sponge_params.F90
commit b7f2dc3f9d3a41851d6057660af0f0350fac71e1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 17:27:04 2015 -0500
f90 -> F90 for sponge
Source/Src_nd/Make.package
Source/Src_nd/sponge_nd.F90
Source/Src_nd/sponge_params.F90
commit 82caf0598ac7f40405ff7ab3930592c4eba8dd95
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 17:26:16 2015 -0500
Remove duplicate file
Source/Src_nd/rotation_nd.f90
commit 6bb34efd5a388794eba330b49cc03e0fa049e998
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 17:24:18 2015 -0500
C bindings for source terms
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/rotation_sources_nd.f90
Source/Src_nd/sponge_nd.f90
Source/Src_nd/sponge_params.f90
Source/Src_nd/update_sponge_params.f90
commit 45b7a1ccc9bac43add722bdd2c56047b7bfcf9a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 17:08:09 2015 -0500
C bindings for diffusion and conductivity
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Diffusion_nd.F90
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/species_diff_coeff_nd.f90
Source/Src_nd/thermal_conductivity_nd.f90
Source/Src_nd/visc_coeff_nd.f90
commit dc460e30a464fc25f0daa1aa5325f280af92d82a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 16:47:02 2015 -0500
C bindings for gravity and multigrid
Source/Diffusion.cpp
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
commit fd00e617cf9b1e61766fda79a61a6726bd17f199
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 13:18:24 2015 -0500
Start of an effort to clean up the C++-to-Fortran interfaces. Instead of using the old BL_FORT_PROC_CALL and BL_FORT_PROC_DECL, we are going to use bind(C) on Fortran subroutines that need to talk to the C++, and extern C {} wrappers around the function declarations in C++. Then we can just call the function name directly, as it will have the same name in both languages. Importantly, this allows the Fortran subroutines that need to be called by C to live in modules. As a first step, create a timestep_module in timestep.F90, and move all of the EstDt routines in there.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/EstDt_burning_nd.f90
Source/Src_nd/EstDt_diffusion_nd.f90
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/timestep.F90
commit 902410098c511922747bf4ff70af1f7e365024b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 13 13:14:00 2015 -0500
Add C bindings for the timestep routines
Src_1d/CastroRad_1d.f90
Src_2d/CastroRad_2d.f90
Src_3d/CastroRad_3d.f90
commit ebfe292a94a484f3ed4293f59fe866457bd87eb7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 16:50:19 2015 -0800
Add a function for computing the volume given cell-centered indices (i,j,k).
Source/Src_nd/Castro_util.F90
commit a98755b8e4f6d0576d2c23e6e8f74cab4cf58828
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 16:18:38 2015 -0800
Add a function for calculating the area of a face perpendicular to a given direction.
Source/Src_nd/Castro_util.F90
commit 1433d9b2105f8350eba14c1d7fbf82bc9e7da1ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 16:06:08 2015 -0500
Wrong index
Source/Src_nd/Castro_util.F90
commit 8ec751bb6e9eff01f8448f805f9d71ff5dd6c109
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 15:48:57 2015 -0500
Move the cross_product function to a new math_module, since sometimes we want to have it without rotation enabled.
Source/Src_nd/Make.package
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/math.F90
Source/Src_nd/rotation_sources_nd.f90
commit 8b83f85872321aa42591870c2b3fac5c843a2ab5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 12:13:57 2015 -0500
Fix some mistakes from the last commit
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/Castro_util.F90
commit 1bb70fcc5ffca913706a67c213b90a63a3100a43
Merge: 272f1df20 f02b207e9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 11:19:03 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 272f1df20f72cb0682474a3e306fd3a2e4f3ab90
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 12 11:10:46 2015 -0500
New approach for the hybrid advection -- do everything in the conservative update
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/enforce_consistent_e_nd.f90
Source/Src_nd/reset_internal_energy_nd.f90
commit f02b207e9fb300a0381c74310a1447e1a7058f93
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 21:05:17 2015 -0500
During estTimeStep and initData, we want to update in the Fortran module which level we're on.
Source/Castro.cpp
Source/Src_nd/Castro_nd.f90
commit 998af4a3483eaac4985f68b35197718250baedee
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 20:50:21 2015 -0500
Move up the set_grid_info call earlier in the setup to the level constructor; since it only runs on level 0 and that's only constructed once, this is safe.
Source/Castro.H
Source/Castro.cpp
commit 35c9d6ad8852d0151a8bfef3c4316321bae85759
Merge: 96289f1cd 02f08c02a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 17:24:28 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 4049d6a22e878fb0a41cc19e90956adc4178a482
Merge: a4b4ecca5 02f08c02a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 17:23:00 2015 -0500
Merge branch 'development' into radmerge
commit 02f08c02af0f322f12e006959091a00d4e8aba4c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 17:21:30 2015 -0500
Forgot to include the actual module file in a previous commit
Source/Src_nd/amrinfo.F90
commit bd4f1e2e8f099e4b0423ca04d1f6064fd10c42c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 17:18:52 2015 -0500
The new position function takes as arguments the (i,j,k) indices on the domain and returns a three-vector containing the spatial position in the domain of those indices. Optionally you can specify edge-centering in any of the three dimensions.
Source/Src_nd/Castro_util.F90
Source/Src_nd/Make.package
commit c33c816103129a00e972d922c1d89994d7ec3b46
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 17:17:03 2015 -0500
Send Interior and Inflow values to prob_params_module
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/prob_params.f90
commit 45e231ec97493bb596d2e95eb69af4f9b2d27d60
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 17:13:32 2015 -0500
Send domlo and domhi on each level to Fortran
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_nd.f90
commit a4b4ecca527c6c921fb1bb5aff6683984b51eb94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 16:51:10 2015 -0500
fix non-radiation compilation
Source/Src_3d/riemann_3d.F90
commit bf088c805936aa7e32575a5c9e42f4fe9ab9229c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 16:34:31 2015 -0500
fix some compilation issues with radiation
Source/Src_3d/riemann_3d.F90
commit afc2a91dacd3e25efb7d906b3026c77c199aabf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 16:33:51 2015 -0500
use the new merged Riemann solver
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit 3e0c83dd264b820321ea99c87c0b3a32b5cb2d6e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 14:18:29 2015 -0500
Create a module that stores some information about the state of the AMR simulation. At the beginning of every advance, we update this info in the module, so that if you access it from the Fortran code at any given time, it should give you the current information about what level you are on and what time it is.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Make.package
commit 8718a7726309b8baabb8bc6b270c4868883eaf95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 12:45:27 2015 -0500
F90
Source/Src_3d/Make.package
commit dbf7eb073f3e2c8525703a59669c470a41bc8e5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 12:42:21 2015 -0500
needs preprocessor
Source/Src_3d/Make.package
Source/Src_3d/riemann_3d.F90
commit d21c4ae7f01312804950d758f2b74bc218f26bb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 12:38:22 2015 -0500
use the unified version
Src_3d/Make.package
Src_3d/riemann_rad_3d.f90
commit aa43348075d53f7f79ffce6d5ccd7bf168dd5350
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 12:37:18 2015 -0500
more rad stuff
Source/Src_3d/Make.package
commit ae08c177d3970c152e02be77e6e71efa75e38642
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 11 12:36:20 2015 -0500
first cut at the radiation merge
Source/Src_3d/riemann_3d.f90
commit 96289f1cd821123f708c9011767f49cd2b504c33
Merge: 41f20bdbe 272f248cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 05:25:28 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 41f20bdbef87e4f48502b61e970820e744ac33cc
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 05:25:22 2015 -0500
Get derkineng consistent with the hybrid advection
Source/Src_nd/Derive_nd.f90
commit 79c82f88db0b15e179f027249e4c03c94700e2e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 05:25:04 2015 -0500
Fix typo -- we were updating the wrong flux
Source/Src_3d/Castro_advection_3d.f90
commit 272f248cf9f0e25cb11380161174434f55954d0f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 04:49:21 2015 -0500
Better formatting for the date and time output, and only print it on the I/O processor
Source/main.cpp
commit 58cacf4466946069ea32aa3e1b02ee681e949b92
Merge: 0ac85696c 5fbab09c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 03:26:19 2015 -0500
Merge branch 'development' into hybrid_hydro
commit 0ac85696c4c9eb96dd7e7e65f0ff9e71f7029833
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 11 03:26:09 2015 -0500
Move the pressure term into the angular momentum so that its explicit conservation property is clearer
Source/Src_3d/Castro_advection_3d.f90
commit 4ccb5c7610fda88d02d4ce5e04b74b47cd77854f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 10 18:09:53 2015 -0500
a little cleaning
Source/Src_2d/riemann_2d.F90
commit 99254b524179764f28722ffcde6a0d71d9bc04b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 10 16:00:01 2015 -0500
Forgot to calculate coordinates when calculating hybrid advection source terms
Source/Src_3d/Castro_advection_3d.f90
commit 577456f13b07957c386cf97268a3e1f7f6396940
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 10 15:55:46 2015 -0500
Forgot to fix the hybrid fluxes in the z-direction
Source/Src_3d/Castro_advection_3d.f90
commit 8235936da018a773efa38f241449469c23b4a091
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 10 12:25:35 2015 -0500
For now undo the momentum name change
Source/Castro_setup.cpp
commit 6bae19c271a866202bbd961affdcddebf33b0670
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 10 12:23:29 2015 -0500
enforce_consistent_e now calculates the momentum correctly in the hybrid advection case.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/enforce_consistent_e_nd.f90
commit 3f80de6fc3f0b1a2ac62bee80d35c48f72aed5da
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 10 02:48:33 2015 -0500
Get reset_internal_e using the new momenta
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/reset_internal_energy_nd.f90
commit c3e07d313ff184c300c66e3b0cd4adf81a8928cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 10 02:34:00 2015 -0500
Fix ugdnvx -> ugdnvy, etc.
Source/Src_3d/Castro_advection_3d.f90
commit 8e76d4ecc1f32d2ccc5fa6346828089731bebc14
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 21:07:19 2015 -0500
First attempt at doing the fluxes and source terms properly for the hybrid advection scheme
Source/Src_3d/Castro_advection_3d.f90
commit ca78c08d7276e654e9d4bf45c7af970e528cc9cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 21:06:48 2015 -0500
Calculate the velocities correctly when estimating the timestep
Source/Src_nd/EstDt_nd.f90
commit ee423442ec0253b5021de27b21d37a9d53455b31
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 21:00:39 2015 -0500
hybrid_hydro should default to 0 and not be used.
Source/_cpp_parameters
Source/castro_defaults.H
commit da971d4b2c58652ec7abb166eb4f7cb0771a26ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 20:19:22 2015 -0500
We also need to pass the edge-based rho and transverse velocities to the consup for the hybrid advection.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
commit 3d17ec0fbf6fc06a9705a792ab1da0095bd323bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 19:44:26 2015 -0500
some fixes in the translation of the radiation into a unified solver
Source/Src_1d/riemann_1d.F90
commit da5854450e4ed29d95ad50d9ba6931d63afb5c2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 19:26:21 2015 -0500
For the hybrid advection we need to pass the edge-state pressure and velocity to consup.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 5fbab09c90ba2dbfc98befc52a60feb50672a6ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 18:51:38 2015 -0500
Print out UTC time and date at the beginning and end of a run.
Source/main.cpp
commit c6ec90abb547f91a6a56099c40c6b93576921a8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 17:12:27 2015 -0500
fix some dimensioning and undeclared stuff -- note that this does
not yet work for rad hydro
Source/Src_1d/riemann_1d.F90
commit 3c558b72f70aeaf13f3b21380f598d81eda31db0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 17:00:44 2015 -0500
update to the new merged interface
Src_1d/RadHydro_1d.f90
commit db5554529eb01b3b8b0d7645baaeb198a962beff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 16:38:14 2015 -0500
update the makefile to section off stuff that is not needd for radiation
Source/Src_1d/Make.package
commit c3a521408d912d37c305098584042072a31cac99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 16:36:21 2015 -0500
no more custom riemann solver
Src_1d/Make.package
Src_1d/riemann_rad_1d.F90
commit 5d01b8d5124a1245b0981d2e15a074c30ba7bc4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 16:35:58 2015 -0500
merge in the radiation
Source/Src_1d/riemann_1d.F90
commit e2e21e24ef8443fbe4b48a945456a04ba4e0a48b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 16:35:24 2015 -0500
merge in the radiation
Src_1d/riemann_rad_1d.F90
commit 336248ad6d61e20c6b2722b9e596aefb18e2940a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 14:41:34 2015 -0500
For starters in the hybrid hydro scheme, rename the variables appropriately and update the conservative to primitive conversion.
Source/Castro_setup.cpp
Source/Src_3d/Castro_advection_3d.f90
commit 67546afe7c07b27faa8115afd3d4afbf5d9ece8b
Merge: e3b59c987 7479b5799
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 13:55:16 2015 -0500
Merge branch 'development' into hybrid_hydro
commit e8e09f00f01aa2054d7b691c07e69f7d72ebb9b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 13:54:00 2015 -0500
import coord_type
Src_2d/RadHydro_2d.f90
commit bf4d688e60c48aa48dc3c4b35eea36df3704064b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 13:37:19 2015 -0500
in the Riemann solver -- we now always add the pressure to the momentum
flux if it is in a Cartesian coordinate direction. This change updates
the conservative update and flux scaling to account for this.
Src_2d/RadHydro_2d.f90
commit 6031db760410fc487d45ecb82c849e7977a57f7f
Merge: fc862a49b 0afe3a784
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 13:28:30 2015 -0500
Merge branch 'development' into radmerge
commit fc862a49b9cdb110b03715a49aa63de3d73b6e2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 13:27:38 2015 -0500
some work on consup
Src_2d/RadHydro_2d.f90
commit 7479b57995af9e68e82e2d96d4302dd221af142c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 12:56:33 2015 -0500
Sync up the radiation hydro approach to source terms with the normal hydro, i.e. add rotation and the sponge.
Source/Castro_advance.cpp
commit 0afe3a7841c82fe250935ab1ebb4be83b8e0a961
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 12:47:30 2015 -0500
We shouldn't be adding dt * src in consup, because we're now adding that separately in Castro_advance.
Src_1d/RadHydro_1d.f90
Src_2d/RadHydro_2d.f90
Src_3d/RadHydro_3d.f90
commit fd7f6ea0e79ee05eedcdb33f37700883bd736069
Merge: ff50a185e 7e523a37b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 12:21:49 2015 -0500
Merge branch 'development' into radmerge
commit 7e523a37b8996d8cff7e40d3abd5fa7632b9637f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 11:36:26 2015 -0500
sync up with the Castro advection_util_module stuff
Src_1d/CastroRad_1d.f90
Src_1d/RadHydro_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit 319eba6168517ceee828eb846127837d54786dd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 22:05:35 2015 -0500
fix declaration
Source/Src_2d/riemann_2d.F90
commit be344424ece6dbfa0727961df8927529147907f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 21:54:50 2015 -0500
if we are doing radhydro, then we always do rad + hydro together.
Source/Castro_advance.cpp
commit ff50a185ef965ec3073dbe8c8d041265fa3f8f5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 21:54:24 2015 -0500
pass domlo/hi
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
commit 36e89b2dddf49926ff983d998cac81e0fd7a799f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 8 20:05:04 2015 -0500
Add parameters castro.react_T_max and castro.react_T_min. We only react in a zone if the temperature is between those two values. By default they are a large number, and zero, respectively, so that reactions always occur.
Networks/burner.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/_cpp_parameters
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit 6a59834affaf634872a73d199bab9ef572d05142
Merge: c1c1a29fd 9590b3122
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 19:27:33 2015 -0500
Merge branch 'development' into radmerge
commit 9590b312201f84878363f4f9f95ed84a4ca6dde8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 19:26:23 2015 -0500
split out some more routines to enable easier reuse by radiation
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_util_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_util_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_util_3d.f90
Source/Src_3d/Make.package
commit f6e231b5128de180abb3edbd3cf93843748750eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 8 19:20:20 2015 -0500
Make omegadot variables actually be a time rate of change and live up to their name.
Exec/toy_flame/Prob.cpp
Exec/toy_flame/Problem.H
Exec/toy_flame/Problem.f90
Exec/toy_flame/Problem_F.H
Exec/toy_flame/sum_integrated_quantities.cpp
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
Source/Src_nd/EstDt_burning_nd.f90
Source/Src_nd/React_nd.f90
commit c1c1a29fd0722d8a76da9c9f5321eee9adee5c6a
Merge: 229996748 96e44b3a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 19:04:52 2015 -0500
Merge branch 'development' into radmerge
commit 96e44b3a97c77ecb57bc63d01d20c331d64cb3fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 19:04:10 2015 -0500
move divu into advection_util_module
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/advection_util_3d.f90
commit 229996748874822ed3b012cc8678b69dd8404923
Merge: e8264a606 2e0c15188
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 18:51:35 2015 -0500
Merge branch 'development' into radmerge
commit e8264a60678ef661d11cb27b037ca8e1b4f2541c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 18:50:27 2015 -0500
only need these for radiation
Source/Src_2d/Make.package
commit 2e0c151883c047b6b3cb6062684e1cacb0d653f6
Merge: b10d6553b 2a9caebaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 18:49:23 2015 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b10d6553b31f0bd781a73493d3109a9561bbfc3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 18:49:02 2015 -0500
break some support routines out into their own module to
make it easier for radiation
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/advection_util_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/advection_util_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/advection_util_3d.f90
commit fb9391ec58211d8cbb92d03df43ac49c8958ca43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 18:16:16 2015 -0500
get this compiling for radiation
Source/Src_2d/riemann_2d.F90
commit f9378b4773c14aee275ca73f3e14e11e7447fecb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 17:50:15 2015 -0500
first attempt at using the merged Riemann stuff
Src_2d/Make.package
Src_2d/RadHydro_2d.f90
Src_2d/riemann_rad_2d.f90
commit 2a9caebaff22c9399920b807cd5d4f766da00b80
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 8 16:02:29 2015 -0500
Add an implementation of the small plotfile functionality in BoxLib.
Source/Castro.H
Source/Castro_io.cpp
commit 99c2d7a2104bed9d6d046be850843ad13649c52e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 16:01:27 2015 -0500
this compiles without radiation
Source/Src_2d/riemann_2d.F90
commit c5f5702c08cf3fefdae6d78336cf537940f4814b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Dec 8 11:21:51 2015 -0800
remove Gravity::getEdgeBoxArray and replace it with AmrLevel::getEdgeBoxArray
Source/Gravity.H
Source/Gravity.cpp
commit 16b1bf10973031ca7ce2fc16e435a39a1b6aa006
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 12:56:01 2015 -0500
start of merging the radiation stuff into the Riemann solver using
the preprocessor
Source/Src_2d/Make.package
Source/Src_2d/riemann_2d.F90
commit 0283fb136390ebdd1ddc2adabd34ccc8a916cde4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 8 11:44:59 2015 -0500
initialize UMY, UMZ
Exec/Sedov/Prob_1d.f90
commit c73781f9db46c0fbf00c02a9208d475a872a3f14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 20:08:12 2015 -0500
add a link to the call graph
README.md
commit aa4b35a06cc5fc01d061369e4779621a35f1e6bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 20:04:11 2015 -0500
Maestro -> Castro
ConvertCheckpoint/GNUmakefile
Util/doxygen/Doxyfile
commit 9a796b3d188aee08490ebf713b6224128871197c
Merge: c10ed2cde 9f1f66d02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 20:01:25 2015 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit c10ed2cdedfb50f061dc2af028c7a6f71441c153
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 20:01:14 2015 -0500
add Doxyfile
Util/doxygen/Doxyfile
commit 9f1f66d02a5d5d73c5024d4324243b394fcae381
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 7 19:04:49 2015 -0500
Problem post timestep hook should go before diagnostics are computed
Source/Castro.cpp
commit fdfbac3173663579d6bb8f53fddf5d0683bad825
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 7 18:54:35 2015 -0500
Add an optional hook for a problem post timestep routine.
Source/Castro.cpp
commit 005a0b9f02657c436e1700aa2a92bf44abbca9a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 18:21:40 2015 -0500
more runtime parameter docs
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 65f2b0a8e2a4e2e375479a96492918f6c7fe78e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 7 18:20:55 2015 -0500
more comments
Source/_cpp_parameters
commit ad8e601190285295625c3bd048702066863a3436
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 18:19:17 2015 -0500
more tables
UsersGuide/runtime_parameters/runtime_parameters.tex
commit d17280e2d148e9d1c95fa41c65a051b52b32c13b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 18:17:39 2015 -0500
more parameters
Source/Castro.H
Source/Castro.cpp
Source/_cpp_parameters
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
commit ac27d06093875170fa65db3c68b799fd66ab0417
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 17:50:02 2015 -0500
more docs
Source/_cpp_parameters
commit b3e82ad7a2317db96ce7325501c6dd7592eb78cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 17:49:52 2015 -0500
more runtime parameters
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 34b10e7b8ed30f79db050d949777c0129ed5a0a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 17:25:56 2015 -0500
more doc
Source/_cpp_parameters
commit 366878c5fb8e69541986f183ed816168f6105726
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 15:02:52 2015 -0500
Add some comments and documentation for rotation parameters
Source/Src_nd/rotation_sources_nd.f90
Source/_cpp_parameters
UsersGuide/Rotation/CastroRotation.tex
commit 630b0f514b9533cb689ad9ccac219b8aa40e4a77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 13:22:40 2015 -0500
more runtime parameter doc
UsersGuide/GNUmakefile
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 6eb21dcf762ffe032d471e607ac2ee4e552fd02d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 13:21:58 2015 -0500
more doc
Source/_cpp_parameters
commit 26206f9da0791d5b7539fd7baf6d37f1f6fda0be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 12:29:38 2015 -0500
style
Source/Src_nd/EstDt_burning_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit e2fbd16f95d3eb08b98e0d58f59643d62572e89e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 12:29:21 2015 -0500
fix latexing
Source/_cpp_parameters
commit e562dc4e89e2d403d8c6f1156d5b5bf0832d94c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 12:07:49 2015 -0500
automagically generated runtime parameter documentation
UsersGuide/CastroUserGuide.tex
UsersGuide/runtime_parameters/rp.py
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 73c32600053d41920647be3da997ea07047b7a03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 11:45:12 2015 -0500
update parameters
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit 0bfcfa654b389016a43dfbe1fdcff7eecab9dfd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 11:44:32 2015 -0500
deterministic is no longer used
Source/Src_3d/Gravity_3d.f90
commit a8df1029efc1fe464af9f59adc228a42f1024a73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 11:43:31 2015 -0500
some docing and put them into categories
Source/_cpp_parameters
commit 946dc717e765751986fb27043987fa717c8bf6c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 10:55:10 2015 -0500
turn on plotfiles
Rad2Tshock/inputs.M2.test
commit b82b81177858ad30d1e77660dc03f2c88a6cb56f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 10:26:58 2015 -0500
add a test suite version
Rad2Tshock/inputs.M2.test
commit 72b259193341620414996288168ea1e4a44550c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 2 13:14:03 2015 -0500
need plotfiles for reg tests
RadThermalWave/inputs.1d.test
commit 4e7e7e4e7dceaddf125785dcd4433671417688e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 2 12:31:58 2015 -0500
for the test suite
RadThermalWave/inputs.1d.test
RadThermalWave/inputs.2d.test
RadThermalWave/inputs.3d.test
commit acecd6f16976da030f1496c22b3f1bac70059cca
Merge: 430644e9c 20960f230
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 2 10:26:02 2015 -0500
Merge branch 'development' into HLLC
commit 20960f2306d99f2ce586eaf97fba5be8e3d6086e
Merge: d01310817 ca800e4a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 2 05:38:48 2015 -0500
Merge branch 'development' into runparams
commit d01310817572ca5cd3ce46d5df78f111c9b48888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 1 20:28:54 2015 -0500
forgot to rerun the param script
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
Source/castro_call_set_meth.H
Source/castro_set_meth.H
commit 7d6bcbf4de7acde4a872bd9e58b9c0259f6515b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 1 20:12:45 2015 -0500
burning_timestep_factor is needed in Fortran
Source/_cpp_parameters
commit ca800e4a52c006e22cbab0044ba6e596d947ad46
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 30 12:25:20 2015 -0500
The implicit rotation update for rot_source_type == 4 is now dimension agnostic with respect to the rotation axis; that is, it will handle correctly the case where omega is not parallel to a coordinate axis.
Source/Src_nd/rotation_sources_nd.f90
commit 93bd3aa8098e50a1ad3e47d64ad268cd5df724fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 19:19:24 2015 -0500
new files
Source/Src_nd/meth_params.f90
Source/Src_nd/set_castro_params.f90
commit d5f84817f06a8b93be83c21cbb0d42bde9e77153
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 18:58:09 2015 -0500
new runtime parameter includes
Source/castro_call_set_meth.H
Source/castro_defaults.H
Source/castro_params.H
Source/castro_queries.H
Source/castro_set_meth.H
commit a418c8cd6b48020a66cdd9ee9b4f4f159aeb9d99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 18:57:34 2015 -0500
deal with runtime parameters that are needed in Fortran but
also have ifdefs
Source/Castro_setup.cpp
Source/Make.package
Source/Src_nd/Make.package
Source/mk_params.sh
Source/parse_castro_params.py
commit eb23e9558d63995b45eb725ce0209e63be75ad65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 16:43:16 2015 -0500
this compiles now, but I am not handling the special case of parameters
that are ifdef'ed and how they interact with Fortran -- in particular,
the rotation stuff
Source/Castro.H
Source/Make.package
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Make.package
Source/_cpp_parameters
Source/parse_castro_params.py
commit 7e3cee445057eadd3bcb9c2cb780694207715c2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 14:35:58 2015 -0500
more progress -- almost have all the Fortran written
Source/Src_nd/Castro_nd.f90
Source/Src_nd/castro_meth_params.template
Source/Src_nd/meth_params.template
Source/parse_castro_params.py
commit cb51e113c0859563220abc1d4efa093f2abb3872
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 14:35:33 2015 -0500
deterministic also changes type from C++ to Fortran
Source/_cpp_parameters
commit d5b24a4f6d91fbfede27c7a8ef488eaf3f862202
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 13:02:04 2015 -0500
add template inputs
Source/parse_castro_params.py
commit eacf08af4b7b42db971f50d8aed541cf72ed45b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 12:32:00 2015 -0500
rename
Source/Src_nd/castro_meth_params.template
commit 14fcda6b3e3cdf9dec98f6eecd742258c8ecfbb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 12:21:59 2015 -0500
some parameters have different data types in Fortran than in C++
Source/parse_castro_params.py
commit cb3a2f18dc0a1b4abe4b6f7caae02954bb1f5722
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 12:16:49 2015 -0500
more progress
Source/Src_nd/meth_params.f90
Source/Src_nd/meth_params.template
Source/_cpp_parameters
Source/parse_castro_params.py
commit f0e9c8db92899ba618e8814107bf235255c97dd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 11:00:29 2015 -0500
add the cpp call + fix the in_fortran parsing
Source/parse_castro_params.py
commit 79ffc529b7da36fca5c58163a8dbc9a740c4b9c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 10:45:05 2015 -0500
get the function prototype working
Source/Castro_F.H
Source/Castro_setup.cpp
Source/parse_castro_params.py
commit ab893d266eb3e0a4aa6daae11b871effaf7d774e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 28 09:49:23 2015 -0500
more work on stripping out the old runtime parameter stuff
Source/Castro.H
Source/Castro.cpp
Source/_cpp_parameters
commit 3f31b611f3366e910c3c8320b64a046f795b6d36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 21:39:20 2015 -0500
strip out the stuff that will be automagically set
Source/Src_nd/Castro_nd.f90
Source/_cpp_parameters
Source/castro_meth_params.template
commit 61196caa62a588c18f2b083bf60e3cc4fa0264f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 20:51:35 2015 -0500
more progress -- list which parameters are needed in Fortran
Source/_cpp_parameters
Source/parse_castro_params.py
commit 626da4d72f8737c414a72a310e7189b758f521b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 20:12:23 2015 -0500
a bit more progress -- we can parse it and write out the Castro.cpp
code, handling special ifdefs and different default for DEBUG and
normal compilation
Source/Castro.cpp
Source/_cpp_parameters
Source/parse_castro_params.py
commit 921c2ef4195c6c0ced1ee0b8fad506a6f27f9b0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 18:26:49 2015 -0500
a little more
Source/TODO.RUNPARAMS
commit 4eb96aaf55969c36a697fcb7a8b931282339058b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 18:26:06 2015 -0500
a plan
Source/TODO.RUNPARAMS
commit 5bc9b943d94312fe00bc7292aba41418360b50e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 17:59:22 2015 -0500
start of a new method of defining runtime parameters, modeled off
of what we do in Maestro
Source/_cpp_parameters
commit 970ac8c45eb2883bc78f62d3b13f8d3498b947a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 27 11:55:06 2015 -0500
time-based plotfiles
Exec/convective_flame/inputs.2d.test
commit 430644e9c11178a0dfd471c798df0fc2130179ed
Merge: 4a7ca7681 806b5c927
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 26 13:15:45 2015 -0500
Merge branch 'development' into HLLC
commit 806b5c927e8116bd780bdff60164afef29acbf62
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 21:13:58 2015 -0500
Cut down on redundant code by writing a function that adds a force term to the sources array. Use it on gravity and rotation.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 4a7ca768131ead96edfed4a1737277ccb12a3421
Merge: c2efa982d ae4a4cf51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 25 19:49:58 2015 -0500
Merge branch 'HLLC' of ssh://github.com/BoxLib-Codes/Castro into HLLC
commit ae4a4cf516615108e352568e11437938e621390f
Merge: 29f7364cf d8d521774
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 19:48:31 2015 -0500
Merge branch 'development' into HLLC
Conflicts:
Source/Src_2d/Castro_advection_2d.f90
commit c2efa982d9c4e97eaab39e345bef122188ae77c0
Merge: 29f7364cf d8d521774
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 25 19:48:09 2015 -0500
Merge branch 'development' into HLLC
commit d8d52177404ebb8ca6877e9521dc9c1677769319
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 19:29:56 2015 -0500
For the source term predictor, we need to put the new-time sources in conservative form before we add them to dSdt. We were already doing this correctly for the old-time sources.
Source/Castro_advance.cpp
commit 00b4ae5680c925218a24000c3e59ea0f0fa9e20a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 14:44:39 2015 -0500
Need to be more careful with ghost zones for the source term arrays
Source/Castro_advance.cpp
commit a9bd66e4f7d2d8b41f02d982d3d5eb1a14eee624
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 13:42:53 2015 -0500
Do the same as the last update, now for rotation.
Source/Src_nd/rotation_sources_nd.f90
commit ba26ab9c3cf42395014fab2e4af0ae31e7dae54a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 13:29:25 2015 -0500
For grav_source_type == 4, we no longer explicitly construct the density change, using the fluxes directly instead. The former approach looks slightly cleaner, but doesn't work out well for non-uniform cell volumes, like we have in spherical coordinates.
Source/Src_nd/gravity_sources_nd.f90
commit 47321122f7bbf82e19eaca97a34c61a6c38f204e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 13:26:55 2015 -0500
Sync up the hydro flux diagnostics in 1D and 2D with how they are in 3D.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
commit ce7895bd1b36377e1c2569b625d060fce7c3af1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 12:18:07 2015 -0500
Don't print out EOS warnings if we're not the IO processor
EOS/eos.f90
commit 319ba4efa74f9d370f5dd2783e3aab141c1bfea8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 25 10:59:42 2015 -0500
Only print small_dens/small_temp warning on the ioprocessor.
Source/Src_nd/Castro_nd.f90
commit 6faa3dc3321e7d5f7220d3f255c731cac72ae444
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 24 21:21:46 2015 -0800
update the call to uflaten in 3D
Src_3d/RadHydro_3d.f90
commit bb15e4f990a0d8f4124fdf9d187c179e4892507d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 24 21:13:56 2015 -0800
update the call to uflaten
Src_1d/RadHydro_1d.f90
Src_2d/RadHydro_2d.f90
commit e387ed83c0185989e9b40cb16320d776ae6ecaec
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 24 21:07:19 2015 -0500
Be slightly more careful with 1D indexing of phi
Source/Src_1d/Gravity_1d.f90
commit 87b3aa6c62533aaa20a7681d7f11b53554622dfe
Merge: d4c787131 62fe82cd6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 24 19:39:48 2015 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit d4c7871319d3652aea8e55b5d30bd7de786c16aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 24 19:39:45 2015 -0500
When using gravity, print out total energy == -0.5 * int(rho*phi) + int(rho*E) in the global sums.
Source/sum_integrated_quantities.cpp
commit 57460e5cccce299f73e525c0edf3dc8c8a91c249
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 24 19:39:17 2015 -0500
In fixing the Poisson gravity boundary value problem for grav_source_type == 4, we were doing it on the boundaries of all boxes, but we should be doing it only on the domain boundaries.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit 29f7364cf63d90aefdeac9254a506882c493e7ae
Merge: 2bee38599 62fe82cd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 24 17:03:44 2015 -0500
Merge branch 'development' into HLLC
commit 62fe82cd6ff44b95faba35b8c7c33627e4f2df03
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 24 11:23:18 2015 -0800
use the new AmrLevel::getEdgeBoxArray
Source/Castro.H
Source/Castro.cpp
commit 82cd2bfdb605123ff15dce719329d9d975ee7b26
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 23 18:08:35 2015 -0800
added explicit virtual
Source/Castro.H
commit 1054d962afd19a52594ea8f42c4f1bc0ba34b51e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 23 16:40:04 2015 -0800
Gravity and Diffusion do not need to have virtrual destructor
Source/Diffusion.H
Source/Gravity.H
commit 57aedd803bd698e788b90bc0574501a856a0b9c7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 23 16:38:54 2015 -0800
added override to virtual functions to catch mismatch bugs at compile time
Source/Castro.H
commit 2bee385995168c30ce8c420c68adf938a24067ef
Merge: f31659243 f5119452d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 22 21:12:01 2015 -0500
Merge branch 'development' into HLLC
commit f5119452d401136eaa35d21b0cb2dcfd09a5ba99
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 22 19:53:43 2015 -0500
Make the maximum y_e just slightly more than 1.0 to avoid possible roundoff issues in comparison operations.
EOS/eos_data.f90
commit f31659243930f9ccaecde2d5b29e4643058a4c2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 22 19:01:40 2015 -0500
a little cleaning
Source/Src_1d/riemann_1d.f90
commit dae2f076dca58a67df2066430f22b5ee2dd2bf55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 22 12:06:48 2015 -0500
move wsqge into riemann_util_module
Source/Src_1d/riemann_1d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/riemann_util.f90
commit f52ea044f134abef9c2742d2e48957e4faf5f224
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 20:27:04 2015 -0500
fix a few axisymmetric cases -- our new convention is actually that
for the z-direction in axisymmetry, we still include the p term
in the momentum, since the grad and divergence look the same,
but for the r-direction in axisymmetry, we do not, and handle that
specially in consup
Source/Src_2d/riemann_2d.f90
Source/Src_nd/riemann_util.f90
commit 407921417b306c705e67a6e6e8aa7b6d05b2176e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 18:53:11 2015 -0500
abort if we do hybrid_riemann is used with non-Cartesian -- this really
doesn't work correctly because of the pressure term in the
momentum flux
Source/Castro.cpp
commit 3d06b1328526ba2ef952b7be5b3d9f632e02b87d
Merge: 4b26e45f3 723b69ae9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 18:15:17 2015 -0500
Merge branch 'HLLC' of ssh://github.com/BoxLib-Codes/Castro into HLLC
commit 4b26e45f368a5f78649f1d909491d850da65c934
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 18:15:08 2015 -0500
turn on hybrid_riemann
Exec/oddeven/inputs.2d
commit 47cddc413e54f07376f9fa31b2fd66b743438b7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 18:13:18 2015 -0500
change how we treat the pressure term in the momentum flux. Previously,
we simply left this out and relieved on consup to difference grad p for us.
Now, in Cartesian geometry, we include the p term in the momentum flux.
This is simpler, and it makes the HLL* solvers work as intended.
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_2d/trans_2d.f90
Source/Src_nd/riemann_util.f90
commit 723b69ae94a8599acd2cb7e79c42b80a07b66448
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 13:14:14 2015 -0500
there really is no reason we cannot use HLLC in hybrid_riemann mode
Source/Castro.cpp
commit 182f98721896fd1ab32736bb6fc0e0618e53e67b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 21:17:59 2015 -0500
use_colglaz is deprecated -- switch these to riemann_solver
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/Sod/inputs-slowshock-x
Exec/Sod/inputs-test1-helm
Exec/Sod/inputs-test2-helm
Exec/Sod/inputs-test3-helm
Exec/StarGrav/inputs_2d
Exec/StarGrav/inputs_2d.test
Exec/convective_flame/inputs.2d.test
Exec/double_bubble/inputs_2d
Exec/double_bubble/inputs_2d.single
Exec/double_bubble/inputs_2d.single.equal
Exec/gresho_vortex/inputs.2d
Exec/test_convect/inputs_2d
commit 390d055688552e3bb35e1460df83001a67b9ae21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 21:13:33 2015 -0500
add a bit about the HLLC solver
UsersGuide/Equations/Equations.tex
commit 3e9a610fa8f50f8db82164e456ae63fb2f597bd0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 20:34:20 2015 -0500
rotational_period_dot --> rotational_dPdt
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
commit c0e312f6ab408e9db5febb2f5185b2e0c1f6b79d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 20:30:16 2015 -0500
remove xmin et al.
Exec/oddeven/probdata.f90
commit 35cd96307e7170108a503bd10d3c41dee91d9e2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 20:09:36 2015 -0500
rename probin
Exec/oddeven/inputs.2d
Exec/oddeven/inputs.3d
Exec/oddeven/probin
commit c9ee12857c9e0626eb5a3e8276356df007e75e56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 20:08:20 2015 -0500
update the inputs to use the HLLC solver
Exec/oddeven/inputs.3d
commit 0976f244ec3edf9ee3e3e7bd53b150402de5f4f8
Merge: ed816b03f 141218a32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 20:06:29 2015 -0500
Merge branch 'development' into HLLC
commit 141218a32c8de74d1639ece866fa333c47ae4f18
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 16:16:28 2015 -0500
Fix another bug in enforce_minimum_density in the case of no nearby zones having rho > small_dens.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit d1b215ad8f099cfd5ef477a4e6131b6bd64e576e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 16:15:39 2015 -0500
Accidentally committed a file that wasn't ready yet
Source/Src_nd/Castro_advection_nd.f90
commit ed816b03fb4a3d16cae154983c2011115096e0be
Merge: 910a7b8fe bcc4e4324
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 15:07:44 2015 -0500
Merge branch 'development' into HLLC
commit bcc4e4324d7e415703e930136dcee0c3dc38bff5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 14:56:12 2015 -0500
Fix indexing problem in density reset code
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/Castro_advection_nd.f90
commit 910a7b8fe8f06a1d192f71614e459692541d39c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 13:55:32 2015 -0500
a 3-d version of the odd-even problem -- this looks great with the
new HLLC solver, and awful with the default solvers
Exec/oddeven/Prob_2d.f90
Exec/oddeven/Prob_3d.f90
Exec/oddeven/inputs.3d
commit 7ece3b356340c4b2abe62399f0d0bec48c4cba3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 11:56:43 2015 -0500
Be a little more careful with a warning output
Source/Gravity.cpp
commit c5cc250fb0d39b76b846f6dc8a171868a594b498
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 11:46:01 2015 -0500
this seems to work now for 3-d HLLC.
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/riemann_util.f90
commit e858d511be2cea81ae4dfbcad2fc23b85de3be31
Merge: 6b5080cea 01ebdc24a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 20 10:06:19 2015 -0500
Merge branch 'development' into HLLC
commit 01ebdc24a91d6fb3e6340ae8af8d9cbe54f52ce5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 20 09:54:54 2015 -0500
Zero out 1D gravity and phi so that they at least have valid data.
Source/Gravity.cpp
commit 9d9b45df2ec2bcba4a6c7af14692a68074079777
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 17:24:37 2015 -0500
More accurate potential calculation for a thick spherical shell of constant density
Source/Src_1d/Gravity_1d.f90
commit ef75ec83edf2348ac564063c09278c4e75521471
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 15:16:08 2015 -0500
When using gravity.get_g_from_phi in 1D, calculate potential on cell edges first, and then average to cell centers later, to avoid the self-contribution problem.
Source/Src_1d/Gravity_1d.f90
commit 6902c44ebcf17bcb989aadb21e0fc78550cb3b8d
Merge: 74f6723ed ba2af2d36
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 14:03:36 2015 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit 74f6723edfc09080773c98d0e63d15aebfe8e715
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 14:03:30 2015 -0500
Integrate rho*phi if we're using gravity.
Source/sum_integrated_quantities.cpp
commit 8a697df0d017f0a6a5b287ce72f62f67cd649880
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 13:58:05 2015 -0500
Add a parameter castro.get_g_from_phi. If set to 1, then its effect is to calculate phi first and then derive g from it by taking the appropriate gradient. This is only active for MonopoleGrav at present. If we're using this, then grav_source_type .eq. 4 will use phi instead of g.
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Gravity_1d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/meth_params.f90
commit ba2af2d36e3b52409078bc94f86c2ae24c9bab20
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Nov 19 09:46:50 2015 -0800
minor changes: the temp mf doesn't need to have 3 components and Divide is replaced faster copy and multiply
Source/Castro_advance.cpp
commit 6b5080cea6b4c873c2bfc7cc38f622ffe966c76d
Merge: 9c0288146 2ce71da78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 19 09:34:24 2015 -0500
Merge branch 'development' into HLLC
commit 2ce71da7808c959950b047d094eeb56608ac5ced
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 08:45:04 2015 -0500
Remove some debugging output
Source/Castro_advance.cpp
commit 5db481b629a01f32d458aa4c5271c2f602fb2075
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 22:05:57 2015 -0500
Only call time_center_source_terms and compute_temp if we are doing add_ext_src. This matches the original code behavior, before recent changes.
Source/Castro_advance.cpp
commit c8553ece366e4350d31e1fa099e60d8cc6c5e0be
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 15:50:23 2015 -0500
The sponge parameter update isn't in a parallel region anymore, so r_old_s doesn't need to be threadprivate.
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/probdata.f90
commit b326f98cb23dca59dbb4b1e950a14ea805e7ac96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 16 09:29:54 2015 -0500
new test suite
Exec/toy_flame/inputs.1d.testsuite
commit c0e74ec744d4ef9b828dc21f3e80aaf1530e481b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 16 07:27:38 2015 -0500
Fix array index in flattening
Source/Src_nd/flatten_nd.f90
commit 9c02881464955d143ff9619a3d84ccb6763477bc
Merge: d268709b9 2b7134182
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 16:42:27 2015 -0500
Merge branch 'development' into HLLC
commit 2b7134182906233dad1dc2bf0426d27c379c3f1b
Merge: fc8a6da60 34aca6748
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 16:23:38 2015 -0500
Merge branch 'development' into source_terms
commit 34aca6748974b2bdf49122a7da9f12f17b0b0671
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 13:41:27 2015 -0500
explicitly set the gamma in these to be 1.4 -- this is what the
exact solutions in Verification/ were computed for
Exec/Sod/probin-sod-x
Exec/Sod/probin-sod-y
Exec/Sod/probin-sod-z
Exec/Sod/probin-test1-helm
Exec/Sod/probin-test2-helm
Exec/Sod/probin-test2-x
Exec/Sod/probin-test2-y
Exec/Sod/probin-test2-z
Exec/Sod/probin-test3-helm
Exec/Sod/probin-test3-x
Exec/Sod/probin-test3-y
Exec/Sod/probin-test3-z
commit d268709b90940f8b7ff8f150c74167c236641ed7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 12:45:30 2015 -0500
forgot to actually return the fluxes -- you know, the main thing
that a Riemann solver should accomplish...
Source/Src_3d/riemann_3d.f90
commit fc8a6da60e2c10155674d403286adb95b7725712
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 15 12:10:21 2015 -0500
Forgot to deallocate some arrays
Source/Src_nd/gravity_sources_nd.f90
commit c9b94dbcaf94f33d5bd1a76728eb766837e3a516
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 12:08:21 2015 -0500
more work on 3-d, some generalizations. 3-d doesn't seem
to work just yet...
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/riemann_util.f90
commit ff3575161b7e410ba0227153aec17b45b290a79b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 10:31:48 2015 -0500
deal with both riemann_solver and use_colglaz
Source/Castro.cpp
commit 21a9c03bb574eccf0726f61f2d8dedef982332df
Merge: be49e5fb2 795873401
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 15 09:22:58 2015 -0500
Merge branch 'source_terms' into HLLC
commit 7958734014757144f45c3e431c0cef25170b3444
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 22:58:39 2015 -0500
Dimension agnostic flattening
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/flatten_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/flatten_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/flatten_nd.f90
commit 254ac5df9be3a73bb1b39ac2da14b75b6f892021
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 22:40:01 2015 -0500
the EOS here needs to be set to gamma_law_general, not gamma_law. We need the
specific heats to be defined for this to work. This means that we need
the Microphysics directory
Exec/diffusion_test/GNUmakefile
commit f6c157ee532a9febbadc46d5e1dc9b3a2ca8f8b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 22:28:00 2015 -0500
wrap the viscous and species diffusion stuff in a dimensional chekc
Source/Castro_advance.cpp
commit be49e5fb2383e577089097626170da75b549259d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 21:44:01 2015 -0500
fix compilation
Source/Src_3d/riemann_3d.f90
commit ec54b0d6b486d18976f82488b09e5faacaa6d640
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Nov 14 18:14:54 2015 -0800
Pass the coordinate system to compute_div_tau_u -- for now it only
works for 1-d spherical but we can generalize it later.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/visc_coeff_nd.f90
commit 8c3563ed8890061b519b9a44b427e542a3033e27
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Nov 14 18:04:45 2015 -0800
We now have the viscous contribution to the total energy.
NOTE THIS ONLY WORKS FOR 1-D.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Src_nd/visc_coeff_nd.f90
commit 4d856f7e12b7a9b7f524e1bb08329d28cef89561
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 20:07:55 2015 -0500
generalize the HLL() solver
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/riemann_util.f90
commit 86fd4e88dc6a9b6daa2966951d9825824adef19d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 19:30:44 2015 -0500
hook in riemann_util
Source/Src_nd/Make.package
Source/Src_nd/riemann_util.f90
commit 52f8b7e9bf6e679b9b3273b0f1a23fcaa37aef38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 19:09:20 2015 -0500
new riemann_util module
Source/Src_2d/riemann_2d.f90
Source/Src_nd/riemann_util.f90
commit 5d304e9a3c21107b9b26d97e5b82a58050f912f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 18:52:04 2015 -0500
strip out all of the redundant BC test code into a separate function
Source/Src_2d/riemann_2d.f90
commit 480403b0c9659ef9061da5f0d7eb09368badc255
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Nov 14 15:47:23 2015 -0800
We add the capability to do viscous terms IN 1-D ONLY!!
This now includes all of the components of the viscous term in the momentum equation
but does not yet include the contribution of the viscous term to the total energy equation.
Conductivity/constant/Make.package
Conductivity/constant/_parameters
Conductivity/constant/constant_viscosity.f90
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_diffusion.cpp
Source/Diffusion.H
Source/Diffusion.cpp
Source/Gravity_F.H
Source/Src_1d/MGutils_1d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_nd/Make.package
Source/Src_nd/species_diff_coeff_nd.f90
Source/Src_nd/visc_coeff_nd.f90
commit 65087cc05d9639140e024a3a5db2fdad9428783d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 16:25:13 2015 -0500
This seems to work correctly now -- I was doing q(QU)*2 instead
of q(QU)**2
Source/Src_2d/riemann_2d.f90
commit d2d9fed4a82d147b84364648a9005268c76c8946
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Nov 14 13:03:59 2015 -0800
We no longer set diffusion.conductivity in the inputs file.
Exec/diffusion_test/inputs.2d
commit 7d52a7022c1a0a530862d3510c84331dcaa7d397
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Nov 14 12:59:26 2015 -0800
Fix the Exec/diffusion_test/GNUmakefile to point to the right EOS stuff.
Exec/diffusion_test/GNUmakefile
commit 16071a9c330f3fa67d2629285749755c6d991ad9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 14:18:19 2015 -0500
some more tweaking -- this runs but doesn't look right yet...
Source/Src_2d/riemann_2d.f90
commit b93ab1c21983a3bd97a89aed00e7007ff7f93e5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 13:29:00 2015 -0500
this compiles
Source/Src_2d/riemann_2d.f90
commit b768d9ad4bb9b6ce0ec6aa13403f15ec7f416f93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 11:17:19 2015 -0500
more progress
Source/Src_2d/riemann_2d.f90
commit ecda0d957fed31bc747c64e6699ef5a636f0f7ad
Merge: a88760007 4a7fadd4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 14 09:33:36 2015 -0500
Merge branch 'source_terms' into HLLC
commit 4a7fadd4b0cb77ce4c2a95bdc33ecc19e1ca3ea3
Merge: a7da3f812 b6b8eed57
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 22:27:24 2015 -0500
Merge branch 'development' into source_terms
commit b6b8eed57185f8a6756fa4f53106c7f4d216bc1d
Merge: 755a5d732 90ad46e2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 21:46:16 2015 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 755a5d73235ac1f4cf4d8a23358411be60d1b214
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 21:44:52 2015 -0500
coefy -> coefz in the z-interface average
Source/Src_nd/thermal_conductivity_nd.f90
commit 90ad46e2bae88ed94750570c4adae9dc4557f143
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 13 18:42:54 2015 -0800
Separate out into two files the computation of thermal diffusion coefficient and species diffusion coefficient.
Source/Src_nd/Make.package
Source/Src_nd/species_diff_coeff_nd.f90
Source/Src_nd/thermal_conductivity_nd.f90
commit a88760007d228082b622f92a94a460be179f6b47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 21:41:58 2015 -0500
fix rhoetot after the merge from source_terms
Source/Src_2d/riemann_2d.f90
commit 7fee030427a823cedcf4212cb6bb67882658f2c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 13 18:38:16 2015 -0800
Added the capability for species diffusion. For now it assumes the same constant
diffusion coefficient for all species, which if the temp coeff is lambda, the
species diff coefficient is lambda / cp.
To use species diffusion you must set USE_DIFFUSION in the GNUmakefile and
castro.diffuse_spec = 1 in the inputs file.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Src_nd/thermal_conductivity_nd.f90
commit 38ff15b44d09d0dfc22926f2e543234a49e09547
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 21:13:16 2015 -0500
a little more progress
Source/Src_2d/riemann_2d.f90
commit e6884b9d6caf31781fcdee06b410d4a03b77703f
Merge: f4caed042 a7da3f812
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 15:25:46 2015 -0500
Merge branch 'source_terms' into HLLC
commit a7da3f8126d45cc74dd766e3c40cf5bca712ecca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 15:18:57 2015 -0500
for completeness, also include the y- and z-velocity in the total
energy in 1-d, just in case, for some reason, someone, someday
decides to advect something with them.
Source/Src_1d/riemann_1d.f90
Source/Src_2d/riemann_2d.f90
commit ed37845a64e096ded85fc6b42ee9d7e1abf79cee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 15:03:19 2015 -0500
actually initialize v2l/r now
Source/Src_2d/riemann_2d.f90
commit 7706904cc5f68ea5831968b83faa823b51f6ac7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 15:00:21 2015 -0500
d'oh -- wl is the wave speed, so I need to use v2l/r for the z-velocity
Source/Src_2d/riemann_2d.f90
commit d901b31b7cefc1bce75d2d33e94802a5beccbcca
Merge: 3da37335c 079aa9e36
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 14:51:51 2015 -0500
Merge branch 'source_terms' of ssh://github.com/BoxLib-Codes/Castro into source_terms
commit 3da37335c078726854e7c210fc414548b22b7841
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 14:51:22 2015 -0500
fix the total energy -- it needs to include the component coming out
of the computational domain (z-velcoity) that is just advected
Source/Src_2d/riemann_2d.f90
commit 079aa9e3677f6f9499b31c8a6a657029894bfff0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 14:40:44 2015 -0500
Fix incorrect number of array components
Source/Src_3d/trace_ppm_3d.f90
commit f4caed0424c8ae7f377bf2f3297609a749e1e807
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 14:39:30 2015 -0500
some progress on HLLC -- stashing it for now
Source/Src_2d/riemann_2d.f90
commit 8f70c597a012e701694febf720cdc075e2715713
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 11:15:31 2015 -0500
Some fixes in 2D for the last commit
Src_2d/trace_ppm_rad_2d.f90
commit 33117b2b0769f47c715cbe32da271e6d650ba393
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 11:11:28 2015 -0500
Get rid of integer parameters and use indexing via state variables
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/trace_ppm_3d.f90
commit d5e979035aac63c01bd4f975916a5f2bf791117c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 10:52:14 2015 -0500
Radiation hydro now uses the generic source term array. One functional change is that it now also uses the gsrc routine which permits it to use the various source term options.
Source/Castro_F.H
Source/Castro_advance.cpp
commit e6ae8539cfcf96e25ab216c00b85bbcc855f9c20
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 10:51:14 2015 -0500
Update hydro code to account for change in how Castro is dealing with source terms
Src_1d/CastroRad_1d.f90
Src_1d/RadHydro_1d.f90
Src_1d/trace_ppm_rad_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/RadHydro_2d.f90
Src_2d/trace_ppm_rad_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/RadHydro_3d.f90
commit b2e0a027385863cbf8be283ec6ebfcaca5711d5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 13 10:20:02 2015 -0500
Fix indexing issue for PPM source term tracing
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 21c8a67c835bd367dfd72ba1cb9414afbf9c95ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 09:58:52 2015 -0500
deprecate use_colglaz
Source/Castro.cpp
commit 777f2dff6879f38763c7135bd2fc9da5be12729d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 13 09:52:42 2015 -0500
add a new riemann_solver parameter that will take over for use_colglaz
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_1d/riemann_1d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit e792e28b1f5a4bdd58cc4e443a5b2d6fb56ae004
Merge: f2de8111e 1e07a4e8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 12 16:28:04 2015 -0500
Merge branch 'development' into source_terms
commit 1e07a4e8a74d24290cd64db67afd36b2afc71f22
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 12 16:27:50 2015 -0500
Initialize an array to zero; leaving it uninitialized was causing problems since there is a step where we multiply the whole array.
Source/Src_3d/Gravity_3d.f90
commit f2de8111e1a07de8c7e4067369ccf31c2922b5d3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 12 13:20:23 2015 -0500
Update local copy of trace_ppm to account for source term changes.
Exec/Sod_stellar/trace_ppm_2d.f90
commit 64ef9f095a8be5105f675bd508959997257536d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 20:05:40 2015 -0500
disable the sponge for now -- it causes bad things to happen to the
temperature and Mach number above the atmosphere
Exec/convective_flame/inputs.2d.test
commit 87bd38e87dbbfb9e8911aabe051b371ec6541776
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 19:23:53 2015 -0500
store the ambient state for the upper boundary condition (2-d only at the moment)
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/hydrostatic_bc_2d.f90
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probdata.f90
commit 7957a14052aa98d0d5d4cc6d02b516edf66013b5
Merge: 76374bd7c 2461e75c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 16:23:49 2015 -0500
Merge branch 'source_terms' of github.com:BoxLib-Codes/Castro into source_terms
commit 76374bd7c3881e5439314ea5160b8f01e68dd9ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 16:23:28 2015 -0500
Don't create a new multifab multiple times
Source/Castro_advance.cpp
commit 2461e75c233ac959f6250086fc6f231b694a429b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 16:10:27 2015 -0500
more domain:
Exec/convective_flame/inputs.2d.test
commit d7a2a4ce89022712443bd57c55b1c4618e906358
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 16:06:12 2015 -0500
Warn the user if they are not setting small_temp or small_dens in the inputs file.
Source/Src_nd/Castro_nd.f90
commit f5452f101733edb447cf626cc74a6df08882aa47
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 15:51:17 2015 -0500
enable some more diagnostics if we are in debug mode
Source/Castro.cpp
commit a19de970383671799d400f54902dee9c2bb0f032
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 15:42:09 2015 -0500
explicitly set small density and tmeperature
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/inputs.3d.test
commit fb02cdcdf282697fb58e83d8a628f622b9a40b93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 14:49:21 2015 -0500
coefy -> coefz
Source/Src_nd/thermal_conductivity_nd.f90
commit 308676b0cba3b5656337e17a2382e3ba4875620b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 14:33:14 2015 -0500
sync up the inputs
Exec/convective_flame/inputs.3d.test
commit bac46e07cc9308995f8a109a8f60b128f14698bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 12:52:01 2015 -0500
this compiles. Hasn't been tested
Exec/convective_flame/Prob_3d.f90
Exec/convective_flame/bc_fill_3d.f90
Exec/convective_flame/hydrostatic_bc_3d.f90
commit 97d61d804ed21a8b0e341e86c94e9dfd12faf497
Merge: c0e7f0249 7558ea940
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 12:24:10 2015 -0500
Merge branch 'source_terms' of ssh://github.com/BoxLib-Codes/Castro into source_terms
commit c0e7f0249af553f8225e429ea14dda911e6424ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 10 12:23:55 2015 -0500
get the 3-d BCs implemented -- not tested yet
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/bc_fill_3d.f90
Exec/convective_flame/hydrostatic_bc_2d.f90
Exec/convective_flame/hydrostatic_bc_3d.f90
commit 7558ea940392ae3d92716033bc19fa3fb2f7182c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 12:10:09 2015 -0500
Remove a redundant operation
Source/Gravity.cpp
commit bc30ec2ba515267eba2315b13dfe71046f938a7b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 16:00:47 2015 -0500
Since we are using the gravity BC fill routines for rotation, define them even when gravity is not enabled.
Source/Castro_F.H
commit 2801910d0259a560afd59521f74db76c3ecd41d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 9 15:39:47 2015 -0500
this is a better version of the problem -- it has a width corresponding
to what the toy_flame problem suggests is reasonable. Note that at the moment
this crashes when run in multilevel.
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probin
commit baf45e9c9a0864182d8ea52fe3b73c5f775c973b
Merge: 9d24ad07e 97ae124eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 9 15:23:14 2015 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 9d24ad07ec6dbc946a17cc7614be9c0347fae1f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 9 15:23:00 2015 -0500
this is a nice set of inputs that gives a good flame
Exec/toy_flame/inputs.1d
commit 97ae124ebecdb62dee5e69b724c0404fc80b3f8e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 14:31:10 2015 -0500
Remove external source terms in reacting_bubble since we aren't actually using the heating.
Exec/reacting_bubble/ext_src_2d.f90
commit 52521175d6d1c8f60fa293bbe423b2b9f23ca359
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 13:51:02 2015 -0500
Expand srcQ indexing in 1D and 2D also.
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
commit b44f657e961c64e5e337fae01240577fd9ab99df
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 13:35:02 2015 -0500
We have to use a temporary MF for adding rotation/gravity to the source term array; can't divide by the momentum like we were doing, because the momentum data might contain zeros.
Source/Castro_advance.cpp
commit 74821a456ece3af305e131150cd2f015598704ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 12:34:45 2015 -0500
Fix indices for srcQ
Source/Src_3d/Castro_advection_3d.f90
commit 7139238adf6b20a303d45b6bcf3f1c06048f6247
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 12:33:13 2015 -0500
Bug fix: when we do a saxpy using ext_src_old we need to specify the box because it defaults to using the ext_src_old box, which has more ghost cells than S_new.
Source/Castro_advance.cpp
commit 2e91be8a8d4dc02e38c9396c0720966d0e9a7e52
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 9 10:46:17 2015 -0500
we were reading in diffuse_cutoff_density wrong. D'oh!
Source/Castro.cpp
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.f90
commit 44bab05a33094ae5b6b51556d44e1a01aeae9f1c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Nov 5 10:31:54 2015 -0800
update to the new particle stuff
Source/Castro.H
Source/Gravity.cpp
commit 720badc92c8d431156b3d8631453512e147f6906
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 20:27:01 2015 -0500
Also don't compile the generic burner module when not using reactions.
Networks/Make.package
commit 1737efab15df6edf68c24692d684e99bd5fc76cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 20:03:37 2015 -0500
Don't compile burner without USE_REACT=TRUE.
Networks/general_null/Make.package
commit 6a75173a503aa2fe3ad3b47dee6a34c8cdbf286c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 16:18:48 2015 -0500
Needed a do_grav check in a couple of places.
Source/Castro.cpp
commit 5f435667426b0dba2fa4059b001a5e8a0d983d48
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 10:25:05 2015 -0500
For source term predictor, need to also multiply ghost cells by dt/2 when using dSdt.
Source/Castro_advance.cpp
commit a2b2ebe80b4d72d71418886453c7af52a4d00d8c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 01:26:01 2015 -0500
Do the MFIter in rotation based on state, not on the rotation data.
Source/Castro_rotation.cpp
commit c23634d56f485f462925103dc4695d728fb8d598
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 00:56:31 2015 -0500
When we detect a NaN, print the name of the component, not its location number.
Source/Castro_advance.cpp
commit f6de7049bc12adb39a106c1df5e2a7b445097101
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 00:42:37 2015 -0500
Need to wrap some code in ifdef's.
Source/Castro_advance.cpp
commit 83d4d8b4000e2ca54ec4ebb0450217dbf938b364
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 4 00:35:29 2015 -0500
Expand the number of ghost cells for srcQ.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 37084e63c00ba506d6b69fe832065a948c1d29e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 18:52:44 2015 -0500
We can save on a fillpatch by using Sborder to fill the rotation data.
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
commit 7acc451a19a50615c96c966651c1559c5b36e386
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 18:44:11 2015 -0500
Create the Sborder multifab explicitly and use a FillPatch from state data to fill it, rather than a FillPatchIterator.
Source/Castro_advance.cpp
commit 61053de8fe0cef712f8f621ac6c566db1ac18f90
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 18:27:22 2015 -0500
Don't add the Source_Type variables to the plotfile, we only need them in the checkpoint.
Source/Castro_io.cpp
commit 2d3212a7336af80dd58117d8675fa0b801036a31
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 18:19:55 2015 -0500
Distinguish the name of the source_type quantities by adding _source.
Source/Castro_setup.cpp
commit bd0495d9d2139f5ac237472cc31715daadbbf87d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 18:11:45 2015 -0500
Gravity_Type and Rotation_Type now have NUM_GROW ghost cells. This permits us to eliminate rot_vector and grav_vector, which saves on memory.
Source/Castro_advance.cpp
Source/Castro_setup.cpp
Source/Gravity.cpp
commit 39729de9e1bca15e7cbfccd6e8ea596827b0c64a
Merge: 8bef119fb ab43dc95d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 18:08:26 2015 -0500
Merge branch 'development' into source_terms
commit 83fd43816752e9945ed981a06eb5bc0b86633c60
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 3 13:41:38 2015 -0800
use BoxLib::average_down because ca_avgdown is gone
Radiation.cpp
commit 8bef119fb25d26b9259942c4932d861c5176c552
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 15:21:11 2015 -0500
Cut down on the number of source-term MultiFabs in advance_hydro, by re-using a single one.
Source/Castro_advance.cpp
Source/Castro_setup.cpp
commit ab43dc95d35d7afd3f883eb278f32035af52a88d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 14:20:53 2015 -0500
Only update sponge parameters if the sponge is active.
Source/Castro_advance.cpp
commit 01eb76356eb922fae516ced799ff469731959d81
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 10:53:44 2015 -0500
Don't initialize a non-constant array. Also, fix a bug that happened when there were more levels allowed than used.
Source/Castro.cpp
commit 81002caa3f37c3027cedb724b5699b3994f6ce63
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 2 21:59:58 2015 -0800
use BoxLib::average_down
Source/Castro.cpp
Source/CastroParticles.cpp
Source/Castro_F.H
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Gravity_3d.f90
commit d2518a0ab4e8a268e806f8804d3a799d4db6fc24
Merge: 6c543b10b 4ce2fef0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 3 00:07:27 2015 -0500
Merge branch 'development' into source_terms
commit 4ce2fef0c528473b84960a5095bffd8637e79b61
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 2 17:04:39 2015 -0800
To quiet gcc fsanitizer. It does not like array with size zero.
Source/Castro_setup.cpp
commit fcf93bb113f541a3710a7784541094f96fe0e28e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 2 16:28:16 2015 -0800
Gravity: get_grad_phi -> get_fluxes
Source/Gravity.cpp
commit 835fe01ead513faee3f50ff8cc4bca6c1daeb478
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 19:11:42 2015 -0500
Send the maximum number of levels, and the grid spacing on each level, to the Fortran prob_params_module.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/Castro_nd.f90
Source/Src_nd/prob_params.f90
commit 0687791cedc5816effcc4ac4cb96f420e395676a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 18:21:41 2015 -0500
Revert "Make buildInfo.cpp a phony target so that it is built every time."
This reverts commit d231f4c07ffcd7affcb339777e4c8e4a354c3855.
Exec/Make.Castro
commit 7d631594fe5971eb9e0f8a177695d15e5693c863
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 2 14:16:35 2015 -0800
songe_params_moudle no longer needs to have threadprivate variables
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/sponge_params.f90
commit d231f4c07ffcd7affcb339777e4c8e4a354c3855
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 15:30:07 2015 -0500
Make buildInfo.cpp a phony target so that it is built every time.
Exec/Make.Castro
commit 6c543b10be61515a253dbafb9584e817893b9440
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 14:24:46 2015 -0500
Fix bug from the merge
Source/Castro_advance.cpp
commit 387dfad8c77fec9e19830fb58c03a3d7f553e876
Merge: e1b9dff0a 3a341417e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 14:16:58 2015 -0500
Merge branch 'development' into source_terms
Conflicts:
Source/Castro_advance.cpp
Source/Src_3d/trans_3d.f90
commit 3a341417e04d36ab383de9569fd2ce02db77220e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 12:47:02 2015 -0500
Dimension agnostic diffusion routines
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Diffusion_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/thermal_conductivity_1d.f90
Source/Src_2d/Diffusion_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/thermal_conductivity_2d.f90
Source/Src_3d/Diffusion_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Diffusion_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/thermal_conductivity_nd.f90
commit 56985fe34a66a673f86229e9dc8bfd0ff938ca81
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 11:36:23 2015 -0500
Move update_sponge_params out of the OpenMP hydro region for thread safety purposes.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_nd/sponge_nd.f90
commit b92ede56d4c058846b2f698993b2662991dcd5f4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 11:29:08 2015 -0500
Fix an incorrect species calculation in enforce_minimum_density
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 6f88d7509658370e30ec69b5c8773d598c555ffa
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 11:16:32 2015 -0500
Revert an earlier mistaken change related to ppm_temp_fix == 2.
Source/Src_3d/riemann_3d.f90
commit 6d4e3e0489e8302329f9a390a62799fede8a4311
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 11:13:17 2015 -0500
Protect against a possible divide by zero
EOS/eos_type.f90
commit 343c1e784b4ddda580da32e16c88ea2b4fb4fef1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 11:12:00 2015 -0500
Revert "In burner.f90, calculate the derivatives of the thermodynamic variables with respect to species abundance, since many networks will need this."
This reverts commit 8b7a018b25c4f5ea17b0d47f7855790548db46f3.
Networks/burner.f90
commit 8b7a018b25c4f5ea17b0d47f7855790548db46f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 2 09:34:07 2015 -0500
In burner.f90, calculate the derivatives of the thermodynamic variables with respect to species abundance, since many networks will need this.
Networks/burner.f90
commit 61ba874ec7384df10572f62621e0589699ba4b6d
Merge: 7b8e9f4f6 73adf1a90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 1 19:25:52 2015 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 7b8e9f4f6d08d7434fa1cefa9c18eb09a7dba339
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 1 19:25:10 2015 -0500
if MICROPHYSICS_DIR is defined, then add the screening directory
into the mix. This fixes some compilation issues now that the
OpenACC sutff has been merged
Exec/Make.Castro
commit 73adf1a9030f5518738ea4be6310578346e589cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 1 19:16:42 2015 -0500
add back in the composition derivatives
EOS/eos.f90
EOS/eos_type.f90
commit 4ed2e7ad6bc5d3eb6705bf723e0718da5dd814b4
Merge: 0a34f6d07 4a4a0b03b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 1 18:49:56 2015 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 0a34f6d073d240aa011c9c97161ab18912e597f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 1 18:49:40 2015 -0500
add a note about the compositional derivatives
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 4a4a0b03b4dc395836919f770d93566b97ff4005
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sun Nov 1 14:19:29 2015 -0800
Make const MultiFab --> MultiFab in Gravity::avgDown so we can happily pass
it to BoxLib::average_down.
Source/Gravity.H
Source/Gravity.cpp
commit 86cdf826c201d2f1b45a9a6bf243fd366a425aaf
Merge: d0812c69c af864e166
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sun Nov 1 13:01:19 2015 -0800
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit d0812c69c26cfdbb6e111eb1696b9e2180081d6e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sun Nov 1 12:57:01 2015 -0800
Replace section of code in avgDown with BoxLib::average_down
Source/Gravity.cpp
commit af864e1667d32f7549382b1fbcee0e0cf210ad22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 31 18:48:07 2015 -0400
add a data log
Exec/toy_flame/inputs.1d
commit 01bc6cf51e6fdf4d1521e469127aac5e40229294
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 10:46:10 2015 -0400
Calculate the flame speed using Equation 7 of Bell et al. 2004. For now we only work on the coarse level because dt is not uniform across levels.
Exec/toy_flame/Prob.cpp
Exec/toy_flame/Problem.H
Exec/toy_flame/Problem.f90
Exec/toy_flame/Problem_F.H
Exec/toy_flame/sum_integrated_quantities.cpp
commit a3e2e8af5b1d151ad141cefb4cc79fdd292290f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 09:36:32 2015 -0400
Forgot to take absolute magnitude of temperature gradient
Exec/toy_flame/Problem.f90
commit cc00683ff0669cc1b4d00360f0264d53e8eebd0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 18:16:27 2015 -0400
Create a local copy of sum_integrated_quantities and use it to calculate the flame width (as defined in Equation 5 of Bell et al. 2004).
Exec/toy_flame/Prob.cpp
Exec/toy_flame/Problem.H
Exec/toy_flame/Problem.f90
Exec/toy_flame/Problem_F.H
Exec/toy_flame/sum_integrated_quantities.cpp
commit 444ea8e890f5f65b3920cac4791ddeafad4cf02a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 11:17:28 2015 -0400
Move some scalars back to eos_data since individual EOSes may need to update them.
EOS/eos.f90
EOS/eos_data.f90
commit 6995484d7e94f98117163f4561091021e9cbc57d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 11:09:30 2015 -0400
Revert the multidimensional EOS code. We're back to only using the scalar eos_t type.
EOS/eos.f90
EOS/eos_data.f90
EOS/eos_type.f90
EOS/gamma_law/gamma_law.f90
Networks/burner.f90
Networks/general_null/general_null_burner.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/React_nd.f90
Source/Src_nd/compute_temp_nd.f90
commit c0bcca09d545ae8f8d5533b438d12e74fec0bc06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 28 21:51:59 2015 -0400
fix the ash state
Exec/toy_flame/Prob_1d.f90
Exec/toy_flame/inputs.1d
Exec/toy_flame/probin
commit e1b9dff0a6e4b31d7137bf3cfb9c41c73e92f464
Merge: 7d222176d d57850ebb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 28 12:39:28 2015 -0400
Merge branch 'development' into source_terms
commit d57850ebba65e30ae947caec89a379c2f2ef177c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 27 21:00:44 2015 -0400
put in some interpolation between the fuel and ash
Exec/toy_flame/Prob_1d.f90
Exec/toy_flame/probdata.f90
Exec/toy_flame/probin
commit 53b05897b50e2bbabfd2b945dd11486b4807552a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 27 20:39:22 2015 -0400
print out some diagnostics + fix the values of rtilde and the
conductivity
Exec/toy_flame/Prob_1d.f90
Exec/toy_flame/probin
commit dab30094e61814a85634c853ba901c5a8570eeee
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Oct 27 10:07:12 2015 -0700
Diffusion: code consolidation
Source/Castro.cpp
Source/Diffusion.H
Source/Diffusion.cpp
commit 182433867d5260cddaefd520774f4d4663c16f4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 27 11:24:11 2015 -0400
In the burner, do the EOS call before copying the state data to the output vector.
Networks/burner.f90
commit 77bdb6cf674fb2f74c40975cae5ac233cd923aaa
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Oct 26 17:40:59 2015 -0700
Diffusion: use FMultiGrid
Source/Castro.cpp
Source/Diffusion.H
Source/Diffusion.cpp
commit 0c2c54dec44c0348777d7c4f702cd106c7196210
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 19:25:21 2015 -0400
fix a bounds issue in 1-d
Source/Src_nd/Derive_nd.f90
commit a23837edd234da9baa9d8e45cc74940c74dbbb1c
Merge: 9a71c73f2 1f06a4641
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 26 18:07:43 2015 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Castro into development
commit 9a71c73f2918b9b79002c8129aa7b10009ef818e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 26 18:07:27 2015 -0400
gravity_type might not be in the inputs file, so use a query and not a get.
Source/Castro_setup.cpp
commit 6dc352f96de3ed92a363d90844bb9ae4b643d0d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 26 18:06:01 2015 -0400
Sign fix
Source/Src_nd/gravity_sources_nd.f90
commit 1f06a464136050c68168b8746632b5ee9c46b322
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 15:11:31 2015 -0400
fix the UMZ
Exec/toy_flame/Prob_1d.f90
commit f96253204fb1e0d239fe2f8ce37a59f42c8eccf0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 15:08:05 2015 -0400
initialize all velocity components
Exec/toy_flame/Prob_1d.f90
Exec/toy_flame/inputs.1d
commit ad9a96da90fa6efab66cd2503242ee9c934fc20e
Merge: d01dd77cd b531a6998
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 15:07:29 2015 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit b531a6998d7a2117f8e4d9db080c2d97df72f7e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 26 12:52:41 2015 -0400
Enable grav_source_type == 4 for non-Poisson grav. We use a variation of the energy update that is valid when you only have the gravitational acceleration, not the potential.
Source/Src_nd/gravity_sources_nd.f90
commit d984d2196dd0fd26b08be20174e9d20807bc9339
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 26 10:42:17 2015 -0400
Pass in the gravity type to the meth_params_module.
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit d01dd77cdb05c413c01a32b424ec232f9378ce0b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 25 19:17:08 2015 -0400
some more progress on setting up the flame -- the fuel and ash states now
appear correct
Exec/toy_flame/Prob_1d.f90
Exec/toy_flame/inputs.1d
Exec/toy_flame/probin
commit d620394eb1b08e0e9e1b68f15343c5093cdd79d0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Oct 25 16:07:16 2015 -0700
Gravity: fixed typo in 1 & 2d
Source/Gravity.cpp
commit d3395b99fbc70a3900e859d65cf550287b65eeea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Oct 25 15:26:02 2015 -0700
Gravity: use FMultiGrid for testing composite phi
Source/Gravity.cpp
commit 6d9172a389e0b8c836a85dfa7791069ccaf895b8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Oct 25 13:11:23 2015 -0700
Gravity: use FMultiGrid for delta phi
Source/Gravity.cpp
commit 2a22541912755592705c5731c13409ecc18c1ec4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Oct 25 12:58:46 2015 -0700
Gravity: use FMultiGrid for eolving multi-level phi
Source/Gravity.H
Source/Gravity.cpp
commit 3f498f37f44ca3d06a3dd455eabc3287d6bb14a4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Oct 24 22:41:23 2015 -0700
Gravity: removed some unused functions
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 066818e54ac4dfeefc4ad732917e91130978dfb0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Oct 24 22:27:04 2015 -0700
fixed a new typo that affected 1 & 2d
Source/Gravity.cpp
commit 5abecd27729889d3203a6285511f66b5822ad89e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Oct 24 21:56:37 2015 -0700
Gravity: use the new FMultiGrid class for solving single-level phi
Source/Castro_advance.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 47d15036bc00f20959889e47000fd7403aa17f48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 25 16:06:05 2015 -0400
new toy flame problem for the XRB
Exec/toy_flame/GNUmakefile
Exec/toy_flame/Make.package
Exec/toy_flame/Prob_1d.f90
Exec/toy_flame/README
Exec/toy_flame/inputs.1d
Exec/toy_flame/probdata.f90
Exec/toy_flame/probin
commit e640d0cd5367cdc57da02fc50925b3bc6f6e88ea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 23 17:47:52 2015 -0700
removed obsolete parameter castro.gamma
Exec/DustCollapse/inputs_3d_poisson_regtest
Exec/DustCollapse/inputs_3d_poisson_regtest_restart
commit 3477d2f39834f20d83cac357dfd401102c2261ba
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 23 17:44:25 2015 -0700
EOS: removed composition_derivatives
EOS/eos.f90
EOS/eos_type.f90
commit e7883d341419c6f7621c84d69743f1dc3801c52d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 22 22:39:54 2015 -0700
Gravity: fixed time
Source/Gravity.cpp
commit ac98030058593a2bd9c6090a7ec9fe98d8c117a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 22 11:45:22 2015 -0400
remove unused variables
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/hydrostatic_bc_2d.f90
commit 43872eb288b0322a7bc0fbbf09516acbacf8ad33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 22 11:07:19 2015 -0400
don't git .xmgr files
.gitignore
Exec/convective_flame/inputs.2d.test
commit 9f9725bb84cf204254c7791ba0fc5382c8f9b95f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 22 08:49:32 2015 -0400
remove some unused UMY
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit 16f0ca08f2151c17574d16e50558262e3d5a6a69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 21 21:03:00 2015 -0400
this now uses an initial model generated by toy_atm. After a short
while it crashes (even faster when we run with multiple levels
of refinement. Probably need to turn on the sponge...
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/convective_flame.hse.tanh.delta_0.040cm.dx_0.040cm
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probdata.f90
Exec/convective_flame/probin.big
commit 4b9fe1c30f2c380f750e49753773c730023fb0d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 21 20:22:04 2015 -0400
remove wrong comment
Exec/reacting_bubble/probdata.f90
commit 8c5204f90ee0b21d0ea706e3d686383aaf7252de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 21:38:05 2015 -0400
also handle the phigrav and react fill routines for inflow
Exec/convective_flame/bc_fill_2d.f90
commit b9c42982d8b2ad0a3ecfe08d34fa8c0ff556f774
Merge: f747fb260 95d549521
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 21:25:45 2015 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit f747fb260d0b8aaaa43c255b5df12e72642c76f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 21:25:40 2015 -0400
add comment
Exec/convective_flame/bc_fill_2d.f90
commit 95d549521b36502f45bb7ecacb19b7c317a1ce2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 21:07:24 2015 -0400
we need to override the BCs for inflow for all the grav?fill routines
(since these are used by rotation too). Here we now create a dummy
bc_temp() array and if we see we are EXT_DIR, we reset that to FOEXTRAP
Exec/convective_flame/bc_fill_2d.f90
commit 3b2305ff8c0dedef40be90f1358a2296a59c007a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 20:55:20 2015 -0400
fix rotation period
Exec/convective_flame/inputs.2d.test
commit 831b46aa4dee7e95a7d7237d6d67cfe9f5d3bb9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 15:38:34 2015 -0400
add a note about castro.diffuse_cutoff_density
UsersGuide/Diffusion/CastroDiffusion.tex
commit cd27cb1f3610e47f052f9528aeac7b1fe129331d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 15:29:52 2015 -0400
fix domain size
Exec/convective_flame/inputs.2d.test
commit 9b340b0fe36a1c01e932c1aa9b95b1ea63a78644
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 15:29:11 2015 -0400
some physically motivated parameters
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probin.big
commit 5b4074e6f7ef0cb7e649edbd499e8cee4782b9f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 15:26:32 2015 -0400
hook in the diffusion_cutoff_density -- below this density, we do not diffuse.
This helps with the surface of a star
Source/Src_1d/thermal_conductivity_1d.f90
Source/Src_2d/thermal_conductivity_2d.f90
Source/Src_3d/thermal_conductivity_3d.f90
Source/Src_nd/EstDt_diffusion_nd.f90
commit 42c8e9f5954d41be31b90d4b4e3b377639bf5921
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 15:18:39 2015 -0400
fix typo
Source/Castro.cpp
commit aa771607ca2fd87de8cd65e3786ab17cb3062759
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 20 14:59:56 2015 -0400
add a diffuse_cutoff_density parameter -- not yet hooked in...
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/EstDt_diffusion_nd.f90
Source/Src_nd/meth_params.f90
commit f4a16efafcb2ee5d352398e3cb0d895cc67cb6cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 19 14:37:34 2015 -0400
Add a normalize_abundances function to the eos vector type and use it to clean up some code in the burner.
EOS/eos_type.f90
Networks/burner.f90
commit 7d222176d4f165be5fa2d2f53a7baeba5ffa1e64
Merge: 14d3bb31d f7b38570f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 19 10:31:37 2015 -0400
Merge branch 'development' into source_terms
commit f7b38570f0f24838de859e7b75408c41ddccbf38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 20:09:41 2015 -0400
update to microphysics
Exec/convective_flame/GNUmakefile
commit c3a0a6657acad202471eb14b7627caebb985b18a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 20:04:31 2015 -0400
update
EOS/README
commit 1dcc37a78665b94acc76c9f146bf2fb25d3484f9
Merge: 3f3a6a70e fe7f10cea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 18:45:51 2015 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 3f3a6a70efee1919ade98f7109f1848f22962770
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 18:44:23 2015 -0400
some more docs
Networks/powerlaw/_parameters
commit fe7f10cea6d56b7cbf982f07381d91e5a0eb7c3d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 18:10:51 2015 -0700
add some comments about thread safety
Source/Src_nd/Tagging_nd.f90
commit 0887f4e8dce31533559f437f0583f39d2cb5dab5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 18:04:08 2015 -0700
added save in several places to follow Fortran standard
Source/Src_nd/prob_params.f90
Source/Src_nd/tagging_params.f90
commit b98125766aa22bc93fe9bfcd5c52b76c8dbb2feb
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 17:59:05 2015 -0700
add some comments about thread safety
Source/Src_nd/Derive_nd.f90
Source/Src_nd/bc_fill_nd.f90
commit fbe93e7ce13984cd1dd8ca8e5a1b18b47d2e8087
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 17:35:32 2015 -0700
made sponge_params_module thread safe
Source/Src_nd/Castro_nd.f90
Source/Src_nd/sponge_params.f90
commit 345caf39799e1fba16cae9c1b225ef716ba00ea7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 17:05:14 2015 -0700
removed an empty probin file in Src_3d
Source/Src_3d/probin
commit 8c7cd19559564b526aa4f9efb07b768abaf5b5f7
Merge: b6e793937 27ab0f290
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 16 16:17:20 2015 -0400
Merge branch 'development' into new_eos. Also, removed the
powerlaw network as it has been moved to Microphysics.
commit b6e7939376f88e7695ca33822e19c79b4f227b19
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 10:37:50 2015 -0700
added save to follow Fortran standard
Networks/general_null/network.template
commit 211144724b1c5eb64d4ca7e8a21e992f8f464815
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 16 12:50:12 2015 -0400
Revert eos_assume_neutral to be a parameter for gamma_law alone, and default it to true as it previously was. To accommodate this the general EOS wrapper no longer calculates mu, only gamma_law does.
EOS/_parameters
EOS/eos.f90
EOS/eos_type.f90
EOS/gamma_law/_parameters
EOS/gamma_law/gamma_law.f90
commit 14d3bb31dd1adce356394733c7f39d9e2f94197d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 16 12:36:17 2015 -0400
Don't double count the momentum source terms.
Source/Src_2d/trans_2d.f90
Source/Src_3d/trans_3d.f90
commit cff04109daa63208e966ec73ddd128bae572eadc
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 16 11:24:26 2015 -0400
Need to add energy source term corresponding to the gravity/rotation momentum sources, to hydro_sources.
Source/Castro_advance.cpp
commit 5e5d0e0cb66dd66c8450cd49762d755669494f0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 15 16:45:08 2015 -0400
Bug fix for non-gravity simulations
Source/Castro_io.cpp
commit c0892263ecdaefbe1f6dc401cb42f838fde8b2e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 15 15:11:21 2015 -0400
Revamp the source term predictor to use the new Source_Type data. We add dt/2 * (d(source) / dt) to the hydro_sources multifab going into the Fortran hydro code. At the end of each timestep, we estimate dS/dt as (sources_new - sources_old) / dt.
Source/Castro_advance.cpp
commit 75b85a3fd5254c0c03631a3b38585d8f7a729e2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 15 13:35:05 2015 -0400
Calculate the time derivative of the source terms.
Source/Castro_advance.cpp
commit a66dcb307f288be0043011624e492678718f82c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 15 13:28:59 2015 -0400
Add new sources together.
Source/Castro_advance.cpp
commit c27bf8eb510e9b5b41b4c15abe1db8d121d00d76
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 14 21:16:23 2015 -0400
Create arrays to store the sum of the sources, instead of double-booking ext_src.
Source/Castro_advance.cpp
commit 569679369f426ed843866e194df2401c024bf2fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 14 20:49:06 2015 -0400
Add a Source_Type to the state data. It has NVAR components, like State_Type, and does live in the checkpoint. However, we ensure that we never allocate old data for it.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
commit cad05d92b29e269529eeb0c775be92f7b2127b95
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 14 16:32:26 2015 -0400
Instead of sending gravity and rotation to the hydro separately, we now pack them all into a single source term MultiFab, including the external source terms. For now we use the new ext_src data to hold it. To do this a couple of separate changes had to be made: 1) we now have a single getSource() function instead of separate getNewSource() and getOldSource() functions. 2) We move the call to add the external source terms outside of the Fortran, appearing right after the umdrv call. 3) We replaced ppm_trace_grav and ppm_trace_rot with ppm_trace_sources, which (when applicable) will do a single tracing over each component of the source term array. However, we haven't changed any of the physics, i.e. we're still only doing this to the velocity terms. Note that this should change results slightly for two reasons -- first, the order of the addition of the sources is very slightly changed; second, and more importantly, we're not doing independent tracing.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_setup.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/slope_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit 0ca360ebad2f1a42d5161a375586f4ea209130b5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Oct 14 13:20:12 2015 -0700
save gamm_const in gamma-law eos
EOS/gamma_law/gamma_law.f90
commit 658f69f0cddbee24e1192365972ef7acfbb101d5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Oct 14 12:03:52 2015 -0700
update to Castro new_eos branch
Rad2Tshock/GNUmakefile
RadShestakovBolstad/GNUmakefile
RadSlope/GNUmakefile
RadSphere/GNUmakefile
RadSuOlson/GNUmakefile
RadSuOlsonMG/GNUmakefile
RadThermalWave/GNUmakefile
commit 6ccdd83fc446b567bf99fb6bac29845f0b7d3fc6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Oct 14 10:30:23 2015 -0700
add cv in the eos_input_rt mode and update Users guide
EOS/gamma_law/gamma_law.f90
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 27ab0f29017cf51031bd83834db7d65000c0dbb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:33:23 2015 -0400
enable diffusion
Exec/convective_flame/README
Exec/convective_flame/inputs.2d.test
commit 440b4ec0fafcd58ad6e363e97ad69d62ed3fef8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:20:20 2015 -0400
fix a typo
Source/Src_nd/Tagging_nd.f90
commit 19ff541bbc55c327ca03d8a3b508f315272e0df0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:17:27 2015 -0400
fix the sign on the energy release
Networks/powerlaw/castro_burner.f90
commit 544936307a791be364b6672110742a038fbbc396
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:14:45 2015 -0400
enable burning
Exec/convective_flame/inputs.2d.test
commit ae1cc0e9b11a3f64bb9fa9abe25da2f6b0169657
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:09:05 2015 -0400
switch to a powerlaw burner
Exec/convective_flame/GNUmakefile
commit 27e1228f2575dee3ef67202198b14f877b736d76
Merge: a5145416a 273270fef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:08:38 2015 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit a5145416a173e09ae356b06ab420aabac2100126
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 21:06:11 2015 -0400
a simple power-law reaction network, with a rate:
r = r0 rho X T**nu
and energy generation:
eps = r Q/rho
Networks/powerlaw/Make.package
Networks/powerlaw/_parameters
Networks/powerlaw/burner_aux.f90
Networks/powerlaw/castro_burner.f90
Networks/powerlaw/f_rhs.f90
Networks/powerlaw/network.f90
commit 273270fefb25f49b5ebd8a83bd1f42211d99416f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Oct 12 17:58:38 2015 -0700
added tagging function for entropy
Source/Src_nd/Tagging_nd.f90
commit 789d2447f796f01c12701d2628d4b15edb5e2bec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 19:48:31 2015 -0400
clean up the perturbvation a little:
Exec/convective_flame/Prob_2d.f90
commit 9d38ff29b6e77e9a016f4f64270b59186bf0cbd3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Oct 12 16:41:19 2015 -0700
make Tagging_nd.f9 match the old Tagging_2d.f90
RadCoreCollapse/Tagging_nd.f90
commit edcfb174ee4ca215938a73e32eedcffca5dc4c04
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Oct 12 16:28:45 2015 -0700
fixed a new bug in tagging
RadCoreCollapse/Tagging_nd.f90
commit 1a1bd86e85639af4a4358f92ed3f711a7453ed67
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Oct 12 15:20:56 2015 -0700
make Tagging_nd.f90 match the old Tagging_?d.f90
RadCoreCollapse/Tagging_nd.f90
commit 5c0e2eba7b407aed8268d5cdc1ea879f50208179
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 12 15:52:29 2015 -0400
add a perturbation
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/probdata.f90
Exec/convective_flame/probin.big
commit 5b27e17c9b9f8af04a4913011f9d21281327434d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 9 21:18:29 2015 -0400
add a check on ustar for symmetry
Source/Src_1d/riemann_1d.f90
Source/Src_2d/riemann_2d.f90
commit 4d0b8a0b5ca88a8c8811a9a9f4fcba7052013a76
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 9 18:16:57 2015 -0700
update tagging routines before Tagging_?d.f90 has long gone and has been replaced by Tagging_nd.f90
RadCoreCollapse/Tagging_1d.f90
RadCoreCollapse/Tagging_2d.f90
RadCoreCollapse/Tagging_3d.f90
RadCoreCollapse/Tagging_nd.f90
RadThermalWave/Tagging_1d.f90
RadThermalWave/Tagging_2d.f90
RadThermalWave/Tagging_3d.f90
RadThermalWave/Tagging_nd.f90
commit d1bff35a33c1ef4441e4ef086db7f4a417b318a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 9 20:20:21 2015 -0400
put in a test if the ustar velocity is really small (compared to ul and ur)
then zero it out. This helps with roundoff
Source/Src_3d/riemann_3d.f90
commit 3049bc89b510949b6720a4e95e3831350db12456
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 9 16:11:58 2015 -0700
removed gamma_law_general. it's now in Microphysics.
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/_parameters
EOS/gamma_law_general/gamma_law_general.f90
Exec/HCBubble/GNUmakefile
Exec/Vortices_LWAcoustics/GNUmakefile
Exec/evrard_collapse/GNUmakefile
Exec/gamma_law_bubble/GNUmakefile
Exec/gresho_vortex/GNUmakefile
Exec/uniform_cube_sphere/GNUmakefile
commit 7a086d12113aebdc84d40f99fdae703d44a01639
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 9 10:50:57 2015 -0400
Fix typo
Source/Castro_advance.cpp
commit 225f221503a51ea210a0bad6d7faaef264b71d7a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 17:02:28 2015 -0700
Give entropy an invalid but nice value for the plotfile. Note that I am trying to avoid the expensive log function in the computation of entropy.
EOS/gamma_law/gamma_law.f90
commit de4346c559b6a2ac33d3b61c64a49f4347bfdeb0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 16:26:45 2015 -0700
add a minimalist version of gamma-law eos and use it in a number of test problems
EOS/gamma_law/Make.package
EOS/gamma_law/_parameters
EOS/gamma_law/gamma_law.f90
Exec/DustCollapse/GNUmakefile
Exec/KH/GNUmakefile
Exec/RT/GNUmakefile
Exec/RT_particles/GNUmakefile
Exec/Sedov/GNUmakefile
Exec/Sod/GNUmakefile
Exec/oddeven/GNUmakefile
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 7063ff861f12d88c8b3007816fda9a4e2ea36534
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 16:18:15 2015 -0700
give priority to EOS_dir in Castro over that in MICROPHYSICS
Exec/Make.Castro
commit 23f5f7f26fad02d307bc9a86a256eb59f25f80aa
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 14:42:06 2015 -0700
fixed logic
EOS/eos.f90
commit a400885d0fd045cc7920e698667d88b0dbd6eff5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 13:50:07 2015 -0700
cleanup
EOS/gamma_law_general/gamma_law_general.f90
commit 832fcec58d1d99db9ed2b9e1fe861795d725283d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 8 16:31:19 2015 -0400
Missed a probin file in a recent update
Exec/DustCollapse/probin.halfstar
commit 6fbf41c6288af70cfbcdd5131f5274e8ed0cd41b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 8 16:27:36 2015 -0400
Make small parameters consistent with what's done elsewhere in Castro
EOS/eos_data.f90
commit 889b4240390bfd2cce0cf2a43e0063bcc366943e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 13:04:05 2015 -0700
fixed a bug in select case eos input
EOS/gamma_law_general/gamma_law_general.f90
commit dfb3580d66ed354b1b7a860d5fc063542dfbc6a5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 10:55:44 2015 -0700
optimization of gamma_law_general
EOS/gamma_law_general/gamma_law_general.f90
commit 41607aef5775307265fb36c1f3c1db593e7c61a0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Oct 8 10:55:19 2015 -0700
fixed directory name for networks
Networks/general_null/Make.package
commit 462965c82478480bd637694e3f9bb784c89fcd64
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 8 10:07:42 2015 -0400
Fix typo in source term predictor, was not adding right number of components
Source/Castro_advance.cpp
commit cda9e1606383bf3c70b09ffb43514d6fcc01a265
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 8 10:06:19 2015 -0400
Remove reference to Microphysics repo
Networks/general_null/Make.package
commit 4eaaed3e9fa6be13c13fa3f5e2b39413fa23f28b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 5 10:10:03 2015 -0400
Add an eos_name parameter to each EOS so that we can test against which are permitted to use certain parameters.
EOS/eos.f90
EOS/gamma_law_general/gamma_law_general.f90
commit e0323dd5104c5adb8f72b3dd74d6a4d2d960fbd0
Merge: 59949c8cc a16f8241d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 5 10:09:31 2015 -0400
Merge branch 'development' into new_eos
commit 59949c8cc3de5dd235bb8b928549c37b11461e34
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 5 09:05:38 2015 -0400
For problems that default to the gamma law EOS, explicitly set eos_assume_neutral = .true. so that we retain prior behavior.
Exec/DustCollapse/probin.fullstar
Exec/DustCollapse/probin.octant
Exec/DustCollapse/probin_3d_poisson_regtest
Exec/HCBubble/probin-sod-x
Exec/KH/probin
Exec/RT/probin
Exec/RT_particles/probin
Exec/Sedov/probin.1d.cyl
Exec/Sedov/probin.1d.sph
Exec/Sedov/probin.2d.cyl_in_cartcoords
Exec/Sedov/probin.2d.cyl_in_cartcoords.tau
Exec/Sedov/probin.2d.cyl_in_cylcoords
Exec/Sedov/probin.2d.sph_in_cylcoords
Exec/Sedov/probin.2d.sph_in_cylcoords.testsuite
Exec/Sedov/probin.3d.cyl
Exec/Sedov/probin.3d.sph
Exec/Sedov/probin.3d.sph.testsuite
Exec/Sod/probin-slowshock-x
Exec/Sod/probin-sod-x
Exec/Sod/probin-sod-y
Exec/Sod/probin-sod-z
Exec/Sod/probin-test1-helm
Exec/Sod/probin-test2-1d
Exec/Sod/probin-test2-helm
Exec/Sod/probin-test2-x
Exec/Sod/probin-test2-y
Exec/Sod/probin-test2-z
Exec/Sod/probin-test3-helm
Exec/Sod/probin-test3-x
Exec/Sod/probin-test3-y
Exec/Sod/probin-test3-z
Exec/Vortices_LWAcoustics/probin
Exec/convective_flame/probin.big
Exec/diffusion_test/probin.2d
Exec/evrard_collapse/probin
Exec/gamma_law_bubble/probin.big
Exec/gresho_vortex/probin
Exec/oddeven/probin.2d
Exec/uniform_cube_sphere/probin
commit a16f8241dc64e4ede0f9847d7f3042c4244014d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 4 14:10:34 2015 -0400
this syncs up with 2-d -- don't try any tracing of the gravity and
rotation sources for the transverse velocity -- we always add them to
the interface states.
Source/Src_3d/trace_ppm_3d.f90
commit a7b1168021c29822af79ea8674e3e9aa04844f19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 4 13:33:37 2015 -0400
add comments
Source/Src_2d/trace_ppm_2d.f90
commit be57f677831ecb89361c2a2e4292dde18adee3e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 4 12:24:30 2015 -0400
fix some styling
UsersGuide/EOSNetwork/EOSNetwork.tex
commit a9e8e6e70044437711c7ca39f08667ccb97b0465
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 3 21:15:53 2015 -0400
update the EOS interface
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 3d4aebeb08afe68a4a7e46637dc3ccc8b13eed4a
Merge: 638ccf111 6c3fd8d16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 2 10:19:38 2015 -0400
Merge branch 'development' into new_eos
commit 6c3fd8d161836c06542c455495a6c7a7ee32bfce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 22:19:09 2015 -0400
update the diffusion docs to reflect the new conductivity interface
UsersGuide/Diffusion/CastroDiffusion.tex
commit bc4f800297c53421a50c09b0cc5aebd9264ade5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 21:53:13 2015 -0400
don't need the fill_temp_cond routine anymore -- this is now all centralized
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Make.package
Exec/convective_flame/fill_temp_cond_2d.f90
commit 30f5d871842f8a4ce150ea55bd3e7bfdeffe89de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 21:40:35 2015 -0400
relative path
Exec/diffusion_test/GNUmakefile
commit 9194f5948e4cbf28445124efdb1f0f354259c23b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 20:44:14 2015 -0400
fix the block that calls the diffusion timestep limiter -- this appears
to work now
Source/Castro.cpp
Source/Src_nd/EstDt_diffusion_nd.f90
commit 8bc21a9af27211f32061738305a91e640d551a35
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 20:38:49 2015 -0400
remove fixed_dt
Exec/diffusion_test/inputs.2d
commit 75a36f180f6732ccc70f48d47056c3566c455c5a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 20:08:13 2015 -0400
start of hooking in the diffusion limiter
Exec/diffusion_test/inputs.2d
Source/Castro.cpp
Source/Castro_F.H
Source/Src_nd/EstDt_diffusion_nd.f90
commit 026d5b8283ee3a623d3d66cdeee54fc9ca478cf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 15:41:44 2015 -0400
add a diffusion timestep estimator
Source/Src_nd/EstDt_diffusion_nd.f90
Source/Src_nd/Make.package
commit dc85034b0086354800fec7da7eb5f6a82a24ebca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 15:28:18 2015 -0400
abandon the diffusion.conductivity parameter -- it is not needed in C++
anyway. Now we have a _parameters in Conductivity/constant that defines
the conductivity for this case, which can be overridden in the &extern
namelist in probin
Conductivity/constant/_parameters
Conductivity/constant/constant_conductivity.f90
Exec/diffusion_test/Prob_2d.f90
Exec/diffusion_test/probin.2d
Source/Castro_F.H
Source/Diffusion.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit c8d34938724cfe7cb73f9f6165ec9f5fbd4e388e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 12:30:37 2015 -0400
split the actual conductivity into a separate subroutine that can be
customized -- it takes an eos_t state and returns the conductivity.
For diffusion problems, you now need to specify a Conductivity_dir in
your GNUmakefile
Conductivity/constant/Make.package
Conductivity/constant/constant_conductivity.f90
Exec/Make.Castro
Exec/convective_flame/inputs.2d.test
Exec/diffusion_test/GNUmakefile
Exec/xrb_mixed/inputs_2d
Source/Src_1d/thermal_conductivity_1d.f90
Source/Src_2d/thermal_conductivity_2d.f90
Source/Src_3d/thermal_conductivity_3d.f90
commit 6f65555424aa5c1e05a7ed90e46be04a1f7b83c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 21:45:41 2015 -0400
work on reseting rho0 to get the desired diffusion coefficient
Exec/diffusion_test/Prob_2d.f90
Exec/diffusion_test/inputs.2d
commit 4cbfa20ac1049d334568f0c50759c7387f61ab97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 21:19:31 2015 -0400
dispense with diff_coeff -- it was never used. Instead we introduce
diffusion.conductivity to set a constant conductivity. We add a
set_method_diffuse_params() routine to interface with method_params
from the diffusion class.
Source/Castro_F.H
Source/Diffusion.H
Source/Diffusion.cpp
Source/Src_1d/thermal_conductivity_1d.f90
Source/Src_2d/thermal_conductivity_2d.f90
Source/Src_3d/thermal_conductivity_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit f34ca4142a82e4dd00a1a7091cae91f748ebf237
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 21:18:38 2015 -0400
no longer need a separate fill_temp_cond_2d.f90 routien -- we now use
the default. Note: this still needs to set the diffusion coefficient
properly, by adjusting rho0 for this test
Exec/diffusion_test/Make.package
Exec/diffusion_test/fill_temp_cond_2d.f90
Exec/diffusion_test/inputs.2d
commit 9ebb7108d1f3937e428836bf56aeac03b85a1d5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 20:49:38 2015 -0400
add in dimension-specific thermal conductivity routines -- these at the
moment assume a constant thermal_conductivity. They need to be
dimension-specific because we need to define it on the interfaces
Source/Src_1d/Make.package
Source/Src_1d/thermal_conductivity_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/thermal_conductivity_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/thermal_conductivity_3d.f90
commit 6a7754bce9a6e2db08c952b6ab33382c716b6653
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 15:32:28 2015 -0400
no need for gravity here
Exec/convective_flame/probin.big
commit 465fa0d992502ab7743edaf63defb0212ddc56b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 13:32:37 2015 -0400
switch from a probin grav to getting const_grav from meth_params_module
Exec/gamma_law_bubble/Prob_2d.f90
Exec/gamma_law_bubble/bc_fill_2d.f90
Exec/gamma_law_bubble/extra_derives_2d.f90
Exec/gamma_law_bubble/probdata.f90
Exec/gamma_law_bubble/probin.big
commit 11ff0153e65a908d901f71c7cdfe172c7ffb9faf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 13:25:19 2015 -0400
remove gravity -- it should come from meth_params_module. Add in
a constant conductivity
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Make.package
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/fill_temp_cond_2d.f90
Exec/convective_flame/probdata.f90
commit d4c773bcfd77a3bedfb0f6f2b6e93b2a1f741548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 11:22:46 2015 -0400
a little more discussion about diffusion
UsersGuide/Diffusion/CastroDiffusion.tex
commit 2f435d7637087c0bfc57abd922b85612388a6368
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 10:17:05 2015 -0400
a simple README describing this problem
Exec/diffusion_test/README
commit 682aedf2ede1e4f63c9c56c841f57715ce5f96bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 30 10:12:24 2015 -0400
this works now and qualitatively looks correct
Exec/diffusion_test/Prob_2d.f90
Exec/diffusion_test/inputs.2d
Exec/diffusion_test/probdata.f90
Exec/diffusion_test/probin.2d
commit 2238a9376e2d7fc6ac32d88396556e6bc7e31c1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 21:50:15 2015 -0400
this isn't quite right yet -- need to specify the Gaussian in terms of the
diffusion coefficient properly
Exec/diffusion_test/Prob_2d.f90
Exec/diffusion_test/inputs.2d
Exec/diffusion_test/probdata.f90
Exec/diffusion_test/probin.2d
commit b9b9f3942abb973570b4945d6d53308ce0b2ffed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 21:04:40 2015 -0400
start of a simple diffusion-only test problem
Exec/diffusion_test/GNUmakefile
Exec/diffusion_test/Make.package
Exec/diffusion_test/Prob_2d.f90
Exec/diffusion_test/fill_temp_cond_2d.f90
Exec/diffusion_test/inputs.2d
Exec/diffusion_test/probdata.f90
Exec/diffusion_test/probin.2d
commit 1813e32dd3861b27821d731cfa82d5bd5edfd229
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 19:36:50 2015 -0400
start of some diffusion notes
UsersGuide/Diffusion/CastroDiffusion.tex
commit 8761ee9b0b2105671386a17068b3980ebf327087
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 29 15:48:34 2015 -0400
fix compilation when DIFFUSION define
Source/Castro.cpp
commit 260e30f846cf651f1f24051f5d1548aeebc7d64d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 17:33:17 2015 -0400
some cleaning
Exec/convective_flame/hydrostatic_bc_2d.f90
commit 5149db3a388cbbebd3ed48a69d25de8683843acf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 14:00:22 2015 -0400
reset plot interval
Exec/convective_flame/inputs.2d.test
commit 1adeb9d7f5de77f12e1fd854f0f9b2ee6d9c3027
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 13:30:29 2015 -0400
don't allow negative energy -- this gets it cooking...
Exec/convective_flame/inputs.2d.test
commit ffd96ab6739ae609baf5a8ba8c0f61bc83184f5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 13:25:36 2015 -0400
start playing around with an upper bounday condition -- regardless of
what I try here, we eventually crash with NaNs... Also start playing
with sponging
Exec/convective_flame/GNUmakefile
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/hydrostatic_bc_2d.f90
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probin.big
commit d1d88fdcc0645cfa6a231d2097b96fb4372dea86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 12:26:50 2015 -0400
we need a special gravity bc fill at the lower boundary since we are
doing a user-specified boundary there
Exec/convective_flame/bc_fill_2d.f90
commit 586afda8a9d1c8e3a098c57fd60d21d3b9ba87b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 27 12:22:02 2015 -0400
break the HSE boundary out into its own thing
Exec/convective_flame/Make.package
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/hydrostatic_bc_2d.f90
Exec/convective_flame/probdata.f90
commit 13fb8b7ba02cf6e86fd22d0f1b4fcc0a0f5f807c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 21:19:25 2015 -0400
update domain size
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probin.big
commit 280b71793a8fb232573778bc7c967e600935631a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 20:45:21 2015 -0400
stray character
Exec/xrb_mixed/bc_fill_2d.f90
commit 70181ccdf2bc9381ff1595af7eb7b93d0fcbf65d
Merge: bd372ed17 0a73f4f7f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 20:26:41 2015 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit 0a73f4f7f0a00ca3fdb4b545b370e3bd28d9b419
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 20:26:31 2015 -0400
initialize UMZ
Exec/xrb_mixed/Prob_2d.f90
Exec/xrb_mixed/bc_fill_2d.f90
commit bd372ed17b9a3c0d0ea905052b097232e1efc9c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 20:25:35 2015 -0400
Get this problem compiling again
Exec/RT_particles/Castro_error.cpp
Exec/RT_particles/bc_fill_2d.f90
commit 017e1f36c69731cbb99d9e35f7cb40c798f25c5d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 20:21:11 2015 -0400
Fix the documentation comments to reflect the new file structure
UsersGuide/AMR/AMR.tex
commit 1bf48fae5a8f9dc498de66f76736594c46030952
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 20:18:34 2015 -0400
This problem doesn't seem to need its own local Castro_error.cpp.
Exec/Detonation/Castro_error.cpp
commit 828401f307a373e6f6f032c96673005c21a49e0a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 20:18:11 2015 -0400
Switch a couple problems over to use problem_tagging_nd.f90.
Exec/toy_convect/Castro_error.cpp
Exec/toy_convect/Problem_F.H
Exec/toy_convect/Tagging_2d.f90
Exec/toy_convect/problem_tagging_nd.f90
Exec/xrb_mixed/Castro_error.cpp
Exec/xrb_mixed/Problem_F.H
Exec/xrb_mixed/Tagging_2d.f90
Exec/xrb_mixed/problem_tagging_nd.f90
commit a99cf80c13f06b58362fa852d043e78c53069d98
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 26 20:11:50 2015 -0400
Fix typo
Exec/xrb_mixed/probin
commit 16fb1bbf4b135d8470481f604ef59e419ea95ec5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 19:43:08 2015 -0400
sync this up with the latst source -- this doesn't compile yet, because of Tagging_2d.f90
Exec/toy_convect/Castro_error.cpp
Exec/toy_convect/Problem_F.H
commit 3ed27302c361cd6e2cda83fd0907883e08129922
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 19:42:29 2015 -0400
fix this for the dimension agnostic stuff -- this now defines UMZ
Exec/toy_convect/Prob_2d.f90
Exec/toy_convect/bc_fill_2d.f90
commit 7f2308e62724dd3216956346458a7bea62b1a65a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 26 19:09:24 2015 -0400
add link to the User's Guide
README.md
commit dc800ef77c237334067e39f8a8e756724f50e342
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 17:34:56 2015 -0400
fix the lower boundary (for now) -- we need to be more general here
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/inputs.2d.test
commit 12fc56cfbef177eedc8cb49c84c4daf3f6c3808e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 17:19:55 2015 -0400
fix UMZ
Exec/convective_flame/Prob_3d.f90
commit 377977671cda90d1b1448c0dc337d5f8ed1f84d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 17:19:03 2015 -0400
fix boundary condition UMZ
Exec/convective_flame/bc_fill_2d.f90
commit bd4d8ae5c1c2471f6baaa2bbe9f220238bec1f6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 17:16:42 2015 -0400
fix uninitialized Z velocity
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/inputs.2d.test
commit 3b87465311531c3ad0248179d0ad4700215993fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 17:10:07 2015 -0400
add a temperature floor -- this allows for bigger domains, but eventually
we crash :(
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/inputs.2d.test
Exec/convective_flame/probdata.f90
Exec/convective_flame/probin.big
commit b59f0c166c3606ab6f0c5f5ca4a17c64492d2793
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 16:52:01 2015 -0400
turn on rotation
Exec/convective_flame/GNUmakefile
Exec/convective_flame/inputs.2d.test
commit 638ccf111b7488128addf6673d406a5b19a43f9b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 25 16:06:37 2015 -0400
Remove initialized check from gamma law EOS
EOS/gamma_law_general/gamma_law_general.f90
commit 377335d0811eabd0118073c730ae702c3080673a
Merge: 1e3feca9f 6c7a0e24a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 25 16:05:55 2015 -0400
Merge branch 'development' into new_eos
commit 6c7a0e24ab34cff29470eb4e9e5d83da80136d34
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 25 14:21:10 2015 -0400
Have small_temp default to a very small number instead of its current value of 1.d-8, as some problems actually might go below that for legitimate reasons.
Source/Src_nd/Castro_nd.f90
commit 1e3feca9fdbf82feae23032e03a8a48809cffcb1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 24 19:52:56 2015 -0400
Remove a parameter that wasn't used and causes conflicts
Exec/StarGrav/Prob_1d.f90
Exec/StarGrav/Prob_2d.f90
Exec/StarGrav/Prob_3d.f90
commit e3b59c9877e3d595cdfe70d0bed730d435e26ca4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 24 19:43:52 2015 -0400
Mixed up argument order
Source/Castro_F.H
Source/Castro_setup.cpp
commit 5dfedb328a6efdaa476d53aa6c1f296de3df6e57
Merge: e63c9e1d5 a7560ad41
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 24 14:26:15 2015 -0400
Merge branch 'development' into new_eos
commit e63c9e1d55bb85d526a78c977879d51e43406043
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 24 14:24:39 2015 -0400
Fix composition calculation and clean it up
EOS/eos_type.f90
commit a7560ad4137cc062d0479d5d09bbb097f96b82d7
Merge: adbf5f5e1 2f60ff891
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 24 12:10:02 2015 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Castro into development
commit adbf5f5e1c523fd3a95c87a4d2e9846f50d687dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 24 12:09:52 2015 -0400
fix Castro_Exec
Util/scripts/get_castro_date.sh
commit 2f60ff8914055604ef0fd6adf88fdec79859a74b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 24 09:43:27 2015 -0400
some more ignores
.gitignore
commit cf74b9edc5645b7ed4090ef971f63009bf2c6cfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 24 09:35:38 2015 -0400
fix the relative paths -- they should always be ../..
Exec/KH/GNUmakefile
Exec/StarGrav/GNUmakefile
Exec/evrard_collapse/GNUmakefile
Exec/gamma_law_bubble/GNUmakefile
Exec/test_convect/GNUmakefile
Exec/uniform_cube_sphere/GNUmakefile
commit 95497a2bdb252b7e695ebbbeda4414627ae82bd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 24 09:33:25 2015 -0400
fix relative paths -- they should never depend on the User's CASTRO_DIR
variable -- they should always point to the source that they are in.
Exec/StarGrav/GNUmakefile
Exec/evrard_collapse/GNUmakefile
Exec/gamma_law_bubble/GNUmakefile
Exec/test_convect/GNUmakefile
Exec/uniform_cube_sphere/GNUmakefile
commit 8ea8c7adde83e16dc1ba5084e820b5ab3c499e65
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 23 12:58:41 2015 -0400
This branch is designed to implement the so-called hybrid advection scheme of Byerly et al. (2014). Instead of advecting the standard linear momenta (xmom, ymom, zmom), the approach is to advect (radial momentum, z-component of angular momentum, z-momentum). We will still advect these on the standard Cartesian mesh. This approach is useful for problems featuring rotation in the x-y plane where strict conservation of the angular momentum associated with that rotation is desired. In the first commit, we have added a runtime option for it, but it is non-functional so far.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_nd/Castro_nd.f90
Source/Src_nd/meth_params.f90
commit deeee40af42831527c1882724515bce289a5927f
Merge: d92b5a8f3 b415e520d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 22 22:11:23 2015 -0400
Merge branch 'development' into new_eos
commit d92b5a8f35e6a76e98108aa84f4a19cede362855
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 22 22:04:04 2015 -0400
if we detect helm_table.dat is a link, the remove it during a make clean
Exec/Make.Castro
commit b415e520dceda6c89a2a3e287bcae5ed46a48932
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 22 21:58:01 2015 -0400
always use a relative path ../.. for CASTRO_DIR so we are sure we are
using the source in this directory
Exec/Detonation/GNUmakefile
Exec/RT/GNUmakefile
Exec/RT_particles/GNUmakefile
Exec/Sedov/GNUmakefile
Exec/Sod/GNUmakefile
Exec/Sod_stellar/GNUmakefile
Exec/StarGrav/GNUmakefile
Exec/convective_flame/GNUmakefile
Exec/double_bubble/GNUmakefile
Exec/test_convect/GNUmakefile
Exec/xrb_mixed/GNUmakefile
commit 1df8129147c20124630d500f0dfcb4953acace7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 18:52:26 2015 -0400
Forgot a variable declaration
Source/Src_nd/EstDt_nd.f90
commit bcfd2bc2b3d1c0cc14cdaf9298441ffb0a8e998c
Merge: 03921bec2 e92d05b2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 14:08:46 2015 -0400
Merge branch 'master' into new_eos
commit 03921bec262ae78712c3738279714e9a048fcf2f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 14:07:35 2015 -0400
Use a eos_t_vector for the single-entry eos_t as well.
EOS/eos_type.f90
commit 271a4a0ad19e3ed4e0dca394bf9048eba9a14072
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 14:06:49 2015 -0400
Fix some output
EOS/eos.f90
commit e92d05b2aa7422d1242d5abc5fc620bb6e177422
Merge: e924f8bfe 4584f2d82
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 11:42:01 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Castro
commit e924f8bfe4ca3980112edeb6bf1fdbb838571870
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 22 11:38:22 2015 -0400
Dimension agnostify the tagging routines.
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_1d/Make.package
Source/Src_1d/Tagging_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/Tagging_2d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/Tagging_nd.f90
commit 4584f2d82dcb3fabd01c7211ec6766e7823aa909
Merge: 228d64a85 1321b6610
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Sep 21 17:09:53 2015 -0700
Merge branch 'master' of https://github.com/BoxLib-Codes/Castro
commit 228d64a851aab86542750f39b7b7235f85270810
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Sep 21 17:08:23 2015 -0700
If ppm_trace_grav = 1, make sure we include gravity in all the right temporaries -- it was being
neglected for a particular transverse case.
Source/Src_2d/trace_ppm_2d.f90
commit 1321b6610f26d2bbea78674454b6d62ebc941bfa
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 14:34:19 2015 -0400
delta_e might be larger on coarse levels
Source/Castro_io.cpp
commit 0a711d87cfe6aac20d457d0efa2b093b356e75a9
Merge: 3f655b7c9 74de3787f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 14:29:09 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Castro
commit 3f655b7c9d5850fb08629e09529475d42c461f16
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 14:28:51 2015 -0400
Enable temperature tagging
Source/Castro_error.cpp
commit e4a00029d00d3c9ed0ceadcb7203d8587980e0a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 14:28:26 2015 -0400
Have the delta_e printed out to the ReactHeader be the maximum on all levels.
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
commit 1a7ff6bea4efd80a1916073dfa13e7954395608d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 13:48:33 2015 -0400
Fix MPI issue from last commit
Source/Castro_io.cpp
commit 74de3787ffe9a0ecdda93e9e2335afafe29a6e74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 21 12:41:24 2015 -0400
add a small_temp
Exec/reacting_bubble/inputs_2d
Exec/reacting_bubble/inputs_2d.test
commit 9b1e3fcf7803c25c33f6cd68ea3dc4c5f7bb3459
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 21 11:51:19 2015 -0400
When writing a checkpoint and using reactions, create a ReactHeader file. Currently this stores a single number, the maximum change in delta_e from the last timestep as indicated by the reactions state data. When doing a restart, read in that value to the reactions state data. This will ensure that we do proper timestep limiting using the burning criterion even after a restart.
Source/Castro_io.cpp
commit bcda5654dde458ac32a1286d24d687111a3949e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 22:54:02 2015 -0400
Forgot to add common block variables to the module instead
Networks/ignition_simple/burner_aux.f90
Networks/ignition_simple/f_rhs.f90
commit 4be00395e236f1e54a29a80f1ec4748a786845ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 22:42:30 2015 -0400
Get the ignition_simple network to be thread-safe.
Networks/ignition_simple/burner_aux.f90
Networks/ignition_simple/castro_burner.f90
Networks/ignition_simple/f_rhs.f90
Networks/ignition_simple/network.f90
commit cbcaec9a1f53f62d506f8eedc941c82dad5521d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 20:04:56 2015 -0400
Avoid testing against exactly zero
Source/Src_nd/EstDt_burning_nd.f90
commit 2cc5a1b743c7d3f4a83b2ab3b077b170beee3234
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 19:34:58 2015 -0400
Don't do the source-term predictor after a restart if there's no valid data to use.
Source/Castro_advance.cpp
commit cc3a845f44d34f07eff15610a0d0c9de246dde93
Merge: 0808d9c6c e6a72ed69
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 20 12:13:58 2015 -0400
Merge branch 'master' into new_eos
commit e6a72ed69465b967f9a3e5f1ef648c31add96888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 18 21:30:35 2015 -0400
first cut at a 2-d problem
Exec/convective_flame/inputs.2d.test
commit f6421b7a1b5eebff8ffc0ef28241704a3db6968f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 18 20:55:38 2015 -0400
get 2-d compiling
Exec/convective_flame/README
Exec/convective_flame/bc_fill_2d.f90
commit 7ae285f9baf11dc65b80d554a3b85f56a895abb9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 17 16:29:48 2015 -0700
update to the new PArray and reuse edge boxarray instead of building it again and again
HypreMultiABec.cpp
MGFLD.cpp
MGFLDRadSolver.cpp
RadSolve.cpp
SGRadSolver.cpp
commit 7a32073a8fa449f0faf70accc9a64123858da1b6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 17 16:09:38 2015 -0700
reuse edge boxarray instead of building it again and again
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.H
Source/Gravity.cpp
commit 126011a98f7fb8c964c2794031b6ba68803c2d0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 17 11:28:58 2015 -0400
remove a print to get this happy again
Util/exact_riemann/GNUmakefile
Util/exact_riemann/exact_riemann.f90
commit 6b8303bfdf231ffd00575202c2c8599fc2c547da
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Sep 16 16:48:35 2015 -0700
update to the new MGT_Solver interface
Source/Diffusion.cpp
Source/Gravity.cpp
commit 40f9c23c53e8244e3e9e97308d40f15999d530f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 16 09:42:17 2015 -0400
remove unneeded UMX and UMY
Exec/reacting_bubble/problem_derive_nd.f90
commit a38ab36a9d8845c3e13bbacffcedacfd26a1399c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 16 09:40:49 2015 -0400
consider UMZ in the BC kinetic energy calculation
Exec/reacting_bubble/bc_fill_2d.f90
commit f60670524157850a82f85765f0df02a49d9b0f28
Merge: f1d0ce4d7 9fc514136
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 16 09:34:10 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit f1d0ce4d7bbe50d4c3d6cd42f9647d3add090805
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 16 09:34:00 2015 -0400
initialize UMZ to 0 too
Exec/reacting_bubble/Prob_2d.f90
Exec/reacting_bubble/inputs_2d
commit 9fc51413654d400f37c5cad6e076ca0baebb3fca
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 16 02:15:07 2015 -0400
Remove stray macro
Source/Castro_F.H
commit a50bd65393282ab6f6fcfbaae397caeb23f2ef6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 16 02:13:08 2015 -0400
Add a predictor for source terms entering the hydro. We predict to time-level n+1/2 using a lagged linear extrapolation from time-levels n and n-1. This should still be second-order but may be more accurate in some cases. It is presently operational for gravity and rotation. It is controlled through the inputs parameter castro.source_term_predictor and is unused by default.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit 90bccb4b1ef3fe8a2b302578f2079d79d20b7cda
Merge: 691011822 2d9244ad8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 15 18:23:43 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Castro
commit 6910118229aa379617f9e7e988b5f1df1acdbb02
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 15 18:23:35 2015 -0400
Enable a basic framework for limiting the hydro timestep based on a burning criterion. The criterion is that we set dt = c_burn * e / delta-e, where e is the current internal energy and delta-e is an estimate of the change of the internal energy from the last timestep. Physically this says that we don't want to let the internal energy change by more than a factor of c_burn from its current value. c_burn is controlled by the new inputs parameter castro.burning_timestep_factor.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_1d/Make.package
Source/Src_1d/estdt_burning_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/estdt_burning_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/estdt_burning_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/EstDt_burning_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/meth_params.f90
commit 2d9244ad8df6556f02a6ed44f33b40657fffd630
Merge: 8d912818b ac142dbb2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Sep 15 14:19:08 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 8d912818be948c7645ea43dedaff4b537ad4ada6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Sep 15 14:11:08 2015 -0700
added some if's so that we don't work on uninitilized data
Source/Src_2d/trans_2d.f90
commit ac142dbb2ac70233139e6269c756832cf61ea0fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 15 15:58:05 2015 -0400
add back a cd ..
Util/scripts/get_castro_date.sh
commit c38b5786483722d1a7324a5fcff654497ee5e34b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 15 15:54:50 2015 -0400
remove some maestroisms
Util/scripts/get_castro_date.sh
commit dd9efbed0c46c8dc5475e6d564f8fd3fedf26161
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 15 15:49:31 2015 -0400
a script to make bisecting easier
Util/scripts/get_castro_date.sh
commit aaa747966e01d2f5793a0351d10ca8e7a13dbc9d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 15 12:56:12 2015 -0400
Set UMZ to 0 in bc_fill
Exec/reacting_bubble/bc_fill_2d.f90
commit 7f8263bda84aafcbc16c37a8de3e463e6342b941
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 15 10:06:24 2015 -0400
Argument shouldn't be const
Source/Castro_F.H
commit e97f254c54bdcfd9d8e01c491bd61791877174c4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 15 10:02:32 2015 -0400
Fix a typo in react_nd.f90
Source/Src_nd/React_nd.f90
commit 0808d9c6cb58560cb117c0f4989558f5d0eea946
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 23:55:39 2015 -0400
Add warning about microphysics repo
Exec/StarGrav/GNUmakefile
commit 99dc2b92ec53ed8874be2025a70a124b4b65665f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 23:48:07 2015 -0400
Use eos_t_3D in a few more places.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/compute_temp_nd.f90
Source/Src_nd/reset_internal_energy_nd.f90
commit e85137789bde19b21168d060823d5335f62a183e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 22:12:46 2015 -0400
Merge all of the EOS constructors into a single eos_allocate function.
EOS/eos_type.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/React_nd.f90
commit d282d6feb6886a6af6932dd6e987314bdc6ae4d5
Merge: f0a05a9ee e02807b60
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 16:28:40 2015 -0400
Merge branch 'master' into new_eos
commit e02807b6061c50b073be1c1e6be0f05fc065ec10
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 16:08:23 2015 -0400
In anticipation of re-enabling nuclear burning-limited timestep criteria, add the reactions multifab to React_nd.f90.
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_nd/React_nd.f90
commit 9a78fa6eca713a8effbae9aacdd05a1fedec2d34
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 14 15:40:19 2015 -0400
Upgrade the checkpoint version to 2. We can now restart from checkpoint versions < 2 that don't have all three space momenta.
Source/Castro_io.cpp
commit 6d928f79a6e94b2b3e20cc4e8110c513b827f5bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 13 19:45:18 2015 -0400
Residual cleanup of volproductsum
Source/sum_utils.cpp
commit 518087508945b5080692a59c9256e20af483e1f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 13 17:32:30 2015 -0400
Get the location-weighted sums working with symmetric boundary conditions, so that for example in cylindrical coordinates the radial center of mass will be zero as expected.
Source/Src_nd/Castro_sums_nd.f90
commit d342a435e1765926351791d8a917f75268b994de
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 13 17:29:49 2015 -0400
Remove unused variable
Source/Castro_react.cpp
commit e24e3c90a6eaa9142751eb28f2711a6c3db01b57
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 13 14:06:18 2015 -0400
Fill the rotation data on initialization or on a restart, as we do for gravity.
Source/Castro.cpp
commit b4f3e558f077e80637beb2f535142aaea289031e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 13 02:12:10 2015 -0400
Make sure to set zero in the reactions data until we've restored their usage.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit f0a05a9eec5c001dabcfeea6fec722f2c5c74657
Merge: 45fa1e363 002022535
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 12 22:39:05 2015 -0400
Merge branch 'master' into new_eos
Conflicts:
Source/Src_3d/Castro_advection_3d.f90
commit 45fa1e363037854bc95164cf4f5f5cace7a4e9a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 12 18:43:13 2015 -0400
Update convective_flame for microphysics repo
Exec/convective_flame/GNUmakefile
commit 002022535f3c9081c8309bf6a649a61c097a0bf2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Sep 12 10:48:01 2015 -0700
filcc_nd.f90 -> filcc_nd.F90
Exec/Make.Castro
Source/Src_nd/Make.package
Source/Src_nd/filcc_nd.F90
commit e2067296eea320377e91852a16212e40e4de2e9d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Sep 12 10:19:08 2015 -0700
added a few missing 'use *_module's
Source/Src_nd/Prob_nd.f90
Source/Src_nd/bc_fill_nd.f90
Source/Src_nd/problem_tagging_nd.f90
commit ea814a414beef30b863606403008585a70629db7
Merge: 5d57e5ff4 4f3e22855
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 12 02:46:20 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Castro
commit 5d57e5ff4d9c6f1e1a75d93cdecd4d3f0f294ae9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 12 02:46:16 2015 -0400
Write a filcc_nd function that converts the dimension agnostic bc_fill_nd data into a form appropriate for the dimensionful FILCC_*d.F
Source/Src_nd/Make.package
Source/Src_nd/bc_fill_nd.f90
Source/Src_nd/filcc_nd.f90
commit 4f3e22855c7e0ce6342703ad1e143fb83b4a5bbf
Merge: 931141bd2 083f2a206
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 21:53:56 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 083f2a206d87151780fed5d7cd453300c8063355
Merge: 4d8b1a78a 98baef353
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 23:54:53 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Castro
commit 4d8b1a78a87b181b4dd1107b421f3d8d67d6a594
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 23:54:49 2015 -0400
Updated dimension agnostic boundary filling
Source/Castro_F.H
Source/Src_nd/bc_fill_nd.f90
commit 931141bd2ab5da95a708adaea15658cb9b83e68a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 20:25:50 2015 -0700
This reverts commit 98baef3530b9fb434b95d0537fdeadf6829ba4b5. The
commit was to make radiation hydro code work. But now it is no longer
necessary.
Source/Castro_advance.cpp
commit a1f8809ffc8b761e67b26ce712d96acdccbb3881
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 17:10:05 2015 -0700
update bc_fill and 1d hydro
Rad2Tshock/bc_fill_1d.f90
RadCoreCollapse/bc_fill_2d.f90
commit 142c10e7d525fc8661459e58839dcfef44e79ebd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 17:10:05 2015 -0700
update bc_fill and 1d hydro
Src_1d/RadHydro_1d.f90
commit 98baef3530b9fb434b95d0537fdeadf6829ba4b5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 17:00:52 2015 -0700
make sure flux for passive velocity components is set to zero in 1d and 2d
Source/Castro_advance.cpp
commit 5e0abbcd3514105dedd8ef40b71918ead81ff389
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 13:51:08 2015 -0700
fixed a typo
Src_2d/RAD_2D.F
commit 5ce8c6e8de245e973537f2447d45404454e8b9bb
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 13:45:05 2015 -0700
better treatment of large and small numbers in black body module
blackbody.f90
commit eaad933a31ae32699a04fb4f9678fe05a2e17b17
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 14:45:51 2015 -0400
Use slice notation in bc_fill for clarity
Source/Src_1d/bc_fill_1d.f90
Source/Src_2d/bc_fill_2d.f90
Source/Src_3d/bc_fill_3d.f90
Source/Src_nd/bc_fill_nd.f90
commit 0979968c676f6b8b25ad17cd8811570cb49bfb5d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 11:12:31 2015 -0700
guard against tiny number
blackbody.f90
commit 3774fff8264ff199043e5f0eaf1afca8cb6d3c0f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 11:01:10 2015 -0700
minor tweak to remove an invalid floating point operation
Src_1d/RAD_1D.F
Src_2d/RAD_2D.F
Src_3d/RAD_3D.F
commit fc6d640749dd6e1c23afc5a5f33e7d8edd5f9514
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 12:58:28 2015 -0400
Fix a bug that was already fixed in another branch related to an incorrect division
Source/Src_3d/Castro_advection_3d.f90
commit 14ecd59f7de81639e84c133e36042d554e19cd1f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Sep 11 09:47:24 2015 -0700
took out a deprecated assertion
Source/Castro_setup.cpp
commit 0cc056b331263fb2bb2dfb69cb7b8147dd0e0728
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 09:04:19 2015 -0400
Add a logical parameter -- reset -- to EOS derived types. If this is set to true, when we call the EOS, we will first check any inputs to see if they are invalid, and if so, try to reset T and rho to small_temp and small_dens, and call the EOS using T and rho. It will then be called as normal during the full EOS sweep.
EOS/eos.f90
EOS/eos_type.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_nd/React_nd.f90
commit b96e7f7b979292e100a7b2de385ce2a2744da1a7
Merge: 138ff620a db05a4d23
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 07:28:16 2015 -0400
Merge branch 'master' into new_eos
commit db05a4d2394d7643f2c4598f211074daeafc8889
Merge: 2b451437f 9c0c210cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 11 03:43:09 2015 -0400
Merge branch 'master' into dimension_agnostic
commit 9c0c210cd1dbd749e78d960faed45af0529fada9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 10 19:17:23 2015 -0400
new test problem -- this checks the 2-d axisymmetric gravity
Exec/StarGrav/inputs_2d.test
commit 930da53315115058e563b6a73d5a98f8f28bceec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 10 19:15:23 2015 -0400
switch to bc_fill defaults
Exec/StarGrav/Prob_1d.f90
Exec/StarGrav/Prob_2d.f90
Exec/StarGrav/Prob_3d.f90
commit 2b451437fdfdd9f32970aa10e6beecb9a26feb23
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 10 18:52:38 2015 -0400
Restore a safe check on negative energies
Source/Src_3d/Castro_advection_3d.f90
commit e476c21c9420ec3f400ecb4712bd6d35969a5533
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 10 13:40:55 2015 -0700
update to Castro dimension_agnostic branch
RadCoreCollapse/bc_fill_2d.f90
commit 476a8312b28fb1a7e1b2e48884d2e01fb0901c6e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 10 13:40:55 2015 -0700
update to Castro dimension_agnostic branch
Radiation.cpp
Src_1d/CastroRad_1d.f90
Src_1d/RAD_1D.F
Src_2d/CastroRad_2d.f90
Src_2d/RAD_2D.F
Src_3d/CastroRad_3d.f90
commit 60f2160697fac7d872221e8ba9c8b01fb75edf33
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 10 13:03:24 2015 -0700
clean up unused variable
Source/Src_1d/Castro_1d.f90
commit 96fbf697acb47e318d08bf157b6002c6eefef197
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 10 15:15:15 2015 -0400
Forgot to set sponge_timescale
Exec/DustCollapse/update_sponge_params.f90
commit 6c9c7006846be96a870535c6b7068bced19233d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 10 14:30:24 2015 -0400
Fix typo
Source/Src_3d/Gravity_3d.f90
commit 2a750fd6dc05df405cf9d8cd0aa938afdb37af55
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 10 14:29:05 2015 -0400
Revert some obsolete changes
Source/Src_2d/Gravity_2d.f90
commit a8e5f0314a0e44e3859dc54b852a863bd9f12114
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 10 14:23:54 2015 -0400
Fix vorticity and divergence calculations in DIM < 3.
Source/Src_nd/Derive_nd.f90
commit 138ff620ab0d23376fabfbc8c3d348e6a440dc2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 22:18:37 2015 -0400
Missed a rhoInv
Source/Src_3d/Castro_advection_3d.f90
commit ba9f132c61f7722de803491becfea783a5751033
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 21:29:41 2015 -0400
Should be a Problem_Derive_F.H, not a Derive_F.H file.
Exec/hydrostatic_adjust/Derive_F.H
Exec/hydrostatic_adjust/Problem_Derive_F.H
commit 38c576a781ece86eeefa5c62bc1c489edeba19d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 21:06:07 2015 -0400
Meant to set only a single component to zero but we were zeroing out the whole multifab.
Source/Gravity.cpp
commit 9a3b8b546648a628f1ec03f04b657dd052191cb5
Merge: 7f8ad9522 0048bd8b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 19:40:25 2015 -0400
Merge branch 'master' into dimension_agnostic
commit 7f8ad9522e9367b060792f5e2022000f65bd742b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 16:26:09 2015 -0400
Get Sod_stellar's local copy of trace_ppm working on this branch
Exec/Sod_stellar/trace_ppm_2d.f90
commit 467b3d5f1993969a7b8b406ead28a172b8094c3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 16:25:15 2015 -0400
Restore the logic that permits the EOS to change small_temp and small_dens
Source/Src_nd/Castro_nd.f90
commit 03ef7312cddc6f40648ba9fa2f9d5e2c6adfd184
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 16:24:50 2015 -0400
Only modify small_temp and small_dens if the user selection is above the internally selected helmeos limits.
EOS/helmeos/eos_stuff.f90
commit 4a0b70774e4f242cc18a77baa0fdb6d33da14029
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 15:20:25 2015 -0400
Bug fix for ppm_temp_fix == 1 -- we're already in primitive variables, don't divide by rho.
Source/Src_3d/Castro_advection_3d.f90
commit 2c6d06f486919ac51e8b69e031ecba79372bd2f2
Merge: 5011c13ef 93cafa878
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 11:15:06 2015 -0400
Merge branch 'dimension_agnostic' of ssh://github.com/BoxLib-Codes/Castro into dimension_agnostic
Conflicts:
EOS/helmeos/helmeos.f90
commit 5011c13eff3340e4091a5e51f5771d5dfbe97986
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 9 11:12:42 2015 -0400
Revert to master branch version of helmeos for this branch.
EOS/helmeos/_parameters
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
EOS/helmeos/vector_eos_f90.dek
commit 93cafa878faccedb20eabfae9ddbf30f2e7fa547
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 8 21:11:20 2015 -0400
initialize y and z velocities
Exec/hydrostatic_adjust/Prob_1d.f90
Exec/hydrostatic_adjust/bc_fill_1d.f90
commit 0048bd8b1f5ed7fe4c7e02b387f3184fe926650f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 8 14:00:47 2015 -0400
break setting BOXLIB_HOME out into its own item
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 5f5dfc26ac25e80bdac7ec6a9324e47357b5e9e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 19:44:32 2015 -0400
drop down to the resolution from Miczek et al.
Exec/gresho_vortex/inputs.2d
Exec/gresho_vortex/probin
commit e487a4499831b27d137dd3b8b0e65539466972b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 19:24:01 2015 -0400
fix the unit vectors for the projection of u_phi into Cartesian coordinates -- much
better now!
Exec/gresho_vortex/Prob_2d.f90
Exec/gresho_vortex/inputs.2d
commit e041d66930ab23688f745fa5792668362d5ee14c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 18:20:56 2015 -0400
add subcell averaging
Exec/gresho_vortex/Prob_2d.f90
Exec/gresho_vortex/inputs.2d
Exec/gresho_vortex/probdata.f90
commit d575e217cdeae2a6d6bcf296ba67511026c7ebab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 17:15:13 2015 -0400
some more parameters
Exec/gresho_vortex/inputs.2d
Exec/gresho_vortex/probin
commit 2526c2ff9e6988c81c0530fdb3e26aa85aac627d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 17:03:04 2015 -0400
forgot how to set periodic BCs in Castro...
Exec/gresho_vortex/inputs.2d
commit cec10de23c5483a5aa11100f2f8f1cb938887b10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 16:58:07 2015 -0400
problem specifies periodic BCs
Exec/gresho_vortex/inputs.2d
commit 9c1ad7817a3a3b8ed0b731fd72b3614acdb6c49a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 16:50:25 2015 -0400
first cut at the gresho vortex problem
Exec/gresho_vortex/Prob_2d.f90
Exec/gresho_vortex/inputs.2d
Exec/gresho_vortex/probdata.f90
Exec/gresho_vortex/probin
commit 69e8aad06cb29a57596bf293e4398760508671dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 7 10:59:42 2015 -0400
start of the gresho vortex problem
Exec/gresho_vortex/GNUmakefile
Exec/gresho_vortex/Make.package
Exec/gresho_vortex/Prob_2d.f90
Exec/gresho_vortex/inputs.2d
Exec/gresho_vortex/probdata.f90
Exec/gresho_vortex/probin.2d
commit 1a1c0709138edfbd513f5bd79a1543039e73c8c3
Merge: 944326cd6 86ba38522
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 6 00:31:08 2015 -0500
Merge branch 'master' into new_eos
Conflicts:
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
commit d277164abe4e8860dfb752bef62e502d578e5e95
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 20:01:47 2015 -0400
Add Fortran routines for problem-specific derived variables.
Exec/reacting_bubble/Derive_F.H
Exec/reacting_bubble/Make.package
Exec/reacting_bubble/Problem_Derive_F.H
Exec/reacting_bubble/extra_derives_2d.f90
Exec/reacting_bubble/problem_derive_nd.f90
Source/Derive_F.H
Source/Make.package
Source/Problem_Derive_F.H
Source/Src_nd/Make.package
Source/Src_nd/problem_derive_nd.f90
commit 10ef0c89c24b8cd24fac5615e481f61444dd7e85
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 19:35:34 2015 -0400
Various bug fixes
Exec/Sod_stellar/trace_ppm_2d.f90
Exec/hydrostatic_adjust/extra_derives.f90
Source/Castro.cpp
Source/Src_2d/Gravity_2d.f90
Util/exact_riemann/riemann_sample.f90
commit 86ba38522476f0ebffb821c013f7739bf4115f1b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Sep 5 14:15:52 2015 -0700
fixed memory leak
Source/Gravity.cpp
commit ba3e65172a5844190c4d30f8c68a43f736115553
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 14:21:29 2015 -0400
Remove errant bracket
Source/Castro_setup.cpp
commit 37f642ea417fa7caa458aa9ccb3bd42783dc5650
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 11:27:45 2015 -0400
Add the passive transverse velocities when computing kinetic energy in the Fortran source routines.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trans_2d.f90
commit 944326cd6e7a862acd874642941c34a4b1d50a90
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 10:54:44 2015 -0400
For compatibility purposes, continue to remove a local network.f90 file when do a clean.
Exec/Make.Castro
commit 6590a0acfdfd68ce0cdca25564aa63db0299fef2
Merge: e1ec515f9 3f1b2746a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 02:57:10 2015 -0400
Merge branch 'master' into dimension_agnostic
commit 3f1b2746a1912b59ea200760f920466c59c707e4
Merge: 6b656d431 53f99a43d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 02:43:36 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Castro
commit 6b656d43161b750912be1e16cfa8c4f9a0001bdd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 02:43:31 2015 -0400
Fix sign of rotational potential, and also add in needed factor of 1/2 in energy update.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit 4d53414a10a7c3a75a98b4ea37223dd13a04ed73
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 5 02:40:41 2015 -0400
Add gravity components to the desc_lst even when not using gravity, for derive purposes.
Source/Castro_setup.cpp
commit 53f99a43d3ea211fca8b9bcf21e7859a7c8384eb
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Sep 4 17:03:28 2015 -0700
Move the average_down_faces routine in BoxLib/.../MultiFabUtil* files to centralize this core functionality.
Source/Gravity.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit e1ec515f9af70ea2ff7190a9d3d92b269fd0f416
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 18:58:54 2015 -0400
Optional dimension agnostic version of problem_tagging_nd.f90
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/problem_tagging_nd.f90
commit 012475c743fb7d54466e7b6b37fbf866316208bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 18:46:46 2015 -0400
Add a dimension agnostic version of ext_src_nd.f90 that is only used if DIMENSION_AGNOSTIC=TRUE in the makefile.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/ext_src_nd.f90
commit c0ec0ce226c77af5617539e218043df4c2078130
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 18:23:32 2015 -0400
Time-varying rotation
Source/Castro.H
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/rotation_sources_nd.f90
commit f621d1ac75b5ec9f272999457934c942c969f603
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Sep 4 15:04:30 2015 -0700
Make sure that the RHS for the gravity_sync solve sums to zero when all periodic...
should have at most a precision-level solve on a simulation using the sync stuff.
Source/Gravity.cpp
commit 28e4ab5f372b4c37f293b45c5ac21c64b95471d5
Merge: 3d70ae673 14b4e3942
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 17:39:19 2015 -0400
Merge branch 'master' into dimension_agnostic
commit 3d70ae673d093aa368be295312dff9bf7aaba0b4
Merge: f79666b97 42f3eca2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 17:35:30 2015 -0400
Merge branch 'master' into dimension_agnostic
commit f79666b97818ebab813b35610fcf3e66d27aee7e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 16:50:26 2015 -0400
Needed to make a couple variables private
EOS/helmeos/helmeos.f90
commit b01843e9ca8ed4ee6b7b8e7363d4ff77ef220fa1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 4 16:06:04 2015 -0400
Move the sponge call up to the C++. This allows it to restore its original order, after the gravity and rotation source terms have been applied. Also, it's now dimension agnostic. More importantly, actual sponge functionality has been implemented to reflect the fact that this is CASTRO code and that the user can use ext_src_*d.f90 if they want to impose their own forcing. You can sponge either on density or on radius from the center of the domain; this is controlled from the new sponge namelist in the probin file. The problems in Exec/ been updated to account for this.
Exec/DustCollapse/sponge_3d.f90
Exec/DustCollapse/update_sponge_params.f90
Exec/README
Exec/StarGrav/probin
Exec/StarGrav/sponge_1d.f90
Exec/StarGrav/sponge_2d.f90
Exec/StarGrav/sponge_3d.f90
Exec/hydrostatic_adjust/Prob_1d.f90
Exec/hydrostatic_adjust/probdata.f90
Exec/hydrostatic_adjust/probin
Exec/hydrostatic_adjust/probin.subchandra
Exec/hydrostatic_adjust/sponge_1d.f90
Exec/reacting_bubble/probin
Exec/reacting_bubble/probin.zoom
Exec/reacting_bubble/sponge_2d.f90
Exec/test_convect/probin
Exec/test_convect/sponge_2d.f90
Exec/toy_convect/probin
Exec/toy_convect/sponge_2d.f90
Exec/xrb_mixed/Prob_2d.f90
Exec/xrb_mixed/probdata.f90
Exec/xrb_mixed/probin
Exec/xrb_mixed/sponge_2d.f90
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_setup.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/sponge_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/sponge_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/sponge_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/rotation_sources_nd.f90
Source/Src_nd/sponge_nd.f90
Source/Src_nd/sponge_params.f90
Source/Src_nd/update_sponge_params.f90
UsersGuide/Equations/Equations.tex
UsersGuide/Parallel/Parallel.tex
commit 54a3bfe10bc49b70cfd50aa85f0db7a005b17966
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 3 17:11:00 2015 -0400
Make the hydro compatible with the gravity by having get_new_grav_vector work on a temporary array of BL_SPACEDIM dimensions and then filling all relevant dimensions of the hydro grav_vector.
Source/Gravity.cpp
Source/Gravity_F.H
commit 14b4e39427930b1413e8015da6fea14688db6b89
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 3 13:32:42 2015 -0700
removed unused SyncInterp
Source/Castro.H
Source/Castro.cpp
commit 1eedc83e7eade5265115f2673903f030398befea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 3 13:27:19 2015 -0700
use BoxLib::average_face_to_cellcenter
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit 16852714bd60d41d2da26c9622a6efe9ec8c36ba
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 3 13:09:19 2015 -0700
use the new BoxLib::fill_boundary function
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.cpp
commit 42f3eca2d1acbc331b8a18ce7868af0cbeecfc74
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 1 03:41:13 2015 -0400
Permit the rotational period to change over time, using the input parameter rotational_period_dot which is its time derivative. Add the corresponding d(omega)/dt term to the rotating source terms (3D only right now for the source terms).
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/Src_3d/probin
Source/meth_params.f90
commit 8561dee6f67c459b9f658402a0dacd1badd57801
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 31 02:40:31 2015 -0400
1) Various pieces of cleanup, most notably using the passive map for advection more uniformly in all dimensions. 2) For 1D or 2D simulations, the unused transverse velocities are now passively advected like other scalar quantities such as the species. 3) Promoted the rotation data (both the potential and the acceleration) to state data. 4) Made both the rotation and gravity source terms dimension agnostic and work the same way, and pulled them out of Fortran umdrv call. 5) The gravitational acceleration now exists in all three dimensions for all simulations. However, this is not yet working with all gravity types in all dimensions.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
Source/Castro_setup.cpp
Source/Gravity.cpp
Source/Gravity_F.H
Source/Make.package
Source/Rotation.H
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Castro_grav_sources_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/riemann_1d.f90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trans_3d.f90
Source/Src_nd/Castro_nd.f90
Source/Src_nd/Gravity_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/Problem.f90
Source/Src_nd/Rotation_nd.f90
Source/Src_nd/gravity_sources_nd.f90
Source/Src_nd/interpolate.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/prob_params.f90
Source/Src_nd/rotation_nd.f90
Source/Src_nd/rotation_sources_nd.f90
Source/Src_nd/tagging_params.f90
commit fdde123f52c4155066f7d64d090a1e1fbcab2985
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 30 01:44:01 2015 -0400
Slightly better calculation of maximum radius for multipole phi.
Source/Src_3d/Gravity_3d.f90
commit ea93ddb2943cd285d132cf450759dc0a1f8380d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 29 02:16:14 2015 -0400
Corresponding to the new DIMENSION_AGNOSTIC makefile variable, permit dimension agnostic versions of bc_fill_nd.f90 and Prob_nd.f90. Also, add stub Prob_*d.f90 files that will throw an error at runtime if you haven't defined a local copy.
Exec/Detonation/Make.package
Exec/DustCollapse/Make.package
Exec/HCBubble/Make.package
Exec/KH/Make.package
Exec/RT/Make.package
Exec/RT_particles/Make.package
Exec/Sedov/Make.package
Exec/Sod/Make.package
Exec/Sod_stellar/Make.package
Exec/StarGrav/Make.package
Exec/Vortices_LWAcoustics/Make.package
Exec/convective_flame/Make.package
Exec/double_bubble/Make.package
Exec/evrard_collapse/Make.package
Exec/gamma_law_bubble/Make.package
Exec/hydrostatic_adjust/Make.package
Exec/oddeven/Make.package
Exec/reacting_bubble/Make.package
Exec/test_convect/Make.package
Exec/toy_convect/Make.package
Exec/uniform_cube_sphere/Make.package
Exec/xrb_mixed/Make.package
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_io.cpp
Source/Src_1d/Make.package
Source/Src_1d/Prob_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/Prob_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/Prob_3d.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/Prob_nd.f90
Source/Src_nd/bc_fill_nd.f90
commit 2b5a72429c022c36c1eed73738afbea273fa4912
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 29 00:12:32 2015 -0400
Replace a couple of instances of assumed indexing for velocities with explicit indexing.
Exec/Sod_stellar/trace_ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 29027b980567425143a9ea97bc2f8e4aac2f09d1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 29 00:08:24 2015 -0400
Some more improvements, including making all three gravity components exist regardless of problem dimensionality.
Exec/RT_particles/bc_fill_2d.f90
Exec/convective_flame/bc_fill_2d.f90
Exec/double_bubble/bc_fill_2d.f90
Exec/gamma_law_bubble/bc_fill_2d.f90
Exec/hydrostatic_adjust/bc_fill_1d.f90
Exec/reacting_bubble/bc_fill_2d.f90
Exec/test_convect/bc_fill_2d.f90
Exec/toy_convect/bc_fill_2d.f90
Exec/xrb_mixed/bc_fill_2d.f90
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/bc_fill_1d.f90
Source/Src_2d/bc_fill_2d.f90
Source/prob_params.f90
Source/sum_integrated_quantities.cpp
commit e2a9a4a2bcce4907b0eff42f2a800a8ab889465e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 28 22:19:10 2015 -0400
Revert the new EOS stuff; we'll save for this for when we merge in the new_eos branch.
EOS/eos_data.f90
Exec/Make.Castro
Networks/general_null/castro_burner.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/React_nd.f90
Source/Src_nd/compute_temp_nd.f90
Source/Src_nd/reset_internal_energy_nd.f90
commit 6b1902635a870a7d65cb302dca8fcd6c8046b58e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 28 21:20:27 2015 -0400
Fix function reference
Source/Derive_F.H
commit 5e9b00ab49bcfe62b67d33f85b57b4e030f73348
Merge: cec441b8c f2d025b2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 28 17:18:41 2015 -0400
Merge branch 'master' into dimension_agnostic
Conflicts:
Exec/RT/Prob_2d.f90
Exec/RT_particles/Prob_2d.f90
commit f2d025b2ae4eea43eaa197a5eeae5875ab5bc05f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 27 10:06:03 2015 -0400
add back in cutoff_density and H_min -- needed for Tagging
also add the phigravfill so this compiles
Exec/toy_convect/Prob_2d.f90
Exec/toy_convect/bc_fill_2d.f90
Exec/toy_convect/probdata.f90
commit 85a9720e78283e0d39857c173c20019de14ad63e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 27 09:55:56 2015 -0400
another note about bc_fill
UsersGuide/Software/CastroSoftware.tex
commit e620bc6a0ea6bc4e8b530f65bb80bf081d276706
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 26 22:06:28 2015 -0400
Remove ztwd from this branch
EOS/ztwd/Make.package
EOS/ztwd/_parameters
EOS/ztwd/eos_stuff.f90
commit 46af3f90e5d72ccb5c5cd4b47dc9bb3b0d1da4f9
Merge: e5b18f6e3 571f46fe2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 26 22:05:49 2015 -0400
Merge branch 'master' into new_eos
commit 571f46fe2764e57315bd26d065ace2736d404796
Merge: 048288fdd d3bac9c12
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 26 10:19:17 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 048288fdd248656071fb6f954cb616fd4cd90b9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 26 10:19:10 2015 -0400
Make a problem have conditional makefile variables
Exec/uniform_cube_sphere/GNUmakefile
commit e5b18f6e306c45377a79a134908e2e6751d0bf54
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 26 10:18:43 2015 -0400
In the burner, we cannot set the EOS types equal to each other to have the output state data be equal to the input state data -- that actually makes the derived types the same, instead of the intended effect which is just to have them each have the same data. So we do an explicit copy now.
EOS/eos_type.f90
Networks/burner.f90
commit d3bac9c126a6e5f0037a9ebe6b6ad5e191e6f9f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 26 10:12:27 2015 -0400
get this compiling again
Exec/double_bubble/bc_fill_2d.f90
commit d72dbbf9ca2d1feeaca8d87b55ae3a4ebc887af6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 26 10:08:13 2015 -0400
get this compiling again
Exec/hydrostatic_adjust/bc_fill_1d.f90
commit adbd4484a632adef1a328399376d5cb0aa28ac06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 26 10:05:29 2015 -0400
get this compiling again
Exec/reacting_bubble/bc_fill_2d.f90
commit 9ca42dea8c0a5920639ef86de3ca7675c3dbbc1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 25 23:11:33 2015 -0400
get this compiling again
Exec/xrb_mixed/bc_fill_2d.f90
commit b4b1a942440d621b839f9e41fffb66198e0738c0
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 25 11:55:01 2015 -0400
Add a network to general_null containing the same species as aprox13.
Networks/general_null/aprox13.net
commit 35ecf364e56f345295046b2c57806fdd2e07b04a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 25 03:34:31 2015 -0400
We can define the 1D working state internally rather than saving it as a separate module variable.
EOS/eos.f90
EOS/eos_type.f90
commit 1501adbd7a3d6219f17f6634733cd255359c436b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 21:08:21 2015 -0400
add the 3-d version
Exec/convective_flame/inputs.3d.test
Exec/convective_flame/probin.big
commit 813fc78e53a9bbe74afa9fcb1f4ceeaa03fa9ff5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 20:54:49 2015 -0400
missing
Networks/kpp/network.f90
commit e8aa17878928bfed6765c0df46f41dbb21096199
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 19:39:22 2015 -0400
compiles
Exec/convective_flame/Prob_3d.f90
Exec/convective_flame/bc_fill_3d.f90
commit 1a66dd4e7b3ecc976b04042a57452ccb52413108
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 19:32:47 2015 -0400
initial 3-d
Exec/convective_flame/Prob_3d.f90
commit d9267147200e7a801ce331f2bea8eb2a943e6117
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 19:20:46 2015 -0400
first cut at the 3-d BCs
Exec/convective_flame/bc_fill_3d.f90
commit 69de48a51b841b2de7204e7dadc3d76a828a4eef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 16:19:32 2015 -0400
hock in the kpp burner
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Prob_2d.f90
commit f8765c8228e9c0bdd7a8cb6224c4750ab6aa09c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 16:18:07 2015 -0400
fixes
Networks/kpp/castro_burner.f90
Networks/kpp/f_rhs.f90
commit 3008251b62a3e35254e1f13332c5d0f6f07ad217
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 16:12:19 2015 -0400
start of a simple KPP reaction
Networks/kpp/Make.package
Networks/kpp/_parameters
Networks/kpp/castro_burner.f90
Networks/kpp/f_rhs.f90
commit 5b08a40319f355eeebb455091e4dee7e656c6b5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 15:57:28 2015 -0400
start of a toy convective flame problem with Andy
Exec/convective_flame/GNUmakefile
Exec/convective_flame/Make.package
Exec/convective_flame/Prob_2d.f90
Exec/convective_flame/README
Exec/convective_flame/bc_fill_2d.f90
Exec/convective_flame/inputs_2d_MAESTRO.big
Exec/convective_flame/probdata.f90
Exec/convective_flame/probin.big
commit 13783237970d7f9bba2775ffb48c38b69caa09a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 15:43:17 2015 -0400
remove some unused stuff from here (including Maestro initialization)
Exec/gamma_law_bubble/Prob_2d.f90
Exec/gamma_law_bubble/probdata.f90
commit b0ac1607854b7d0ebf87afe19f0ad8ccc106e3b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 15:43:02 2015 -0400
add the phigravfill routine
Exec/gamma_law_bubble/bc_fill_2d.f90
commit 7c20d95342a2242557f0e9ef6f573dac8613eab6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Aug 21 17:06:00 2015 -0700
added a 3-level regression test with Poisson gravity
Exec/DustCollapse/inputs_3d_poisson_regtest
Exec/DustCollapse/probin_3d_poisson_regtest
commit c78100aab45822df6096cfe3f52d12bf7fffac49
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Aug 21 15:55:03 2015 -0700
FineAdd in sync solve should only be done in the last iteration
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
commit c9ec6ecf6d255e151b1b5cdd1f6100dab4e43c18
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 21:56:20 2015 -0700
area was missing in a FineADD
Source/Gravity.cpp
commit e92536711f3fb85bde45cfa688451ddde24e9dad
Merge: 420716c6a efea71679
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 20:34:46 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 420716c6a954d0be464a7676986966bcb2bc946a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 20:25:00 2015 -0700
fixed a bug that was fixed and then reintroduced
Source/Gravity.cpp
commit efea7167984077c220baa1a2fc5285bb1c7589cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 20 20:02:32 2015 -0400
ok, this has the co-moving frame stuff working
Util/exact_riemann/exact_riemann.f90
commit 2562d03d5f2c8cf3cc3cb001f4d3c681e0ae0f2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 20 19:42:27 2015 -0400
these files are pulled from ppm-blend -- I accidently commited them there
Util/exact_riemann/_parameters
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/inputs.moving
commit 1019f9d00ae8a4475a702e68a152beff5172c169
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 14:22:03 2015 -0700
use previous as guess in post_regrid multi-level solve
Source/Castro.cpp
Source/Gravity.cpp
commit b7e71b691f47e3f348447a3883c1a3f910c9b724
Merge: ab92e5857 56935ff29
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 13:49:04 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit ab92e58578afba632dc97a044918ec0b31ef4416
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 13:47:22 2015 -0700
phi is only used in Poisson gravity, but we need to make sure it doesn't contain nans
Source/Castro_advance.cpp
commit d0453a6de8daf89d1a61125eb08a3ee5f2dd9fa8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 10:54:34 2015 -0700
update bc fill functions
Rad2Tshock/Prob_1d.f90
Rad2Tshock/bc_fill_1d.f90
RadBreakout/Prob_1d.f90
RadCoreCollapse/Make.package
RadCoreCollapse/bc_fill_1d.f90
RadCoreCollapse/bc_fill_2d.f90
RadCoreCollapse/bc_fill_3d.f90
RadShestakovBolstad/Prob_1d.f90
RadSlope/Prob_1d.f90
RadSphere/Prob_1d.f90
RadSuOlson/Prob_1d.f90
RadSuOlsonMG/Prob_1d.f90
RadThermalWave/Prob_1d.f90
RadThermalWave/Prob_2d.f90
RadThermalWave/Prob_3d.f90
commit 56935ff29c4b115f28eea055b28e22ca16af0662
Merge: 70b814801 0d14dbae4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 20 13:35:41 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 70b814801c692be0129408a403e5ff6be6efa55f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 20 13:35:26 2015 -0400
add a description of the transverse_* runtime parameters
UsersGuide/Equations/Equations.tex
commit 0d14dbae4b5d97510f9528011b45f34a70d7d4d7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 10:33:38 2015 -0700
forgot to put new_grav_mf inside ifdef GRAVITY. added radfill to
bc_fill functions for radiation.
Source/Castro.cpp
Source/Src_1d/bc_fill_1d.f90
Source/Src_2d/bc_fill_2d.f90
Source/Src_3d/bc_fill_3d.f90
commit 0a53642799fe31b5ffcea81d746687192a68ff79
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 09:07:15 2015 -0700
fill phi in Castro::init called in regrid
Source/Castro.cpp
commit fc9fbf755c6b698360fd1fb45f538d21afb9bafb
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 07:47:31 2015 -0700
don't need to set new phi to zero in Castro constructor so that it could have previous or newly interpolated values when a new Castro AmrLevel is created
Source/Castro.cpp
commit 8f8185316f96ff4e14ab6f824580667a1d3292cf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 07:15:29 2015 -0700
put Poisson solver stuff into if block
Source/Castro_advance.cpp
commit 5166db6272bdf9cdefe4637e85cc881a1b6b8c15
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Aug 20 06:55:49 2015 -0700
swap grad_phi only of the gravity type is Poisson
Source/Gravity.cpp
commit 5dfb815fe03933c59e4e2aa7f27a29c77157433f
Merge: 8f9c135fe 15fd33f53
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 20 01:40:10 2015 -0400
Merge branch 'master' into new_eos
commit 8f9c135feef6e3ce2c471d71ffdf40ea6b63f745
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 20 01:36:44 2015 -0400
Missing module include
EOS/eos_type.f90
commit a5c4475fb3c66f948bd08ceef9079c540b8f05fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 20 01:25:30 2015 -0400
Use bl_allocate and bl_deallocate, and add an explicit destructor function after we've created an EOS type. Only implemented in 3D right now.
EOS/eos.f90
EOS/eos_type.f90
Networks/burner.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/React_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit 15fd33f53ade9bba89e711b827075fcac1f89301
Merge: ef2befc94 ecfa22001
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 20 01:11:48 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit ef2befc9459931623e991c7f9575d3d365a11f67
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 20 01:11:27 2015 -0400
Make some variable declarations conditional.
Exec/KH/GNUmakefile
commit ecfa220012e02e8764dc3c5105fb41b4c656b826
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 19 21:12:59 2015 -0700
use phi_old - comp_minus_level as initial guess for new phi solve
Source/Castro_advance.cpp
commit ad5c75dc5a33f9b7ff325d40ecb29456aab5ba72
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 19 17:45:29 2015 -0700
use previous old phi as initial guess
Source/Gravity.cpp
commit efc9470ac5d79c0d2c75974b0811d63958426a4e
Merge: d3dc52126 4b29303cf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 19 17:18:30 2015 -0700
Merge branch 'phi'
commit 4b29303cf2648f963d5e33faf0aeb4fe8c0cd3cd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 19 16:49:29 2015 -0700
always use bnorm unless it's periodic
Source/Gravity.cpp
commit d3dc521261e3719d2dea1e8dfdd9ddc074e8cd5b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 19 15:06:03 2015 -0400
Make KH problem callable from external locations.
Exec/KH/GNUmakefile
Exec/KH/inputs.2d
Exec/KH/inputs.3d
commit 174b16f07acbe690f12764741a69119199262049
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 19 11:15:40 2015 -0700
Revert "made level + sync = composite". We will achieve level + sync
= composite to tolerance error by simply making MG use bnorm for
convergence test.
This reverts commit 88e47094abcb6e1dd247ec4b3300560c9c55c1bf.
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.H
Source/Gravity.cpp
commit a0e306554b78ac78725903fc3ba91275970fd00e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 16 21:15:40 2015 -0400
Remove unused variable reference
Source/Src_3d/Gravity_3d.f90
commit c0ebbdb3b9d159fdbb40dd964fb5f7d808fd6338
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 18 21:22:13 2015 -0400
Compute multipole moments (both upper and lower) for a set of concentric shells that have the same slicing as the radial_mass array used in MonopoleGrav. At present we only use the outermost one for the purposes of computing the boundary conditions in a PoissonGrav solve.
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
commit e89005a59296e8c0fc3bfc048220be15264bb78f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 16 04:15:44 2015 -0400
Update to reflect name changes in Microphysics
EOS/eos.f90
EOS/gamma_law_general/gamma_law_general.f90
commit 88e47094abcb6e1dd247ec4b3300560c9c55c1bf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Aug 14 09:54:12 2015 -0700
made level + sync = composite
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.H
Source/Gravity.cpp
commit c51ad881c776cfa108e46476cf4613b1b5ed1d28
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 12 22:35:11 2015 -0700
use proper boundary conditions in testing composite phi
Source/Gravity.cpp
commit 9a4259e271bf1a5c399e0e7891d62e3d612e08ae
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 11 16:40:44 2015 -0400
Amend previous commit so that we get the contribution from the refluxing as well.
Source/Gravity.cpp
commit c2887ef939bb161af05fadf8b1f8c926fcb38ec3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 11 16:31:43 2015 -0400
When we do a gravity sync starting at level 0, change two things: 1) take the part of the source term corresponding to the contribution from the average down and use it to calculate new boundary values on delta phi. This ensures that the boundary value for phi on the coarse grid is equal to what we would do if we did a coarse grid level solve after the average down. 2) Subtract that part of the source term from the source term that goes into solve_for_delta_phi, since the algorithm is intended to use only changes just outside the coarse-fine boundary anyway.
Source/Gravity.cpp
commit b7f79a02179bf6cc399749d4f7f10a8b5621e693
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 11 01:09:32 2015 -0400
Add the zero-temperature electron degenerate white dwarf equation of state of Chandrasekhar (1935).
EOS/README
EOS/ztwd/Make.package
EOS/ztwd/_parameters
EOS/ztwd/eos_stuff.f90
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 2b8c139c547bf1647240581fd2c725a9cc209459
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 10 17:46:15 2015 -0700
fixed curly braces mismatch in 2d
Source/Castro_setup.cpp
commit 9479fad7f21d86ed09353060918a76d4c3015e7b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 8 23:45:52 2015 -0400
We need to use pointers instead of allocatables inside the EOS structure, for the Cray compilers to be happy.
EOS/eos_type.f90
commit 46ef40da296c9d91b51ee2808555aad5f3c6439e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 8 17:51:09 2015 -0400
We were forgetting to set the initialized variable.
EOS/eos.f90
commit 12e849979507c9509e693d97624b88fa5b2a57e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 7 14:24:27 2015 -0400
Castro has gone through the paperwork for BSD license
license.txt
commit f23ab347dace7ecaea034856498f08763cb3a36f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Aug 5 15:06:56 2015 -0400
On a restart, we want to use the previous phi (i.e. what we've read in from the checkpoint) as a guess to the multilevel solve, so do this explicitly. In principle the multilevel solve should not need to do any iterations, if the phi in the checkpoint satisfied the Poisson equation within the given tolerance. Also, in the multilevel solve, don't erase the interior values with make_radial_phi if we said we want to use the previous phi.
Source/Castro.cpp
Source/Gravity.cpp
commit f92fc5469b3a1ed54d65e555b19319143381a4d6
Merge: 9b9b19066 026471390
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 18:40:55 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 9b9b19066e98d3ac3b6c5df54ff47d56fcbabac4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 18:40:46 2015 -0400
a better inputs files
Exec/StarGrav/inputs_2d
commit 026471390edba4a505cdf8c19c3c1f333b5f23b3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jul 31 13:44:57 2015 -0700
changed default tile size for hydro
Source/Castro.cpp
commit cc8733419bb4d98231faaeb507e0e61209fb55ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 15:48:19 2015 -0400
trace gravity
Exec/StarGrav/inputs_2d
commit 72ad99f898cb31619cbc3b624eddce20d9fa443b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 15:44:41 2015 -0400
update the parameters -- this runs but looks crappy right now.
Exec/StarGrav/inputs_2d
Exec/StarGrav/probin
commit ff4988d3120550a897457176907d816cb6d2341e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 15:26:45 2015 -0400
change defaults
Exec/StarGrav/GNUmakefile
commit bbdd2629cfb80b40b5d25349e10570153bafab6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 15:12:24 2015 -0400
move an updated version of the original stargrav problem from
Castro paper I over to the main Castro source distriubtion.
At a minimum, this demonstrates how to map a star on a grid.
I still need to tweek the settings for this problem to get things
running optimally
Exec/StarGrav/GNUmakefile
Exec/StarGrav/Make.package
Exec/StarGrav/Prob_1d.f90
Exec/StarGrav/Prob_2d.f90
Exec/StarGrav/Prob_3d.f90
Exec/StarGrav/WD_rhoc_2.e9_M_1.1.hse.2560
Exec/StarGrav/inputs_1d
Exec/StarGrav/inputs_2d
Exec/StarGrav/inputs_3d
Exec/StarGrav/probdata.f90
Exec/StarGrav/probin
Exec/StarGrav/sponge_1d.f90
Exec/StarGrav/sponge_2d.f90
Exec/StarGrav/sponge_3d.f90
commit 8b799d546db921a8ad8cc944e38f339dcc95f54f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 15:03:12 2015 -0400
add a new net for Maestro compatibility
Networks/general_null/ignition_wdconvect.net
commit a9c77afd692755e229a6ebc597859f6af0f8f8fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 14:23:58 2015 -0400
npts_model should not be in the namelist -- it comes from model_parser
Exec/reacting_bubble/Prob_2d.f90
Exec/reacting_bubble/probin
Exec/reacting_bubble/probin.zoom
commit 3e8e2745dc0ad446fb8fe2c40a4d87f0777ccc6f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 30 15:31:34 2015 -0500
Define parsec as a double precision number, not in terms of other constants.
constants/constants_cgs.f90
commit 9d6ad513edb89f47c43f71006ebd6a5eb0484787
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jul 29 11:00:34 2015 -0700
added a regression test inputs file
Exec/DustCollapse/inputs_3d_poisson_regtest_restart
commit 71ac344967227c0fe72ec690ed9b971feed463eb
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 27 16:54:33 2015 -0700
Checkpoint files now save checkpoint version in CastroHeader file.
The current version is 1. If CastroHeader file is missing, we call
that checkpoint version 0. The code can read versions 0 and 1.
Because version 0 checkpoint files do not contain phiGrav, we simply
set phiGrav zero in restart.
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
commit d506c8b7a8f6547dcaebbd082c589339ff6e227b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 27 13:45:30 2015 -0700
Do not need to do anything special to write phiGrav into plotfile because it's already in the state; otherwise we end up with two copies of phiGrav in plotfiles.
Source/Castro_io.cpp
commit 6ed6c33ce4e58183b2b1d108f26d65fd63514c3f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 27 13:26:37 2015 -0700
added subroutine ca_phigravfill for 3D DustCollapse
Exec/DustCollapse/bc_fill_3d.f90
commit 043f21c10913b29a68a51ab7b2b10102450338e2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 27 11:16:39 2015 -0700
update the dimension agnostic codes because the interface has changed
Rad_nd.f90
commit 3521a6cf7561dc52c42d57aab254f7eb5d23d2ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 24 14:04:22 2015 -0400
Fix reference to no longer existing macro
Source/Castro_F.H
commit 23f2fbc6b2a0d4e86e8e28619cde6593793e6a26
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 24 14:03:54 2015 -0400
Fix reference to no longer existing macro
RAD_F.H
commit dfdd3629fa477e2d04a463ce23d0a7394d7ad0b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 24 11:04:58 2015 -0500
Bug fix: we were getting new phigrav data when we should have been getting old phigrav data.
Source/Gravity.cpp
commit 980b5d0c7d07b443d3232251f819c100500c93ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 23 15:04:51 2015 -0400
Switch from specific_* to actual_*
Networks/burner.f90
Networks/general_null/general_null_burner.f90
Networks/general_null/network.template
Networks/network.f90
commit 946b5af6d901ba88fcd7454eac9b4ac5b6f41b07
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 22 14:25:15 2015 -0400
Update of the EOS and network sections in the user's guide to reflect the fact that most of the equations of state are living in Microphysics now.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit aed91cc93fcc749e23f4dc7dc51bee892b8160a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 22 14:24:29 2015 -0400
For the test suite problems that require Helmholtz EOS or other advanced networks, throw an error and fail to compile if we don't have MICROPHYSICS_DIR set as an environment variable.
EOS/README
Exec/Detonation/GNUmakefile
Exec/Sod/GNUmakefile
Exec/Sod_stellar/GNUmakefile
Exec/hydrostatic_adjust/GNUmakefile
Exec/reacting_bubble/GNUmakefile
Exec/test_convect/GNUmakefile
Exec/toy_convect/GNUmakefile
Exec/xrb_mixed/GNUmakefile
Util/exact_riemann/GNUmakefile
Util/exact_riemann/README
commit 111c878ff75474d3bc9659c20029cc816e3cd32b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 22 11:38:29 2015 -0500
Since we are always using the previous phi as a guess in the Poisson solve, we don't want to use fill_interior in Castro::advance() when calling solve_for_phi.
Source/Castro_advance.cpp
commit a4989ae46cabbca332d955a75d8260c4b5c1b9ad
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 22 02:16:17 2015 -0400
Move all of the EOS and network interface source from Microphysics to here. However, we only retain the gamma_law_general EOS and the general_null network.
EOS/Make.package
EOS/_parameters
EOS/eos.f90
EOS/eos_data.f90
EOS/eos_type.f90
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/_parameters
EOS/gamma_law_general/eos_stuff.f90
EOS/gamma_law_general/gamma_law_general.f90
EOS/gamma_law_general/test/GNUmakefile
EOS/gamma_law_general/test/GPackage.mak
EOS/gamma_law_general/test/dummy.probin.template
EOS/gamma_law_general/test/testeos.f90
EOS/helmeos/Make.package
EOS/helmeos/README
EOS/helmeos/_parameters
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helm_loop.dek
EOS/helmeos/helm_table.dat
EOS/helmeos/helmeos.f90
EOS/helmeos/test/GNUmakefile
EOS/helmeos/test/GPackage.mak
EOS/helmeos/test/dummy.probin.template
EOS/helmeos/test/testeos.f90
EOS/multigamma/Make.package
EOS/multigamma/_parameters
EOS/multigamma/eos_stuff.f90
EOS/multigamma/test/GNUmakefile
EOS/multigamma/test/GPackage.mak
EOS/multigamma/test/dummy.probin.template
EOS/multigamma/test/testeos.f90
EOS/polytrope/Make.package
EOS/polytrope/_parameters
EOS/polytrope/eos_stuff.f90
EOS/stellarcollapse/Make.package
EOS/stellarcollapse/README
EOS/stellarcollapse/_parameters
EOS/stellarcollapse/eos_aux_data.f90
EOS/stellarcollapse/eos_stuff.f90
EOS/stellarcollapse/test/GNUmakefile
EOS/stellarcollapse/test/GPackage.mak
EOS/stellarcollapse/test/dummy.probin.template
EOS/stellarcollapse/test/probin
EOS/stellarcollapse/test/simple.net
EOS/stellarcollapse/test/testeos.f90
Exec/Make.Castro
Networks/Make.package
Networks/burner.f90
Networks/general_null/Make.package
Networks/general_null/castro_burner.f90
Networks/general_null/general_null_burner.f90
Networks/general_null/general_null_network.f90.test
Networks/general_null/network.template
Networks/ignition_simple/Make.package
Networks/ignition_simple/burner_aux.f90
Networks/ignition_simple/castro_burner.f90
Networks/ignition_simple/f_rhs.f90
Networks/ignition_simple/network.f90
Networks/ignition_simple/test/GNUmakefile
Networks/ignition_simple/test/GPackage.mak
Networks/ignition_simple/test/dummy.probin.template
Networks/ignition_simple/test/eval.f90
Networks/ignition_simple/test/testburn.f90
Networks/ignition_simple/test/testjacobian.f90
Networks/network.f90
Networks/screen.f
commit b2bf8ed56eb0392e2cdfb00b196e6bf45b7412cb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 21 20:58:22 2015 -0400
In the Gravity class, remove the phi_curr and phi_prev MultiFabs and replace references to them everywhere with the new and old PhiGrav_Type data. This effectively makes the gravitational potential a state variable.
Source/Castro_advance.cpp
Source/Castro_io.cpp
Source/Castro_setup.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/sum_utils.cpp
commit eca3fbe1ecc92dfa8759777d2fefc47be54de753
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 21 14:58:08 2015 -0400
We now plot the PhiGrav_Type data instead of the phi MultiFab in Gravity, and we remove the castro.plot_phiGrav parameter; it will automatically be put in the plotfile if we're using gravity. However this isn't currently filled with real data.
Exec/uniform_cube_sphere/inputs
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
UsersGuide/Inputs/CastroInputs.tex
commit 7380a119083c0070ff756cdc9990f18703a6629b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 21 04:49:43 2015 -0400
Define a PhiGrav_Type that lives in the StateData.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_setup.cpp
Source/Src_1d/bc_fill_1d.f90
Source/Src_2d/bc_fill_2d.f90
Source/Src_3d/bc_fill_3d.f90
UsersGuide/Software/CastroSoftware.tex
commit 136154ee7c303c1deded2bceeb2c3b6cc89d80e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 21 04:07:04 2015 -0400
Move the boundary condition fill routines to a separate file, bc_fill_*d.f90. They no longer need to be included in your Prob_*d.f90 file, nor in your problem setup at all unless you want to specify specific fill routines that overwrite the generic routines.
Exec/Detonation/Prob_1d.f90
Exec/Detonation/Prob_2d.f90
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/bc_fill_3d.f90
Exec/HCBubble/Prob_3d.f90
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/RT/Prob_2d.f90
Exec/RT/Prob_3d.f90
Exec/RT_particles/Prob_2d.f90
Exec/RT_particles/bc_fill_2d.f90
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
Exec/Sedov/bc_fill_1d.f90
Exec/Sedov/bc_fill_2d.f90
Exec/Sedov/bc_fill_3d.f90
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
Exec/Sod_stellar/Prob_1d.f90
Exec/Sod_stellar/Prob_2d.f90
Exec/Sod_stellar/Prob_3d.f90
Exec/Vortices_LWAcoustics/Prob_2d.f90
Exec/double_bubble/Prob_2d.f90
Exec/double_bubble/bc_fill_2d.f90
Exec/evrard_collapse/Prob_3d.f90
Exec/gamma_law_bubble/Prob_2d.f90
Exec/gamma_law_bubble/bc_fill_2d.f90
Exec/hydrostatic_adjust/Prob_1d.f90
Exec/hydrostatic_adjust/bc_fill_1d.f90
Exec/oddeven/Prob_2d.f90
Exec/test_convect/Prob_2d.f90
Exec/test_convect/bc_fill_2d.f90
Exec/toy_convect/Prob_2d.f90
Exec/toy_convect/bc_fill_2d.f90
Exec/uniform_cube_sphere/Prob_3d.f90
Exec/xrb_mixed/Prob_2d.f90
Exec/xrb_mixed/bc_fill_2d.f90
Source/Src_1d/Make.package
Source/Src_1d/bc_fill_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/bc_fill_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/bc_fill_3d.f90
UsersGuide/Software/CastroSoftware.tex
commit 3ae09a24d6b26661da3d298b0756190f5087241b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 18:14:17 2015 -0400
Add a new parameter castro.dual_energy_eta3. Like dual_energy_eta1, this determines whether we use (E - K) or e, but in this case it is used for reactions. By default it is set to 0, meaning that it is effectively non-functional and we retain the old behavior of always using e. This should allow us to experiment in the future with which energy we want to send to the burner.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/React_1d.f90
Source/Src_2d/React_2d.f90
Source/Src_3d/React_3d.f90
Source/meth_params.f90
commit 09047c7173fdf03b8b630ab81e1456ee3d4179ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:48:33 2015 -0400
Some bugfixes from the transfer
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_react.cpp
commit 5d0b63c6e29d3340497f10639cd92ed3aaf8ea22
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:33:24 2015 -0400
In compute_temp, don't reset the total energy to internal + kinetic. Instead, just add the change in internal energy.
Source/Src_1d/compute_temp_1d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_3d/compute_temp_3d.f90
commit b3541bcb7e9fb551af8005246719b675ebfca4e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:28:36 2015 -0400
Revert "Make the react_state function dimension agnostic using the new BoxLib macros."
This reverts commit 0f420e79fd3b6700c881a6f3a6d59344c8782b6b.
Conflicts:
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_3d/React_3d.f90
Exec/Make.Castro
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_1d/Make.package
Source/Src_1d/React_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/React_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/React_3d.f90
Source/Src_nd/Make.package
commit a2041c387d1a5de6238ee3dc7df3fe5e30bfcc4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:22:07 2015 -0400
Revert "Dimension agnosticify compute_temp, plus a bugfix for react_state."
This reverts commit 3c7f7ebb7fe8dd20cb600c9bc7f70d4d371f151e.
Conflicts:
Source/Src_nd/React_nd.f90
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_1d/compute_temp_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/compute_temp_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/compute_temp_3d.f90
Source/Src_nd/Make.package
commit 6687fb69571922357edaa71e3ff137339e95399d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:21:03 2015 -0400
Revert "Always include y- and z-momenta in the state vector, even in 1D or 2D."
This reverts commit b5fa34c9a87de0123e1fbeb15144ff44c9db1e9c.
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
commit 9a0a2d8b63acf6abc1405d8d4393aefc85e5c6dc
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:20:56 2015 -0400
Revert "Accidentally deleted QLAST"
This reverts commit 38580eefee48189d82f96013880c39153ffddcd0.
Source/Castro_nd.f90
commit cf388ce67c53f81cf9ff0ba166d7cbd3ac864021
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:20:25 2015 -0400
Revert "Dimension agnostic version of reset_internal_e."
This reverts commit 71df28cc637434b9be7095d7385a8d4548275383.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_nd/Make.package
commit 500786ea1709ca985592f4261949e4e8474ccbbe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:20:17 2015 -0400
Revert "Dimension agnostic version of enforce_consistent_e"
This reverts commit 058f749755f043083f774297864822134f6391d6.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_1d/enforce_consistent_e_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/enforce_consistent_e_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/enforce_consistent_e_3d.f90
Source/Src_nd/Make.package
commit 2e1b4856b3094294f07a7956ad2c8a283abdbafe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:20:05 2015 -0400
Revert "Dimension agnostic version of integral quantities in Castro_sums_nd.f90."
This reverts commit feee1270d0b61fdf282cf912924c65b3cc552b0e.
Conflicts:
Source/Castro_react.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Gravity.cpp
Source/Src_1d/Castro_sums_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Castro_sums_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/sum_utils.cpp
commit 7902d82592a3e6c340a97c0a979e4d8682ebb8a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:18:55 2015 -0400
Revert "Dimension agnostic EstDt_nd.f90."
This reverts commit dd3afccb1e1a3f42ef36229d9887d315e4d2b250.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
commit 935ab53fd6a075505f9891f74efa49fddec46828
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:18:47 2015 -0400
Revert "Dimension agnostic prescribe_grav_nd.f90."
This reverts commit 19f52489b35decdb421c092be719d623bf3797d5.
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_2d/Make.package
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/prescribe_grav_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/prescribe_grav_nd.f90
UsersGuide/Gravity/CastroGravity.tex
commit 63553896e2d57d1ca7c4eccde078ba7e17911f51
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:18:12 2015 -0400
Revert "In compute_temp, don't reset the total energy to internal + kinetic. Instead, just add the change in internal energy. If the user desires to force rho*E = rho*e + rho*K then that will be enforced in reset_internal_e."
This reverts commit 4c98dc3431279d378fdbb436320a5c5040b9bd1e.
Source/Src_nd/compute_temp_nd.f90
commit 2ecadc2e26308df79c51533c551f5acb7f0d67e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:17:51 2015 -0400
Revert "Dimension agnostic Derive_nd.f90. Relies on recent BoxLib changes defining a dimension agnostic DeriveFunc3D type."
This reverts commit cec441b8cd38e9016f049d93e1b8d468fd043e5b.
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_1d/Derive_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Derive_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Derive_3d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
commit 19c9a1c02bae24666faa376e3d740075cdc5e779
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:17:37 2015 -0400
Revert "Remove _nd specifier on dimension agnostic Fortran routines; there's only one of each by design, so it's redundant."
This reverts commit 3c44c8a3f77610e20276245f76a6df1305b47e80.
Source/Src_nd/Castro_sums_nd.f90
Source/Src_nd/Derive_nd.f90
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/Make.package
Source/Src_nd/React_nd.f90
Source/Src_nd/compute_temp_nd.f90
Source/Src_nd/enforce_consistent_e_nd.f90
Source/Src_nd/prescribe_grav_nd.f90
Source/Src_nd/reset_internal_energy_nd.f90
commit e995746ed971f2a04fb1cd13163dd0aeade75cbf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:17:25 2015 -0400
Revert "Move existing dimension agnostic routines to Src_nd"
This reverts commit 1ccf9f1ffc4831bbf6f2a0799ed853390c70d6ee.
Source/Castro_nd.f90
Source/Gravity_nd.f90
Source/Make.package
Source/Problem.f90
Source/Src_nd/Make.package
Source/extern_probin.template
Source/interpolate.f90
Source/meth_params.f90
Source/prob_params.f90
Source/tagging_params.f90
commit 8d913f8255786e592d2c2de7eb7abe9e32b7015d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:17:14 2015 -0400
Revert "Dimension agnostic problem tagging routine."
This reverts commit a122b40de5aae72ea27a6012a6b685292616eecf.
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_1d/Make.package
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/problem_tagging.f90
commit 40751f5053d14adc4946de4a918d8dad8dfe13d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:17:02 2015 -0400
Revert "Argument is not constant in the BoxLib interface"
This reverts commit c4157f65b7dee88b376fa13bfca05ef3cc0aefab.
Source/Derive_F.H
commit c4157f65b7dee88b376fa13bfca05ef3cc0aefab
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 14:01:10 2015 -0400
Argument is not constant in the BoxLib interface
Source/Derive_F.H
commit a122b40de5aae72ea27a6012a6b685292616eecf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 12:26:54 2015 -0400
Dimension agnostic problem tagging routine.
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_1d/Make.package
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/problem_tagging_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/problem_tagging.f90
commit 1ccf9f1ffc4831bbf6f2a0799ed853390c70d6ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 12:15:44 2015 -0400
Move existing dimension agnostic routines to Src_nd
Source/Make.package
Source/Src_nd/Castro.f90
Source/Src_nd/Gravity.f90
Source/Src_nd/Make.package
Source/Src_nd/Problem.f90
Source/Src_nd/extern_probin.template
Source/Src_nd/interpolate.f90
Source/Src_nd/meth_params.f90
Source/Src_nd/prob_params.f90
Source/Src_nd/tagging_params.f90
commit 3c44c8a3f77610e20276245f76a6df1305b47e80
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 12:13:00 2015 -0400
Remove _nd specifier on dimension agnostic Fortran routines; there's only one of each by design, so it's redundant.
Source/Src_nd/Castro_sums.f90
Source/Src_nd/Derive.f90
Source/Src_nd/EstDt.f90
Source/Src_nd/Make.package
Source/Src_nd/React.f90
Source/Src_nd/compute_temp.f90
Source/Src_nd/enforce_consistent_e.f90
Source/Src_nd/prescribe_grav.f90
Source/Src_nd/reset_internal_energy.f90
commit cec441b8cd38e9016f049d93e1b8d468fd043e5b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 11:59:50 2015 -0400
Dimension agnostic Derive_nd.f90. Relies on recent BoxLib changes defining a dimension agnostic DeriveFunc3D type.
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Src_1d/Derive_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Derive_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Derive_nd.f90
Source/Src_nd/Make.package
commit 67253602fe7acfc8bf10511051a36624e3b8db9a
Merge: 1bdae512d 10144fb0c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 19 07:00:41 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 4c98dc3431279d378fdbb436320a5c5040b9bd1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 19 01:20:07 2015 -0400
In compute_temp, don't reset the total energy to internal + kinetic. Instead, just add the change in internal energy. If the user desires to force rho*E = rho*e + rho*K then that will be enforced in reset_internal_e.
Source/Src_nd/compute_temp_nd.f90
commit b1c0af954d43e88722a678d35474e37295f5fa9c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 18 13:24:57 2015 -0400
Add a parameter ngrow to react_half_dt that determines the number of ghost cells to burn in. Defaults to zero, and will only have any effect if the MultiFab actually has ghost cells.
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 7796db56b5b0d6405d1f9f7e4f96aea19330818a
Merge: 924017617 10144fb0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 18 02:08:59 2015 -0400
Merge branch 'master' into openacc
Conflicts:
.gitignore
commit 10144fb0c280ee83f27eab30ff7d5af0a10231f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 18 02:08:15 2015 -0400
Add user's guide PDFs to the .gitignore list
.gitignore
commit 924017617c657e41be6a15a36b23956661a2e62a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 18 02:05:10 2015 -0400
Remove ReactMF multifab, as it isn't presently used in the code anywhere. It looks like estdt_burning may have relied on it at some point -- but we can always reconstruct de/dt and dX/dt using the old and new state data, if needed, rather than making another copy of the data.
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_nd/React_nd.f90
commit 36f176856bebf5f45853d06f5a89fe5fe6ea8890
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 18 01:47:58 2015 -0400
Remove the S_old/S_new distinction in react_state -- we just update the state in place. Also, use mfi.growntilebox() instead of mfi.tilebox(); this correctly gives us non-overlapping interior boxes for the second-half burn, and also non-overlapping interior boxes with ghost cells outside the domain for the first-half burn.
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_nd/React_nd.f90
commit 1bdae512d7cae2560c1190cd06a061e40575303f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jul 17 18:15:37 2015 -0700
clean up
Source/Gravity.cpp
commit 4727246280cc41abdd019613d659e3da6a081c14
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jul 17 17:53:32 2015 -0700
clean up
Source/Gravity.cpp
commit c10ad926611cfde4be688608094d87ae06f9e4a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 16:45:58 2015 -0400
Since we react with the same function, eliminate reactState and place all the functionality in react_half_dt.
Source/Castro.H
Source/Castro_react.cpp
commit 9d6ce29fd8447e8fcbe3080bb2f88783ef2a929d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 16:39:49 2015 -0400
Remove the option to react on ghost cells in react_second_half_dt since the S_new state doesn't have ghost cells.
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit a5ea524a5cbe63863bb7c5cb9655538cd5280637
Merge: 19f52489b 2efbfabc3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 02:52:20 2015 -0400
Merge branch 'master' into openacc
Conflicts:
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
commit 19f52489b35decdb421c092be719d623bf3797d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 02:45:24 2015 -0400
Dimension agnostic prescribe_grav_nd.f90.
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_2d/Make.package
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/prescribe_grav_3d.f90
Source/Src_nd/Make.package
Source/Src_nd/prescribe_grav_nd.f90
UsersGuide/Gravity/CastroGravity.tex
commit dd3afccb1e1a3f42ef36229d9887d315e4d2b250
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 02:25:59 2015 -0400
Dimension agnostic EstDt_nd.f90.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/EstDt_nd.f90
Source/Src_nd/Make.package
commit f6998fee81786ced504680b346f4c34108e998b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 00:11:28 2015 -0400
Only do react_state I/O if do_react == 1.
Source/Castro_react.cpp
commit 7fab51f79258aa4d7946afbff951b1223398b98e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 00:09:34 2015 -0400
Some cleanup of sum_integrated_quantities.cpp, and also make sure that we don't attempt to open a data log if we didn't enter any in the inputs file.
Source/sum_integrated_quantities.cpp
commit feee1270d0b61fdf282cf912924c65b3cc552b0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 17 00:08:57 2015 -0400
Dimension agnostic version of integral quantities in Castro_sums_nd.f90.
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_react.cpp
Source/Gravity.cpp
Source/Src_1d/Castro_sums_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Castro_sums_nd.f90
Source/Src_nd/Make.package
Source/sum_utils.cpp
commit 636432494d4c5f709e08651e14529b5aefe07d66
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 21:21:43 2015 -0400
Store number of dimensions in prob_params
Source/Castro_nd.f90
Source/prob_params.f90
commit c25db198741014447170a204f637a19f199f8b2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 21:17:14 2015 -0400
network.f90 is now general_null_network.f90 when created, so that's what we want to ignore.
.gitignore
commit 058f749755f043083f774297864822134f6391d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 21:15:36 2015 -0400
Dimension agnostic version of enforce_consistent_e
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_1d/enforce_consistent_e_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/enforce_consistent_e_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/enforce_consistent_e_nd.f90
commit 71df28cc637434b9be7095d7385a8d4548275383
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 21:07:58 2015 -0400
Dimension agnostic version of reset_internal_e.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/reset_internal_energy_nd.f90
commit 38580eefee48189d82f96013880c39153ffddcd0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 21:05:13 2015 -0400
Accidentally deleted QLAST
Source/Castro_nd.f90
commit b5fa34c9a87de0123e1fbeb15144ff44c9db1e9c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 20:25:36 2015 -0400
Always include y- and z-momenta in the state vector, even in 1D or 2D.
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
commit 5381acd7d851feb0a20fe704aab2b66c65fae665
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 20:20:18 2015 -0400
Cannot have temp = 0, setting to small_temp instead.
Exec/RT/Prob_2d.f90
Exec/RT/Prob_3d.f90
Exec/RT_particles/Prob_2d.f90
commit 2834d45680eb76ebbafc930b9a4393a8e6bf30ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 16 19:41:02 2015 -0400
add the gamma_law_bubble problem from Castro_Exec -- this has a Maestro
counterpart
Exec/gamma_law_bubble/Derive_F.H
Exec/gamma_law_bubble/GNUmakefile
Exec/gamma_law_bubble/Make.package
Exec/gamma_law_bubble/Prob_2d.f90
Exec/gamma_law_bubble/Problem_Derives.H
Exec/gamma_law_bubble/extra_derives_2d.f90
Exec/gamma_law_bubble/inputs_2d_MAESTRO.big
Exec/gamma_law_bubble/probdata.f90
Exec/gamma_law_bubble/probin.big
commit 2efbfabc33a2853db81085f41133b5eb3c45d662
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 16 18:57:25 2015 -0400
move from Castro_Exec -- this was used in the 3-d XRB paper for
timing comparisons to Maestro
Exec/xrb_mixed/Castro_error.cpp
Exec/xrb_mixed/GNUmakefile
Exec/xrb_mixed/Make.package
Exec/xrb_mixed/Prob_2d.f90
Exec/xrb_mixed/Problem.H
Exec/xrb_mixed/Problem_F.H
Exec/xrb_mixed/README
Exec/xrb_mixed/Tagging_2d.f90
Exec/xrb_mixed/inputs_2d
Exec/xrb_mixed/probdata.f90
Exec/xrb_mixed/probin
Exec/xrb_mixed/sponge_2d.f90
Exec/xrb_mixed/sum_integrated_quantities.cpp
Exec/xrb_mixed/toy_xrb.hi_dens.hse.tanh.delta_12.000cm.dx_6.000cm.CNO
commit 6109df694ec04dad4369f0d33cdfd31a4af1dd84
Merge: dc7025115 a44af23d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 16 18:54:42 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit dc7025115d73144b80a67828ff70013ac6516664
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 16 18:54:32 2015 -0400
we were computing E_added wrong
Exec/reacting_bubble/sponge_2d.f90
commit a44af23d56759b72fe01f0b501f7c0c80bbbb61c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 15:09:43 2015 -0700
Answer a marginpar question
UsersGuide/Software/CastroSoftware.tex
commit 6be11d1fdec9197148c9fe09033887a1ad43e265
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 15:14:16 2015 -0400
Add basic I/O messages indicating when we're in react_state.
Source/Castro_react.cpp
commit 3c7f7ebb7fe8dd20cb600c9bc7f70d4d371f151e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 15:04:30 2015 -0400
Dimension agnosticify compute_temp, plus a bugfix for react_state.
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Make.package
Source/Src_1d/compute_temp_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/compute_temp_2d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/React_nd.f90
Source/Src_nd/compute_temp_nd.f90
commit 0f420e79fd3b6700c881a6f3a6d59344c8782b6b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 14:12:46 2015 -0400
Make the react_state function dimension agnostic using the new BoxLib macros.
Exec/Make.Castro
Source/Castro_F.H
Source/Castro_react.cpp
Source/Src_1d/Make.package
Source/Src_1d/React_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/React_2d.f90
Source/Src_3d/Make.package
Source/Src_nd/Make.package
Source/Src_nd/React_nd.f90
commit e9e8b8e428f682b4bae49718193441883557891f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 16 13:40:21 2015 -0400
Clean up the C++ side of the reactions a bit, and add tiling + OpenMP ability. The version that needs ghost cells isn't OpenMP-ify'ed yet, so we don't call that at present.
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 71e13fde5a18c153f2a2ba8d87dd6712a4a24449
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 15 22:26:28 2015 -0400
Remove the checks for negative density and energy in react_state. These should be irrelevant because we call enforce_minimum_density and reset_internal_energy before the burning happens. We could always add additional checks to the eos_type setup as needed.
Source/Src_1d/React_1d.f90
Source/Src_2d/React_2d.f90
Source/Src_3d/React_3d.f90
Source/Src_nd/Make.package
commit 6f3c5a35671861049dc67eafbe8c0500be2fcaa1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 15 22:16:52 2015 -0400
Switch to the structure of arrays method to be consistent with the new EOS interface.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/React_1d.f90
Source/Src_1d/compute_temp_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/React_2d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/React_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit aee1819704623033ca2cde06b32e280a47bb6f11
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jul 14 16:52:34 2015 -0700
added ivdep to riemann
Source/Src_3d/riemann_3d.f90
commit ae4092d313fc0730a230554bc9027fec53a50b5c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jul 14 15:32:38 2015 -0700
added a number of ivdep pragmas and changed the array bounds in uflatten
Source/Src_3d/flatten_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.f90
commit 8fd9bfa486321de4768168c8c0e087cc18e165be
Merge: cca500471 d3f703b32
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 13 16:23:28 2015 -0700
can use smaller arrays
commit d3f703b323ade84bf506ded361c67bae3738732b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 13 16:21:50 2015 -0700
can use smaller arrays
Source/Src_3d/riemann_3d.f90
commit cca500471c525c666b36e9c1a96db36ae7b24e93
Merge: b29e696a8 c3a89d6b1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 13 15:56:13 2015 -0700
fixed the number of components in rot; note that this bug caused more memory used, but did not affect results;
commit c3a89d6b1b1b0e67ed96717aaa07aef5f96a5b7e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 13 15:54:42 2015 -0700
fixed the number of components in rot; note that this bug caused more memory used, but did not affect results;
Source/Src_3d/Castro_3d.f90
commit b29e696a8508fd6200f3c58a341e68bef4d5e923
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 13 11:24:33 2015 -0700
use bl_allocate instead of allocate
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/Src_3d/flatten_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/slope_3d.f90
commit c06b8cbeb163ddac16de05ebaea5673892b00ef8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 13 10:57:41 2015 -0700
use bl_allocate instead of allocate
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 84bb4a7d7d8b6ccaebad2dd6514ebb156ef2daf3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 13 02:59:12 2015 -0400
Move the uniform cube/sphere test of Poisson gravity from wdmerger to CASTRO.
Exec/uniform_cube_sphere/GNUmakefile
Exec/uniform_cube_sphere/Make.package
Exec/uniform_cube_sphere/Prob_3d.f90
Exec/uniform_cube_sphere/README
Exec/uniform_cube_sphere/inputs
Exec/uniform_cube_sphere/probdata.f90
Exec/uniform_cube_sphere/probin
commit b146f0ea3f051b9d4b7dcd0b619eedd164d854ca
Merge: 971847a8a bd7874136
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 13 01:53:08 2015 -0400
Merge branch 'master' into openacc
commit bd7874136b1baf4c5b29a987dd7fb377dfdbccf7
Merge: c9c3f3317 020f6b9d3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 22:19:02 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit c9c3f33172e22374bb315a1472ca040f128967b4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 22:15:12 2015 -0700
fixed a new typo
Source/Src_3d/Castro_advection_3d.f90
commit 3d2bfd4735e56f70ff8b452a458816432300a505
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 21:47:40 2015 -0700
removed some arrays in ppm module
Source/Src_3d/ppm_3d.f90
commit 020f6b9d3954ee4cfe675f67218c9105ab461959
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 13 00:20:27 2015 -0400
Change up the KH test so that it mirrors what was in wdmerger. It now has two more tests in addition to the one it already had.
Exec/KH/Castro_error.cpp
Exec/KH/GNUmakefile
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/KH/README
Exec/KH/Tagging_2d.f90
Exec/KH/Tagging_3d.f90
Exec/KH/inputs.2d
Exec/KH/inputs.3d
Exec/KH/probdata.f90
Exec/KH/probin
commit 122358d392bcc59cc50a9c181a6c24247c0141d5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 21:18:30 2015 -0700
removed some divisions
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit cf5af3cf53bf33742b7bfa60a0d378bbcf56e496
Merge: 8a94b604f 176f1f48b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 20:39:26 2015 -0700
Merge branch 'master' into weiqun
commit 8a94b604f3bc1186742310f9a26ae20336ea6c30
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 19:21:45 2015 -0700
removed some divisions
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/enforce_consistent_e_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit 2709bcabfb5dafd3dcc0e5e01eb3e05ab9c3015b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jul 12 18:45:40 2015 -0700
fixed a bug in point mass
Source/Src_3d/pointmass_3d.f90
commit 176f1f48b08fea767d9dcf9df2d14bd5faeb36a4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 12 20:47:26 2015 -0400
Add the collapse problem of Evrard (1988) as discussed in Springel (2010). This is coming over from the wdmerger repository.
Exec/evrard_collapse/GNUmakefile
Exec/evrard_collapse/Make.package
Exec/evrard_collapse/Prob_3d.f90
Exec/evrard_collapse/inputs
Exec/evrard_collapse/probdata.f90
Exec/evrard_collapse/probin
commit 662a7ec502547b4d3d3061b50d9253690479921f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 12 16:50:12 2015 -0400
Only require castro.do_react if we compile with reactions on.
Source/Castro.cpp
commit 971847a8a3e6fd93efe1b463f9556b52349d8176
Merge: 6bc98149f 08536738a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 12 01:15:36 2015 -0400
Merge branch 'master' into openacc
commit 08536738a360dca6ac78eeafc9de9ad8312c48ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 12 01:15:20 2015 -0400
Add number of cm in an AU, and define the parsec in terms of that.
constants/constants_cgs.f90
commit 6bc98149fbbba4ebf69ae357311a9a52c86a24f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 00:55:43 2015 -0400
Vectorize the react_state function so that it's compatible with the new interface in Microphysics.
Source/Src_1d/React_1d.f90
Source/Src_2d/React_2d.f90
Source/Src_3d/React_3d.f90
commit 662a0eb1a0eba98c7eff43b31ab0651b7f6f4b98
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 00:54:48 2015 -0400
If we have MICROPHYSICS_DIR, use the networks directory there.
Exec/Make.Castro
commit 05d46b93f777f3f6a4a5ebb9181f6a41cab4b3b8
Merge: e19245eb2 d07ddf6fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 10 13:04:55 2015 -0400
Merge branch 'master' into openacc
commit e19245eb2e022455b199978f6cd3189214d7aed0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 23:49:46 2015 -0400
Check the HDF5_INCL directory for includes if it is set.
Exec/Make.Castro
commit ccc58deb31ce82ca5197616c6bdf2fe5adfedc74
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 14:47:25 2015 -0400
Check the EOS_HOME for extern parameters too.
Exec/Make.Castro
commit 32e34b07f6b25cf8dc5d94d720d7ddc1f25f2e40
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 14:47:11 2015 -0400
Clean up Exec/ directory references to EOS interface.
Exec/HCBubble/Prob_3d.f90
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
Exec/Sod_stellar/Prob_2d.f90
Exec/Sod_stellar/trace_ppm_2d.f90
Exec/hydrostatic_adjust/extra_derives.f90
Exec/reacting_bubble/initdata_others.f90
commit c5d4d641e4bb81ffd7d3217f740967ab45581ba9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 14:17:41 2015 -0400
Remove remaining pt_index references and replace them with eos_state % loc.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/React_1d.f90
Source/Src_1d/compute_temp_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/React_2d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
commit feefbfd9e5576159877394bcb9210743c3d816de
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 14:01:23 2015 -0400
Remove obsolete references to EOS interface.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/React_1d.f90
Source/Src_1d/compute_temp_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_1d/riemann_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/React_2d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
commit 83651c4a0f495e96597017344e9c4c891d1f22a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 12:47:18 2015 -0400
Don't rely on the EOS to set smallt and smalld; they belong here, and are sent to the EOS to be acted upon there as necessary.
Source/Castro_nd.f90
commit cb03a22d413b8cea775e2ce8ffa99674bbe81c80
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 12:44:28 2015 -0400
Couple more latex ignores
.gitignore
commit b8980b9c55873f8b6924a0558deb2650e785871a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 9 12:14:56 2015 -0400
If we locate MICROPHYSICS_DIR, then we can now rely on it entirely for the EOS.
Exec/Make.Castro
commit bda9c8f818868e3e2a10f8794f98d9dce2ea03c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 8 17:54:55 2015 -0400
Add the location index to the EOS calls so that we know where things went wrong if the EOS crashes.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/React_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit 944d6076c5dd0bbff7100861676c52e0429e4f2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 8 13:51:42 2015 -0400
Add a three-dimensional index to the eos_type.
EOS/eos_type.f90
commit cd856acafc3fb2d195743533d0431eb1f252543e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 8 13:05:35 2015 -0400
Rewrite the EOS calls using eos_state arrays that are of the same rank as the calling state. This will work with the Helmholtz EOS in the Microphysics repo, at present.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/riemann_3d.f90
commit d07ddf6fb65fcceecf2295dd8d3e9034ccd45d81
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 7 14:57:22 2015 -0400
Add to the physical constants module the number of centimeters in a parsec.
constants/constants_cgs.f90
commit 3149f937d12a09784690483df4265bae812c3d2e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 3 03:11:48 2015 -0400
Remove some unneeded saves
EOS/eos_data.f90
commit 4f9a1d8e585713a2b41fd55f2e4761f8814ac19f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 3 03:09:15 2015 -0400
If we have set the environment variable MICROPHYSICS_DIR, then Castro will look there for the EOS_dir you set instead of in Castro/EOS. We still have the eos_type and eos_data modules in Castro though.
Exec/Make.Castro
commit 57afcc4988759c35f07751f61eb680dde7a81235
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 3 02:58:30 2015 -0400
Switch from dp type to Fortran double precision so that we don't need to use bl_types module in the EOS.
EOS/eos_data.f90
EOS/eos_type.f90
commit 78ba483a568f01a6b2fc2b3536b05dd48c5ee31a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jul 2 21:10:22 2015 -0700
flatten: swap ijk loop order
Source/Src_3d/flatten_3d.f90
commit 477852c3f23e4d802ac633cb0b4921971c1da5ab
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jul 2 21:09:28 2015 -0700
ctoprim: split a loop into two for vectorization
Source/Src_3d/Castro_advection_3d.f90
commit 826a99cbf42ad82a4f710ac43a1b817b32b47639
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jul 2 17:50:21 2015 -0700
trans: move EOS calls into separated loops
Source/Src_3d/trans_3d.f90
commit 226a5240ec9d1ead126cba0520cf788af808697b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jul 2 14:07:58 2015 -0700
trace_ppm: vectorization
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit 5be5a3aead515a26997fa9bf2507ae61dc2c3355
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 1 19:57:16 2015 -0400
In places in the hydro where we are calling the EOS with only a single element, revert to using the scalar eos_type.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit 0aeb49deba87ded67d099e0da05daea4c5799c0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 1 19:42:47 2015 -0400
Add an interface to the helmeos so that we can call it either with a rank-0 scalar eos_type or a rank-1 vector eos_type.
EOS/helmeos/eos_stuff.f90
commit a24e9a7597f36a327caf89fac110bebd67b2bebe
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 1 17:49:21 2015 -0400
Since we now use OpenMP only at the tiling level, remove the option to do OpenMP parallelization of the EOS loop.
EOS/helmeos/helmeos.f90
commit 13c77e8e11325c20068e6f5c42c3dd14a066c8d0
Merge: 3cdc243f2 fe7e099c5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 1 17:31:46 2015 -0400
Merged in last year's worth of commits from master into OpenACC
commit c7e0bd31bcc5809389c811aa50f2c99fa232d5ac
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jul 1 06:15:20 2015 -0700
fixed a new bug at boundary
Source/Src_3d/riemann_3d.f90
commit 5625e07ac108168c949a7b404e1479d41b61e7c9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jun 30 11:36:02 2015 -0700
riemann: vectorization
Source/Src_3d/riemann_3d.f90
commit 5573211cd4f755bbeeb82fe8634b2fd1aa4379bc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 29 15:36:40 2015 -0700
removed some if (idir...)
Source/Src_3d/riemann_3d.f90
commit fe7e099c5246cb0444c3937b4bb92877040e8185
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jun 28 20:58:33 2015 -0700
riemann: removed if (idir...)
Source/Src_3d/riemann_3d.f90
commit 1dac2d7071b5f69fede5768280f19abb00e75222
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 23:22:56 2015 -0700
fixed a typo in last commit
Source/Src_3d/trans_3d.f90
commit 6ef6c253cd8a96ede351bbd2538b3fc0dbbea636
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 21:39:10 2015 -0700
trans: some part should be inside if block
Source/Src_3d/trans_3d.f90
commit 17210a54f0dea1ac8cb027da3167c64dc0ca7996
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 21:12:34 2015 -0700
minor
Source/Src_3d/trans_3d.f90
commit 1277ca2ca50e67a595c4cab9d4ca3db6a0a63ace
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 21:10:46 2015 -0700
transz: some part should be inside if block
Source/Src_3d/trans_3d.f90
commit f1d068725e2a6f1cbb7a15417f9d3903ddfd97fc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 21:00:42 2015 -0700
transy1: some part should be inside if block; transy2: minor
Source/Src_3d/trans_3d.f90
commit ab4eeb4645d342379ef640f8a150d61a1f6f74f6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 20:51:23 2015 -0700
minor
Source/Src_3d/trans_3d.f90
commit a40b5db1d05dd68e99615a54222d84b747d2fa6f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 16:03:58 2015 -0700
transx1: some part should be inside if block
Source/Src_3d/trans_3d.f90
commit 8b4035e56c779fa2c9f7398e79b22acbe18364c1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 15:36:39 2015 -0700
turn if (ppm_temp_fix /= 1) and if (ppm_temp_fix == 1) into if () ... else ...; switch loop order
Source/Src_3d/Castro_advection_3d.f90
commit 5128fbcdcaa2fb8fa709775bcb87d72bfc1665c3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 15:32:49 2015 -0700
allocate Ip and Im only when ppm_type .gt. 0; allocate dqx, dqy and dqz only when ppm_type .le. 0
Source/Src_3d/Castro_advection_3d.f90
commit f899f42ca0303341a87dfd4c04ef52c6f7888475
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 27 07:45:25 2015 -0700
inputs for the dungeon
Exec/RT/inputs.dungeon
commit a6ba4126e205d3bfc81c88c786aca465a187009f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 26 13:41:24 2015 -0400
fix the rotation number of ghost cells in 2-d too -- not sure if we
have a test problem for 2-d rotation yet.
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_rot_sources_2d.f90
commit 146729a160ab16d74b7353ac920e74915d1e4bb1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 26 05:55:26 2015 -0700
fixed bug in my recent commit
MGFLD.cpp
RAD_F.H
commit 73e2b947dd4fa104a0790e051ad50ea076046fe4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 25 16:40:38 2015 -0400
fix the rot() number of ghostcells, we now set it to NHYP, since
we do reconstruction and tracing under it.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit e6545abf55ad14ae740071b0747eb5a863b58a8f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jun 20 20:38:59 2015 -0700
minor change
RadHydro_nd.f90
commit e35e714f5aa528a5ebedfeca30e3aff0f3a2b43c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 19 16:51:55 2015 -0700
comment
RadHydro_nd.f90
commit dc6d4eef45114526f745893f7618f771e227d1fd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 19 16:21:32 2015 -0700
added inelastic electron scattering for photons
MGFLD.cpp
RAD_F.H
RadHydro_nd.f90
Rad_nd.f90
Radiation.H
Radiation.cpp
radhydro_params.f90
commit 2eced775187767ef8280edc9fec6c9e90b4ccf8c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 19 16:05:38 2015 -0700
RadBreakout: make Prob_1d work for multigroup
RadBreakout/Prob_1d.f90
commit 2cbe3c3aa237a079bf10ce6c4ccce5769c8622a7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 19 16:04:01 2015 -0700
Radiation: added inelastic electron scattering for photons
Exec/Make.Castro
Source/Castro_F.H
Source/Castro_advance.cpp
commit 5f5cb685f1c1f1f30b63bb667a8e395b28aa6033
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 19 16:03:07 2015 -0700
added some LAPACK subroutines
Util/LAPACK/Make.package
Util/LAPACK/dgtsv.f
Util/LAPACK/xerbla.f
commit c625904cf3fb0db23a155afce6a24d9f96c306f3
Merge: 1c8eb2706 077c97b46
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 29 17:34:48 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 1c8eb270620df5ffcb080a66ee14136751eac87d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 29 17:34:41 2015 -0500
Fix variable declaration bug
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit 077c97b466ece7c92d46bba19525153988ff8fb6
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 29 11:46:46 2015 -0700
A few hydro parameters that were previously mandatory are now optional to set.
Source/Castro.cpp
commit 04ca3630db02b221e82550524a05d55b1a1729d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 29 13:29:34 2015 -0500
Similar to gravity, for rot_source_type = 4 we now explicitly construct density fluxes to make the energy update more comprehensible.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit f13070f5fc7d52d699d706264a0cd3f5ec78f24a
Merge: 59812ddd3 930bdfd33
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 28 22:55:25 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 59812ddd370bec9bbeaba2a783bed9ffd5639723
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 28 22:55:09 2015 -0500
We don't do grav_source_type = 4 in 2D, remove the reference to it.
Source/Src_2d/Castro_grav_sources_2d.f90
commit 930213d46c46dad8dcc11fd27f51be11500adadb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 28 22:54:09 2015 -0500
Slight rewrite of the form of grav_source_type = 4. We now explicitly construct the density changes at each zone boundary; this makes it easier to see how the gravitational potential energy is changing.
Source/Src_3d/Castro_grav_sources_3d.f90
commit 930bdfd332f3982c92638d9762fce33ba5d74c23
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 25 23:53:01 2015 -0400
The rot_source_type == 4 energy update was being applied incorrectly. The correct update that is conservative is to simply evaluate the flux of rho * phi_R at the zone boundary. We don't need the gravity formalism for this because the rotational potential doesn't depend on the fluid motions, unlike the gravitational potential.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit e809d66970d3eee367cc92ba7fb5072841a84639
Merge: 11e2a2548 f1e97c18e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue May 19 10:58:37 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit f1e97c18eaa8feb9eec885e355f75bd18aa6332e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 19 00:52:10 2015 -0500
float -> dble in rotation sources to be consistent with what we do elsewhere in the code.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit 11e2a2548086e48ab9cea216fa74e03be305aeab
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon May 11 13:51:55 2015 -0700
new parameter for hydro MFIter: hudro_tile_size
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
commit d3dd27eaed7918aac419f6da7842d1bb313d2c06
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue May 5 16:56:09 2015 -0700
call S_new.setVal(0.) in initData so that every thread touches it
Source/Castro.cpp
commit ea72977264d5f3353f4aac12c1199e7d0615305b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue May 5 13:12:45 2015 -0700
no need to define volume and area again in advance
Source/Castro_advance.cpp
commit fb04c5a604b7f02776e428a099790df7a13c5022
Merge: be4a5e304 fbab0dc55
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 4 12:36:08 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit fbab0dc55ede4328f6baede88446dbf762819b82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 4 13:16:21 2015 -0400
more comments
Source/Src_3d/Castro_rot_sources_3d.f90
commit 2e86ecca9fe799d54fe7b6d4c4ef71197761da24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 4 12:22:16 2015 -0400
add a comment
Source/Src_3d/Castro_rot_sources_3d.f90
commit 626ef66e1703c4b634c5f5c46ced68ecbb7c6fa6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun May 3 14:26:25 2015 -0700
protection against division by zero
Src_1d/RadPlotvar_1d.f90
Src_2d/RadPlotvar_2d.f90
Src_3d/RadPlotvar_3d.f90
commit 9895de3d0c0fc2400d6b1a3073965c23fc0366f8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun May 3 14:12:07 2015 -0700
fixed index for flux in plotvar
Src_1d/RadPlotvar_1d.f90
Src_2d/RadPlotvar_2d.f90
Src_3d/RadPlotvar_3d.f90
commit 8c00bfd3c8bf4117532cfd4917ddb34f35f9feb5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun May 3 14:05:51 2015 -0700
fixed index for lab Er in plotvar
SGRadSolver.cpp
Src_1d/RadPlotvar_1d.f90
Src_2d/RadPlotvar_2d.f90
Src_3d/RadPlotvar_3d.f90
commit db0e88bb835be76419b0ef1536a82ae871a42b26
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 20:32:44 2015 -0700
add to plotfile some extra radiation plot variables
Source/Castro_io.cpp
commit 75389a8648d9a7bd79de3c8885862d5ce873dcec
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 17:50:03 2015 -0700
removed Test_Type from Radiation
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_setup.cpp
commit fe08d19939817fd90fa9eea03ce96953be46df23
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 16:13:02 2015 -0700
Radiation: set up for saving flux etc. in plotfiles
Source/Castro_setup.cpp
commit 6c4c046660d7caa58159097d93a74a46fd382afd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun May 3 12:10:04 2015 -0700
fixed a new bug
SGRadSolver.cpp
commit 162ba69626dc55cbc79400980d5bedd1d71cf5f5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun May 3 11:22:32 2015 -0700
plotvar in 1d and 3d
Src_1d/RadPlotvar_1d.f90
Src_3d/RadPlotvar_3d.f90
commit 6b174a06cf075f0e9c2c171f1c0d62b66652195c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun May 3 10:26:20 2015 -0700
cleanup
MGFLDRadSolver.cpp
RAD_F.H
RadPlotvar.cpp
SGRadSolver.cpp
Src_2d/RadPlotvar_2d.f90
commit 2f704063778c04cf239f2b78a3feeaa9472beda4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 2 22:53:42 2015 -0700
added some new files for plotvar
RadPlotvar.cpp
Src_1d/RadPlotvar_1d.f90
Src_2d/RadPlotvar_2d.f90
Src_3d/RadPlotvar_3d.f90
commit 7e9a4cb79d0c8383fd86bccd5ea8863464bfac00
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 2 22:51:04 2015 -0700
implemented Lorentz trandformation for plotfiles in 2D
RadBreakout/inputs.1d
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
commit 3cdf99ead674ffc601c5f1e341b88e8bbbc2070f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat May 2 22:51:04 2015 -0700
implemented Lorentz trandformation for plotfiles in 2D
MGFLDRadSolver.cpp
Make.package
RAD_F.H
Radiation.H
Radiation.cpp
SGRadSolver.cpp
Src_1d/Make.package
Src_2d/Make.package
Src_3d/Make.package
commit be4a5e304cdc0bf33d6870c4d5fc1ddde31c1b8b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 2 15:04:21 2015 -0500
Fix a sign in the rotation corrector step for rot_source_type == 4.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit 34bd5f2e6bde63e9634e2fd7ea123a34af0b6227
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri May 1 15:54:49 2015 -0700
save only 1 group of lambda when limiter==0 because they are all 1/3
MGFLDRadSolver.cpp
Radiation.cpp
commit d307bd805f136eed53f5c97e10efd831a83238fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 15:31:22 2015 -0400
update the e-mail list
README.md
UsersGuide/Introduction/CastroIntroduction.tex
commit 80c79cc82c89f18caa6a8bb50ec355c47eb6efc5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 21:11:06 2015 -0700
removed deprecated files
Src_1d/Make.package
Src_1d/SGFLD_1d.f90
Src_2d/Make.package
Src_2d/SGFLD_2d.f90
Src_3d/Make.package
Src_3d/SGFLD_3d.f90
commit 30654a48fe4a67dc215511f3dc626f956b602ceb
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 21:06:59 2015 -0700
update inputs: Test_Type_Flux --> plot_flux
RadBreakout/inputs.1d
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
commit fc97bba300ec0427bc7e51254c42faa8d49a060c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 20:34:22 2015 -0700
make plotvar public for Castro
Radiation.H
commit 8fc269b639c00ea2a497f9e9c3d00e0250170178
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 19:54:35 2015 -0700
initialize plotvar to zero
Radiation.cpp
commit 704d1ff89add1972ffe8d44e778c4452c8ee4f48
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 17:49:41 2015 -0700
removed Test_Type and added plotvar
MGFLDRadSolver.cpp
Radiation.H
Radiation.cpp
SGRadSolver.cpp
commit d0286ac244aa50c6bdf2839a2182cba32fdb014d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 16:30:23 2015 -0700
fixed index for plot_kappa_r and removed a duplicate multifab in SGRadSolver
MGFLDRadSolver.cpp
SGRadSolver.cpp
commit b21b5c4111c9e0a9e5a3e8d6c43145f44b9732f9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 16:10:14 2015 -0700
save kappa_p and kappa_r for plotfiles in MGFLD
MGFLDRadSolver.cpp
commit 97d11610fc808b44ca6f3651a53fed1296cf787c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 30 16:02:31 2015 -0700
option to save lambda, flux, kappa_p and kappa_r in plotfiles
MGFLDRadSolver.cpp
RAD_F.H
RadSolve.H
RadSolve.cpp
Radiation.H
Radiation.cpp
SGRadSolver.cpp
Src_1d/CastroRad_1d.f90
Src_1d/MGFLD_1d.f90
Src_1d/SGFLD_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/MGFLD_2d.f90
Src_2d/SGFLD_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/MGFLD_3d.f90
Src_3d/SGFLD_3d.f90
commit cb92607eff5492a56395bb768ce263fa34e9d7fd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Apr 24 14:34:37 2015 -0700
fixed a bug
Source/Src_3d/trans_3d.f90
commit fa745a3b05fd8a95aa798c963c785149a3cf0335
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Apr 21 21:42:32 2015 -0700
update the interface of sponge
Src_1d/CastroRad_1d.f90
Src_2d/CastroRad_2d.f90
Src_3d/CastroRad_3d.f90
commit b3f31ef446a472aeed87a762af45b702693071d4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Apr 21 12:33:46 2015 -0700
Tell BoxLib that boundary functions are thread safe. The user needs to make sure this is in fact true.
Source/Castro.H
Source/Castro.cpp
commit 264d367f7fd0b0ee6d2a1d527598c5dec91448d1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Apr 20 17:18:56 2015 -0700
update users guide: boundary fill functions are now inside OMP
UsersGuide/Parallel/Parallel.tex
commit b7df59f74fb71455407eb4010573486a3b15f885
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Apr 20 17:13:13 2015 -0700
remove OMP from hypfill because it's already inside OMP
RadCoreCollapse/bc_fill_3d.f90
commit 02f234735f9795f78be43571848cb311105cb11a
Merge: 3299fcb55 240002cd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 12 18:55:30 2015 -0400
Merge /home/zingale/temp/Castro_Exec
commit 240002cd1b3f4f66d824169a57fae62fbbba68b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 12 18:54:59 2015 -0400
move from Castro_Exec/ to Castro/Exec/
Exec/Detonation/Castro_error.cpp
Exec/Detonation/GNUmakefile
Exec/Detonation/Make.package
Exec/Detonation/Prob_1d.f90
Exec/Detonation/Prob_2d.f90
Exec/Detonation/README
Exec/Detonation/inputs-det-x
Exec/Detonation/probdata.f90
Exec/Detonation/probin-det-x
commit 3299fcb555b9e101fc40a3da8a2e23369de3ecdf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 10 13:18:20 2015 -0400
update README
Exec/README
commit 564530b04e74af66a5a789557667736df731ec3a
Merge: 848c0a9ac 171289365
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 10 13:14:50 2015 -0400
Merge /home/zingale/temp/Castro_Exec
commit 1712893654a0d344519def2ad70f05955e505c22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 10 13:14:35 2015 -0400
move to Castro/
Exec/test_convect/GNUmakefile
Exec/test_convect/Make.package
Exec/test_convect/Prob_2d.f90
Exec/test_convect/Problem.H
Exec/test_convect/Problem_F.H
Exec/test_convect/ext_src_2d.f90
Exec/test_convect/inputs_2d
Exec/test_convect/model.hse
Exec/test_convect/probdata.f90
Exec/test_convect/probin
Exec/test_convect/sponge_2d.f90
Exec/test_convect/sum_integrated_quantities.cpp
commit 1aac2016fc389134ac13adaf6edf94cbe80232c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 10 12:08:33 2015 -0400
need to set small_temp, otherwise we crash :(
inputs_2d
commit d0d8589ca098f8575442f41e6923034ef24edd58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 6 09:57:00 2015 -0400
point to MICROPHYSICS_DIR
GNUmakefile
commit 848c0a9ac548278c158cf7c9d3dbc599c304049c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 5 09:41:43 2015 -0500
Use the rotation predictor-corrector approach even for rot_source_type == 4.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit d9186aac3783e8deb80aac0d8c5ab92f083d2957
Merge: a839bf16b 9f6e17c46
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 4 14:36:19 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit a839bf16b681037a1457e8815e19d7f3959434a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 4 14:35:58 2015 -0500
It is possible for a zone's velocity to violate the CFL criterion during a subcycled timestep if the previous subcycle generated large velocities in the hydrodynamics. We now have an integer parameter castro.hard_cfl_limit that determines whether we abort the simulation in this case. By default it is 1 and we do abort (retaining old behavior); but by setting it to zero in the inputs file we can continue the simulation with a warning.
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
UsersGuide/Inputs/CastroInputs.tex
commit 9f6e17c46f24b94ddc739770d632b765a224851a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 2 08:56:50 2015 -0400
get this compiling again
Exec/reacting_bubble/sponge_2d.f90
commit e6531c79a364ea99f64481cb6d4a897306951b85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 2 08:53:11 2015 -0400
fix compilation
Exec/hydrostatic_adjust/sponge_1d.f90
commit 2828f6ee2e4a3eebb7ac6051b670651af02abfef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 21:03:26 2015 -0400
sync up with Maestro
probin
commit c430af44f40daa0216e9f582e31dea7973fd5c54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 21:02:03 2015 -0400
no longer require gravity to be set twice. Add the toy_convect
perturbations
Prob_2d.f90
inputs_2d
probdata.f90
probin
commit 94f1bb77fe9dbc6d19d20d34cf675ec1fd36387a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 21:00:32 2015 -0400
get this compiling again
Exec/toy_convect/sponge_2d.f90
commit 0b3faf56ffaa48f3f535c54c08042781be949f45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 20:58:32 2015 -0400
get this compiling again
sponge_2d.f90
commit 05ea5b93f666a4268e9f406633d7d17b28dcdb09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 20:57:51 2015 -0400
remove some unused variables
Exec/toy_convect/Prob_2d.f90
Exec/toy_convect/probdata.f90
commit af303586887e4f61912a67f98be2fbe187223362
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Mar 30 08:51:35 2015 -0700
updated sponge for DustCollapse
Exec/DustCollapse/sponge_3d.f90
commit 05b5755a5b4b2b022cd21913831fcba49ba23c5e
Merge: ce12de212 fc2842828
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 28 13:12:20 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit ce12de212fb3ab90c73240dd6a3c1afb4cb17ac5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 28 00:24:17 2015 -0500
Add diagnostic variables -- energy and momenta added -- to the sponge routine, and print them out like the other diagnostics if we have that verbosity level set.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/sponge_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/sponge_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/sponge_3d.f90
commit fc28428288255d5a6f0a6343b180643a7965c868
Merge: d37054da9 0263e780c
Author: Max <MDGonzalez@lbl.gov>
Date: Wed Mar 25 12:25:38 2015 -0700
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit d37054da9a6a77c3178d8ec04cf7bc7446e6837d
Author: Max <MDGonzalez@lbl.gov>
Date: Tue Mar 24 15:53:18 2015 -0700
Co-rotating vortices problem
Exec/Vortices_LWAcoustics/GNUmakefile
Exec/Vortices_LWAcoustics/Make.package
Exec/Vortices_LWAcoustics/Prob_2d.f90
Exec/Vortices_LWAcoustics/README
Exec/Vortices_LWAcoustics/inputs.2d
Exec/Vortices_LWAcoustics/probdata.f90
Exec/Vortices_LWAcoustics/probin
commit 0263e780cfdeb0494efb6afb9d66ba9a514ad482
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 21 09:03:53 2015 -0500
Fix some indexing issues
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit 596cbcdbb9f0ed0a43a9428f3903f87350299d4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 14:04:48 2015 -0500
Fix some modular arithmetic
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit d7d214967ee34b5d3a87f415b784173e3f9897b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 12:47:16 2015 -0500
Only print out the message about stopping run at OkToContinue if we're on the IO processor.
Source/main.cpp
commit 90d60d06e9d73ef9362d176d4aef651cd9257495
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 12:45:29 2015 -0500
In cmpflx for ppm_temp_fix==2, add a check to protect against possible negative energies in the edge states.
Source/Src_2d/riemann_2d.f90
Source/Src_3d/riemann_3d.f90
commit eb6583a227d005e96d06a435db769a330b40c894
Merge: a2799487e 44518496b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 13:50:37 2015 -0400
Merge branch 'master' into hydro_sync
commit 2d8775dc6742ace5f8112b56de90c7d8f876c01c
Merge: baeed1c9f 4ccb1caed
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 16 13:25:50 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit baeed1c9f5e3d7282d8f325a894e7f34b757bbba
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 16 13:25:24 2015 -0500
Slightly generalize the message in case we are not okToContinue().
Source/main.cpp
commit a2799487e93efe43342e28ef46bb2cb084a295bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 11:05:34 2015 -0400
compilation fixes
Src_1d/trace_ppm_rad_1d.f90
commit 2df96f0195c515b288731e6d18a8160ea9cc8df4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 10:57:05 2015 -0400
first hack at syncing up the 1-d hydro
Src_1d/trace_ppm_rad_1d.f90
commit 4ccb1caed4a1d9ed54ee36a60e777bfd1bdce9a6
Merge: b0f4ecb49 27b0398e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 09:20:35 2015 -0400
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit b0f4ecb496ccb004394ba4685d5fa86e03c88e8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 09:20:18 2015 -0400
some updates to the initial visualization
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 27b0398e84e6de70159fb3d097827cf0cdc518da
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 19:24:19 2015 -0500
Move up the mass_offset subtraction in the solve_for_phi subtraction.
Source/Gravity.cpp
commit e903836ff6f3eee526d3341c45f1a067026bbf6e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 13:00:43 2015 -0500
Remove mass_offset subtraction from solve_for_old_phi and solve_for_new_phi; that operation is now in solve_for_phi.
Source/Gravity.cpp
commit 3dfff0ed731a0b0870e9fae4a45ff2a4a0023688
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 11 11:42:54 2015 -0500
For rot_source_type == 4 we now implement the approach of solving the coupled implicit system of equations for the Coriolis update. A description of this will be in the first wdmerger paper.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit 44518496b965a819d2bcfd65c8c8583bb34cbe3e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 16:19:51 2015 -0700
cleanup
RAD_F.H
Src_1d/Make.package
Src_1d/RAD_1D.F
Src_1d/RadN_1d.f90
Src_2d/Make.package
Src_2d/RAD_2D.F
Src_2d/RadN_2d.f90
Src_3d/Make.package
Src_3d/RAD_3D.F
Src_3d/RadN_3d.f90
commit 25d0273fbd78b9e2ca5f5224093476628bb64f69
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 15:39:56 2015 -0700
fixed new bugs and cleaned up
RAD_F.H
Src_1d/RAD_1D.F
Src_2d/RAD_2D.F
Src_3d/RAD_3D.F
commit faf29cda846868a9beb6840179f1a33779a73769
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 15:06:54 2015 -0700
fixed typos
RadSolve.cpp
commit 039ddb7466673613e1dd1231cb3cbf8ceb4952b3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 15:01:31 2015 -0700
finished tiling in RadSolve
HABEC_F.H
RadSolve.cpp
Src_1d/HABEC_1D.F
Src_1d/RAD_1D.F
Src_2d/HABEC_2D.F
Src_2d/RAD_2D.F
Src_3d/HABEC_3D.F
Src_3d/RAD_3D.F
commit d61685c8399eb659931f37d63ef75504e365fb4e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 13:24:07 2015 -0700
tiling and cleanup
MGFLD.cpp
RAD_F.H
RadSolve.H
RadSolve.cpp
Src_1d/RAD_1D.F
Src_2d/RAD_2D.F
Src_3d/RAD_3D.F
commit dbbaa20af496d58d4424d25a4e68bc696086fd0b
Merge: 4a5c234a7 ec45a936e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 14:40:12 2015 -0400
Merge branch 'master' into hydro_sync
commit 4a5c234a74857ea51e98a82d97bbc3b8493d14df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 13:32:11 2015 -0400
need ppm_type
Src_2d/RadHydro_2d.f90
commit 1d028de5c85a88af89a6fce7c1b125b67de3fa50
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 10:31:26 2015 -0700
finished tiling in Radiation.cpp
Radiation.cpp
commit 394a1615f86aa6c112f6a6f8b63fbecc1a379920
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 13:28:54 2015 -0400
only add gravity to the edge states if we didn't trace it in the ppm routine
Src_2d/RadHydro_2d.f90
commit ec45a936e4531affc2a75f3d84245e656ac03027
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 10 10:14:32 2015 -0700
fixed new tiling bug
RAD_F.H
Radiation.cpp
Src_2d/RAD_2D.F
Src_3d/RAD_3D.F
commit d446df2e21eae333d87ea7ed956f145404a7f1ae
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Mar 9 18:18:10 2015 -0700
more tiling
RAD_F.H
Radiation.cpp
Src_1d/RAD_1D.F
Src_2d/RAD_2D.F
Src_3d/RAD_3D.F
commit dae6ebeae0ae3cfe8d420c9133f312114f1e58a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 9 19:30:07 2015 -0400
fix some missing reference states
Src_2d/trace_ppm_rad_2d.f90
commit 084afcebae0f70926a5f16406113a18a73a34ba2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Mar 9 14:37:41 2015 -0700
Changes to gravity in all periodic case:
(1) At the end of a Coarse Timestep, mass_offset is updated.
(2) Subtract mass_offset in single level solve for all levels.
(3) When solving for delta phi, do local correction only when the
lowest level covers the whole domain.
Source/Castro.H
Source/Castro.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/sum_utils.cpp
commit c731c6d5b40df563f0a73d7eef61567f419011d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 9 16:17:42 2015 -0400
add a note to denfill
UsersGuide/Software/CastroSoftware.tex
commit 5a157cf1785e8ebb5b849b542024981cba5bbfdc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 9 12:22:30 2015 -0400
remove the rot source for now and pass in the grav source
Src_2d/RadHydro_2d.f90
Src_2d/trace_ppm_rad_2d.f90
commit 16cad568be59ca299355373e3b409f0b95222f3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 9 12:04:51 2015 -0400
get this compiling
Src_2d/trace_ppm_rad_2d.f90
commit 0d628d8afe57fe721f5f90528f4613d11d2e1881
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 9 10:29:30 2015 -0400
forgot to define p_ref (in addition to ptot_ref)
Src_2d/trace_ppm_rad_2d.f90
commit 534dd9c48afd46d826cb5423bd13b1b2979ff763
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 20:41:28 2015 -0400
start of syncing up the hydro reconstruction with the main
castro. This fixes the flattening and adds the correct reference
states. The interface has changed, and needs to be updated.
We also need to make sure that if ppm_trace_{grav,rot} is enabled,
that we don't double add in the trans routines.
Eventually, hopefully, we can merge this rad and norad routines
into a single one, perhaps with preprocessing.
Src_2d/trace_ppm_rad_2d.f90
commit 766b544d07c74486a51f1900661fa82856869698
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 20:40:00 2015 -0400
remove some ununsed reference states
Source/Src_2d/trace_ppm_2d.f90
commit d8a4b4affcdb8058bbbffeeff7f1fc316102e3a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 16:02:19 2015 -0400
some syncing up with the Castro version -- no functional changes,
just cleaner diffing
Src_2d/riemann_rad_2d.f90
commit 4972abc19c725c454c8003ae799ec475efe89567
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 15:34:03 2015 -0400
split the tracing stuff out.
Src_3d/Make.package
Src_3d/RadHydro_3d.f90
Src_3d/trace_ppm_rad_3d.f90
commit 67287a34da01774960b68843ca62072d6bd9c4da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 15:10:55 2015 -0400
split out the ppm tracing stuff and switch it over to qpass_map
Src_1d/Make.package
Src_1d/RadHydro_1d.f90
Src_1d/trace_ppm_rad_1d.f90
commit 8d36111f8fd0df850b31ec93f3f850add150b0bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 8 14:56:33 2015 -0400
switch to qpass_map
Src_2d/RadHydro_2d.f90
commit df308efb6d232c35c7ceb47234542007ecad3e28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 17:00:03 2015 -0500
split the ppm tracing out into its own module ot match castro
and switch over to qpass_map
Src_2d/Make.package
Src_2d/RadHydro_2d.f90
Src_2d/trace_ppm_rad_2d.f90
commit dc1ea6933c8b3e9d78c2d96c683b3f561d20abc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 16:27:52 2015 -0500
switch to qpass_map/upass_map
Src_1d/riemann_rad_1d.f90
Src_2d/riemann_rad_2d.f90
Src_3d/riemann_rad_3d.f90
commit b3a55e51242c40bfbf068ac862be09a651d27fc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 15:54:05 2015 -0500
move cmpflx and the Riemann solver into a new riemann_rad_module to mirror
what we do in Castro
Src_1d/Make.package
Src_1d/RadHydro_1d.f90
Src_1d/riemann_rad_1d.f90
Src_2d/Make.package
Src_2d/RadHydro_2d.f90
Src_2d/riemann_rad_2d.f90
Src_3d/Make.package
Src_3d/RadHydro_3d.f90
Src_3d/riemann_rad_3d.f90
commit b211bb0e35368464115811daa020454a7af20aa4
Merge: c23f50f24 e6636652e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 14:36:15 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/CastroRadiation
commit 637f7c68fb30d16971d8ffb745c8fd1f6833b07a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 14:36:00 2015 -0500
link in the new Src_?d subdirectories
Make.Radiation
commit c23f50f24f25248ea026da46f44c15a6ef1f40d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 7 14:35:14 2015 -0500
separate the different dimension sources into Src_?d subdirectories
-- this mirrors what we do in the main Castro
Make.package
Src_1d/CastroRad_1d.f90
Src_1d/DumpModel1d.H
Src_1d/DumpModel1d.cpp
Src_1d/HABEC_1D.F
Src_1d/MGFLD_1d.f90
Src_1d/MGFLDneut_1d.f90
Src_1d/Make.package
Src_1d/RAD_1D.F
Src_1d/RadBndry_1d.f90
Src_1d/RadDerive_1d.f90
Src_1d/RadEOS_1d.f90
Src_1d/RadHydro_1d.f90
Src_1d/RadN_1d.f90
Src_1d/SGFLD_1d.f90
Src_1d/filt_prim_1d.f90
Src_2d/CastroRad_2d.f90
Src_2d/HABEC_2D.F
Src_2d/MGFLD_2d.f90
Src_2d/MGFLDneut_2d.f90
Src_2d/Make.package
Src_2d/RAD_2D.F
Src_2d/RadBndry_2d.f90
Src_2d/RadDerive_2d.f90
Src_2d/RadEOS_2d.f90
Src_2d/RadHydro_2d.f90
Src_2d/RadN_2d.f90
Src_2d/SGFLD_2d.f90
Src_2d/filt_prim_2d.f90
Src_3d/CastroRad_3d.f90
Src_3d/HABEC_3D.F
Src_3d/MGFLD_3d.f90
Src_3d/MGFLDneut_3d.f90
Src_3d/Make.package
Src_3d/RAD_3D.F
Src_3d/RadBndry_3d.f90
Src_3d/RadDerive_3d.f90
Src_3d/RadEOS_3d.f90
Src_3d/RadHydro_3d.f90
Src_3d/RadN_3d.f90
Src_3d/SGFLD_3d.f90
Src_3d/filt_prim_3d.f90
commit e6636652eb8414dd844abdcbcbc933f6eb1551bd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 6 16:40:26 2015 -0800
more tiling
RAD_1D.F
RAD_2D.F
RAD_3D.F
RAD_F.H
Radiation.cpp
SGFLD.cpp
SGRadSolver.cpp
commit e80c01e516d3398b69f107b707864d3bd6b73b2e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 6 14:32:43 2015 -0800
more tiling
MGFLD.cpp
MGFLDRadSolver.cpp
commit 41f4435ceb93777fef9c8befd851e354cfd8b682
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 6 14:02:38 2015 -0800
more tiling
MGFLD.cpp
RAD_F.H
RadN_1d.f90
RadN_2d.f90
RadN_3d.f90
Radiation.cpp
commit bfe4f93e058e5cbcc734950e0917886f128781fd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 6 13:44:38 2015 -0800
removed outdated comments
HypreABec.cpp
commit 911fc97dab8a02197ce1fcb196890659dbb3ae11
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 6 13:44:14 2015 -0800
removed intent(out) for tiling
MGFLD_2d.f90
commit aadd223e34018a9a82d3a7bd27c237e0368d0393
Merge: bf6cd61c0 db940c43a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 5 23:06:53 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit bf6cd61c0592f42e1278febd4258ccc889ef05bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 5 23:06:44 2015 -0500
Because of tiling the new state isn't guaranteed to have valid data outside of the tilebox. So when we do a density reset we only look at adjacent zones that are within the valid region of the tilebox.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit db940c43a07ed3be1bb6a1e7791fa1310159c7fc
Merge: 11b530b07 89aec55bd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 5 13:35:28 2015 -0600
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 11b530b0796fd96f2efc6303812b4f5d805251d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 5 13:35:11 2015 -0600
When we do the solve for delta phi in a gravity sync, subtract the RHS average on the coarse grid from all levels. Previously we were only subtracting it on the coarse level and the multigrid solver didn't converge.
Source/Gravity.cpp
commit 89aec55bdd0b5c966639dc31c338035ca75e7f90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 5 13:21:51 2015 -0500
update the docs for the grav?fill routines -- in particular note
that these do not come into play for constant gravity
UsersGuide/Software/CastroSoftware.tex
commit f76076f0647476d1acb1737a25a679a3e8f53f9c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 5 08:34:39 2015 -0800
removed an unnecessary reduction because dt_new returned by Castro::advance is not used
Source/Castro_advance.cpp
commit 9630380cf592406a9e0a556d38e6d6a17e3e8ec0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 21:40:39 2015 -0500
make do_real_eos a static member variable and initialize it. This
fixes a segfault when we ran with radiation support compiled in,
but with castro.do_radiation=0
Radiation.H
Radiation.cpp
commit 55b2e2df2ae4709d5c2e1f4d43ffcaca743d5b24
Merge: 3993f8e26 da05305ec
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 4 17:47:00 2015 -0800
Merge branch 'lazy'
commit 3993f8e26c9911b0a51b190d6cbcef045c27ed82
Merge: 824179e99 0d96e0e8c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 4 17:46:47 2015 -0800
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit da05305eccf04bd8e264c8fb7d164605c33a1194
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 4 17:31:43 2015 -0800
do not need to do reduction when checking nans because we will abort if any nan is found
Source/Castro_advance.cpp
Source/Gravity.cpp
commit 3cb2df97e55c1601c3c379d4c6c201ec38dff644
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 4 17:19:29 2015 -0800
LAZY: moved data log stream into lambda
Source/sum_integrated_quantities.cpp
commit 84b3bc1845cecc11ac17d3ce43cc644c7c905ea2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 4 17:01:25 2015 -0800
made a number of reduction lazy
Source/Castro.H
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_react.cpp
Source/Gravity.cpp
Source/sum_integrated_quantities.cpp
Source/sum_utils.cpp
commit 0d96e0e8c6386074e50b54d2d7a9605263b4b2af
Merge: ea393b9ea 6444da76d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 4 18:14:40 2015 -0600
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit ea393b9ea58bcd3359abf3f2ae5ce324b79577b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 4 18:14:20 2015 -0600
We were forgetting to make the temperature consistent during a small density reset.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 824179e99f5d2c2aaff3ba65fc1fb199d5435fd3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 4 14:09:33 2015 -0800
print out run time w/o init
Source/main.cpp
commit 6444da76df92db4edddbb5d9717a078d4e3b8e3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 2 02:28:58 2015 -0500
Allow the user to set a problem_post_init() routine by defining the do_problem_post_init preprocessor directive. It will be executed just after the multilevel Poisson solve and just before we do diagnostics.
Source/Castro.cpp
commit c703535911e0d339e1a2ac13cdc4fadded1f2da0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 28 17:46:11 2015 -0500
Fix a couple reference inconsistencies
UsersGuide/GettingStarted/CastroGettingStarted.tex
UsersGuide/refs.bib
commit e8d2c48c49ee66dd7ae5056c3cb0b23caceaf089
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Feb 28 10:57:53 2015 -0800
added an optional argument, mask, to computeAvg; don't mask off fine grids when ensuring solvability for single level solve
Source/Gravity.H
Source/Gravity.cpp
commit ce518e16374ba2f64594b044ac40cdf58046d4d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 27 22:08:00 2015 -0600
Two bug fixes in Gravity.cpp: incorrect level being handled to computeAvg(), and incorrect argument ordering in a MultiFab plus operation.
Source/Gravity.cpp
commit ac1cab35fbddfa1ec9cd55efa0e822507cdb30bf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 27 17:12:59 2015 -0800
In post_regrid, delete fine_mask before multilevel_solve_for_phi is called so that a new mask can be built
Source/Castro.cpp
commit fe62c11e061b3c7b494a0c028fe964d591cc852d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 27 10:28:39 2015 -0500
add another reference for the elusive CGF solver
UsersGuide/Equations/Equations.tex
UsersGuide/refs.bib
commit b95c9d2ccc27b3259a24c29710401de59d075f41
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 18:09:05 2015 -0800
more tileing in ca_test_type_*
RAD_F.H
RadSolve.cpp
SGFLD_1d.f90
SGFLD_2d.f90
SGFLD_3d.f90
SGRadSolver.cpp
commit 8155dab1ea2e32ebb0cde00a219aa75657b85e6a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 17:44:12 2015 -0800
removed more intent(out) because of tiling
RadEOS_1d.f90
RadEOS_2d.f90
RadEOS_3d.f90
commit 360a0b4ea56c01719633f9c6a8f844548e229ac7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 17:27:37 2015 -0800
removed intent(out) because of tiling
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
commit 84c1ab3c605d46faac473df36437f123b5d63f6a
Merge: 06581af31 64bd92163
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 23 20:18:28 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
Conflicts:
Exec/toy_convect/Prob_2d.f90
commit 06581af3163de98bcf97a1d9136de54a3cb1de01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 23 20:17:35 2015 -0500
style updates
Exec/toy_convect/Prob_2d.f90
commit 95f702a9be7dd62cc2d54fc142fbbe3cd1e39be7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 13:49:39 2015 -0800
tiling spalpha
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
RAD_F.H
RadSolve.cpp
commit 10807f6db2e71c82b1786b091afa3d47b6f85527
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 13:23:42 2015 -0800
tiling ca_compute_powerlaw_kappa for SGFLD
SGFLD.cpp
commit c3dd0f09fe4a5bd5513afec64e8ab4076cad48be
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 13:22:17 2015 -0800
tiling ca_compute_powerlaw_kappa_s for SGFLD
SGFLD.cpp
commit 5d037d38df3d3b393d0df5ffe56c52cacf91d71a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 13:16:45 2015 -0800
fixed a typo
MGFLD_3d.f90
commit 0b92d9b496c1da88a91ce58adf0fdf8514bebc65
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 23 13:15:57 2015 -0800
tiling rhs2er
MGFLD.cpp
MGFLDRadSolver.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
RAD_F.H
Radiation.H
commit 64bd921631c09b9792c52493ed4b234e10c3cf0b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 22 21:08:12 2015 -0500
gravity is available through meth_params_module (as const_grav), so we don't need
to also set it in the probdata/&fortin namelist. Now there is only one
value of gravity (as there should be...)
Exec/toy_convect/Prob_2d.f90
Exec/toy_convect/probdata.f90
Exec/toy_convect/probin
commit b1a94017dfd302673ca53147478a0c5c3aa2d0ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 22 15:28:57 2015 -0500
add more to the clean
UsersGuide/GNUmakefile
commit 91d5f37f259ba87961b90075cf80adc399abfbb0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 21 21:39:37 2015 -0600
Missed some locations in the last commit
UsersGuide/CastroUserGuide.tex
UsersGuide/Parallel/Parallel.tex
UsersGuide/Visualization/CastroVisualization.tex
commit 29e803964051cda8af7e569ba9effbeb5edd61b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 21 21:28:37 2015 -0600
Automatically convert all EPS files in the User's Guide to PDF, rather than specifying which directories have them. Also, add some more graphicspath locations to the main latex file so that we don't need to specify relative locations in the individual chapters.
UsersGuide/CastroUserGuide.tex
UsersGuide/CastroVerification/Verification.tex
UsersGuide/ConvertCheckpoint/ConvertCheckpoint.tex
UsersGuide/GNUmakefile
UsersGuide/Scaling/Scaling.tex
commit c554092cbe902b5192290b7d7b1bf0a2bd1fac14
Merge: dd14e7016 2723a7523
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 21 20:41:04 2015 -0600
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit dd14e7016c598b313398f87a4253cecf2ef0a4ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 21 20:38:15 2015 -0600
Remove the castro.allow_untagging parameter. In practice it had no effect since none of the default tagging routines clear zones anyway. Now, if a user sets a tagged zone to CLEAR either by overwriting the default routines or by using the set_problem_tags function, it will be cleared. The user's guide now has a section on how the tagging works as well.
Source/Castro.H
Source/Castro.cpp
UsersGuide/AMR/AMR.tex
UsersGuide/CastroUserGuide.tex
UsersGuide/GNUmakefile
UsersGuide/Inputs/CastroInputs.tex
UsersGuide/Parallel/Parallel.tex
commit 2723a752305e4704404398710c2017117ab3170e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 18:57:02 2015 -0500
stop -> bl_error
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
commit c59ca11f58fdf3f7d7399b18715819e6c76b1bfe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 18:49:55 2015 -0500
stop -> bl_error, indenting
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
commit d87e70e0ea7d99904800faad8bdee0d06fedc7d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 18:39:13 2015 -0500
stop -> bl_error
Exec/hydrostatic_adjust/Prob_1d.f90
commit f6192356c69e72343ccee8432ab76b3c699a9445
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 17:06:56 2015 -0500
a little more on the *fil BC routines
UsersGuide/CastroUserGuide.tex
UsersGuide/Software/CastroSoftware.tex
commit daa31ad582fac8c8cc3bc0a6b648f4d90f93c2a1
Merge: 242ec525e b57da8e63
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 21 15:06:04 2015 -0600
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 242ec525ec09f202358f3b95ad4ebee1698ec8d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 21 15:05:30 2015 -0600
Move sum_interval over to Castro.H
Source/Castro.H
Source/Castro.cpp
commit b57da8e63df69bfe316e2ce075f15e3976a9f031
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 16:01:58 2015 -0500
lots of stubs for boxlibby things to fill in
UsersGuide/Software/CastroSoftware.tex
commit 16b65474226957141e0784c8215abe1b03e013b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 10:55:52 2015 -0500
a lot more documentation about problem writing
UsersGuide/Software/CastroSoftware.tex
commit 4fbb9247624916b96a1e2a887ab43b16715d9805
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 21 10:24:46 2015 -0500
float -> dble
Exec/toy_convect/Prob_2d.f90
commit 0b87d5e9fc4e1cbc6d1b5ff402851644361e038e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 20 20:29:17 2015 -0500
add some helper modules
UsersGuide/Software/CastroSoftware.tex
commit 31e11cd3be78664d9c11a7256e2fcc72033b97ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 19 20:18:12 2015 -0500
more work on updating the hydro section
UsersGuide/Equations/Equations.tex
UsersGuide/FlowChart/FlowChart.tex
UsersGuide/refs.bib
commit c6e17c19668f51f71a6ce4c6a28c38fcbfa27b2b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 19 03:36:56 2015 -0600
Print the build git hash to the stdout if it exists.
Source/Castro_setup.cpp
commit 0694af6349557a1b8fa302ad9759e31ac0c586d3
Merge: d4a372906 a8c0b7e78
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 19 00:12:23 2015 -0600
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit d4a3729064e8cd0404b9f81555c4fe705e106108
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 19 00:08:32 2015 -0600
Fix the density reset strategy so that it is actually consistent with what I said in the commit with hash ee25594. Also, sync up the strategies in 1D and 2D.
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit a8c0b7e783ddd68b15cfbb047c42e3bf59e2ce77
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 18 20:24:44 2015 -0500
some more cleanup
UsersGuide/Equations/Equations.tex
UsersGuide/Gravity/CastroGravity.tex
commit 01d1c8c958dca49ae2617559f295569644ec866e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 18 20:18:05 2015 -0500
add description of castro.spherical_star from Ann
UsersGuide/Equations/Equations.tex
commit 26262e92467f4485ae47abba33ae5540da2a96bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 18 16:50:24 2015 -0500
Sync up output spacing for extra build git line
Source/Castro_io.cpp
commit 33d9db2ab5f7b2b5dcdafc6947d456b22c06028d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 18 15:47:41 2015 -0500
add some problem descriptions
UsersGuide/GettingStarted/CastroGettingStarted.tex
UsersGuide/refs.bib
commit 5a7a03cfd676c1afdb3f69df13113ca67b5338ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 18 10:10:25 2015 -0500
add a problem-specific build directory git hash with name. THis
requires the updated Make.Castro and script in BoxLib/Tools/C_scripts
Source/Castro_io.cpp
commit c7f74a3299441d7ce65311e4657d63b68106b642
Merge: 63e373f8a d7fdbcd8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 18 10:10:00 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 63e373f8addc86b5b45fd820d58c6058b6f4975c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 18 10:09:12 2015 -0500
if we define BUILD_GIT_NAME and BUILD_GIT_DIR in our problem's
GNUmakefile, then take an addition git hash for output into the
job_info file. For example:
BUILD_GIT_NAME := wdmerger
BUILD_GIT_DIR := $(WDMERGER_HOME)
Exec/Make.Castro
commit d7fdbcd8d2e0604dc76a5dbc270a3d83895f1230
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 17 11:27:42 2015 -0800
explicitly initialize center to 0.0
Source/Castro_setup.cpp
commit b82eca6f86a8ab74d83b1f40d60a6b2c592c9b75
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 17 11:20:58 2015 -0800
tiling ca_test_type_flux
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
RAD_F.H
RadSolve.cpp
commit 9f66b3f687d4ff02e1823c5bb6c878a8ee9ad2dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 17 14:09:02 2015 -0500
fix some refs
UsersGuide/Equations/Equations.tex
UsersGuide/refs.bib
commit c439b645a76754dc7c832ad09f471c1bb4e2ec60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 17 13:12:36 2015 -0500
some more updates to the software chapter
UsersGuide/Software/CastroSoftware.tex
commit d155d3d94ef24af243c64c5af49bd368ac866909
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 21:18:38 2015 -0500
more parameters
UsersGuide/Equations/Equations.tex
UsersGuide/FlowChart/FlowChart.tex
UsersGuide/Gravity/CastroGravity.tex
commit 665a2a7e7ef69acc52cf42250902634f836f4584
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 20:52:56 2015 -0500
more updating of parameters in the hydro section
UsersGuide/Equations/Equations.tex
UsersGuide/refs.bib
commit 8e67169d97a790b4fa65a62a3c6da0f8c4642a4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 18:23:18 2015 -0500
more work on the software framework section
UsersGuide/CastroUserGuide.tex
UsersGuide/Software/CastroSoftware.tex
commit 2fa6ba9f1e49f4407258b4bfe137040ba99d40bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 18:12:14 2015 -0500
finish a pass through the runtime parameters, also some random
style updates
UsersGuide/CastroUserGuide.tex
UsersGuide/Equations/Equations.tex
UsersGuide/FlowChart/FlowChart.tex
UsersGuide/Inputs/CastroInputs.tex
UsersGuide/MAESTRO_restart/MAESTRO_restart.tex
UsersGuide/Software/CastroSoftware.tex
commit e4932edf923836e4260cce43dc7ad6bebb7477e3
Merge: f26e9d883 bd6f87e89
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 16 16:22:34 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
Conflicts:
UsersGuide/Inputs/CastroInputs.tex
commit f26e9d88319409947c239d023ed5a49c897619a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 16 16:11:42 2015 -0500
The user can now set castro.center in the inputs file, to determine the location of the problem center at initialization. It can still be overwritten later in Fortran^Crom the prob_params_module.
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
UsersGuide/Inputs/CastroInputs.tex
commit bd6f87e895f05371c7fc1d76d446e5d39a08bb71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 14:50:03 2015 -0500
more styling
UsersGuide/Equations/Equations.tex
UsersGuide/FlowChart/FlowChart.tex
UsersGuide/Inputs/CastroInputs.tex
commit 9ce81a6eb47764edf083c79888bcc6ae8c2c5920
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 13:38:18 2015 -0500
big reorganization -- move physics-specific runtime parameters into
their relevant chapters. Add a stub diffusion chapter
UsersGuide/CastroUserGuide.tex
UsersGuide/Diffusion/CastroDiffusion.tex
UsersGuide/Equations/Equations.tex
UsersGuide/GNUmakefile
UsersGuide/Gravity/CastroGravity.tex
UsersGuide/Inputs/CastroInputs.tex
UsersGuide/Rotation/CastroRotation.tex
UsersGuide/refs.bib
commit a031999c9f76ca97f34471a604fcd824511f8563
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 12:19:17 2015 -0500
start working through the inputs section and restructure / add notes
UsersGuide/Inputs/CastroInputs.tex
commit 7080cd1ca84f59497aaf9950d1ae4f2c260edfab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 16 11:04:01 2015 -0500
update the preface. Add the names of contributors as reported by
git shortlog -s -n
UsersGuide/Introduction/CastroIntroduction.tex
commit 72476c823949058de5ef97b5a9c502108872a3c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 11:03:24 2015 -0500
update the analysis scripts to accept the right directory now that
these live in Castro/
Exec/Sod_stellar/testsuite_analysis/test1-helm.py
Exec/Sod_stellar/testsuite_analysis/test2-helm.py
Exec/Sod_stellar/testsuite_analysis/test3-helm.py
commit baccf6cad57e6de569ee19806cc499378566e9a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 10:46:01 2015 -0500
move the hydrostatic_adjust problem over from Castro_Exec/
This problem is designed to test the 1-d base state evolution
algorithm from Maestro. Note that you need to make sure that
you are running with the same network as Maestro does (to
get the species and therefore thermodynamics correct).
Exec/hydrostatic_adjust/Derive_F.H
Exec/hydrostatic_adjust/GNUmakefile
Exec/hydrostatic_adjust/Make.package
Exec/hydrostatic_adjust/Prob_1d.f90
Exec/hydrostatic_adjust/Problem_Derive.H
Exec/hydrostatic_adjust/README
Exec/hydrostatic_adjust/ext_src_1d.f90
Exec/hydrostatic_adjust/extra_derives.f90
Exec/hydrostatic_adjust/inputs
Exec/hydrostatic_adjust/inputs-subchandra
Exec/hydrostatic_adjust/probdata.f90
Exec/hydrostatic_adjust/probin
Exec/hydrostatic_adjust/probin.subchandra
Exec/hydrostatic_adjust/spherical.hse.640
Exec/hydrostatic_adjust/sponge_1d.f90
Exec/hydrostatic_adjust/sub_chandra.M_WD-1.00.M_He-0.05.hse.C.768
commit 5e36dbd022853063f547773aca2cdfc5a09b3078
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 10:41:43 2015 -0500
make CASTRO_DIR relative
Exec/oddeven/GNUmakefile
Exec/toy_convect/GNUmakefile
commit 6386fa5f7c233b0e6391206a17081e4efb7ce30d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 10:40:21 2015 -0500
make CASTRO_DIR relative
Exec/reacting_bubble/GNUmakefile
commit bb817b894eb3768a54eac10efcf018f12f5ab908
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 10:39:35 2015 -0500
make CASTRO_DIR relative now that we live in Castro/
Exec/double_bubble/GNUmakefile
commit 47f64b256bddc769fc26a8926755980628d17626
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 10:14:20 2015 -0500
add double_bubble
Exec/README
commit f4d25de23c3fec16d7bed97274d51088ef21f1d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 10:12:32 2015 -0500
add the double_bubble problem from Castro_Exec/
Exec/double_bubble/GNUmakefile
Exec/double_bubble/Make.package
Exec/double_bubble/Prob_2d.f90
Exec/double_bubble/README
Exec/double_bubble/inputs_2d
Exec/double_bubble/inputs_2d.single
Exec/double_bubble/inputs_2d.single.equal
Exec/double_bubble/model_stuff.f90
Exec/double_bubble/probdata.f90
Exec/double_bubble/probin
Exec/double_bubble/probin.single
Exec/double_bubble/probin.single.equal
commit baa93ef20288706a3b9cfb99b6d54591a7c21598
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 09:16:52 2015 -0500
update names
Exec/README
commit a43a9982dff9a852904336f0f1b166a94a246235
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 15 07:11:43 2015 -0500
rename tes2 -> reacting_bubble
Exec/reacting_bubble/Derive_F.H
Exec/reacting_bubble/GNUmakefile
Exec/reacting_bubble/Make.package
Exec/reacting_bubble/Prob_2d.f90
Exec/reacting_bubble/Problem_Derives.H
Exec/reacting_bubble/bc_fill_2d.f90
Exec/reacting_bubble/ext_src_2d.f90
Exec/reacting_bubble/extra_derives_2d.f90
Exec/reacting_bubble/initdata_others.f90
Exec/reacting_bubble/inputs_2d
Exec/reacting_bubble/inputs_2d.test
Exec/reacting_bubble/inputs_2d_noentropy
Exec/reacting_bubble/inputs_2d_smalldomain
Exec/reacting_bubble/inputs_2d_zoom
Exec/reacting_bubble/model.hse.cool.coulomb
Exec/reacting_bubble/model.hse.cool.coulomb.6400
Exec/reacting_bubble/probdata.f90
Exec/reacting_bubble/probin
Exec/reacting_bubble/probin.zoom
Exec/reacting_bubble/sponge_2d.f90
commit f646bc9e1d9c82691e0d65131d291afad589af5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 14 15:03:58 2015 -0500
update problems
Exec/README
commit 559d4c4299bd03fefad9dbd07fcb32cc85510aa0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 14 15:03:20 2015 -0500
TODO done
Exec/test2/README
commit f8569f9bdf4dbf85126fee05f3371eca6ac30734
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 14 15:01:16 2015 -0500
move this from Castro_Exec/. THis is the Castro analogue to the Maestro
test2 problem which was used in Maestro paper III. This is a reacting
bubble problem.
Exec/test2/Derive_F.H
Exec/test2/GNUmakefile
Exec/test2/Make.package
Exec/test2/Prob_2d.f90
Exec/test2/Problem_Derives.H
Exec/test2/README
Exec/test2/bc_fill_2d.f90
Exec/test2/ext_src_2d.f90
Exec/test2/extra_derives_2d.f90
Exec/test2/initdata_others.f90
Exec/test2/inputs_2d
Exec/test2/inputs_2d.test
Exec/test2/inputs_2d_noentropy
Exec/test2/inputs_2d_smalldomain
Exec/test2/inputs_2d_zoom
Exec/test2/model.hse.cool.coulomb
Exec/test2/model.hse.cool.coulomb.6400
Exec/test2/probdata.f90
Exec/test2/probin
Exec/test2/probin.zoom
Exec/test2/sponge_2d.f90
commit 13d0ebbcdab7bbd2e32c921f830fb7dd19dec572
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 14 14:40:04 2015 -0500
remove the tagging stuff from probdata.f90 and set it in the tagging
namelist
Exec/oddeven/Prob_2d.f90
Exec/oddeven/probdata.f90
Exec/oddeven/probin.2d
commit dd3c4dc7822d61bf5e1118ae839560f3a2efcccc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 14 14:39:30 2015 -0500
fix error message for namelist read
Source/Castro_nd.f90
commit bead4183c15f4f3d12c8608bca5b83e99a920695
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 13 19:08:14 2015 -0500
tweak some names / style
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 53c30146819e3fb01b260211366ba61c08df5364
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 13 14:46:17 2015 -0500
clean up the equations section a little
UsersGuide/Equations/Equations.tex
commit 734eb28ead15a7f2ddce0c17f4813d6f2487e6f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 13 13:57:36 2015 -0500
take a pass through Chapter 1
UsersGuide/CastroUserGuide.tex
UsersGuide/GNUmakefile
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit de417f901c7aa5982a1b70ed5cdaa25731212228
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 13 13:13:19 2015 -0500
add the oddeven problem
Exec/README
Exec/oddeven/GNUmakefile
Exec/oddeven/Make.package
Exec/oddeven/Prob_2d.f90
Exec/oddeven/inputs.2d
Exec/oddeven/probdata.f90
Exec/oddeven/probin.2d
commit 71111320329bf492a032ebd10e0784f896e59fb8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 13 12:19:20 2015 -0500
I keep forgetting that the 3-d Riemann momentum fluxes have the pressure
term by the 2-d ones don't. So add the pressure term into the HLL solver
for 3-d.
Source/Src_3d/riemann_3d.f90
commit fb167d3a5e0408a2d3c74373a8287b0cf538a7fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 13 11:04:50 2015 -0500
add the hybrid_riemann option to 3-d -- this should fix the problem of
odd-even decoupling with grid-aligned shocks. I need to do a 3-d test
problem for this, but this implementation follows the 2-d version I
did a while back and tested with the oddeven setup.
Also took the opportunity to comment more clearly what kc, k3d, km,
and kflux mean for the slab implementation in 3-d
Source/Castro.cpp
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
commit ac5005c8a2f9535c0d5bab9a8fb15220685e7195
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 12 20:30:53 2015 -0500
try to explain the whole k3d, kc, km business
Source/Src_3d/Castro_advection_3d.f90
commit f0465d91c98fd14485465a41d800489ebc275c1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 12 19:23:32 2015 -0500
add an HLL Riemann solver -- not used yet (but will be part of the
hybrid Riemann option for 3-d
Source/Src_3d/riemann_3d.f90
commit 71afbae97a0afa8552911acbb93c3f6d3834d57b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 12 18:57:08 2015 -0500
add the multi-d shock detection method for 3-d
Source/Src_3d/riemann_3d.f90
commit 7998f5580d8f3ed15305d2ae2e20852f32e41f80
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 12 18:45:24 2015 -0500
fix a bug in the y component of divU for the multi-d shock detection
algorithm
Source/Src_2d/riemann_2d.f90
commit 8abf7a671d93ffaffe07caf032381704da9b4402
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 12 12:51:33 2015 -0800
tiling accel_ccoe
MGFLD.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
RAD_F.H
RadN_1d.f90
RadN_2d.f90
RadN_3d.f90
commit dad07e46b76fc8274495697cf252bb6942bcc7e9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 12 12:35:56 2015 -0800
tiling compute_rosseland
MGFLD.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
commit 27fba2a45ce3c510a1fd56a42365d6f0b675cf80
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 12 11:13:35 2015 -0800
tiling update_matter
MGFLD.cpp
MGFLDRadSolver.cpp
Radiation.H
commit 7174e5bdc408084793c1a8f9a1b344ebb3794b10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 20:27:51 2015 -0500
add a README to describe the included problem
Exec/README
commit 12a0464162d6ceb858ac59f27faa6d502510402a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 19:44:24 2015 -0500
bug fix in the y state for rhoe when using tau in the characteristic limiting
(this bug was introduced in my cleanup/sync earlier today)
Exec/Sod_stellar/trace_ppm_2d.f90
commit 84ce4bdc6ce99e2234cbdc47c9b36bb622423ed9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 11 16:43:01 2015 -0800
removed center form probdata_module
RadBreakout/probdata.f90
commit 2ee35d76335b6e3fdc43561ac16e6275c4191480
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 11 16:42:34 2015 -0800
minor
RadThermalWave/Prob_2d.f90
commit 79416f179a1c15c5a70219701da6d5a08daa57db
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 11 16:17:44 2015 -0800
added entropy to tagging namelist since it is already in taggin_params_moudle
Source/Castro_nd.f90
commit 50eb78eef6236bb00fa98ee4b39456e2df64fd9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 19:03:56 2015 -0500
move this problem from Castro_Exec -- it provides a good example of
how to:
-- use the model parser
-- use a custom tagging routine
-- sponge
-- use a custom sum_integrated_quantities.cpp
Exec/toy_convect/Castro_error.cpp
Exec/toy_convect/GNUmakefile
Exec/toy_convect/Make.package
Exec/toy_convect/Prob_2d.f90
Exec/toy_convect/Problem.H
Exec/toy_convect/Problem_F.H
Exec/toy_convect/Tagging_2d.f90
Exec/toy_convect/ext_src_2d.f90
Exec/toy_convect/inputs_2d
Exec/toy_convect/probdata.f90
Exec/toy_convect/probin
Exec/toy_convect/sponge_2d.f90
Exec/toy_convect/sum_integrated_quantities.cpp
Exec/toy_convect/toy_nova_constg_tanh2.hse.smooth_3.00.1024
commit ef00898d1e7cdcde3712c5ef4f7b24d0fe5d4db2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 11 15:56:25 2015 -0800
sync up with Castro
Rad2Tshock/Prob_1d.f90
Rad2Tshock/probdata.f90
RadBreakout/Prob_1d.f90
RadBreakout/probdata.f90
RadBreakout/probin.1d
RadCoreCollapse/Prob_1d.f90
RadCoreCollapse/Prob_2d.f90
RadCoreCollapse/Prob_3d.f90
RadCoreCollapse/Tagging_1d.f90
RadCoreCollapse/Tagging_2d.f90
RadCoreCollapse/Tagging_3d.f90
RadCoreCollapse/bc_fill_2d.f90
RadCoreCollapse/bc_fill_3d.f90
RadCoreCollapse/probdata.f90
RadCoreCollapse/probin.1d.mgfld
RadCoreCollapse/probin.2d.mgfld
RadCoreCollapse/probin.3d.mgfld
RadShestakovBolstad/Prob_1d.f90
RadShestakovBolstad/probdata.f90
RadSlope/Prob_1d.f90
RadSlope/probdata.f90
RadSphere/Prob_1d.f90
RadSphere/probdata.f90
RadSuOlson/Prob_1d.f90
RadSuOlson/probdata.f90
RadSuOlson/probin
RadSuOlsonMG/Prob_1d.f90
RadSuOlsonMG/probdata.f90
RadSuOlsonMG/probin.common
RadThermalWave/Prob_1d.f90
RadThermalWave/Prob_2d.f90
RadThermalWave/Prob_3d.f90
RadThermalWave/Tagging_1d.f90
RadThermalWave/Tagging_2d.f90
RadThermalWave/Tagging_3d.f90
RadThermalWave/probdata.f90
RadThermalWave/probin.1d
RadThermalWave/probin.2d
RadThermalWave/probin.3d
commit be29d476042ce236a1bb6a0f6b538826ef962716
Merge: 73288f236 38e0b113f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 11 15:09:26 2015 -0800
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 73288f23664223138587de11c1583d1a59c5a652
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 11 15:09:18 2015 -0800
set the default of center to 0, which makes more sense; minor cleanup;
Source/Castro_nd.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_2d/Castro_sums_2d.f90
commit 38e0b113f294ad7100891626cabe283a281ec038
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 18:06:51 2015 -0500
update the locations of the various analysis tools
UsersGuide/CastroVerification/Verification.tex
UsersGuide/MAESTRO_restart/MAESTRO_restart.tex
UsersGuide/ManagingJobs/managingjobs.tex
commit 9414c8005b90ccd3fe13a38258543a604150e3f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 14:16:16 2015 -0500
scripts to make pertty plots for the regression testing
Exec/Sod_stellar/testsuite_analysis/test1-helm.py
Exec/Sod_stellar/testsuite_analysis/test2-helm.py
Exec/Sod_stellar/testsuite_analysis/test3-helm.py
commit eacdf5583dae63729b117f00c0aee7d3333d323b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 14:14:25 2015 -0500
fix the location of CASTRO_DIR since this exists in Castro/
Exec/Sod_stellar/GNUmakefile
commit a4fb96fbc36646e57dd7a442eba764e5e26717b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 14:05:56 2015 -0500
sync up with &tagging
Exec/Sod_stellar/runs/CW-ev/probin-test1-helm
Exec/Sod_stellar/runs/CW-ev/probin-test2-helm
Exec/Sod_stellar/runs/CW-ev/probin-test3-helm
Exec/Sod_stellar/runs/CW-ev/probin-test4-helm
Exec/Sod_stellar/runs/CW/probin-test1-helm
Exec/Sod_stellar/runs/CW/probin-test2-helm
Exec/Sod_stellar/runs/CW/probin-test3-helm
Exec/Sod_stellar/runs/CW/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC/probin-test1-helm
Exec/Sod_stellar/runs/MC/probin-test2-helm
Exec/Sod_stellar/runs/MC/probin-test3-helm
Exec/Sod_stellar/runs/MC/probin-test4-helm
commit 73b25f1716d2c92d09d1f55a7c8627fb5ad33a8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 14:02:12 2015 -0500
sync up with the version used for our paper
Exec/Sod_stellar/Verification/test1.exact.128.out
Exec/Sod_stellar/Verification/test2.exact.128.out
Exec/Sod_stellar/Verification/test3.exact.128.out
Exec/Sod_stellar/Verification/test4.exact.128.out
Exec/Sod_stellar/runs/CW-ev/probin-test1-helm
Exec/Sod_stellar/runs/CW-ev/probin-test2-helm
Exec/Sod_stellar/runs/CW-ev/probin-test3-helm
Exec/Sod_stellar/runs/CW-ev/probin-test4-helm
Exec/Sod_stellar/runs/CW/probin-test1-helm
Exec/Sod_stellar/runs/CW/probin-test2-helm
Exec/Sod_stellar/runs/CW/probin-test3-helm
Exec/Sod_stellar/runs/CW/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test4-helm
Exec/Sod_stellar/runs/flash/test1/flash.par.test1.data
Exec/Sod_stellar/runs/flash/test1/flash.par.test1.nocharlimit.data
Exec/Sod_stellar/runs/flash/test1/flash.par.test1.nosteep.data
Exec/Sod_stellar/runs/flash/test2/flash.par.test2.data
Exec/Sod_stellar/runs/flash/test2/flash.par.test2.nocharlimit.data
Exec/Sod_stellar/runs/flash/test2/flash.par.test2.nosteep.data
Exec/Sod_stellar/runs/flash/test3/flash.par.test3.data
Exec/Sod_stellar/runs/flash/test3/flash.par.test3.nocharlimit.data
Exec/Sod_stellar/runs/flash/test3/flash.par.test3.nosteep.data
Exec/Sod_stellar/runs/flash/test4/flash.par.test4.data
Exec/Sod_stellar/runs/flash/test4/flash.par.test4.nocharlimit.data
Exec/Sod_stellar/runs/flash/test4/flash.par.test4.nosteep.data
Exec/Sod_stellar/runs/makePlot-MC-CGF.py
Exec/Sod_stellar/runs/makePlot-MC-CW.py
Exec/Sod_stellar/runs/makePlot-MC-final.py
Exec/Sod_stellar/runs/old/makePlot-MC-dt.py
Exec/Sod_stellar/runs/old/makePlot-MC-eigen.py
Exec/Sod_stellar/runs/old/makePlot-Tfixes.py
Exec/Sod_stellar/runs/old/makePlot.py
Exec/Sod_stellar/runs/old/makePlotZoom.py
Exec/Sod_stellar/runs/relnorms.py
commit 2c9cc0c6e717a50df1c83f4aee841a8aaa5adb87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 13:58:58 2015 -0500
sync up with the main version
Exec/Sod_stellar/trace_ppm_2d.f90
commit 6b9e146eba28abb8078c3cf93aa302e0df18b5f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 12:35:35 2015 -0500
fix dimensioning of rot()
Source/Src_2d/trace_ppm_2d.f90
commit b0e8c7114928c71b82b932c58aad146a58814304
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 12:07:35 2015 -0500
move the tiliing discussion into the Software Framework chapter
UsersGuide/CastroUserGuide.tex
UsersGuide/Parallel/Parallel.tex
commit 96f9d3cb7a634ec8e809fdba61d1714062943590
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 11 12:04:01 2015 -0500
update verification to point the regression test stuff to the BoxLib
User's Guide
UsersGuide/CastroVerification/Verification.tex
commit 902721f4e455a840617d8d49ca7914b2cd6f293c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 17:08:51 2015 -0800
removed prob_center
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/probdata.f90
Exec/DustCollapse/sponge_3d.f90
Exec/HCBubble/Prob_3d.f90
Exec/HCBubble/probdata.f90
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/KH/probdata.f90
Exec/RT/Prob_2d.f90
Exec/RT/Prob_3d.f90
Exec/RT/probdata.f90
Exec/RT_particles/Prob_2d.f90
Exec/RT_particles/probdata.f90
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
Exec/Sedov/probdata.f90
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
Exec/Sod/probdata.f90
Exec/Sod_stellar/Prob_1d.f90
Exec/Sod_stellar/Prob_2d.f90
Exec/Sod_stellar/Prob_3d.f90
Exec/Sod_stellar/probdata.f90
commit c8e594499520351c1228fbfb32cd754086f7c2b8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 17:08:08 2015 -0800
fixed local trace_ppm_2d.f90
Exec/Sod_stellar/trace_ppm_2d.f90
commit 8d7a113b64aea18f88dece0eecd474220d12f74c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 15:53:01 2015 -0800
rotation in 3d: made the array smaller
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/trans_3d.f90
commit d235088cef5cd63d3ad55decc296c9c0ec9a8271
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 15:42:05 2015 -0800
rotation in 2d: made the array smaller; fixed index for q
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
commit 32513ecb666b3b76557bc6e6e1ed6d9c4ddee9ed
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 15:39:56 2015 -0800
made the correction of rotation source terms thread safe; minor changes
Source/Castro_advance.cpp
commit 9d679b6402989f452adf97cf55888b5e19119f13
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 12:23:49 2015 -0800
hack for non-Poisson gravity
Source/Castro_advance.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
commit 7a7da27ea031a67c3886de25a20c2d2908644194
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 10:52:00 2015 -0800
removed some const
Source/Castro_F.H
commit 3ee2bf76bdf50815e5283ac891f266c703a58956
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 10:51:50 2015 -0800
added a number of new variables to omp reduction
Source/Castro_advance.cpp
commit 6ead11a02c585631a22d4849a392d6cf6ef269c3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 10:18:33 2015 -0800
center --> prob_center
Exec/DustCollapse/sponge_3d.f90
commit 90283d67ce34661861f6db3da29e4409db85876d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 10 10:05:19 2015 -0800
user specified tagging using the full state should be outside the loop over err_list
Source/Castro.cpp
commit 508b8f135514201f30c22b8bc91979158eca62c4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 10 00:47:07 2015 -0500
Change center -> prob_center in local test files to avoid overwriting center variable in prob_params_module.
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/probdata.f90
Exec/HCBubble/Prob_3d.f90
Exec/HCBubble/probdata.f90
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/KH/probdata.f90
Exec/RT/Prob_2d.f90
Exec/RT/Prob_3d.f90
Exec/RT/probdata.f90
Exec/RT_particles/Prob_2d.f90
Exec/RT_particles/probdata.f90
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
Exec/Sedov/probdata.f90
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
Exec/Sod/probdata.f90
Exec/Sod_stellar/Prob_1d.f90
Exec/Sod_stellar/Prob_2d.f90
Exec/Sod_stellar/Prob_3d.f90
Exec/Sod_stellar/probdata.f90
commit d233abfbf0b95cdf532e5e71e53a1796091fdaa5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 9 23:55:06 2015 -0500
Move extern_init() to be after read_params().
Source/Castro_setup.cpp
commit 929dae16ff6e99a587cabee36357fbcbde0a9fce
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 9 22:30:35 2015 -0500
Move some more tagging parameters to the new namelist.
Exec/DustCollapse/probin.fullstar
Exec/DustCollapse/probin.halfstar
Exec/DustCollapse/probin.octant
commit 419503c18b41b515b15ce0efbaaebcc8dce9d9dc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 9 16:15:37 2015 -0800
fixed last two commits
MGFLD.cpp
commit 0226529e7b8bdfc4c52bba9d0c3ef68a3d8db8a6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 9 15:59:24 2015 -0800
tiling lcoal_accel
MGFLD.cpp
MGFLDRadSolver.cpp
Radiation.H
commit 0f17be577966991769a239fceea62b2c373c7b56
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 9 15:54:55 2015 -0800
tiling compute_rhs
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
RAD_F.H
RadSolve.cpp
commit 2d7ace67c48d81c029fcc9ff9fb3269345e90461
Merge: f0f5c70fc 7a3a9c136
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 9 18:47:48 2015 -0500
Merge branch 'master' into conservative_gravity
Conflicts:
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Rotate_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Rotate_3d.f90
Source/prob_params.f90
commit 7c893ea4fa391a28008a27e3e62a85341c9e597a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 6 16:26:05 2015 -0800
tiling accel_spec
MGFLD.cpp
commit 6cd40be71fe7e8af846ded6a8bf82016882292c2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 6 16:08:12 2015 -0800
tiling ca_accel_rhs
MGFLD.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
RAD_F.H
commit 126bc79e9fa6991a424f3e455f02c02c8eae8013
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 6 16:07:49 2015 -0800
DEBUG=FALSE by default
Rad2Tshock/GNUmakefile
RadCoreCollapse/GNUmakefile
RadSphere/GNUmakefile
RadSuOlsonMG/GNUmakefile
commit 7a3a9c13622c04299f43d1f54cc3018caf3bfdca
Merge: fe040bef9 9438810b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 6 14:55:15 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit fe040bef92677d84a8d3649a078ae5f69d7bfacd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 6 14:55:05 2015 -0500
test notifications
README.md
commit 4cf09bc34d0e2a50c9361aa94f527e2992e2003a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 5 12:48:24 2015 -0800
tiling for accel acoe
MGFLD.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
RAD_F.H
commit 4768be2de77683313112725afa9f16ac28b86585
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 5 12:35:33 2015 -0800
tiling in filter_prim
Radiation.cpp
commit 3c7da340cd2d5fd02863cdba84e0ffd651ad14de
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 5 11:11:08 2015 -0800
fixed a bug in mask for filtering primitives
Radiation.cpp
commit c400df87ac43e75b5781e8c0190bdea99cb471cc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 5 10:59:07 2015 -0800
comments
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
commit 1f51da0628c617ee924d55f953d03dee3cfd3427
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 5 10:51:00 2015 -0800
more tiling
CastroRad_1d.f90
CastroRad_2d.f90
RadSolve.cpp
commit fba2b917f856d52a51dfd3bb9cba6a6ef5309711
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 17:25:22 2015 -0800
tiling in leveldterm
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RAD_F.H
RadSolve.cpp
commit cc705fb211fe7b0053c1fc0cc57ed2f282c585df
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 17:15:07 2015 -0800
tiling in set_dterm_face
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RAD_F.H
RadSolve.cpp
commit c54638feb94ba9172b72b04704d9f5dd2194a9b6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 17:06:11 2015 -0800
tiling in update_dcf
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RAD_F.H
Radiation.cpp
commit f6c5779028c43d23c1d92a16399b764e1f0af32d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 16:59:16 2015 -0800
tiling in levelDCoeffs
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RAD_F.H
RadSolve.cpp
commit ad11edb2cc65bdefea6993d372bf5f22d936d5e5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 16:27:10 2015 -0800
tiling in get_rosseland_v_dcf
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RAD_F.H
Radiation.cpp
commit 90f6b16e7a4150b1d72c22427ae9834439ab40be
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 15:43:26 2015 -0800
added omp to compute_limiter
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
MGFLD.cpp
commit 2a2a2d8381ea57bb5682c2618daaed9736f41831
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 15:05:51 2015 -0800
fixed FORT_GCV for tiling
MGFLD.cpp
RAD_1D.F
RAD_2D.F
RAD_3D.F
RAD_F.H
Radiation.cpp
commit 9438810b753eb79ccdefcd0d92d236ead4fa309d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 13:31:33 2015 -0800
some cleanup and float --> dble
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/Rotate_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/Rotate_3d.f90
commit c6c0d47dc72f7d63cb597c57decf8e0cbc0b2c77
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 4 13:00:11 2015 -0800
fixed a bug in sum_utils due to tiling
Source/sum_utils.cpp
commit c0eeee422541abcc400b5c265a63d9e07a5b2a3d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 21:07:17 2015 -0800
fixed some derived variables for tiling
RadDerive_1d.f90
RadDerive_2d.f90
commit a4a575fedf46931306c21d9a656e969c58084685
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 16:55:15 2015 -0800
more tiling and removed lots of unused variables
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
MGFLD.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
MGRadBndry.cpp
RAD_F.H
RadBndry.cpp
RadHydro_1d.f90
RadHydro_2d.f90
RadHydro_3d.f90
commit 0b87325c755bcb6e4683c7e35cf7bb84d4e928a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 17:46:54 2015 -0500
some updates to the tiling from Weiqun
UsersGuide/Parallel/Parallel.tex
commit b7adfdedb2d4c9d33daddd1ba4b2e844fc04002c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 14:41:50 2015 -0800
fixed size for srcQ in tiling
CastroRad_3d.f90
commit 9b8ed5f233f9b418527e054ab992fa5a201b025d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 14:01:00 2015 -0800
fixed a new bug introduced in tiling for radiation hydro
Source/Castro_advance.cpp
commit 4185cb1288ec739e494a729fba24572233bf7350
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 12:28:52 2015 -0800
tiling umdrv_rad
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RadHydro_1d.f90
RadHydro_2d.f90
RadHydro_3d.f90
commit 82323a7d69be2979c7a360b8fe1c917e024f2df4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 11:25:01 2015 -0800
fixed misleading const
Source/Castro_F.H
commit aa9157527177845017b04275d0df14595de4a091
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 11:13:25 2015 -0800
fixed typos
Source/Castro_F.H
Source/Castro_advance.cpp
commit a1d71d7f1374d9dad2f32dfdf0321aa655a5c8fd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 10:48:09 2015 -0800
tiling umdrv_rad
Source/Castro_advance.cpp
commit a21b9c5f8a788ec3a8ed068575fe9e38be0d62ad
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 3 10:06:03 2015 -0800
cleanup
Source/Castro_setup.cpp
commit 06cd0da7be2de5ec13bf8c174980990898ef3d96
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 2 16:27:24 2015 -0800
tiling in estdt for radiation
Source/Castro.cpp
commit 7299d10755a80e1178d863f95da2ace90f3d3c1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 15:16:59 2015 -0500
more stuff to ignore
.gitignore
commit fc8e5ff37e1d099b24a6cb17af3f8705ed4c2ce7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 15:11:30 2015 -0500
add a graphics path
UsersGuide/CastroUserGuide.tex
commit 0bac9268232a2fdfa705c32f102fca9b8760ba19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 15:11:16 2015 -0500
finish first pass at tiling Docs
UsersGuide/Parallel/Parallel.tex
commit 1c43b4131bf681415589609001783ab627b15439
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 14:36:47 2015 -0500
more figure tweaking
UsersGuide/Parallel/Parallel.tex
UsersGuide/Parallel/domain-tile.eps
UsersGuide/Parallel/domain.py
commit 1e4b392d05fc2bed2670cfadfc86253c4d8b07b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 13:38:48 2015 -0500
more tiling editing
UsersGuide/Parallel/Parallel.tex
commit f1dff401e0fd5293e87881f247616fa41527c32c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 13:16:10 2015 -0500
more on the non-tiling approach
UsersGuide/Parallel/Parallel.tex
commit bfcce6dd74c46974f62b517ae1e097ae3444604c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 3 12:24:37 2015 -0500
Start of a Parallel chapter that discusses tiling -- at the moment this
is just Weiqun's notes. Committing this to save it before customizing
it.
UsersGuide/CastroUserGuide.tex
UsersGuide/GNUmakefile
UsersGuide/Parallel/Parallel.tex
commit cfb1ae66208bde6109200d785eba2492caed6343
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 2 17:16:44 2015 -0800
tiling in estdt for radiation
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
MGFLD.cpp
RAD_F.H
commit 4f3447b5fa95ed80f3d6ea27cf87606e13cdbdd3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 2 14:20:02 2015 -0800
removed a number of omp critical
Source/Gravity.cpp
commit 2e251df5c96446f50eb3e460120cf3c938e0fbc2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 2 14:19:45 2015 -0800
int --> long for safety
Source/Castro.cpp
commit f0f5c70fc7bf4755c3a15ed561fa96ad07c7753f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 1 21:50:38 2015 -0600
Add a set_problem_tags subroutine call to errorEst() that calls a Fortran function and passes it the state. This allows the user to write their own tagging function. To do so, the user should copy problem_tagging_$(DIM)d.f90 to their problem directory and edit the function accordingly.
Source/Castro.cpp
Source/Castro_error_F.H
Source/Src_1d/Make.package
Source/Src_1d/problem_tagging_1d.f90
Source/Src_2d/Make.package
Source/Src_2d/problem_tagging_2d.f90
Source/Src_3d/Make.package
Source/Src_3d/problem_tagging_3d.f90
commit 84264ab497fc2a51876b000ae892585887ae4bf3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 1 14:37:42 2015 -0600
Get the Sod_stellar problem working with the new changes.
Exec/Sod_stellar/trace_ppm_2d.f90
Source/Src_2d/Castro_advection_2d.f90
commit 0a1d02edd20f1dfa60307c37ce610ece8fbac06e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 1 13:56:53 2015 -0600
Some fixes to get things compiling again in 1D and 2D.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_setup.cpp
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
commit 767ca92a4933f874e19b02381ae3be7c109f2af5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 1 12:48:34 2015 -0600
Move all of the tagging parameters (e.g. denerr, max_denerr_lev) into a separate module, and read them in from a separate namelist, tagging, from the probin file. This means we no longer need to include these variables in the probdata_module, and completes the removal of references of probdata_module in the code. All of the tests in Exec/ have been updated accordingly.
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/probdata.f90
Exec/HCBubble/Prob_3d.f90
Exec/HCBubble/probdata.f90
Exec/HCBubble/probin-sod-x
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/KH/Tagging_2d.f90
Exec/KH/Tagging_3d.f90
Exec/KH/probdata.f90
Exec/KH/probin
Exec/RT/Prob_2d.f90
Exec/RT/Prob_3d.f90
Exec/RT/probdata.f90
Exec/RT/probin
Exec/RT_particles/Prob_2d.f90
Exec/RT_particles/probdata.f90
Exec/RT_particles/probin
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
Exec/Sedov/probdata.f90
Exec/Sedov/probin.1d.cyl
Exec/Sedov/probin.1d.sph
Exec/Sedov/probin.2d.cyl_in_cartcoords
Exec/Sedov/probin.2d.cyl_in_cartcoords.tau
Exec/Sedov/probin.2d.cyl_in_cylcoords
Exec/Sedov/probin.2d.sph_in_cylcoords
Exec/Sedov/probin.2d.sph_in_cylcoords.testsuite
Exec/Sedov/probin.3d.cyl
Exec/Sedov/probin.3d.sph
Exec/Sedov/probin.3d.sph.testsuite
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
Exec/Sod/probdata.f90
Exec/Sod/probin-slowshock-x
Exec/Sod/probin-sod-x
Exec/Sod/probin-sod-y
Exec/Sod/probin-sod-z
Exec/Sod/probin-test1-helm
Exec/Sod/probin-test2-1d
Exec/Sod/probin-test2-helm
Exec/Sod/probin-test2-x
Exec/Sod/probin-test2-y
Exec/Sod/probin-test2-z
Exec/Sod/probin-test3-helm
Exec/Sod/probin-test3-x
Exec/Sod/probin-test3-y
Exec/Sod/probin-test3-z
Exec/Sod_stellar/Prob_1d.f90
Exec/Sod_stellar/Prob_2d.f90
Exec/Sod_stellar/Prob_3d.f90
Exec/Sod_stellar/probdata.f90
Exec/Sod_stellar/probin-test1-helm
Exec/Sod_stellar/probin-test1-helm-y
Exec/Sod_stellar/probin-test1-helm-z
Exec/Sod_stellar/probin-test2-helm
Exec/Sod_stellar/probin-test3-helm
Exec/Sod_stellar/probin-test4-helm
Exec/Sod_stellar/runs/CW-ev/probin-test1-helm
Exec/Sod_stellar/runs/CW-ev/probin-test2-helm
Exec/Sod_stellar/runs/CW-ev/probin-test3-helm
Exec/Sod_stellar/runs/CW-ev/probin-test4-helm
Exec/Sod_stellar/runs/CW/probin-test1-helm
Exec/Sod_stellar/runs/CW/probin-test2-helm
Exec/Sod_stellar/runs/CW/probin-test3-helm
Exec/Sod_stellar/runs/CW/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test4-helm
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Make.package
Source/Src_1d/Tagging_1d.f90
Source/Src_2d/Tagging_2d.f90
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_3d/Tagging_3d.f90
Source/Src_3d/prescribe_grav_3d.f90
Source/tagging_params.f90
commit 19186c053344a9f31eab6e5e5e4518d26ce3e046
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 1 02:27:31 2015 -0600
Replace instances of xmin, xmax, etc. in the code with problo, probhi.
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/prob_params.f90
commit bded809ae9fbb301472c1df1dfcf21825f270f23
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 1 00:19:10 2015 -0600
Replace xmin, xmax, etc. with problo and probhi in the prob_params_module.
Source/Castro_nd.f90
commit 83070fa4c66c6c2a3ab3dba310aa6ef4257d492c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 31 23:48:03 2015 -0600
Replace all instances where probdata_module was being used to obtain center, with prob_params_module.
Source/Castro_nd.f90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/Src_3d/Castro_sums_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/pointmass_3d.f90
commit 39bf50c4817810de9805d4f6daa0510a37ffe368
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 31 23:05:20 2015 -0600
Add center variable to prob_params_module.
Source/Castro_nd.f90
Source/prob_params.f90
commit ee255941630f16bfa5219249f5bfd973e17dab90
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 31 22:59:13 2015 -0600
Change strategy for density resets. We now find the neighboring zone of the largest density, and reset the zone to this neighboring zone's characteristics. If no neighboring zone has density greater than small_dens, then we reset the zone to small_dens and small_temp with zero velocity.
Source/Src_3d/Castro_advection_3d.f90
commit 3ec756e2b300f03b1809686f9b525cc26ceef155
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 31 02:08:32 2015 -0600
Print out a message when we've discontinued the simulation due to the timestep being too small.
Source/main.cpp
commit 7153ee34d7fbef60bd20773743b4d71b1f11f1df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 30 19:41:42 2015 -0500
comments
Source/prob_params.f90
commit 402632e705a15e2deeb31fb2e29e0a1f8492c000
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 30 03:02:50 2015 -0500
Only do ppm calculations with gravity and rotation if do_grav and do_rotation are enabled, respectively.
Source/Castro_advance.cpp
Source/Src_2d/Castro_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit 09b9aff63f025f84ed046ecccd801f0acada9456
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 29 16:17:11 2015 -0800
sync up makefile with Radiation
Exec/Make.Castro
commit 3cc7ce050af1f4b2d12a18e92ef39e52e5a675be
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 29 16:16:08 2015 -0800
tweak the make system to use openmp enabled hypre when USE_OMP is TRUE
Make.Castro
commit e09924546525152f333f1a6de14c58297c1dd17f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 29 17:50:52 2015 -0500
Pass in do_grav and do_rotation to Fortran
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 6d65eb17bc731824feb03aad8e7228fbea9cd35b
Merge: 6104aacb8 53f57a725
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 29 13:46:15 2015 -0800
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 53f57a725cad1cbcaca1d3a6c96b80eab9a1736f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 29 16:10:04 2015 -0500
don't need naux
Source/Src_2d/trace_ppm_2d.f90
commit d5e115af30f9b7fb5dd43a871d5713513870b2af
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 29 04:27:53 2015 -0500
Fix incorrect array indexing
Source/Src_3d/Castro_grav_sources_3d.f90
commit 485eb39e4779cdff15a92df3a78d8a82bee7c5f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 29 03:28:21 2015 -0500
Fix typo
Source/Src_3d/Castro_rot_sources_3d.f90
commit 6104aacb8a0085b5198fb922a854566b1e5c1caa
Merge: a26a5b22e d9671b88a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 28 10:05:58 2015 -0800
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 7ccb95be1454272f1b91b0a3bd828e2fdd4f309c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 28 02:17:07 2015 -0500
Sync up the recent changes to gravity in 1D and 2D.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_grav_sources_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
commit c1cc0dfd8c3e6a3df9317a3ea49f95dd23b6bada
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 28 00:39:29 2015 -0500
Sync 2D rotation module with the recent updates to 3D.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_2d/Castro_rot_sources_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/Rotate_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit e9228202224106f96c9636fe0c7adf02d6500068
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 21:06:47 2015 -0500
Enable tracing of the rotation source term using ppm_trace_grav == 1. This works identically to the gravity update since both only update the velocities among the primitive variables.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit c0deb3dedd59582ee0b342faaf3bf746c4725124
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 16:22:02 2015 -0800
changed how some saved variables are set for thread safety
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
RAD_F.H
Radiation.cpp
radhydro_params.f90
commit a26a5b22ededd4e9f0f4a72e41d2608c3b613ec0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 16:07:27 2015 -0800
sync up with Radiation
Source/Castro_F.H
Source/Castro_advance.cpp
commit 2ec9a28b2f6ae5bc8f233b0e9c0798d85a834ff9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 19:01:24 2015 -0500
Add a ppm_trace_rot option. This has no effect yet.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/trans_3d.f90
Source/meth_params.f90
commit d9671b88a588d4c1e61a518f29fc5c8cd388937d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 27 18:54:41 2015 -0500
more doc of parameters
UsersGuide/Equations/Equations.tex
commit ef9b8f4291919c55990572c0cb2633c196ce75ba
Merge: 851cb1c23 3be43751c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 27 18:51:30 2015 -0500
Merge branch 'master' of ssh://github.com/BoxLib-Codes/Castro
commit 851cb1c237672e737c3044e827dd1bcce27c8b79
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 27 18:51:07 2015 -0500
add some notes on various ppm parameters
UsersGuide/Equations/Equations.tex
commit 89e153e35f7c0239603e47440eed5b34e7b3074b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 15:36:07 2015 -0800
more OMP and cleanup
HypreABec.cpp
HypreExtMultiABec.H
HypreExtMultiABec.cpp
HypreMultiABec.cpp
commit 781d5811fac4eae8415fc9f2cd59c30fc2a0abea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 15:21:16 2015 -0800
added OMP
HypreABec.cpp
commit 290f7f5550a6403d998bf33eb5acf081b72f7804
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 18:20:54 2015 -0500
Allow the rotation axis to be arbitrary by setting the rot_axis parameter. By default it will be 3, corresponding to the z-axis.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/Castro_rot_sources_3d.f90
Source/meth_params.f90
commit 3be43751c1f616218338bee4069d64d2d0a68723
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 15:00:25 2015 -0800
minor cleanup
Source/Castro.cpp
Source/sum_utils.cpp
commit 11bb77c7141e3b07b248893688f5a9917583ab36
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 14:59:37 2015 -0800
minor cleanup
HypreABec.cpp
HypreMultiABec.H
HypreMultiABec.cpp
RadBndry.cpp
Radiation.cpp
commit b209b491009910171a8fd5bd9aebc91b542f23a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 17:46:21 2015 -0500
Create a separate function to return the omega vector.
Source/Src_3d/Castro_rot_sources_3d.f90
commit 2e344777a8ad0dd024a564df8e493fcaaf43c9f5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 14:45:49 2015 -0800
fixed SolverType assertion
Radiation.cpp
commit 95d75a374af0e0fc987595399ddb15bbcba4ba68
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 17:33:37 2015 -0500
Remove some unused variables
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit da95e64011df242031c3cb3384aef9e147e5e5d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 17:26:25 2015 -0500
Explicitly add the rotation field as a source term to the edge states. This is necessary because the rotation terms are no longer part of the external source terms.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/Src_3d/trans_3d.f90
commit 199a42ca412d5e12655fd3049d4d360f2bacea05
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 14:18:24 2015 -0800
fixed setabecflux; this new issue was caused different macros were used in HABEC_?D.F and COMPSOLVER_?D.F
HABEC_1D.F
HABEC_2D.F
HABEC_3D.F
RadSolve.cpp
commit f6c6deb720e6415f4f1743fe0811736e97048f05
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 13:48:36 2015 -0800
Since sync_solve is gone, we can clean up RadSolve and remove _CompSolver.
Make.Radiation
commit 593f81a4bcb1360171db8c2029882820a9e06a30
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 13:48:36 2015 -0800
Since sync_solve is gone, we can clean up RadSolve and remove _CompSolver.
HABEC_1D.F
HABEC_2D.F
HABEC_3D.F
HABEC_F.H
RadSolve.H
RadSolve.cpp
_CompSolver/COMPSOLVER_1D.F
_CompSolver/COMPSOLVER_2D.F
_CompSolver/COMPSOLVER_3D.F
_CompSolver/COMPSOLVER_F.H
_CompSolver/CompSolver.H
_CompSolver/CompSolver.cpp
_CompSolver/CompSolverLevel.H
_CompSolver/CompSolverLevel.cpp
_CompSolver/EDGEVAR_1D.F
_CompSolver/EDGEVAR_2D.F
_CompSolver/EDGEVAR_3D.F
_CompSolver/EDGEVAR_F.H
_CompSolver/EdgeVar.H
_CompSolver/EdgeVar.cpp
_CompSolver/Make.package
commit ec1be6023fcc1dcc622964bf3f31e31887fc279e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 15:57:37 2015 -0500
Add rot_source_type = 4, the method for updating the energy so that the total energy (E + rho * phi_rotation) is conserved. This is analagous to grav_source_type = 4 and in fact is implemented the same way since both sources can be expressed in terms of a potential.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_rot_sources_3d.f90
commit 9173e1cb53375b90faf75ca015947c30fffca302
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 12:34:24 2015 -0800
more cleanup
Radiation.H
Radiation.cpp
commit b05906fd1f4ad013805906109e6010c404f344e3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 12:13:37 2015 -0800
fixed a warning about omp
Source/Castro_advance.cpp
commit 2dc04914916f88dd25d8dbeccb4ebace092b151f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 12:08:18 2015 -0800
clean up sync_solve
Rad2Tshock/inputs.M2
Rad2Tshock/inputs.M5
RadBreakout/inputs.1d
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
commit 15c0c81a37f448693e10e6af05dfe97db81149d3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 12:08:18 2015 -0800
clean up sync_solve
Radiation.H
Radiation.cpp
SGRadSolver.cpp
Using.H
energy_diagnostics.cpp
commit bc058d616890031cef0ef1085a68cc85f91a475e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 14:29:29 2015 -0500
Query for the rot_source_type
Source/Castro.cpp
commit 2b35510d80aeca95bc187554cf2abafd11a7a1ca
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 11:08:24 2015 -0800
clean up deprecated sync_solve
Source/Castro.cpp
commit 29acd8c821916ec77fe6805f1b855d3f6a5f5f57
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 10:25:00 2015 -0800
put an accidently deleted line back
RadHydro_3d.f90
commit 78773d8577879a57e6395ae621a33bd58af57012
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 13:23:37 2015 -0500
Add a hook for rot_source_type == 4.
Source/Src_3d/Castro_rot_sources_3d.f90
commit f7fda16c914b5479578468cc7b736afce9b402f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 13:14:14 2015 -0500
Add rot_source_term == 1, 2, and 3 that are the analogue of grav_source_type == 1, 2, and 3. Setting this to 1 should leave the old behavior unchanged.
Source/Src_3d/Castro_rot_sources_3d.f90
commit f80ac53bc1192322b14e81551b34c7d7816e8794
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 27 10:07:02 2015 -0800
removed OMP from fortran routines in preparation for tiling
CastroRad_3d.f90
MGFLD_3d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
RAD_3D.F
RadEOS_3d.f90
RadHydro_3d.f90
commit 943779be1d71e193a17b28e5b949b8c9a39c3422
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 04:32:44 2015 -0500
Move rotation correction after gravity correction since that was the original order.
Source/Castro_advance.cpp
commit 0c1ea77c8fefac9dab947084b101b5fe5a8508d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 04:26:51 2015 -0500
Add diagnostic outputs to the rotation sources.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
commit d13dedb60e32fa70b086fa62fac3a0b43b826c46
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 04:01:47 2015 -0500
Instead of adding the rotation terms to the external source terms, we now have separate routines for the rotation source and correction steps, similar to the way we do gravity. As a result, the rotation source is no longer included in the edge state prediction; I'll need to add this in later.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
Source/Make.package
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_rot_sources_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/Rotate_3d.f90
commit 7ea2cb19b8d26115c0bf116b84c57e02acf350f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 27 00:23:20 2015 -0500
Add a rot_source_type parameter that determines how we will include the rotation source terms. This has no effect yet.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 6e225c0ad4ee2eae9ed73b5a61bbe004f4415e57
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 26 15:16:19 2015 -0800
turn off tiling for hydro
Source/Castro_advance.cpp
commit 30880007fea2b8f5798f86396ad05ab0c4a021a1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 26 14:00:58 2015 -0800
have to allocate fluxes MF, whenever do_reflux is true
Source/Castro_advance.cpp
commit d0eed586e756a4110fcdbba23b55d6a85d160d32
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 26 13:41:21 2015 -0800
fixed new bug in REACTIONS
Source/Castro_advance.cpp
commit ee6c4ebfb77fadcf857e43828664866bc328a83d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 26 12:31:01 2015 -0800
limit the scope of fpi
Source/Castro_advance.cpp
commit 490d15f5ffbee70f1f24bdc85a23ebce2b710afc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 26 12:23:27 2015 -0800
fixed a new bug: forgot to update fpi to mfi
Source/Castro_advance.cpp
commit c5809dd3b60ec56e523d2484f81a21dd46bd021b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 16:18:49 2015 -0600
Updated the dual energy formalism so that it is more consistent with Bryan et al. (2014). We now have two flags: one checks whether we use (E-K) or (rho e) in generating the primitive variable e, and the other determines whether we use (E-K) or e when updating UEINT. Values for the etas are set by default so that past behavior should not change.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/meth_params.f90
commit 01d3f9f576b2a3bec08a3065ada6b87ae275ad91
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 13:50:37 2015 -0600
Clean up the g source correction routine. We're no longer using a flux-based approach.
Source/Src_3d/Castro_grav_sources_3d.f90
commit f403b80b86d0b406bcfb86be6998924773bfaf8a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 13:50:02 2015 -0600
Query the inputs file for the dual energy parameters.
Source/Castro.cpp
commit eaed28ef69fcbe3609b8298298f55d7e9bc1dc5a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 04:04:42 2015 -0600
Remove the old grav_source_type = 4 and 5 because these just don't work well due to the truncation error in the gravitational field. We retain as grav_source_type = 4 the AREPO approach.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
commit 659529127fc02f8ac2348b66d533453209db511b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 02:59:36 2015 -0600
Set the default so that the total energy is updated in the dual energy formalism, so that previous behavior remains unchanged.
Source/Castro.cpp
commit 50826a4c876962377f0fe8efae8fad6af4e1d6b6
Merge: 5a4f77d39 29b6a4885
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 02:58:23 2015 -0600
Merge branch 'conservative_gravity' of ssh://github.com/BoxLib-Codes/Castro into conservative_gravity
commit 5a4f77d398525d798b1a83b8c45611c100e3bc3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 25 02:58:07 2015 -0600
Fix a sign error in the grav_source_type = 6 update for the energy. It now no longer appears as the divergence of a flux, but is conservative for the total energy (internal + kinetic + potential). Also, revert to using the old momentum update. This is actually conservative up to the truncation error of the gravitational potential.
Source/Src_3d/Castro_grav_sources_3d.f90
commit 29b6a4885318a91183a68eb9585b694a1af5a96b
Merge: b15f58b9a 179b8801e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 24 23:39:47 2015 -0500
Merge branch 'master' into conservative_gravity
commit b15f58b9ac6711f00cffdb6fedaa98fa465a7444
Merge: 0fce8413d 56a9ac5b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 24 23:22:01 2015 -0500
Merge branch 'conservative_gravity' of ssh://github.com/BoxLib-Codes/Castro into conservative_gravity
commit 0fce8413d21e9aea2c11e24fc44f71c98cda3cd9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 24 23:21:55 2015 -0500
Add two flags: one that determines the threshold in the dual energy formalism for when we use (E-K) for e, and another that determines whether we update (rho E) when we don't reach that threshold.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/reset_internal_energy_3d.f90
Source/meth_params.f90
commit 56a9ac5b08a1c276c12decb3c8271d4b9319ab8f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 24 22:09:51 2015 -0600
Update of the runtime energy and momentum diagnostics. We have now have energy and momentum diagnostics for both the hydro step, the grav source step, and the grav correction step, and the names in the output are more consistent.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
commit 9b7c2a3786658556b9f7c55f22c9f6780741dbde
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 20:30:47 2015 -0800
fixed RADIATION
Source/Castro_advance.cpp
commit 8a6a710efbd0a8210e0e87961d4c0ddd5924be47
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 20:24:21 2015 -0800
sync up with Castro: Sborder technically does not have ghost cells now
MGFLD.cpp
commit a3f9a205f74cc4710cdf4049d1ae7ccc1ee12fdc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 20:23:51 2015 -0800
forgot u_gdnv has a ghost cell
Source/Castro_advance.cpp
commit 6f40bd482ee8fbc25c0d4cbbc2de66491ae026ef
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 17:23:59 2015 -0800
fixed the bounds of srcQ
Source/Src_1d/Castro_advection_1d.f90
commit d30d43c3768eda648171525db38371c82053466f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 17:21:50 2015 -0800
fixed the bounds of srcQ
Source/Src_2d/Castro_advection_2d.f90
commit 2b6d038f981badd113d7afa1ef4d5777f4d3e9a5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 17:18:54 2015 -0800
fixed the bounds of srcQ
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 7f26c0ae916699013f2fccc751899f44699fcea1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 17:08:59 2015 -0800
tiling from C++ side
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
commit f8c93eed633a017d935f56fa838ddd208a7bb176
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 17:08:07 2015 -0800
make it less confusing
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 6691e3543d0e2e000cfbc0a81c3aff72dc1a09b2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 23 17:07:35 2015 -0800
no reason to floor here
Source/Src_1d/pointmass_1d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_3d/pointmass_3d.f90
commit c26d257f6cf2aa5bd3fb25b5ef7f350654e9003c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 22 10:32:13 2015 -0800
added a comment about the RadCoreCollapse problem
RadCoreCollapse/GNUmakefile
commit 179b8801e0a3515fafe717da8d88c268580e9dab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 21 21:19:12 2015 -0500
add some getting started notes
README.md
commit 5098930c14666029b2253ee2a7f1c95b0d51c235
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 21 17:37:17 2015 -0500
Test commit for GitHub
README.md
commit ff10da99e76e90604e2f4f415411d36f9b2e8138
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 21 16:32:08 2015 -0500
now on github
UsersGuide/CastroUserGuide.tex
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit 45f47eabb7a6ffd1a0730ed6e554b304d3cb3292
Merge: f22c36007 397d9cd14
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 20 23:49:17 2015 -0600
Merge branch 'master' into conservative_gravity
commit 397d9cd146ccaa39c29c6751e8d36d5b10fc59a7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 20 17:11:52 2015 -0800
nodalbox -->> nodaltilebox to sync up with BoxLib
Source/Diffusion.cpp
Source/Gravity.cpp
commit f22c360076b519d522e65c8d00b05387ee45fee7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 19 21:25:02 2015 -0600
Uncomment a function call that had been commented for debugging purposes.
Source/Castro.cpp
commit 881d313a8390b955385f0d08a6da6f89447ad5f5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 14 10:27:06 2015 -0800
sync up
RadCoreCollapse/Tagging_1d.f90
RadCoreCollapse/Tagging_2d.f90
RadCoreCollapse/Tagging_3d.f90
RadThermalWave/Tagging_1d.f90
RadThermalWave/Tagging_2d.f90
RadThermalWave/Tagging_3d.f90
commit 250228dc00e3eb33274933b149d546c0f6a98f35
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 13 20:27:36 2015 -0600
Added a small_ener minimum energy.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 8096cd9accef4bee2ddbd0768ad26635041b7497
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 13 16:26:50 2015 -0800
fixed a recent bug in fine mask
Source/Gravity.cpp
commit 8d86bba247466da2bebfe29b0dbae62160deb4b2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 13 15:39:05 2015 -0800
be safe
Castro_radiation.cpp
commit 33a407ff97f4117873b59bbe8c7acdeebd0575e0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 13 15:37:17 2015 -0800
sync up with Castro
RadDerive_3d.f90
commit d67d4faf2f53307d2702918e5eb05aa2dd9860b0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 13 15:32:06 2015 -0800
fixed a recent bug
Source/Src_1d/Tagging_1d.f90
commit abdd6cdc2c566dcc56e6bb882505b312031e6dda
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 13 14:38:05 2015 -0800
fixed fortran function names
Source/sum_utils.cpp
commit 5bd02ec6567efec6ed97bb8f5a527d579a27c7d2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 13 14:35:30 2015 -0800
fixed a new bug in no hydro case
Source/Castro_advance.cpp
commit 00018a1342347d81ffe0da6624d573bb51a76703
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 13 12:43:49 2015 -0600
We don't actually need to explicitly construct the gravitational tensor, the three components in flux1, flux2 and flux3 do the job as well.
Source/Src_3d/Castro_grav_sources_3d.f90
commit bbf94780c51ac0b3a2138f2f9d6cf8692b98dbe1
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 13 04:13:14 2015 -0600
For the grav_source_type = 6 option, we now do things slightly differently from the AREPO code paper. First, both the mass flux and the gravitational acceleration are evaluated on the cell boundaries, which allows the formalism to be explicitly conservative. Second, instead of using the tensor formalism for the momentum update as recommended by Jiang et al., we use the approach of the AREPO paper to evaluate the momentum update from gravity (rho * g) on the boundaries using the divergence theorem. To do this, we need rho on cell faces, which we're getting by dividing the mass flux by the velocities on the cell faces (which is ugdnv from the Riemann solver). If the mass flux is zero, then the hack we're using to get rho will fail. This can be temporarily resolved by making sure the initial velocity on the grid is not exactly zero. Also, we still need a way to deal with the possibility that the source term update will result in a negative total energy.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
commit c945f183ad5332f58cc2ad9225f6d8bef2c992f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 12 23:48:13 2015 -0600
The gravitational tensor for the momentum equation was being calculated incorrectly. It now uses the correct approach of calculating all three components of the gravitational acceleration on cell faces, using second-order reconstruction from phi.
Source/Src_3d/Castro_grav_sources_3d.f90
commit 6cc4fa96fd77aeaf80819aed2cf100ca961ea16f
Merge: 1b0d88261 75b987c28
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 12 23:00:06 2015 -0600
Merge branch 'master' into conservative_gravity
Conflicts:
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
commit 1bfb4ed0d6e7266a9cdf9502505aed2526914216
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 12 17:21:10 2015 -0800
get_new_grav_vector fills ghost cells too
Source/Gravity.cpp
commit 75b987c2891415c19aa5fe1f84440ac934861b53
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 12 13:09:01 2015 -0800
fixed last commit
Source/Gravity.cpp
commit 3160a09cd8cf993ef8842433397e755d698f5b57
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 12 12:52:04 2015 -0800
finished tiling in Gravity
Source/Gravity.cpp
Source/Src_3d/Gravity_3d.f90
commit 2c262f92ae1263b0a955d66920143c60c26b9a0f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 12 12:11:27 2015 -0800
fixed last commit
Source/Gravity.cpp
commit 65492dc0f2862a4a8f0a90c8ef6bc6ba02346523
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 12 11:15:26 2015 -0800
more tiling in Gravity
Source/Gravity.cpp
commit a98afa7391220ca7c8246419e1d05a21b33663b4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 12 11:02:44 2015 -0800
more tiling in Gravity
Source/Gravity.cpp
Source/Src_3d/Gravity_3d.f90
commit 8a7885fa67f943e400fb93af42d1670fc95400da
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 10 20:34:22 2015 -0800
remmoved another OMP for similar reason in last commit
Source/Castro.cpp
commit 4641f410d8ea861b9ca78c28241171a209f21000
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 10 20:33:09 2015 -0800
removed omp of the MFiter loop of ca_fill_temp_cond because ca_fill_temp_cond is under Castro/source
Source/Castro.cpp
commit 00edf0c9361ddf250772802f6f604846f606137a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 10 20:19:24 2015 -0800
clean up
Source/Castro.cpp
commit 7b4cf550c19498719534c133cb4d5eaaa998e505
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 9 20:32:01 2015 -0800
fixed the realbox for tagging and updated comments
Source/Castro.cpp
Source/Src_1d/Tagging_1d.f90
Source/Src_2d/Tagging_2d.f90
Source/Src_3d/Tagging_3d.f90
commit 7febc688eeebb2ecc36e4aacd639070028572f63
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 9 20:30:12 2015 -0800
Revert "fixed how x,y,z are computed in derive functions"
because BoxLib has been fixed.
This reverts commit 869ca5937e2e539b1a76255bd01f89e21aff13d8.
Source/Src_2d/Derive_2d.f90
Source/Src_3d/Derive_3d.f90
commit 0331386d624605a1e6941b56d425142016f65a05
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 9 21:12:33 2015 -0600
Added the git commit hashes for Castro and BoxLib to the stdout during setup, so that a record is kept of what code versions you were using during a run.
Source/Castro_setup.cpp
commit 869ca5937e2e539b1a76255bd01f89e21aff13d8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 9 17:14:37 2015 -0800
fixed how x,y,z are computed in derive functions
Source/Src_2d/Derive_2d.f90
Source/Src_3d/Derive_3d.f90
commit 7d1a5520042e79b84388a1870dde510e186dfb1d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 9 16:07:38 2015 -0800
tiled Derive
Exec/Make.Castro
Source/Src_1d/Derive_1d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_3d/Derive_3d.f90
commit ea9f3492a6ea25279ca1e24e7a513a90c115cd15
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 9 15:17:29 2015 -0800
removed ca_derlapvar
Source/Derive_F.H
Source/Src_1d/Derive_1d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_3d/Derive_3d.f90
commit 8bbaabc5b142977f04cf822f93b861b8d7d3cf93
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 9 10:33:59 2015 -0800
more sync up
ext_src_2d.f90
commit 185bde74d39bf6686069ac82fb9648c027430522
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 9 12:29:39 2015 -0500
add a null pphotcno network`
Networks/general_null/pphotcno.net
commit 60436f1a14e479debea0f1ae4ba71acc558ccde2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 9 11:49:29 2015 -0500
remove unused variables
Source/Src_2d/Castro_advection_2d.f90
commit d541f911652d9bf016961c08a09def4a8a78d3df
Merge: 14d950ecc e1707fb9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 9 11:46:20 2015 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 14d950eccf525bb4bc9e0e8e0713c85694b76159
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 9 11:46:05 2015 -0500
remove unused variables
Source/Src_2d/riemann_2d.f90
commit e1707fb9a11b1d9bc7c2802e04f061b640cdd94c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 9 11:35:47 2015 -0500
remove unused variables
EOS/gamma_law_general/eos_stuff.f90
commit e0fc74ba3b0bab0d38816196f890f51e342ab2a3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 8 14:55:12 2015 -0800
sync up Exec/KH
Exec/KH/Tagging_2d.f90
Exec/KH/Tagging_3d.f90
commit dbfca3084f7757e4f2cf3c6eed850e5a672a89d7
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 8 14:21:00 2015 -0800
fixed a new bug: passed the wrong box
Source/Castro.cpp
commit bc55510ec53dba50c32c24ea2ee56b61d5f1aa1b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 8 13:32:16 2015 -0800
updated Tagging_?d.f90
Source/Src_1d/Tagging_1d.f90
Source/Src_2d/Tagging_2d.f90
Source/Src_3d/Tagging_3d.f90
commit 48623502206293b218728d2f0fbcc692067b6e44
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 8 13:10:04 2015 -0800
tiled TagBox using the new BoxLib
Source/Castro.cpp
commit 37a2d87e18850c0fac6e13b47c892d5d9d4e6b29
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 7 14:51:20 2015 -0800
fixed a bug in my last commit: we might have diffusion or rotation when do_ext_src is false
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_rotation.cpp
commit d2a5c3987de84cf0e396f5d6db2f2eee79ac759f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 7 12:42:53 2015 -0800
time-center diffusion and rotation more efficiently
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_rotation.cpp
commit e0c2889264a88c6b241e110e09aac509d663001e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 7 10:49:13 2015 -0800
extrapolate diffusion term to ghost cells
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Diffusion_1d.f90
Source/Src_1d/Make.package
Source/Src_2d/Diffusion_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Diffusion_3d.f90
Source/Src_3d/Make.package
commit 6605fb0cbec6aac8987074ded797717bac311959
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 6 17:19:56 2015 -0800
fill ghost cells for diffution source terms
Source/Castro.cpp
Source/Castro_diffusion.cpp
Source/Castro_rotation.cpp
commit 2351ff3dd8585d4236a3897234c7e21c9adcf7ee
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 6 16:22:17 2015 -0800
cleaned up Gravity
Source/Castro_advance.cpp
Source/Gravity.cpp
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit 6862cd5aef7306639613db33a36a57daabe83977
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 6 14:23:34 2015 -0800
fill ghost cells for rotation source terms too
Source/Castro_diffusion.cpp
Source/Castro_rotation.cpp
commit aed9f1d5026924c6a90daddb5289666c87093899
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 6 14:01:14 2015 -0800
fixed my last commit
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
commit abeb4f84f34c668e7b63e2326ad959888eeba711
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 6 13:55:48 2015 -0800
Don't need to use FillPatchIterator in getNewSource because we don't need to fill ghost cells
Source/Castro.cpp
commit 97ba55e3568ca32affee7e9fb745329d7d5ad9c9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 6 13:41:37 2015 -0800
tiled ext_src
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Src_1d/ext_src_1d.f90
Source/Src_2d/ext_src_2d.f90
Source/Src_3d/ext_src_3d.f90
commit a64d90354e0c7cef09df2c08dbabbc2e37aca88b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 5 20:56:33 2015 -0800
use the new AmrLevel::FillPatch
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.cpp
commit dc483f137f5fc21c518d2ee164f37a5581812126
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 5 15:23:55 2015 -0800
new way of using FillPatchItrator that can utilize OMP'd MultiFab::Copy
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.cpp
commit 4d47a0088ecfd9183a77da247241427cf819d46e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 5 14:55:35 2015 -0800
minor optimization
Source/Castro_advance.cpp
commit b5653d7c0e37ad400414fa310e2b21f0c49b49cf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 5 14:38:59 2015 -0800
remove duplicated codes in sum_utils.cpp
Source/Castro.H
Source/Castro.cpp
Source/Gravity.cpp
Source/sum_utils.cpp
commit f7af8dd6bb667fe99163b136f722644b06f39f26
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jan 5 13:00:49 2015 -0800
For consistence, fill the ghost cells of prescribed gravity too
Source/Gravity.cpp
commit 8b01830e88433d096fadf555d483b7d47e3b9f8c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jan 4 08:05:48 2015 -0800
tiled Castro sums; this is likely to break regression tests because of omp reduction of sum
Source/Src_1d/Castro_sums_1d.f90
Source/Src_3d/Castro_sums_3d.f90
Source/sum_utils.cpp
commit f7f4984d133d2b7fa2047cb703f9b3bcab2e9a72
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sun Jan 4 07:16:37 2015 -0800
almost done tiling in Gravity
Source/Gravity.cpp
Source/Src_3d/Castro_sums_3d.f90
commit 2fa662bd85f0f412e2f750c0b615645d54a771bd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 3 11:17:48 2015 -0800
more tiling
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/pointmass_1d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_3d/pointmass_3d.f90
commit 619af809ad7b626a5152381bc288ad46f3b794fc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 3 11:00:01 2015 -0800
fixed a new bug
Source/Gravity.cpp
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit 5d3fcd94f32b89d15a1eff535ee36d1d090c9caa
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 3 10:49:23 2015 -0800
more tiling in Gravity
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/MGutils_1d.f90
Source/Src_2d/MGutils_2d.f90
commit bbeb89e7898a9d64c92c691d4eeb169cadc96dda
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 3 09:08:06 2015 -0800
removed omp from some 2d f90 files
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_2d/Castro_sums_2d.f90
commit cbbb2a0f0da6b57e518f0485f60830f98e611fb9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 3 08:28:02 2015 -0800
fixed a data race
Source/Castro.cpp
commit 9e598d8c8a0716fe09c271a2d41c877f4d1f10ba
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Sat Jan 3 08:00:10 2015 -0800
changes due to that MFIter::fluxbox has been renamed nodalbox in BoxLib
Source/Diffusion.cpp
Source/Gravity.cpp
commit 05f9e82cc411c371ac3f4f5656973ff284fb6ea1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 2 22:07:17 2015 -0800
tiled ca_apply_metric
Source/Diffusion.cpp
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/MGutils_1d.f90
Source/Src_2d/MGutils_2d.f90
commit 24fd93a4bfd9f4b053c2152f08ebd8d7e09d1d4d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 2 21:42:14 2015 -0800
more tiling in Gravity
Source/Gravity.cpp
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/prescribe_grav_3d.f90
commit e4d5ba7fe5da1f1d65dad81ac4a1799e218cd294
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 2 20:32:06 2015 -0800
fixed typos
Source/Gravity.cpp
commit c6f937cae542cc99b21fdd2ba6d3534463295ddd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 2 15:29:28 2015 -0800
fixed a typo
Source/Gravity.cpp
commit a236acbe2414ca4df786418b5f2d1d072542628c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 2 15:26:40 2015 -0800
more tiling in Gravity
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Gravity_3d.f90
commit afe17cdd7a09a16b8b91873b902744ae14d94962
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jan 2 11:58:41 2015 -0800
more tiling in Gravity
Source/Gravity.cpp
commit b6a491bd021672a8fb3340fce2c6a94d74a340de
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jan 1 14:25:38 2015 -0800
tiled part of Gravity
Source/Gravity.cpp
Source/Src_3d/Gravity_3d.f90
commit f9e43dde935e1f0785e84305d31828662111e723
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 31 20:06:20 2014 -0800
tiled Diffusion
Source/Diffusion.cpp
commit ba5fc9e3389cae2184aef021a7b32205ad9bb877
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Dec 31 19:55:05 2014 -0800
tiled rotation routines
Source/Castro_rotation.cpp
commit 528d66394e9a9ab2693fa7b8b13ce4090c4d0d41
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Dec 30 20:50:15 2014 -0800
more tiling
Source/Castro.cpp
Source/Src_3d/Castro_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/enforce_consistent_e_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
commit 2bf8f05fce961777aae7fa91fe60535c212069fe
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Dec 30 20:31:49 2014 -0800
more tiling
Source/Castro.cpp
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 0a7c02024f2b0954e02c3da4942eeacc18c1c70c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Dec 30 20:21:21 2014 -0800
started using tiling version of MFIter
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/EstDt_3d.f90
commit e25e0f23136837089caa6d1734ca5cf24fec1e95
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 22 09:26:21 2014 -0500
remove a hardcoded iorder flag -- that was for my own personal debugging
Source/Src_2d/trace_2d.f90
commit 28f8b4db7039c46f3a0b724559401962c7540d0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 16 20:43:10 2014 -0500
add xmin, xmax, ymin, ymax, zmin, zmax to prob_params_module -- this information
is sometimes useful to have easily accessible in F90 land.
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_2d/trace_2d.f90
Source/prob_params.f90
commit b7e9b59a461cfe9c0b29cebbfe35b26b884ff108
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Dec 8 10:10:09 2014 -0800
fixed a new bug: BoxArray is reference counted
Source/Gravity.cpp
commit 1b0d882613e0d977c85e88578b76960b1b69d508
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 6 03:15:29 2014 -0500
Fixed sign error in AREPO gravity source. The mass change due to incoming fluxes is positive for fluxes on the left side of the cell and negative for fluxes on the right side. This makes the source actually equivalent to Eq. 96 in the Springel paper.
Source/Src_3d/Castro_grav_sources_3d.f90
commit 7d30bbfb2ba940b5a6567fbf3424104ffce02858
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Dec 5 14:22:14 2014 -0800
minor
MGFLD.cpp
Radiation.cpp
commit 39730e32372872fa643239f601f6d3a98a1d6a00
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Dec 5 14:00:27 2014 -0800
const T --> const T& to avoid copying
Source/Castro.cpp
Source/CastroParticles.cpp
Source/Castro_advance.cpp
Source/Diffusion.cpp
Source/Gravity.cpp
commit 4364c5042c52cff26090a631b2754a2f422886cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 15:57:30 2014 -0500
use npassive and qpass_map/upass_map
Source/Src_3d/riemann_3d.f90
commit 7f45836a8177dc7ed1eb24f6b1f85e733ac0d11a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 15:47:10 2014 -0500
switch over to using npassive and upass_map/qpass_map
Source/Src_2d/riemann_2d.f90
commit 3535480f17da845656f3d87ad42214a281a4b563
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 14:27:39 2014 -0500
use npassive and qpass_map/upass_map
Source/Src_3d/Castro_advection_3d.f90
commit 70e7e941622f658fee05049b80eb0ad59f19dbb2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 12:34:37 2014 -0500
remove some magic '4's in favor of NUM_GROW. Now the number of
ghost cells is set in F90 (and brought into C++ in Castro_nd via
get_method_params)
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Castro_rotation.cpp
commit baa387d8c1239f140898e869a89fe5e021a37748
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 12:27:15 2014 -0500
merge some loops
Source/Src_2d/Castro_advection_2d.f90
commit b085ed35ad724e664bd2b03c27c3f76b0245627d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 11:36:44 2014 -0500
switch over to using npassive and upass_map/qpass_map in ctoprim
Source/Src_2d/Castro_advection_2d.f90
commit 8f10dcad2e71c368221464d9716aac1c693d7637
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 10:40:17 2014 -0500
add a max on small_pres for the pressure
Source/Src_3d/trans_3d.f90
commit 429cff6a0954a27c4b737fd4cc362d8dac98bd87
Merge: ca0bbdfe8 35a336cb2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 5 09:41:37 2014 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 35a336cb265af65f3af0d3492ce25f07974213c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 4 19:59:57 2014 -0500
remove MAXADV -- this is not used
Source/meth_params.f90
commit ca0bbdfe8ac61767c62217e81c6ecc826d158fcc
Merge: fe0b6080a 3589c12ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 1 09:09:18 2014 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit a48e0b86529bb6ebf2588f34fbf7d648051f5b59
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 30 14:30:01 2014 -0500
New gravity coupling: grav_source_type = 6. This implements the method described in Springel (2010), the AREPO code paper. The discretization for the gravitational source term is written so that the formulation is explicitly conservative.
Source/Src_3d/Castro_grav_sources_3d.f90
commit 7a76dcc5fce13685690ef80944ecba22fe2495c8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 24 23:05:59 2014 -0800
make MG_SU_OLSON compile again
RadBndry.cpp
RadSolve.cpp
commit ecc9b42fabd3168c7dcf469c7d48902ff35e72af
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 24 22:40:52 2014 -0800
mf[mfi.index()] -> mf[mfi]
_CompSolver/CompSolver.cpp
_CompSolver/CompSolverLevel.cpp
_CompSolver/EdgeVar.cpp
_interpbndry/RadBndryData.cpp
_interpbndry/RadInterpBndryData.cpp
commit dfe092e028f869deae5dfe1d0ff70c43ae95951d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 24 22:07:18 2014 -0800
mf[mfi.index()] -> mf[mfi]
_CompSolver/CompSolver.cpp
commit e14757d615e19432a048c6d65343af8b0d9c1446
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 24 22:02:59 2014 -0800
mf[mfi.index()] -> mf[mfi]
HypreABec.cpp
HypreExtMultiABec.cpp
HypreMultiABec.cpp
MGFLD.cpp
MGFLDRadSolver.cpp
MGRadBndry.cpp
RadBndry.cpp
RadSolve.cpp
Radiation.cpp
SGRadSolver.cpp
commit 3589c12ff3163020b26c64985f983d65bc43809c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 24 13:40:48 2014 -0800
mf[mfi.index()] -> mf[mfi] for efficiency
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Gravity.cpp
Util/plot1d/XGraph1d.cpp
commit fe0b6080abfebb33a2a48f114c325d81d0d04112
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 19 12:49:09 2014 -0500
add flattening
Source/Src_2d/slope_2d.f90
commit 251f9dc57823ef8ec209ad685b1072cca4ec1382
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 19 12:44:49 2014 -0500
add an bilinear reconstruction to get the slopes for piecewise linear,
based on the BDS stuff. This seems to do a better job in the concave
corners of a poorly-resolved star.
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
commit 4fe822414b2034d1c864b02729dac173c9fd1e1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 19 12:34:46 2014 -0500
remove a print
Source/Src_2d/trans_2d.f90
commit e3f2a422e0163b2ae03830b4958f6ba52b15c073
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 19 10:33:08 2014 -0500
fix a comment
Source/meth_params.f90
commit 371a49a8ccf4ebdaa2dfcb13b8a942152b552d81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 18 22:37:24 2014 -0500
don't pass dx() into and outof trace_2d -- we only use it within trace_2d.
Also declare separate space for the x- and y- versions in prep
for an unsplit limiter
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trace_2d.f90
commit 9f84ba1b25c4a16fcae4d4a3d455363d84eb959c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 18 22:17:30 2014 -0500
use a reference state when doing the characteristic tracing. This brings
the form of this more in line with the original Colella 1990 paper,
and should be more robust.
Source/Src_2d/trace_2d.f90
commit 58061b52c35078d896fd577668faa676a8008fa9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 18 21:37:19 2014 -0500
some comments
Source/Src_2d/trace_2d.f90
commit 1df49cde7f9a69759c480ee323117789df26c71f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 18 21:27:30 2014 -0500
formatting + in the y-direction, we were always doing pslope regardless of
where use_pslope was set
Source/Src_2d/riemann_2d.f90
Source/Src_2d/trace_2d.f90
commit 0335a85171a67815bb967dd316ae6370f147ff92
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 14 15:04:56 2014 -0500
fix indexing of the energy fluxes
Source/Src_2d/riemann_2d.f90
commit 479fa91af6ed1cca3fe6bed49280fe12850b31de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 14 15:02:30 2014 -0500
I was not using the conserved quantities in the HLL fluxes
Source/Src_2d/riemann_2d.f90
commit 365adc74c7226c65859f496fdbda3d12a4d67593
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 14 14:35:46 2014 -0500
add an HLLE Riemann solver that can be used in a hybrid fashion to
overcome the odd/even carbunkle error that plagues our current
solvers. Not tested yet.
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/riemann_2d.f90
commit 6c82d6300ffb354efc60b58e3fb3706836c606a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 14 10:52:33 2014 -0500
add a hybrid_riemann option -- not yet implemented
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 82565ff582bc9f19d8f90c9eb5722d57ac768235
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 14 10:42:02 2014 -0500
add a multi-dimensional shock detection method that will be needed
for implementing a hybrid Riemann solver
Source/Src_2d/riemann_2d.f90
commit b4bd3961b966f2d1b4d2bfa9c495fbe0491db8a5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Nov 13 14:40:23 2014 -0800
Cray compiler is not smart enough to do OMP collapse, so I have do it manually for this crucial piece of code.
Source/Src_3d/Castro_3d.f90
commit 99954451737127751905f7dc937d4b093bfe9e4c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 12 20:04:15 2014 -0500
Added as grav_source_type = 5 the version of Jiang et al. (2013) from their appendix, which uses a different form of the flux and gravitational energy. This version is Galilean invariant.
Source/Src_3d/Castro_grav_sources_3d.f90
commit c0c8b4b96a28bc82eacb137674d529fe7fa41a2f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Nov 12 16:57:38 2014 -0800
turn off some OMP for regression tests
Source/Src_3d/Gravity_3d.f90
commit bb6b7aa49ecdc17dabed741c4ebf9ad19ddfacae
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Nov 12 13:36:04 2014 -0800
Added a parameter castro.deterministic for regression testing. The
default is false. If it is set to true, make OMP deterministic. So
far it only has effects on compute_radial_mass in Gracity_3d.f90. In
the future, we could use this to turn off dynamic scheduling if it
causes problems for regression tests.
Exec/DustCollapse/inputs_2d_monopole_regtest
Exec/DustCollapse/inputs_2d_poisson_regtest
Exec/DustCollapse/inputs_3d_monopole_regtest
Exec/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/DustCollapse/inputs_3d_poisson_regtest
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/Sedov/inputs.3d.sph.testsuite
Exec/Sod/inputs-sod-rt1
Exec/Sod/inputs-sod-rt2
Exec/Sod/inputs-sod-rt3
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/meth_params.f90
commit ebca16929404df545a257b3761c7792740bea723
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Nov 12 12:28:40 2014 -0800
OMP'd compute_radial_mass
Source/Src_3d/Gravity_3d.f90
commit 642e7335394f25a5301e79b403e0ff2ae135f939
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Nov 12 12:26:15 2014 -0800
indentation
Source/Gravity.cpp
commit ae065ee14790a9fa9bf10f15ba0ced7705717977
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 12 11:27:34 2014 -0500
fix sign error in gammae terms
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
commit 5f2ccb9c767da5f247fdc9b81fba0d97b661955b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 12 11:03:47 2014 -0500
fix a sign in the transverse part of the gamma_e update
Source/Src_3d/trans_3d.f90
commit 694b49279a53ed7caff28a538a60e4d0cebf4775
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 12 10:57:57 2014 -0500
fix a sign error in the gammae evolution
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit cdd30a70828cb1132e50b3777ea030a53bbde69b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 11 14:14:53 2014 -0800
fixed comments
Source/Src_3d/riemann_3d.f90
commit 9fa76be87ba7c929182b2f726a61113549788d5d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Nov 11 13:24:24 2014 -0800
Fix the comment to now be correct.
Source/Src_3d/riemann_3d.f90
commit 8fd35661cdb7714b53562c2745af9d5fffe819b2
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Nov 11 13:15:35 2014 -0800
Fix the tests against domlo and domhi -- we should be using k3d not kflux --
I have also added comments about what kc,kflux and k3d are
Source/Src_3d/riemann_3d.f90
commit 914de433e1adfd5c32fa08dba831275342eb921f
Merge: 3e919afbf 8e8acb721
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 11 10:33:17 2014 -0800
Merge branch 'master' into tiling
commit 3e919afbff8fad0c42e557ee0bb4ebc55fdb5495
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 11 10:30:15 2014 -0800
removed some redundant codes introduced by threadbox version jof umdrv
Source/Src_3d/Castro_3d.f90
commit ac661e2bf5dcf8db7948ae5a350309054d8b76cd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 11 10:18:03 2014 -0800
moved threadbox.f90 to boxlib
Source/Make.package
Source/threadbox.f90
commit 6363999824f5b51754cb71616ff8609fd4480c4a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 11 06:51:28 2014 -0800
merged some mpi reduce calls
Source/Castro_advance.cpp
commit 283f242b56d4a961084e8b580f8ad7d8bc65665b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 11 05:55:14 2014 -0800
turn off tiling when OMP is not used
Source/Src_3d/Castro_3d.f90
commit 0156526fc13f5781f21b4cb5abdc2fea33751c8d
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 10 20:37:56 2014 -0800
converted umdrv to tiling version
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/probdata.f90
Exec/DustCollapse/sponge_3d.f90
Source/Make.package
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/flatten_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/slope_3d.f90
Source/Src_3d/sponge_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
Source/threadbox.f90
commit 8e8acb721ff2e939d65dba88fc069d24c4d5838b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 21:46:24 2014 -0500
turns out we were never really doing ppm_predict_gammae! It wasn't
being set properly
Source/Castro_nd.f90
commit 0800ba32c80b790ff956a43da1c62704dedbf0a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 20:44:15 2014 -0500
implement the gamma_e reconstruction -- now we can run with ppm_predict_gammae = 1
in 2-d
Source/Src_2d/trace_ppm_2d.f90
commit 312f88cb22008a02514dabec6a003ea625de650e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 19:03:30 2014 -0500
work on getting the transverse terms for the gammae prediction in
place -- this is not yet complete -- we still need to do the
normal prediction
Source/Src_2d/trans_2d.f90
commit 7fa08ad1099c94a2d7b3ab6d12d98dbab7267de8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 18:29:02 2014 -0500
the transverse gamma_e reconstruction was wrong -- we need to add
the transverse differences to the old normal state when defining
the new one.
Source/Src_3d/trans_3d.f90
commit ab604535eecae6214c9bd4538dccc4fba1b7e3bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 15:49:07 2014 -0500
pass the Godunov gamma_e into the transverse routines
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trans_2d.f90
commit 7f850f9deca36175ff2588c34323aaa6c7eac10e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 15:32:47 2014 -0500
pass the Godunov edge state of gamma_e through the Riemann solver
into the Castro_advection_2d routine so we can play with this in the
transverse terms. This shouldn't actually do anything just yet.
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_2d/trans_2d.f90
commit ab650059b9af7d90c004b30db0edd07b6d8a7205
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 10 15:19:42 2014 -0500
Fix incorrect function name in sum_utils
Source/sum_utils.cpp
commit 293a7e95c8b5133de9238fc642783fbf939b5886
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 14:26:04 2014 -0500
put some checks on the zones when doing the transverse_reset_rhoe fix
-- in 3-d we have things more robust. Here, in 2-d, we can operate on
data that is not valid, which is troublesome when the EOS gets involved.
I'll port the 3-d restrictions over shortly.
Source/Src_2d/trans_2d.f90
commit 1342dbf1d03cd2a173de8217158f2cdbb111744c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 13:46:13 2014 -0500
finish the implementation of the transverse_reset_rhoe stuff. Fix
a bug in the previous part just added too.
Source/Src_2d/trans_2d.f90
commit 05cade7a95a4e34be2c7d5d64b20c428b2909057
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 10 12:53:12 2014 -0500
fix the transverse pressure update when we are in axisymmetric 2-d
coordinates. The area factors were not in the p div{U} term.
Also start adding the transverse_reset_rhoe stuff, syncing up with
3-d.
Source/Src_2d/trans_2d.f90
commit eaf9bcdfea8b28ff1e6f9781b9058efd09f9d8cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 6 09:49:31 2014 -0500
add transverse_reset_density to the 2-d transverse stuff -- this was
already in 3-d
Source/Src_2d/trans_2d.f90
commit 7cd9460104ea7dbda45008f6a5ced303f17ae092
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 5 12:05:42 2014 -0500
add some comments
Source/Src_2d/trans_2d.f90
commit aca697f2a37c643511164b6f3f654d04e5fb4418
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 27 10:45:44 2014 -0400
Restore some commented lines.
Source/Castro_advance.cpp
commit 73f8fa9cee7567559177e2f184c44d3952280844
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 27 09:51:14 2014 -0400
Added conservative gravity source as grav_source_type = 4. This implements the method of Jiang et al. (2013) for implementing the gravitational source term as the divergence of a flux (tensor for the momentum equations).
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
commit c0af43cd4b3ec46bad616c6a754e73be5f8da28a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 27 09:49:04 2014 -0400
Now in compute_temp we add the difference between the old rho*e and the new rho*e to rho*E instead of explicitly recomputing it.
Source/Src_1d/compute_temp_1d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_3d/compute_temp_3d.f90
commit bd989fe1a588aeb693ebb1a818639f5db9a89fb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 3 10:31:32 2014 -0400
bc.f90 in this directory was conflicting with the F_Baselib bc.f90
Rad2Tshock/Tools/bc.f90
commit 99b2390af4429c3b14d33bf89554d35758362b12
Merge: 133d9b4e9 c76fde0b4
Author: Chris Malone <cmalone@lanl.gov>
Date: Thu Aug 28 10:59:24 2014 -0600
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 133d9b4e90026498dba58b3afa4f534383542b91
Author: Chris Malone <cmalone@lanl.gov>
Date: Thu Aug 28 10:58:28 2014 -0600
cleanup and add helper function to get neutrino chemical potential
EOS/stellarcollapse/eos_stuff.f90
commit ca0748524debb9dbfcf94f5432ebc1d3f6b491d5
Author: Chris Malone <cmalone@lanl.gov>
Date: Thu Aug 28 10:57:33 2014 -0600
cleanup and add dpde|_rho
EOS/stellarcollapse/eos_aux_data.f90
commit c76fde0b4f8aaf998ee072c628dc749e2f7dcb8f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Aug 27 10:45:46 2014 -0700
Forgot to wrap AddParticlesToRhs in ifdef PARTICLES.
Source/Gravity.cpp
commit c6d4f2e5fdf087d6c70960f09af5237dac58eee3
Merge: d02b01212 6b789ca1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 27 13:35:30 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
Conflicts:
Source/Src_3d/trans_3d.f90
commit d02b012125d9e79a308e2448b9f83a86998e4331
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 27 13:34:27 2014 -0400
fix
Source/Src_3d/trans_3d.f90
commit 6b789ca1bd1eb21abec2ffbd468abdafb6596157
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Aug 27 10:32:32 2014 -0700
1) Remove some unused variables
2) Correct oops where gegp or gegm was accidentally set to ugdnv instead of gegdnv array ...
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit ca30f431e46a6f230ed2e4cf5253f31cd44950d5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Aug 27 10:20:45 2014 -0700
Fix oops in writePlotFile
Source/Castro_io.cpp
commit d515722d47c16269b48db54159559d526b70fbe6
Merge: 6f08c1427 e78f3b6e8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Aug 26 15:28:43 2014 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 6f08c1427eca84310288199df833e93fda3925ba
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Aug 26 15:28:00 2014 -0700
Add a test problem RT_particles that tests the ability of
Castro to intialize and randomly move particles. Fixed
the Castro source code so that particles now work correctly.
Exec/RT_particles/Castro_error.cpp
Exec/RT_particles/GNUmakefile
Exec/RT_particles/Make.package
Exec/RT_particles/Prob_2d.f90
Exec/RT_particles/README
Exec/RT_particles/amrvis.defaults
Exec/RT_particles/inputs_2d
Exec/RT_particles/particle_file
Exec/RT_particles/probdata.f90
Exec/RT_particles/probin
Source/Castro.cpp
Source/CastroParticles.cpp
Source/Castro_io.cpp
Source/Gravity.H
Source/Gravity.cpp
commit e78f3b6e8d392a557d6d6bc895d147bfdc3346f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 25 11:05:29 2014 -0400
forgot a continuation character
Source/Src_3d/trans_3d.f90
commit 96679455c90ac933edf9679a91c83db27619ffb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 22 10:39:48 2014 -0400
fix some OMP issues (missing commas in the PRIVATE)
Source/Src_3d/trans_3d.f90
commit 64c321a5b8f893c80fd85fe0a8b39efcc0d02ce6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 21 15:41:10 2014 -0400
this completes the changes necessary to reconstruct gammae instead of p and
account for the transverse terms
Source/Src_3d/trans_3d.f90
commit 620fef9aff2dfcbe3756c8d9ffd4641a2dff40ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 21 13:46:56 2014 -0400
was missing a block for ppm_predict_gammae
Source/Src_3d/trans_3d.f90
commit 4038ff648baee86fd3deaf35fdb1a1b1da25ad84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 21 13:31:01 2014 -0400
compute the quantities that will be used for the transverse gamma stuff
-- the term is still not in, but this change makes everything we need
in place.
Source/Src_3d/trans_3d.f90
commit 2bc73873a6d96ef2fffa076ab374f336de2946ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 21 11:43:38 2014 -0400
add the infrastructure for dealing with the edge-based gammae in the
transverse terms
Source/Src_3d/trans_3d.f90
commit 5efe95d057ae8b50302a8cb3daa34cb600b0f3ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 20 21:45:12 2014 -0400
store gamma_e on the interfaces from the Riemann solve
Source/Src_3d/riemann_3d.f90
commit a7de3022f2a23c959e7df089470e55b20491fea4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 20 21:18:50 2014 -0400
create a gamma_e on the interfaces that will be returned from the Riemann
solver just like ugdnv and pgdnv are. At the moment, this just creates
the arrays and passes everything through the necessary interfaces..
Still need to fill it in riemann and use in the trans routines.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit b30602f15703d4b5bf479f592e0a493cb68a393d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 20 20:06:09 2014 -0400
put in the stubs to where the transverse gamma terms will go -- they aren't in
here yet, and nothing should change otherwise as a result of this change.
Source/Src_3d/trans_3d.f90
commit 6726565e7cf56d9eab36e039f0a8f0d76cfba95e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 20 17:02:33 2014 -0400
predict gammae to the interfaces -- this compiles, but is incomplete.
We still need to implement the transverse bits.
Source/Src_3d/trace_ppm_3d.f90
commit 42fabd703ab783c544c1a4248fabedfa438f010c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 20 14:52:46 2014 -0400
add ppm_predict_gammae -- yet another option. Not implemented yet. This
just gets the runtime parameter in place.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 8467f102f55d2cfa5df3255f20ccc431ad414b24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 20 14:22:07 2014 -0400
lots of comments to help make sense of this in prep for adding gamma_e
reconstruction
Source/Src_3d/trans_3d.f90
commit 87053a06002ead0f11639c737d4581fbc7598438
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Aug 20 10:03:15 2014 -0700
fixed React_3d so that it can compile
Source/Src_3d/React_3d.f90
commit 7417daad505cab45fb374022d4c32b146419e3b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 19 15:46:03 2014 -0400
Add a stub Prob.cpp file, which is intended to implement any declarations in Problem.H
Source/Make.package
Source/Prob.cpp
commit 9870f26ab9849b3b5bd543c7c66a9791801f99d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Aug 14 14:48:54 2014 -0400
Now if we set regrid_int < 0 then we disable regridding. Added this information to the user's guide.
UsersGuide/Inputs/CastroInputs.tex
commit 9f6c13c8d5a6b82b486565601ed3f775e4cfc516
Merge: 5ffe897e3 a39011864
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 5 10:41:25 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 5ffe897e33a27b57079eeb1cc8247e5fe9d78cf1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 5 10:40:57 2014 -0400
threadsafe fixes
Source/Src_3d/EstDt_3d.f90
commit 4155c1c422b002089f42444d188898ee95b5e659
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jul 30 15:52:00 2014 -0700
fixed constant ZERO
CastroRad_1d.f90
commit 0ccb80bee09efeff9a34e93c0f185c22ea494363
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jul 30 15:39:50 2014 -0700
more protection against nagative energy
RadEOS_1d.f90
RadEOS_2d.f90
RadEOS_3d.f90
commit 8f61fd19e9ca237faaa921b2b78d7837da262fe8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jul 30 14:29:47 2014 -0700
protect against negative energy
CastroRad_1d.f90
RadHydro_1d.f90
commit 3cdc243f2f4e7210dbb0085a08a75fc88fe31f21
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 27 00:55:23 2014 -0400
We now have the ability to run the helmeos either using OpenMP or using OpenACC. The latter is activated only if the vector size is greater than eos_acc_cutoff, and if castro.do_acc = 1 in the inputs file. Otherwise, we default to OpenMP for threading the loop. Since nesting of OpenMP and OpenACC regions is not allowed by the Cray compiler, we now use a helm_loop.dek file that is included in helmeos.f90, which contains the actual text of the helmeos loop.
EOS/helmeos/helm_loop.dek
EOS/helmeos/helmeos.f90
commit 918ec07f2eaddb45d494f5001fc8ece2c33634af
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 27 00:52:33 2014 -0400
Fix bug in dermachnumber; we were multiplying by rho instead of dividing by it.
Source/Src_3d/Derive_3d.f90
commit 26b0d891588ef19ef7880a1d0d3177eacb2398e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 26 23:55:25 2014 -0400
Add a parameter, castro.do_acc, which controls whether or not we will use the accelerator on systems where OpenACC is available. Doing so will require setting USE_ACC=TRUE in the makefile to ensure that the compiler is set to read OpenACC directives.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 443d20def9f84d1e9cfba172f567cacf96e808d0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 25 17:09:25 2014 -0400
Only activate the use of the accelerator if the size of the vector in the EOS is greater than acc_cutoff.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
commit ebbf53fa7732879f61ea257c71604c7d6f07c9ea
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 25 16:22:22 2014 -0400
Add an extern parameter to the helmeos, eos_acc_cutoff.
EOS/helmeos/_parameters
EOS/helmeos/eos_stuff.f90
commit 4f45703446600855ca75058e0df38e17b5ebcaf5
Merge: 2be282f89 a39011864
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 25 16:08:12 2014 -0400
Merged in master and fixed two conflicts.
commit 2be282f89b5f43faff84749b559ea1f79b670acb
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 24 20:22:23 2014 -0400
Initial update to allow the hydrodynamics to use the accelerator version of the EOS. The OpenACC commands are not currently set up to work in conjunction with OpenMP so some loops have this disabled -- that will be fixed in a future commit.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/trans_3d.f90
commit a390118645c85411614c7edbdb94c4de2a217309
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 16 19:57:09 2014 -0400
update for the new method of makebuildinfo_C.py
Exec/Make.Castro
commit 86002f239944187b53ace90be7d7aa53d5792d00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 12 19:25:40 2014 -0400
switch to the python buildInfo.cpp script -- it's cleaner. This
fixes the breakage from the recent make_build_info_cpp changes.
Exec/Make.Castro
commit d7a579286b499c3036524888f32e97be7db05e0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 4 20:58:16 2014 -0400
frac wasn't doing what it was supposed to be doing. Now it does.
Prob_1d.f90
commit 62181926a9f6480b56370d40c71e031d3e659834
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 3 19:52:35 2014 -0400
we are inheriting idens, itemp, ... from eos_data_module, but these are commonly declared
in other routines as well -- make them private in this module, so we don't have name
clashing/.
EOS/helmeos/eos_stuff.f90
commit 45fd4a2424bdf0f75319cfd91224f614128251d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 1 15:17:09 2014 -0400
maller CFL
inputs-det-x
commit 5ecd8b180f639e7663736dfcc0c86e475abe4905
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 1 14:13:47 2014 -0400
add temperature-based error estimation
Castro_error.cpp
GNUmakefile
Prob_1d.f90
inputs-det-x
probin-det-x
commit 965e29262091cb386ee1f8e67bc86f64a93ad450
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 1 13:09:52 2014 -0400
allow for He burning
GNUmakefile
Prob_1d.f90
probdata.f90
probin-det-x
commit 4e4426eed6fe6ae8969a8f9b99c81e7c7ac8fb2d
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Jun 30 16:03:49 2014 -0600
initial commit of EOS interface to tabulated CCSN EOS from stellarcollapse.org
EOS/stellarcollapse/Make.package
EOS/stellarcollapse/README
EOS/stellarcollapse/_parameters
EOS/stellarcollapse/eos_aux_data.f90
EOS/stellarcollapse/eos_stuff.f90
EOS/stellarcollapse/test/GNUmakefile
EOS/stellarcollapse/test/GPackage.mak
EOS/stellarcollapse/test/dummy.probin.template
EOS/stellarcollapse/test/probin
EOS/stellarcollapse/test/simple.net
EOS/stellarcollapse/test/testeos.f90
commit bd72d18d80c69586c1efc7b664d4dab394a2a6d6
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Jun 30 15:13:50 2014 -0600
swap to using a subroutine so tri_interp can return 1st derivs for Newton iters
Source/interpolate.f90
commit 24b52bb5793ff63d441afaf0ec65a1abb033b356
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jun 20 10:14:50 2014 -0700
XGraph1d: increased the max number of vars and BoxLib::Error will be called if there are too many variables.
Util/plot1d/XGraph1d.H
Util/plot1d/XGraph1d.cpp
commit d4eb767de5f83948b3062bbd781bb182870ff33a
Merge: 0bd68a904 82f9f77e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 19 20:53:52 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 0bd68a904c6616071d10d42b224fde44ddf8a879
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 19 20:53:24 2014 -0400
rhoInv was not declared as private in the OMP directive.
Source/Src_3d/compute_temp_3d.f90
commit 82f9f77e0f6cba1a98cd29535bf57fb1fc295ac0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 19 15:36:50 2014 -0700
speed up the interpolate module by using bisection to locate the location
Source/interpolate.f90
commit fe43279137f4a5d4298f0ac9ad9c564c78391b91
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 16 14:19:40 2014 -0700
minor changes to mute valgrind
RadHydro_1d.f90
RadHydro_2d.f90
RadHydro_3d.f90
commit a71fa75b5a869834cdd204fc68c51ce064ada484
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 16 17:13:57 2014 -0400
Add OpenACC directives to the Helmholtz EOS.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
commit b6ade804afabbd9904f8452ac82a861d27247937
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 16 13:30:26 2014 -0700
If xgraph.format=all, all variables will be put into a single file for each dump.
Util/plot1d/XGraph1d.H
Util/plot1d/XGraph1d.cpp
commit 0a8f8b58f3397431e58575996eb7e03046d52208
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 16:15:06 2014 -0400
Update T and rho after EOS iterations.
EOS/helmeos/helmeos.f90
commit 70ac413f4f4466ab109234392d35fe634a3b8796
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 15:52:57 2014 -0400
Add input_is_constant functionality to helmeos.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
commit f34532e141b1aa27b149e8177377b258773cfcde
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 15:31:01 2014 -0400
The statement functions in helmeos are now real functions.
EOS/helmeos/helmeos.f90
commit 324b8f1eef01144c85c8699c9ad97f4384a9afb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 15:17:30 2014 -0400
Move the initial error checking back up to eos_stuff.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
commit cd49a4189b7e42fab0f336c881e1d6cca7cf06e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 15:01:35 2014 -0400
helmeos now accepts a vector of arbitrary length and operates on it. The iteration logic now lives inside helmeos and the wrapper only does elementary calculations like abar and zbar. Later they could be merged into one module.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
commit a83d1f9b37792f330ec70c250cc8c58bdda9eff3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 11:57:17 2014 -0400
Insert all of the physical constants from the latest version of the EOS into the helmeos module. Some are initialized in helmeos_init.
EOS/helmeos/helmeos.f90
commit 1c9635757172dec6f832c2d9048beb082f3e8926
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 11:54:25 2014 -0400
No longer use case statements since the eos_data values are not parameters.
EOS/helmeos/eos_stuff.f90
commit 44117cdc09a0427778e737ec56c1c175d2a22b7f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 11:32:24 2014 -0400
eos_data module integer types are no longer parameters -- necessary so they can be sent to the accelerator.
EOS/eos_data.f90
commit 81466c1098d116208260d3f8da42fc8ceaa1e90f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 13 11:30:55 2014 -0400
Create a helmeos_module that contains the table data and the helmeos routines.
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helmeos.f90
EOS/helmeos/vector_eos_f90.dek
commit 677f00e0e063d58a0b77a1154c5cd8ca9451aa1a
Author: Chris Malone <malone@ucolick.org>
Date: Mon Jun 2 15:38:38 2014 -0700
add ability to get aux variable indices from network_species_index
Networks/general_null/network.template
commit 15a2b26d60eb6246ccac684d89248eed010ecaf8
Merge: 5629898a9 2f8fcd6a6
Author: Chris Malone <malone@ucolick.org>
Date: Mon Jun 2 15:27:42 2014 -0700
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 5629898a915ed166e7571f3412a1b13c3c005f3b
Author: Chris Malone <malone@ucolick.org>
Date: Mon Jun 2 15:27:10 2014 -0700
give aux vars a bad initial value
EOS/eos_type.f90
commit b3fd1258fbb4f119d4f17deb5532f5179e3e84e1
Author: Chris Malone <malone@ucolick.org>
Date: Mon Jun 2 15:26:38 2014 -0700
add some more error codes
EOS/eos_data.f90
commit 2f8fcd6a649dec4886ef3ccadec45d6c55aa47cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 1 12:54:05 2014 -0400
Updated to the latest version of the Helmholtz interpolation table. This ranges from 3 <= log(T) <= 13 and -12 <= log(rho) <= 15. It also uses updated versions of the physical constants, so results will be slightly different using this EOS.
EOS/helmeos/helm_table.dat
EOS/helmeos/helmeos.f90
EOS/helmeos/vector_eos_f90.dek
commit a6a7315d5b3273afb4362f37f54615c51e37088a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 31 04:04:09 2014 -0400
Replace 1 --> ONE in tri_interpolate so that we can compile in gcc.
Source/interpolate.f90
commit 0eaa1c7d5f40a7b5c101d08e1ec6e7e1e7503c38
Author: Chris Malone <malone@ucolick.org>
Date: Fri May 30 12:50:51 2014 -0700
add option to have auxiliary variables defined in netFile with the prefix "__aux_"
Networks/general_null/network.template
Networks/general_null/write_network.py
commit 62077f569e5ca042097a4b90864c2348ae8b4227
Author: Chris Malone <malone@ucolick.org>
Date: Fri May 30 11:54:53 2014 -0700
added tri-linear interpolation function
Source/interpolate.f90
commit 276baffc4812cc3608fce226973dc8b2db92b24c
Merge: 98e9427f7 6081b2971
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue May 27 09:32:59 2014 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 98e9427f7267e35affab4517d60a6c85707fc15f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue May 27 09:32:30 2014 -0700
Move test on CFL inside an IOProcessor test so that we only get one error
message -- this works because courno is identical on all processors.
Source/Castro_advance.cpp
commit 6081b2971858fd87a822c3e73a2f371a458f8635
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu May 22 08:36:52 2014 -0400
use a different backend so these work when headless
Exec/Sedov/testsuite_analysis/sedov_2d_cyl_in_cart.py
Exec/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
Exec/Sedov/testsuite_analysis/sedov_3d_sph.py
commit c3d58aa7bc14e3e6249d0e48d4a4e0f9849551a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 21 15:00:04 2014 -0400
That last fix for sum_utils created its own problems. I changed the way we deal with phi, so that the function is more limited but we don't have to worry about memory issues.
Source/sum_utils.cpp
commit 529a37cf2fc625c8d00b7b1f378df0eb9d71fd77
Merge: dd433fde5 bab370138
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 15 21:38:28 2014 -0400
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit dd433fde51f79cee3c8ee8e6565b47b36b471c5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 15 21:38:22 2014 -0400
Fixed an issue in volProductSum that was causing a memory leak.
Source/sum_utils.cpp
commit bab370138e9ee1684b5344f38b5dac3270cb3d90
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 11:11:14 2014 -0400
different probin with different gamma
Exec/Sedov/inputs.2d.cyl_in_cartcoords.tau
commit 9fac8d604a00f780b904bebf115f2192fb6866ee
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 11:10:35 2014 -0400
update gamma
Exec/Sedov/probin.2d.cyl_in_cartcoords.tau
commit ef5bb3e35681d2c479b25d89dbb1a60f0965b28e
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 11:09:29 2014 -0400
specify analysis script is to run from current directory; add cyl in cart script
Exec/Sedov/testsuite_analysis/sedov_2d_cyl_in_cart.py
Exec/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
Exec/Sedov/testsuite_analysis/sedov_3d_sph.py
commit 135e6c1855f2c6d41e6ef4fdb208f5b1b66a6d10
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 11:04:46 2014 -0400
comment header
Exec/Sedov/Verification/cylindrical_sedov.dat
commit 245af595cc5b8f69022c998fbff17b4acdc5ae13
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 10:59:54 2014 -0400
more descriptive output names
Exec/Sedov/inputs.2d.cyl_in_cartcoords.tau
commit ff044a381980952de4e78c84448abac094f40f49
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 10:22:58 2014 -0400
accidentally commited an altered version of this
Exec/Sedov/probin.3d.sph
commit aae2ee89fefaefdc0a638a63bb173b4499d26f55
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 10:21:46 2014 -0400
test suite version -- different gamma
Exec/Sedov/inputs.3d.sph.testsuite
Exec/Sedov/probin.3d.sph.testsuite
commit 98943405933d45b7f3e3b1cadbd4d16e24e3d9af
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 10:20:47 2014 -0400
3-d version
Exec/Sedov/testsuite_analysis/sedov_3d_sph.py
commit 698f2a22422e6d318203277e60e56c7fa2c5333b
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 09:58:01 2014 -0400
for testing
Exec/Sedov/GNUmakefile
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords.testsuite
Exec/Sedov/inputs.3d.sph
Exec/Sedov/probin.2d.sph_in_cylcoords
Exec/Sedov/probin.3d.sph
commit 91388daacce574eb9fbfcaccd9ee47a51eadcac1
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 09:56:53 2014 -0400
to compare we need a different gamma
Exec/Sedov/probin.2d.sph_in_cylcoords.testsuite
commit 2f295779125adf381cf21e1b30982df6aaf13db2
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 09:55:04 2014 -0400
quiet things
Exec/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
commit 790fc5b549e6f2912cc60f81ce415952bab9b7c7
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 09:43:25 2014 -0400
fix the update :)
Exec/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
commit d2c82c206f66c01e8c1d4b98b99a47d84db75c64
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue May 13 09:43:04 2014 -0400
update to accept plotfile
Exec/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
commit 90450811942fd16e6aad6eeb4d6e916dea3855c4
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon May 12 21:28:09 2014 -0400
script to run from the test suite
Exec/Sedov/testsuite_analysis/sedov_2d_sph_in_cyl.py
commit fb88d85b65d7cc25784f8d7ce9af4fbac18ee2e1
Merge: 4df012f98 3951fed4b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon May 12 19:10:30 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 3951fed4bd8b210532fcb04debefc63713beb440
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon May 12 13:43:27 2014 -0400
get these compiling again -- GNUmakefile was very out of date
Diagnostics/Sedov/GNUmakefile
commit 644a7d010c59db09694f68f41f1d67e427a77eee
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon May 12 13:38:39 2014 -0400
update Diag file location
Exec/Sedov/Verification/Readme
commit 30b822968b10eb56bf684d59b59899241eb0f145
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon May 12 13:32:45 2014 -0400
more descriptive output names
Exec/Sedov/inputs.2d.cyl_in_cartcoords
commit 41290594ff3cf20862001793303c6259f4dcd01f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 22:15:34 2014 -0400
get the inputs filename into job_info -- this syncs up more with Maestro.
Note, my C++ here might not be the most elegant. I added a Castro_io.H
with a global variable to minimize the changes needed to main.cpp
(where we have access to argc/v).
Source/Castro_io.H
Source/Castro_io.cpp
Source/Make.package
Source/main.cpp
commit 67dfac35b2e0c297343644646b6dd9077384f42d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 22:14:58 2014 -0400
sync the transverse velocities up with the 3-d case
Source/Src_2d/trace_ppm_2d.f90
commit e028992a9df52550ec554da81b96b1579bedba7b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 15:45:10 2014 -0400
comments
Source/Src_3d/trace_ppm_3d.f90
commit 765e01c5e2a18d71a63fcb2b60684a3a889568e9
Merge: 9755968dc b998c5c67
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 11:53:53 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 9755968dc142283e03e553a5e873f864eb4ae560
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 11:53:30 2014 -0400
prematurely removed the transverse reference states -- that will come
with the next big change...
Source/Src_2d/trace_ppm_2d.f90
commit b998c5c67525c5a0b80e547a1133b724466378aa
Merge: bcb6fa800 7dade69ff
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Sun May 11 11:48:57 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 7dade69ff1fd8a9cfb39f0515d8a42086c870819
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 11:46:27 2014 -0400
more syncing with Ann's changes to 3-d from yesterday
Source/Src_2d/trace_ppm_2d.f90
commit 6d4698920e2caaa7d533be56fa07d40c4d1dcf36
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 11:44:44 2014 -0400
remove comment
Source/Src_3d/trace_ppm_3d.f90
commit bcb6fa800a00e494425b99b6bac28847701ac4ce
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Sun May 11 11:43:16 2014 -0400
new test with tau in tracing
Exec/Sedov/inputs.2d.cyl_in_cartcoords.tau
commit e21f1d5eb437f6bb9f900b994b3ef4053449874d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Sun May 11 11:24:33 2014 -0400
new test
Exec/Sod_stellar/inputs-test1-helm.tau
commit 0657b4d9e772dc7f873f0f35386f4fea0f1b23c8
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 11 11:18:21 2014 -0400
remove unneeded ref states
Source/Src_3d/trace_ppm_3d.f90
commit 4df012f9811285211bdf99f546839684913db049
Merge: 159d72407 274c84568
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat May 10 18:54:18 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 159d724078185d5baebfe03b68764a9a9717f0ac
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat May 10 18:53:55 2014 -0400
add force_type to allow for an override of the global ppm_type
Source/Src_3d/ppm_3d.f90
commit 274c845684fbab7671f09b0fe2d13745fa68b13a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat May 10 13:27:04 2014 -0700
Fixed stupid typo in previous changes.
Source/Src_3d/trace_ppm_3d.f90
commit 8134cecf14957c10a07d1df2fa13875c1016a182
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat May 10 12:09:20 2014 -0700
Code clean-up; less repeated code plus remove some unused variables.
If this makes any difference at all in the results I have screwed it up.
Source/Src_3d/ppm_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 8a94b32d0feb332af94e5cc05b26d1812b51ab32
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri May 9 19:23:45 2014 -0700
Fix comment.
Source/Castro.cpp
commit db1626ebb0e69f0ee7dab3aebca62c8e219eec7a
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri May 9 19:25:46 2014 -0400
change how we do the transverse velocities -- this traces under the
middle wave and picks the appropriate state based on the direction
on the contact.
This significantly cleans up the Sedov problem (divu)
Source/Src_3d/trace_ppm_3d.f90
commit fb0f2ae7243888c9156a9f5476a99a89a79c21b2
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri May 9 10:36:40 2014 -0400
sync up with 3-d: move flattening and enforcing of the small_* to
after the different tracing methods
Source/Src_2d/trace_ppm_2d.f90
commit f6506a5e20fbf77d6fa95250bd7f8ea0f8510603
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri May 9 09:56:53 2014 -0400
isolate the flattening stuff out at the end of the different tracing types.
This makes it much clearer that it is optional in this routine (depending
on ppm_flatten_before_integrals). This shouldn't affect any answers
(although, there may be a round-off level change).
Source/Src_3d/trace_ppm_3d.f90
commit 79f97a3bce00763c9787fd8dcb575c6dd67152f8
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri May 9 09:05:09 2014 -0400
remove unused variables
Source/Src_3d/trace_ppm_3d.f90
commit e94c59af6d64c6277ea49a2f6356b39d86b2cb8e
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri May 9 08:46:58 2014 -0400
move the enforcement of the small_* stuff to outside of the if block
on which tracing method we use
Source/Src_3d/trace_ppm_3d.f90
commit 6065f877dc7dda93a0fd8ed9aeab7be791448dad
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu May 8 19:08:55 2014 -0400
make the 1-d use qpass_map.
Source/Src_1d/trace_ppm_1d.f90
commit 521bf8d1d742ad9768483f5cdcb3fd004989910c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu May 8 18:56:19 2014 -0400
switch to qpass_map and upass_map to sync with 3-d and cut a lot of
redundant code
Source/Src_2d/trans_2d.f90
commit eed3698a81adafe62ff361715750894145ed6c61
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu May 8 18:26:12 2014 -0400
switch to using qpass_map -- remove a lot of redundant code
Source/Src_2d/trace_ppm_2d.f90
commit b76166d5ae839ccd3b174fa4d0eb4656ec4cea65
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu May 8 15:36:58 2014 -0400
we were defining mappings into U and q for the passively advected
quantities many MANY times (qpass_map and upass_map). Now we define
this once in meth_params.f90 and we can use it everywhere. This will
make it easier to extend this to the 2-d code.
Source/Castro_nd.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
Source/meth_params.f90
commit 508c8d9907e771356f8c58c972e3dd6d14240cbb
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu May 8 14:32:19 2014 -0400
remove duplicate flattening code and consolodate
Source/Src_3d/trace_ppm_3d.f90
commit ff2a73570d8bb4cd98a7b85fafaedb55041c5871
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu May 8 14:27:50 2014 -0400
move the transverse velocity parts at the end of the interface code
blocks. This consolodates code and makes it easier to update to
the correct way later
Source/Src_2d/trace_ppm_2d.f90
commit e4f04422c3de362f30b69657cc40c5e642a52469
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu May 8 13:43:17 2014 -0400
revert back to the old behavior regarding transverse velocity,
but reorganize things so that all the transverse stuff is together.
This way we can update in two passes -- first make sure the reorg
didn't break any tests, and then implement the fixes more robustly.
Source/Src_3d/trace_ppm_3d.f90
commit 7406d616e5b50af1be3800f11834a6ccaea99827
Merge: 4ebdc4ce4 015648389
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Wed May 7 11:35:24 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 0156483892f1be120fa5aaaa05a8ce74eb4c7941
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Apr 22 21:30:18 2014 -0400
output the names of the boundary conditions into the job_info file.
This syncs us up with Maestro (we output idenfically now) and this
will help with yt, which sometimes will need to know the BC types.
Source/Castro_io.cpp
commit f0568a7e2d687e7f8a1801b3b3f6af48972048e2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Apr 14 12:09:35 2014 -0700
use bl_constants_module in tranverse_module explicitly
Source/Src_2d/trans_2d.f90
Source/Src_3d/trans_3d.f90
commit a5b9c9ccaca672f1dd2f9390e177c7385d3566d6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Apr 9 20:05:58 2014 -0400
comments
Source/Src_3d/trans_3d.f90
commit 4ebdc4ce48a487eea0f605d5b58e33db9df2351a
Merge: 545e9222b 65ea7f752
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Wed Apr 9 16:13:22 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 545e9222ba0c6c6655ccb3435efab88599f2c8d9
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Wed Apr 9 16:12:48 2014 -0400
do the correct thing for the transverse velocities with respect to the
reference state -- they should simply jump across the contact
Source/Src_3d/trace_ppm_3d.f90
commit 65ea7f7525af5e554bfab181870a9c976928d342
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Apr 9 14:30:24 2014 -0400
we were setting the wrong state in one of the transz transverse_use_eos
blocks
Source/Src_3d/trans_3d.f90
commit e3d6dcf689dda305f80513b2f28945f01f19a54b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Apr 9 12:25:14 2014 -0400
define q(...,QGAME)
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit eebf116cf73e5c6ee906582f125e3297ebce301c
Merge: c49164866 36ded42a7
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Apr 9 11:11:36 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit c491648660449f76bada41effa7c34e33ff8e84b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Apr 9 11:10:31 2014 -0400
we don't need QGAMC if we are running with use_colglaz = 1 -- that
is a remnant of the old version of the algorithm. Also, we now
always define QGAME -- this will be used for an experimental mode
to help with getting the thermodynamic state on the interfaces correct
Source/Castro_nd.f90
commit 36ded42a761990bf4bc8e19c37e6415f105c2132
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Apr 8 09:49:20 2014 -0400
add solar mass
constants/constants_cgs.f90
commit d84352753275c2a09600bc9e66983b0da0e4ae2d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon Apr 7 20:50:02 2014 -0400
fix typo in error message
Source/Castro.cpp
commit 4635658452dc88be8bed1b21b7daf71a0b4cc9ba
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon Apr 7 20:16:31 2014 -0400
if we reset (rho e) using the EOS, we may as well reset p too
Source/Src_3d/trans_3d.f90
commit b7df0220aac7c5d3fdd4e7d18387b7e6a3f60c1e
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon Apr 7 14:28:55 2014 -0400
check if p < small_pres, not <= small_pres -- we reset it to
small_pres in the trace routines if needed.
Source/Src_3d/riemann_3d.f90
commit 7079a14132d34fcb6798e6096b440abb5a6a2ee3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Apr 6 20:56:34 2014 -0400
parsing transverse_reset_rhoe wrong
Source/Castro.cpp
commit c89520f85c8dce6d2833b53509a2eb9c249455a6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Apr 6 20:47:00 2014 -0400
make the new rho e reset controlled by a parameter transverse_reset_rhoe
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/trans_3d.f90
Source/meth_params.f90
commit ef58ec90819a608f0bea7fe63539cec1f3db3ccc
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Sun Apr 6 19:22:35 2014 -0400
prevent us from every leaving the trans routines with a negative e -- we try
to remedy this in 2 ways. First, if (rho e) is negative after the transverse
update, we difference the internal energy equation instead. If it is still
negative, then we call the EOS with small_temp.
Source/Src_3d/trans_3d.f90
commit 7d09efeb8f197d9a9e4bf8201a877a69b9eb8067
Merge: 1c0ce72cc 9493cc407
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Apr 4 10:34:13 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 1c0ce72ccc3e19bc13d5817037ee5bb7b819ec21
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Apr 4 10:33:10 2014 -0400
add transverse_reset_density -- this implements what Nyx does by default (3-d only). Namely,
if adding the transverse terms result in making the density negative, then we reset them
to the original state.
Exec/Sod/GNUmakefile
Exec/Sod/probin-sod-x
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/trans_3d.f90
Source/meth_params.f90
commit 9493cc4078c854966b3dbb1a3d3dfb7170978e7d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 27 18:53:15 2014 -0400
some more restructuring. The bisection simply does not work...
Util/exact_riemann/riemann_support.f90
commit e808340c36f37385506335102ab3fbfbbc89add4
Merge: 364e642cc b3792ced0
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 18:47:00 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 364e642cc66c1ded6fe7d6930b11c0e1c22be28f
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 18:46:48 2014 -0400
more tests
Util/exact_riemann/inputs.bug7
Util/exact_riemann/inputs.bug8
commit b3792ced0720464b8b6e5b7ccbfce009f75aa44d
Merge: 542e92d35 aec77fd8a
Author: Regression Tester account <regtester@battra.(none)>
Date: Thu Mar 27 14:59:08 2014 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 542e92d35891b63a8e76510a068c1036245feb54
Author: Regression Tester account <regtester@battra.(none)>
Date: Thu Mar 27 14:58:54 2014 -0700
changed ppm type in one of the regression test
Exec/Sod/inputs-sod-rt1
commit aec77fd8a03b72d5db108924b65fadca66db87e5
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 16:36:44 2014 -0400
128 zones
Util/exact_riemann/inputs.test1.helm
Util/exact_riemann/inputs.test2.helm
Util/exact_riemann/inputs.test3.helm
Util/exact_riemann/inputs.test4.helm
commit 8d33d03e551163212101d7118c3eda2211e1f742
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 16:36:25 2014 -0400
move the bisect method into a subroutine
Util/exact_riemann/riemann_support.f90
commit 4e73fc0e56b3c4d0a19528f55d7ae2f2b9f9684c
Merge: 0a9f89b72 f67857568
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 16:24:57 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 0a9f89b726587889f22d42a0690d4e90bb8af235
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 16:24:39 2014 -0400
move the Newton solve to its own loop
Util/exact_riemann/riemann_support.f90
commit f678575681e5adc35ee8660cfe7068d665b23671
Merge: 1c4041c6b bb670cc6e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 27 15:16:06 2014 -0400
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 1c4041c6b5745c5d8f94f45de37ad5976a3af86a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 27 15:15:53 2014 -0400
Use speed of light from fundamental constants module in GR gravity.
Source/Src_1d/GR_Gravity_1d.f90
commit 3cebc636d7c200dbe267df531e88df8618a2249a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 27 15:12:52 2014 -0400
Synced up 1D with numerical value changes.
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Castro_grav_sources_1d.f90
Source/Src_1d/Castro_sums_1d.f90
Source/Src_1d/Derive_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/enforce_consistent_e_1d.f90
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/flatten_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/slope_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
commit 71480dbde2ff217bb7c1e405c0e41cdbfa89c19a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 27 14:54:35 2014 -0400
Sync up 2D with the numerical value replacements.
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/LevelSet_2d.f90
Source/Src_2d/Rotate_2d.f90
Source/Src_2d/enforce_consistent_e_2d.f90
Source/Src_2d/ext_src_2d.f90
Source/Src_2d/flatten_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_2d/slope_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
commit a38c9a89aed1125085ea609935dbdf18649ea335
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 27 14:29:07 2014 -0400
Some fixes to numerical values update for level set stuff.
Source/Src_3d/LevelSet_3d.f90
commit bb670cc6e798c1cb62f776fc2d72096b2904cf3a
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 14:18:37 2014 -0400
add the gam1 stuff
Source/Src_1d/TODO
Source/Src_1d/trace_ppm_1d.f90
commit d90de2199704365c11601a5b7d4837ad2c30b883
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 27 12:06:18 2014 -0400
fix compilation error from constants replacement
Source/Src_3d/ext_src_3d.f90
commit 7405d7d163337a810d2eca2a14696a9eaa487676
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 25 17:40:11 2014 -0400
Replaced numerical values with named constants from bl_constants_module where possible.
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Castro_sums_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/LevelSet_3d.f90
Source/Src_3d/Rotate_3d.f90
Source/Src_3d/enforce_consistent_e_3d.f90
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/flatten_3d.f90
Source/Src_3d/pointmass_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/prescribe_grav_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/slope_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 7becb67485b8db9eb7778dd44f94fb1a7063d6ab
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Mar 25 12:46:14 2014 -0400
lots of index typos
Source/Src_2d/trans_2d.f90
commit e5ca3b43a9abd4002daef12b7931f8f5765eaab9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 25 11:56:41 2014 -0400
Replace numerals with named constants in trans routines.
Source/Src_2d/trans_2d.f90
Source/Src_3d/trans_3d.f90
commit 688625268a6d0c5f8e799fe542dd923b8073325b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 25 11:51:24 2014 -0400
Sync up 2D with the transverse_use_eos option. Also, guard against pressures that are less than small_pres.
Source/Src_2d/trans_2d.f90
commit 162ae2f51063957ecb2cd4267875f6a3a74c590a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 25 11:39:55 2014 -0400
Add the castro.transverse_use_eos option. When set to 1, this will use the EOS to calculate the pressure on the interface states in the transverse routines. This is more expensive but guarantees thermodynamic consistency. Implemented in 3D currently.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/trans_3d.f90
Source/meth_params.f90
commit 0f9671b6b365a209ac6dcaefffbd019096e886a8
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Mar 21 15:11:43 2014 -0400
add the ppm_flatten_before_integrals support to ppm_type = 2
Source/Src_2d/ppm_2d.f90
commit a1085fc5a2e4de196b28c65d6bc9487b731a6494
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Mar 21 14:24:46 2014 -0400
add ppm_flatten_before_integrals support to ppm_type = 2
Source/Castro.cpp
Source/Src_3d/ppm_3d.f90
commit 21029db76398c4292a1ff63364380a908289845b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Mar 21 12:15:18 2014 -0400
we weren't doing the edge_limit stuff for ppm_type = 2 because the
two ppm types don't share the same integral construction portion
of the code. Now we remedy this.
Source/Src_3d/ppm_3d.f90
commit 99ccb0e3b4d70bf3934b58a75aa8f1dd7a69d86f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 22:24:58 2014 -0400
update README
EOS/README
commit 7354596b89ed23b55a098837c5df14ce93caf0fc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 20 15:54:24 2014 -0700
updated PPM interface
RadHydro_1d.f90
commit d35fa19ff575ae827aa7a07f986ba7d5253962ce
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 15:26:42 2014 -0400
the list of tables and the list of figures were being added to the TOC
as if they were parts, and this messed up the navigation in PDF viewers
UsersGuide/CastroUserGuide.tex
commit e310532c379b49e02f5a33fe9761f84cd321937b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 15:20:05 2014 -0400
more on the multigamma EOS
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 54bc635c916c9cd47da43ab82c8a9d2b1349ddec
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 14:09:58 2014 -0400
3-species tracing
Networks/general_null/simple3.net
commit 64f06761f73d759d25401afb03c6da68ef7a2a31
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 13:36:54 2014 -0400
roll back the castro.ppm_reference_eigenvectors=1 new default -- this option
causes trouble with ppm_type = 2
Source/Castro.cpp
commit cf31d67a73a9f336b9190dd3450c591304f7642a
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 12:20:10 2014 -0400
more fixing...
Source/Src_2d/Castro_2d.f90
commit 2bf46994856a88f11eea6e31e38a6d2f0efc121b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 12:11:39 2014 -0400
clean up the output message for the "fixing negative species" bit -- it was printing
n as referenced in the U vector, but it is clearer if we print out n as the
index of the species in the composition vector
Source/Src_2d/Castro_2d.f90
commit 25f05a3e389efd60e4464084ced6028404a57c07
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 20 11:10:58 2014 -0400
better initialization output
EOS/multigamma/eos_stuff.f90
commit 1b3772b8ad2a6668b5909d4430e706b81fd2e5eb
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 19:41:48 2014 -0400
some formatting
UsersGuide/GettingStarted/CastroGettingStarted.tex
UsersGuide/Introduction/CastroIntroduction.tex
commit bb0f388093988f44bd4400314eaeda703f4a2b44
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 18:48:03 2014 -0400
add a description of the multigamma EOS
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 9088a01616d11d50c783245db73d5b7f7faa9500
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 18:02:41 2014 -0400
varying gamma test
EOS/multigamma/eos_stuff.f90
EOS/multigamma/test/testeos.f90
commit ee65597739649513f5fdca217d1d4b274035a9aa
Merge: 15ead3727 a09a6eda3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 19 17:01:03 2014 -0400
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 15ead372702514b44ed271cab097c27b7f92ac7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 19 17:00:57 2014 -0400
Fix some errors in the gamma law thermodynamics, and disallow use of input_th mode for this EOS since the system is underconstrained.
EOS/gamma_law_general/eos_stuff.f90
commit a09a6eda332bc23506a988e5aa5dc5895300d1ba
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 16:56:25 2014 -0400
fix error in e
EOS/multigamma/eos_stuff.f90
EOS/multigamma/test/testeos.f90
commit a4594dd82614036ef9d5c654c5be64885bb918b9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 16:31:05 2014 -0400
start of a new multigamma EOS for a new Castro/Maestro test problem
EOS/multigamma/Make.package
EOS/multigamma/_parameters
EOS/multigamma/eos_stuff.f90
EOS/multigamma/test/GNUmakefile
EOS/multigamma/test/GPackage.mak
EOS/multigamma/test/dummy.probin.template
EOS/multigamma/test/testeos.f90
commit 82c3d73434467ed3667f599504fb64201455ac10
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 11:03:49 2014 -0400
just formatting
Source/Src_3d/Castro_3d.f90
commit 375d334c4b8adf7cfbd588422935659031ea64a4
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 10:57:18 2014 -0400
new defaults: ppm_reference_edge_limit = 1 and ppm_reference_eigenvectors = 1
Some problems will change answers slightly, but these give generally better results.
Source/Castro.cpp
commit 52f064df19a4c67727ff39527060365dfeca4c4f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 19 10:55:27 2014 -0400
more runtime parameter checks
Source/Castro.cpp
commit 33dbeabb6c869878cdb0b0585c71ab2fc7f7855e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 18 22:26:22 2014 -0400
rmeove CG
Source/Src_1d/TODO
commit 6c7afa9c428480eb9c2ac5f9bd95814f5c7c1483
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 18 22:04:24 2014 -0400
comment typos
Source/Src_2d/riemann_2d.f90
commit e3236499c1144ecdd764680f6aca176087823cdf
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 18 22:03:20 2014 -0400
sync up the Colella & Glaz stuff. Previously, this was actually doing the
original CG 1985 algorithm, even if we had selected a ppm_type > 0. Now
it does what happens in the 2- and 3-d solvers -- it simply used the CG
two-shock iterative Riemann solver.
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/riemann_1d.f90
commit 03486ab6df22d4ea5f66b5c9050ae90e3d10f14d
Merge: 85327dc13 10b189aa9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 18 12:19:45 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 85327dc13e14e0c77eefa6f27748cf00e7cce892
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 18 12:19:21 2014 -0400
make trans{x,y} a module
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trans_2d.f90
commit 10b189aa9f7896e47cfe3822b2288060acc9eaca
Merge: 35f84d219 b2c6119c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 18 11:37:24 2014 -0400
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit b2c6119c87470b51f429e2149c9fd9752b786567
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 18 09:43:37 2014 -0400
move cmpflx into riemann_1d.f90 as in 2- and 3-d
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/riemann_1d.f90
commit 88b6e827559208508f513c999fc448b3201b0c6c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 23:20:26 2014 -0400
some comments
Source/Src_3d/trans_3d.f90
commit 5b42ba91024483a48f63f32cf23a57058504a63c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 22:58:51 2014 -0400
put the trans stuff in a module. Remove unused variables
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/trans_3d.f90
commit ec3a16f2a312103fb72d68caf0f3be29f35b7318
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 21:57:57 2014 -0400
space out plotfiles
Exec/Sod/inputs-slowshock-x
commit 890df6e0841290738257753ea32d64dea72bae31
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 21:55:09 2014 -0400
add the use_flattening parameter to sync up more with 2- and 3-d
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/flatten_1d.f90
commit aa792d07ad4e4dcea158350b0d6fb37f60821030
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 21:45:03 2014 -0400
remove unused iorder parameter
Source/Src_2d/flatten_2d.f90
commit 5d653bdfc3f8b6f29b69837aebb1060b5067a578
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 21:26:58 2014 -0400
more todo
Source/Src_1d/TODO
commit ad0c39c8b79e32f1edb4b4572e3a6f6d199af15c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 21:25:33 2014 -0400
more sync changes needed
Source/Src_1d/TODO
commit f30dbe8c6a867806e369ccd89fd15091cd1bdbc1
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 21:25:04 2014 -0400
lots of syncing up with the 2- and 3-d solvers. Many of the ppm_reference
options are now supported. See TODO for what's missing.
Source/Src_1d/ppm_1d.f90
Source/Src_1d/trace_ppm_1d.f90
commit 35f84d219a24e2079e0f71ab13d29e0a0fee6378
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 17 16:56:31 2014 -0400
Some performance improvements for the multipole BCs. Removed redundant calculations and the conditionals inside the main loop.
Source/Src_3d/Gravity_3d.f90
commit e60173f3b8df5d97cf7b5a4679d74458b85bcd4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 17 16:09:29 2014 -0400
Replaced floating point numbers with named constants in multipole and direct sum BCs.
Source/Src_3d/Gravity_3d.f90
commit 67feb001838336d9bc2d1025c58307656ec89e22
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 15:57:06 2014 -0400
favorite params
Exec/Sod/inputs-slowshock-x
commit c68b001d013b6f5092f33fd2148c754be0d5b759
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 15:28:32 2014 -0400
a slow shock problem that I wrote a long time ago for my simulation
class. This shows oscillations behind the shock.
Exec/Sod/inputs-slowshock-x
Exec/Sod/probin-slowshock-x
commit 4c16e2bf19a0d44f5df94723dbd8eed7a77b8cf6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 17 13:18:31 2014 -0400
just formatting
Source/Src_2d/trans_2d.f90
commit 576bb05486c7a3bfdbbd0b1f84214e42e3e72d0d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Mar 13 13:28:11 2014 -0400
add a few comments
Source/Src_3d/riemann_3d.f90
commit 6cddd7097b4a8d5ad43cd112490117809cb14bb6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 12 15:51:05 2014 -0400
just formatting to make it easier to read/compare to 2-d
Source/Src_3d/trace_ppm_3d.f90
commit c5fae9ff03a70a279c6680c6b0f8e20de3dc5062
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Mar 12 12:22:48 2014 -0400
add building note
Util/exact_riemann/README
commit b7c74c8a47d846b59b0d208fecece5e6802333ae
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 10 22:08:06 2014 -0400
implement the ppm_flatten_before_integrals methods for ppm_type == 1 -- this syncs
us up to the 2-d solver
Source/Src_3d/ppm_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit 4338cdd1cf06942277fa5a7ee03a42b94d0ccd15
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Mar 9 19:41:04 2014 -0400
add test4
Exec/Sod_stellar/inputs-test4-helm
Exec/Sod_stellar/probin-test4-helm
commit 2e5c9745ef6ac8d870f3a945251e9f5248315b9b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Mar 9 19:40:31 2014 -0400
sync up with the Castro_Exec version
Exec/Sod_stellar/inputs-test1-helm
Exec/Sod_stellar/inputs-test2-helm
Exec/Sod_stellar/inputs-test2-x
Exec/Sod_stellar/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test4-helm
Exec/Sod_stellar/runs/CW-ev/probin-test4-helm
Exec/Sod_stellar/runs/CW/inputs-test1-helm
Exec/Sod_stellar/runs/CW/inputs-test2-helm
Exec/Sod_stellar/runs/CW/inputs-test3-helm
Exec/Sod_stellar/runs/CW/inputs-test4-helm
Exec/Sod_stellar/runs/CW/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-CGF/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev-dt/probin-test4-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test4-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test4-helm
Exec/Sod_stellar/runs/MC/inputs-test1-helm
Exec/Sod_stellar/runs/MC/inputs-test2-helm
Exec/Sod_stellar/runs/MC/inputs-test3-helm
Exec/Sod_stellar/runs/MC/inputs-test4-helm
Exec/Sod_stellar/runs/MC/probin-test4-helm
Exec/Sod_stellar/runs/PROCESS
Exec/Sod_stellar/runs/exact/test1.exact.128.out
Exec/Sod_stellar/runs/exact/test1A.exact.out
Exec/Sod_stellar/runs/exact/test2.exact.128.out
Exec/Sod_stellar/runs/exact/test3.exact.128.out
Exec/Sod_stellar/runs/exact/test4.exact.128.out
Exec/Sod_stellar/runs/exact/test4.exact.out
Exec/Sod_stellar/runs/flash/test1/flash.par.test1.data
Exec/Sod_stellar/runs/flash/test1/flash.par.test1.nocharlimit.data
Exec/Sod_stellar/runs/flash/test1/flash.par.test1.nosteep.data
Exec/Sod_stellar/runs/flash/test1/old/flash.par.test1
Exec/Sod_stellar/runs/flash/test1/old/flash.par.test1.nocharlimiting
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm.dat
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm.out
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_dens.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_dens_nocharlimiting.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_initial.out
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_nocharlimiting.dat
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_pres.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_pres_nocharlimiting.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_temp.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_temp_nocharlimiting.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_velx.data
Exec/Sod_stellar/runs/flash/test1/old/flash_test1_helm_velx_nocharlimiting.data
Exec/Sod_stellar/runs/flash/test1A/flash_test1A_helm.out
Exec/Sod_stellar/runs/flash/test2/flash.par.test2.data
Exec/Sod_stellar/runs/flash/test2/flash.par.test2.nocharlimit.data
Exec/Sod_stellar/runs/flash/test2/flash.par.test2.nosteep.data
Exec/Sod_stellar/runs/flash/test3/flash.par.test3.data
Exec/Sod_stellar/runs/flash/test3/flash.par.test3.nocharlimit.data
Exec/Sod_stellar/runs/flash/test3/flash.par.test3.nosteep.data
Exec/Sod_stellar/runs/flash/test4/flash.par.test4.data
Exec/Sod_stellar/runs/flash/test4/flash.par.test4.nocharlimit.data
Exec/Sod_stellar/runs/flash/test4/flash.par.test4.nosteep.data
Exec/Sod_stellar/runs/makePlot-MC-CGF.py
Exec/Sod_stellar/runs/makePlot-MC-CW.py
Exec/Sod_stellar/runs/makePlot-MC-dt.py
Exec/Sod_stellar/runs/makePlot-MC-eigen.py
Exec/Sod_stellar/runs/makePlot-MC-final.py
Exec/Sod_stellar/runs/makePlot-Tfixes.py
Exec/Sod_stellar/runs/makePlotEigenT.py
Exec/Sod_stellar/runs/norms.py
Exec/Sod_stellar/trace_ppm_2d.f90
commit 8d12b638473a5d6acf3161addeaf4a4f8dc5ec66
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 16:53:26 2014 -0800
test
Radiation.H
commit 5a182bb1593b77199a6a2af34f6bc57f4f0ad737
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 16:40:13 2014 -0800
test
Radiation.H
commit 3c8085b932a2ceace26f6098420a40951db2bcaf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 14:12:38 2014 -0800
updated due to change in Castro
RadHydro_3d.f90
commit 1d719b0c56baf6a1d11b684aa523de27aaa4f4db
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 14:03:40 2014 -0800
fixed a mistake just committed
RadBreakout/GNUmakefile
commit 54493c2779fc4a7daf283d1fae74bed54f01a58f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 13:54:44 2014 -0800
clean up
RadSolve.cpp
commit 01f1494b639d01034c9e3f9e03c8668d160d8bf5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 13:09:56 2014 -0800
clean up makefiles
Make.Castro
Rad2Tshock/GNUmakefile
RadBreakout/GNUmakefile
RadCoreCollapse/GNUmakefile
RadShestakovBolstad/GNUmakefile
RadSlope/GNUmakefile
RadSphere/GNUmakefile
RadSuOlson/GNUmakefile
RadSuOlsonMG/GNUmakefile
RadThermalWave/GNUmakefile
commit cb6b346a8fa7115812ee35c85d2bb47b5394e3e0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Mar 7 10:47:06 2014 -0800
tidy
CastroRad_2d.f90
RadEOS_2d.f90
RadEOS_3d.f90
RadHydro_2d.f90
RadHydro_3d.f90
commit 5df37bdf7352b29937451a72c6ccfd02bd45ba03
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 6 21:36:06 2014 -0500
pass flatn into ppm() so we can change the ordering of the flattening
as we did in 2-d. No changes yet..
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/ppm_3d.f90
commit 49fe5ac452de9f91951ee47df737ed7bb47a884b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 17:44:34 2014 -0800
update Prob_?d.f90
RadSphere/Prob_1d.f90
RadSuOlson/Prob_1d.f90
RadSuOlsonMG/Prob_1d.f90
RadThermalWave/Prob_1d.f90
RadThermalWave/Prob_2d.f90
RadThermalWave/Prob_3d.f90
commit 13d039acfd6835ab8ec03368bd032f96b98cad1f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 17:11:25 2014 -0800
updated 2D and 3D
CastroRad_2d.f90
CastroRad_3d.f90
MGFLD.cpp
MGFLDneut_2d.f90
MGFLDneut_3d.f90
RAD_F.H
RadEOS_1d.f90
RadEOS_2d.f90
RadEOS_3d.f90
RadHydro_1d.f90
RadHydro_2d.f90
RadHydro_3d.f90
Radiation.H
Radiation.cpp
commit e9688a5c0afed8aa910f3cc0440f625f12eee7c6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 17:11:25 2014 -0800
updated 2D and 3D
RadCoreCollapse/Prob_2d.f90
RadCoreCollapse/Prob_3d.f90
RadCoreCollapse/bc_fill_2d.f90
RadCoreCollapse/bc_fill_3d.f90
commit 5123fde5b27b39396439731e85cf28c1e7504e7c
Merge: 312cc3bee fcafefdaf
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 6 18:37:45 2014 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 312cc3beec282651386a8f32583c83558e6a2d84
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Mar 6 18:37:01 2014 -0500
revert back to the correct sanity check on ppm_reference
Source/Castro.cpp
commit fcafefdaf12f7e0fcc9f3e324c23e401c93410ff
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 15:24:03 2014 -0800
cleaned up some Radiation stuff
Source/Castro_F.H
commit 830fe29cbd6ab61a1bf24e7636050b368d64e1cc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 14:56:20 2014 -0800
fixed undefine constant ZERO; it worked for many tests because some EOS modules have ZERO.
Source/Src_3d/riemann_3d.f90
commit d01ac699acb72e34af1ac93410522941e735bea9
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 14:38:45 2014 -0800
fixed undefined constant ZERO
Source/Src_2d/riemann_2d.f90
commit 8ea0abe282b79b80fbb914f0e62397f3cf6dbdb3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 14:08:44 2014 -0800
updated collapse EOS and 1D neutrino routines
MGFLDneut_1d.f90
RadHydro_1d.f90
commit 5948d5785bdd7113db833bc79192005549159231
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Mar 6 14:08:44 2014 -0800
updated collapse EOS and 1D neutrino routines
RadCoreCollapse/Prob_1d.f90
RadCoreCollapse/filt_prim_1d.f90
commit 6a0af653889ef16412ec7db3d0a8a3efbcce4ace
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 5 15:01:03 2014 -0800
Radiation: set ghost cells of state data to zero so that valgrind
doesn't complain when checkpoints are written.
Source/Castro.cpp
Source/Castro_advance.cpp
commit 78ec04163cb4c6bc390c91296f45316f3bdce742
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 5 14:42:38 2014 -0800
save some memory
Radiation.cpp
commit e8f7a7cf1c32b643faea452fc5288328fe833f09
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 5 13:50:57 2014 -0800
copy T into state along the way
Radiation.cpp
commit 4d8bfecacadef996f44954892a6373bcedb0f6f2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 5 13:20:43 2014 -0800
add lo and hi to a number of routines for opacities to have more control on which region to update
MGFLD.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
RAD_F.H
Radiation.cpp
SGFLD.cpp
commit 8251445989f8a2783f305a129d8e7e416a2684c8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 5 09:28:03 2014 -0800
cleanup
_interpbndry/RadInterpBndryData.cpp
commit eabe92d3ccfac97697e1c70d3284ed94cbc95482
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Mar 5 09:22:23 2014 -0800
clean up unused variables
Radiation.cpp
commit a5f37a02667c922b03a9fb64057239f33519f84e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 4 16:44:22 2014 -0800
updated EOS/breakout
RadBreakout/Prob_1d.f90
RadBreakout/filt_prim_1d.f90
commit 441445e1a4fe001116f3afe0478c8446c58d64c4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 4 15:53:18 2014 -0800
updated EOS calls
CastroRad_1d.f90
RadEOS_1d.f90
RadHydro_1d.f90
filt_prim_1d.f90
commit 582234d3cd81e085731ae4b624ea46b340d6e9d4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Mar 4 15:53:18 2014 -0800
updated EOS calls
Rad2Tshock/Prob_1d.f90
commit 10cd41d352ca134db4f051c7cf8a3ff40a65d244
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Mar 4 14:55:13 2014 -0500
no more gamma_in
Util/exact_riemann/exact_riemann.f90
commit 8c7b5c191c8bf68c4a7c01a0d538328caba9a9bf
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Feb 25 09:37:19 2014 -0500
get this compiling again
Prob_2d.f90
commit 0fd2cea0b8ab707148384688c529a00dce61037e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Feb 24 18:52:11 2014 -0500
get this compiling
Prob_2d.f90
commit 9ce9d2c21bb4cbb86795c9fd68cece885c660cab
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Feb 24 18:44:29 2014 -0500
get this compiling
Source/Src_1d/React_1d.f90
commit 0cb566e566b295d37ea5e7d1e66be52f408b6802
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Feb 24 18:44:08 2014 -0500
get this compiling
Prob_1d.f90
commit 268fbbf38842ee2198dbcb1d0d87c883ea59564d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 24 14:14:03 2014 -0500
Removed reference to core-collapse network in User's Guide, which is not currently bundled with CASTRO.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 8eaf1aaaa4e67bc453c32475e0e1e7ec9dd25075
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 24 13:59:51 2014 -0500
Added comment to the User's Guide on how the auxiliary variables have changed with respect to the EOS interface.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 70f3025ee4410d6de848e54fb0e146e2b8b3e7c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 24 13:42:01 2014 -0500
Added description of non-constancy of EOS input to the User's Guide.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 45d946884928ba9020b86885b87f2c7ea2f88aea
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Feb 23 10:57:03 2014 -0500
formatting
Source/Src_2d/React_2d.f90
commit 2488d70e4b2392ce0fa638680d92e9110ef1344d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Feb 23 10:41:44 2014 -0500
get this working with Castro
Networks/ignition_simple/test/GNUmakefile
Networks/ignition_simple/test/GPackage.mak
Networks/ignition_simple/test/dummy.probin.template
Networks/ignition_simple/test/testburn.f90
commit 3836c28ac1de3591acdebe89ea234201bdfadaf3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 20:20:31 2014 -0500
we were not setting e_in correctly. Also declare n
Source/Src_2d/React_2d.f90
commit f59aecf2b0c124412716f511e8da98d4d160b6cd
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 20:00:57 2014 -0500
there were multiple sign errors in the derivatives used for the 2-d Newton solver
with this change, all the input methods seem to work to high precision (as
demonstrated by the test/ unit test
EOS/helmeos/eos_stuff.f90
commit 76ea89d4e725cfd1b891437b92065cfb79bd04a4
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 19:40:17 2014 -0500
fix part of the eos_input_ph -- we were not setting p_want correctly
EOS/helmeos/eos_stuff.f90
commit 763b6bf0129a64d77da6dd42ff4af946dadecfda
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 19:35:28 2014 -0500
fix the calculation of the density when we do eos_input_ps -- we were using
the input T instead of the T that we just calculated from p & s
EOS/gamma_law_general/eos_stuff.f90
commit f757a8cb9a97abb7f8d7adbf089bb1b4f2f1b2c3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 19:04:28 2014 -0500
update the unit test to be the same as the one for helmeos -- it tests
every input method
EOS/gamma_law_general/test/GNUmakefile
EOS/gamma_law_general/test/GPackage.mak
EOS/gamma_law_general/test/dummy.probin.template
EOS/gamma_law_general/test/testeos.f90
commit 0d4ef43e99a4f8b135da3fc671cd2b414e927239
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 18:49:11 2014 -0500
a unit test that exercises EVERY input method
EOS/helmeos/test/testeos.f90
commit 33beafcae6aeb88f3ab776bc44b9336eeee82530
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 18:28:14 2014 -0500
update for the new EOS interface
Networks/ignition_simple/castro_burner.f90
Networks/ignition_simple/f_rhs.f90
commit 1b7defd2b00a7c83ac71746c7a193d1666d78644
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 18:25:24 2014 -0500
remove old Maestro interface
Networks/ignition_simple/burner.f90
commit ff049a409891782ffbda97afea1d91e2d202164e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 17:50:06 2014 -0500
need to compute ymass in the new loop
EOS/eos_type.f90
commit 52fc9889d8b2178e8cf83c03d8730f1256b7f367
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 15:58:00 2014 -0500
only compute ysumi if it is needed
EOS/eos_type.f90
commit 3550abc88149791c93a00435f1bfbdb0445a1715
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 15:37:07 2014 -0500
fix a typo
Source/Src_3d/React_3d.f90
commit 242e339605a035f6cd9d261434286df78f6cb09c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 22 12:56:43 2014 -0500
Added an aux array to the eos_t derived type, that holds auxiliary variables, and updated the hydro calls correspondingly.
EOS/eos_type.f90
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Derive_1d.f90
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/React_1d.f90
Source/Src_1d/compute_temp_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/React_2d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/React_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/riemann_3d.f90
commit 4eb05711bc13d632696e77b18c0a7fe26bf8f5dd
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Feb 22 07:16:18 2014 -0500
we need an initial T guess when calling the eos in eos_input_re mode
Source/Src_1d/compute_temp_1d.f90
commit 51149a195f65baa44028c6b65f0580b2c8855315
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Feb 21 20:11:49 2014 -0500
should be dpdr_e
Source/Src_1d/CastroCG_1d.f90
commit 514cdd7c3c9e6bee4d07977276ee6b62d504ee4d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Feb 21 20:08:36 2014 -0500
there were a number of undefined thermodynamic quantities
Source/Src_1d/CastroCG_1d.f90
commit a9b848ab79464de48d78e33a102e4837a4c20929
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 21 16:54:07 2014 -0800
fixed a bug: ysumi was not initialized to 0
EOS/eos_type.f90
commit 9553d1fb865f750f48090f34f74a69fc2047065d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Feb 21 15:27:49 2014 -0800
Remove x_in from the OMP list since we no longer use this.
Source/Src_3d/reset_internal_energy_3d.f90
commit 8b55086116361869ded5298de09b48e2b29074c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 17:55:46 2014 -0500
Added missing thermodynamic derivatives to gamma law EOS.
EOS/gamma_law_general/eos_stuff.f90
commit 4241b6287718346d8d618ad52d57e3392f37edcd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 17:34:41 2014 -0500
Temp and dens weren't being properly assigned for every input in gamma law EOS.
EOS/gamma_law_general/eos_stuff.f90
commit 20c5c1d782106ba47c76d6abd1de0feb921cad62
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 17:11:32 2014 -0500
Removed errant 2D indices from a couple places.
Source/Src_1d/Derive_1d.f90
Source/Src_1d/compute_temp_1d.f90
commit acc0b1733d7e21ab2845111a6bfe14b740ba36e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 17:05:54 2014 -0500
More 1D fixes for EOS interface update.
Source/Src_1d/Derive_1d.f90
commit c92c03704c824febd8eaea0c03fb789f7d3fcb1d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 16:56:22 2014 -0500
Synced up compute_temp_1d with 2D and 3D.
Source/Src_1d/compute_temp_1d.f90
commit 1051c2304a67232cfad6ac459c565029b22e346d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 16:49:42 2014 -0500
Fixes for the gamma law EOS, using the new interface.
EOS/gamma_law_general/eos_stuff.f90
commit a7292a3c364a9b48014bbb0fbab161d1919bdd70
Merge: 9b695a413 80f768660
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 16:32:38 2014 -0500
Merged new EOS interface changes into main repository.
commit 80f76866014c5c2ea2b485b2ee34317a99aba3c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 16:28:34 2014 -0500
The last fix to input_th for a polytrope was wrong; now it's really right.
EOS/polytrope/eos_stuff.f90
commit 9b695a4137da54920c345c646ceb410138c73f4e
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Feb 21 14:37:57 2014 -0500
sync up with the 2-d solver -- mostly just order-of-operation stuff to
minimize roundoff errors
Source/Src_3d/riemann_3d.f90
commit 4a29733e84180c67c4f5247cc5b3a42d3d976036
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Feb 21 13:47:11 2014 -0500
1.0 -> 1.0d0
Source/Src_2d/riemann_2d.f90
commit 6e44697f77f6d44f7675966677f3ac40643e4e1d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Feb 21 12:21:02 2014 -0500
to
this allows for a custom Derive_F.H in our problems
Source/Castro_setup.cpp
commit 722fc62c2a7538d2fe9bb95f123c50a6060e46dd
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Feb 21 11:59:56 2014 -0500
add a Problem_Derives.H that can be put in individual problem
directories to allow us to specify custom derived variables without
having to have a completely separate Castro_setup.cpp
Source/Castro_setup.cpp
Source/Make.package
Source/Problem_Derives.H
commit ea11f0f574a2b8040d4239aa3623ab748acb7c75
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 00:06:19 2014 -0500
Fixed error in input_th mode for polytrope EOS.
EOS/polytrope/eos_stuff.f90
commit 9555f404b34568406f32b12fce58d85b052c29f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 20 22:39:48 2014 -0500
Change the location of the convergence check in the helmeos iterations.
EOS/helmeos/eos_stuff.f90
commit 25b83b03a435e05ed137f5db719f3d6aa82ff58e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 20 20:06:37 2014 -0500
Fixed some thread safety issues with new eos_state.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/React_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
commit 65742c75fd649cac8585cdb4c2664e66cb3670c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 20 19:17:28 2014 -0500
We don't need to have a separate first pass to call the helmeos in the Newton iterations.
EOS/helmeos/eos_stuff.f90
commit 6517ff5e0fd34bc95dcd81e5c4fc4940de90f417
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 20 18:51:37 2014 -0500
In helmeos, moved all of the error handling to a separate subroutine for performance reasons.
EOS/eos_data.f90
EOS/eos_type.f90
EOS/helmeos/eos_stuff.f90
commit 4e335216740e3f6ac293396c75e3679e93d16c3d
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 20 13:58:26 2014 -0500
Slight modifications for backward compability with the old EOS method.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
commit c53e671af230376e8c40b35a7494a10e79b56654
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 19 15:13:58 2014 -0500
Removed some redundant calculations from helmeos.
EOS/helmeos/helmeos.f90
commit 7deba10725c22abf6388c8ccb3ac14f783ba2d6c
Merge: 0322ff42c 197c35822
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 19 14:17:13 2014 -0500
Merge branch 'eos_new' of gamera:/usr/local/gitroot/Castro into eos_new
commit 0322ff42c89ae9b47dae75cdcf3b9e0b8f57340a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 19 14:17:00 2014 -0500
Instead of using strings to represent variables we're iterating on, we now use integers that are stored in eos_data_module.
EOS/eos_data.f90
EOS/helmeos/eos_stuff.f90
commit 0c0c8120fa63b78d3d6a01492e17510ff7bac86e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 19 14:06:12 2014 -0500
Fixed typo in compute_temp for resetting the energy.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/compute_temp_3d.f90
commit 197c35822dbf8729bb89bec1413fd25ea881928d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Feb 19 13:50:48 2014 -0500
this should compile once the EOS stuff is fixed
EOS/helmeos/test/GNUmakefile
EOS/helmeos/test/GPackage.mak
EOS/helmeos/test/dummy.probin.template
commit 0541bb35ea653a9e1de7f9a3d97029d8a01b0943
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 19 10:39:56 2014 -0500
We now calculate dpdA, dpdZ, etc. in each EOS before calling the derivatives to get dpdX, etc.
EOS/eos_type.f90
EOS/gamma_law_general/eos_stuff.f90
EOS/helmeos/helmeos.f90
EOS/polytrope/eos_stuff.f90
commit 53815b613ce41637f936987ad54fcd18f02be1ef
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 18 23:59:04 2014 -0500
Fixed subroutine that calculated the derivatives w.r.t. abundances, and adjusted gamma/polytrope EOS to use abar/zbar accordingly.
EOS/eos_type.f90
EOS/gamma_law_general/eos_stuff.f90
EOS/polytrope/eos_stuff.f90
commit 9fe635654d13bd1684b54ef6f66b10620c2d4f65
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 18 00:55:09 2014 -0500
mu_e can only be equal to 2.0 at present for the polytrope EOS. Also, added check to make sure the species abundances were set before coming into the EOS.
EOS/eos_type.f90
EOS/helmeos/eos_stuff.f90
EOS/polytrope/eos_stuff.f90
commit 03df91195a820d9575102cf8fd7c53a3f8810a02
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 17 23:36:40 2014 -0500
Some fixes to the polytrope and gamma law EOS.
EOS/gamma_law_general/eos_stuff.f90
EOS/polytrope/_parameters
EOS/polytrope/eos_stuff.f90
commit 5a1f38677fe642bb743ebef89d881a0764f1ae3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 23:35:34 2014 -0500
Updated the description of the EOS in the User's Guide.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 4f604690d67c7022a7382c443ed62959ef75f936
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 20:25:06 2014 -0500
Moved compositional information and calculations to the eos_data module, since this is the same calculations for all equations of state.
EOS/eos_type.f90
EOS/gamma_law_general/eos_stuff.f90
EOS/helmeos/eos_stuff.f90
EOS/polytrope/_parameters
EOS/polytrope/eos_stuff.f90
commit e3fafa6592122bb796aa3f9ae65d1e1ac818e1fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 19:12:33 2014 -0500
Add eos_input_th and eos_input_ph modes to the gamma law EOS.
EOS/gamma_law_general/eos_stuff.f90
commit 4dda7b85e0a084b86adb9d7b802978c9f25c1e44
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 18:53:51 2014 -0500
Moved some data and subroutines that are common to all equations of state into a separate module, eos_data_module.
EOS/Make.package
EOS/eos_data.f90
EOS/gamma_law_general/eos_stuff.f90
EOS/helmeos/eos_stuff.f90
EOS/polytrope/eos_stuff.f90
Source/Src_3d/compute_temp_3d.f90
commit 5503045d7bab51da1913ec1d0217f8f959e73930
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 17:33:46 2014 -0500
Updated the polytrope and gamma law EOS to match the new interface.
EOS/gamma_law_general/eos_stuff.f90
EOS/polytrope/eos_stuff.f90
commit 6e161dd717502201365276b63e58a366bb9f00d5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 15:20:04 2014 -0500
Updated Helmholtz EOS so that the interface now uses a derived type struct (eos_t). All references to the old interfaces (eos_given_*) are now removed from the main code.
EOS/eos_type.f90
EOS/helmeos/README
EOS/helmeos/_parameters
EOS/helmeos/helmeos.f90
EOS/helmeos/test/GNUmakefile
EOS/helmeos/test/testeos.f90
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Derive_1d.f90
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/React_1d.f90
Source/Src_1d/compute_temp_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/React_2d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/React_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
commit 927e9036ac6abc4bf022b42f0a9050a5d5ec71a1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 17:26:10 2014 -0800
comments in inputs
Rad2Tshock/inputs.M2
Rad2Tshock/inputs.M2.mg
Rad2Tshock/inputs.M5
Rad2Tshock/inputs.M5.mg
RadBreakout/inputs.1d
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadShestakovBolstad/inputs.common
RadSlope/inputs
RadSphere/inputs
RadSuOlson/inputs
RadSuOlsonMG/inputs.common
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
commit ddd9db29623129fa8f1c758ec2bd855ed8ea3d58
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 17:17:13 2014 -0800
update comments in inputs
Rad2Tshock/inputs.M2
Rad2Tshock/inputs.M2.mg
Rad2Tshock/inputs.M5
Rad2Tshock/inputs.M5.mg
RadBreakout/inputs.1d
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadShestakovBolstad/inputs.common
RadSlope/inputs
RadSphere/inputs
RadSuOlson/inputs
RadSuOlsonMG/inputs.common
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
commit b7b24147630b28e90220a1e29e94299f5d9d744f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 17:02:18 2014 -0800
better default for struct_flag
HypreMultiABec.cpp
commit 824cb005c3d4a2eb12b7c09e47005fe7b1ae10ea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 17:02:18 2014 -0800
better default for struct_flag
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadSlope/inputs
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
commit 49039b91414831fc1d4870e43fc6c897402ef0f8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 15:41:22 2014 -0800
sync with Castro
RadHydro_2d.f90
RadHydro_3d.f90
commit f479b389cd340791ee732902e3ffba569d6b673f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 15:29:13 2014 -0800
cleanup
HypreMultiABec.cpp
commit 9ec220ef00961f7c03a5a2ff49a96c661e1d93e1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 15:28:48 2014 -0800
update inputs
RadSlope/inputs
commit 5e8dc88b6a2ad9d3bba81957f934b9ae0fd48970
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 14:15:39 2014 -0800
redo cleanup of internal boundary
HABEC_1D.F
HABEC_2D.F
HABEC_3D.F
commit 63f78e6eea1875b4b6b7a7b192601a62f701cdd6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Feb 13 14:08:18 2014 -0800
Revert "clean up internal boundaries"
This reverts commit 439da83a01a75d2dfd09a304f0aa24cc9990974f.
HABEC_1D.F
HABEC_2D.F
HABEC_3D.F
commit bb4c105f025670c8d9194158776c584bb38dc843
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Feb 13 11:59:23 2014 -0500
remove unneeded variables
Source/Src_2d/flatten_2d.f90
commit 2c2da637993ce539a74c449b785b18e2c404ed46
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Feb 13 10:59:43 2014 -0500
clean up the indexing in uflaten -- now everything refers to the
same index space so there is no mapping needed -- this makes it a lot
easier to read. No functionality change should be seen.
Source/Src_2d/flatten_2d.f90
commit 1877c032b7ba69c355eeb2737c0364f90fcde45c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 12 17:13:55 2014 -0800
fixed non-zero flux Neumann boundary
HABEC_1D.F
HABEC_2D.F
MGRadBndry.H
MGRadBndry.cpp
RadBndry.H
RadBndry.cpp
commit 1b230f9d19857ce8cbeec7ecbdca128c658c76de
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 12 15:58:11 2014 -0800
working on adding FORT_RADBNDRY
MGRadBndry.cpp
Make.package
RAD_F.H
RadBndry.cpp
RadBndry_1d.f90
RadBndry_2d.f90
RadBndry_3d.f90
commit cc1abc794127b9f03c2d23dc39d3345bd81ccf52
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Feb 12 15:54:50 2014 -0800
clean up internal boundaries
HABEC_1D.F
HABEC_2D.F
HABEC_3D.F
commit bb32802d84c627555b8c4b3b1ecddf5ab4599358
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Feb 12 16:33:18 2014 -0500
remove the bit that looked if iorder = 3, and if so, disabled
flattening. This seems like it was only relevant for ppm_type = 0
(i.e. piecewise linear slopes), and even then, it appears to be
undocumented. Now we have use_flattening to make everyone
happy.
Source/Src_2d/flatten_2d.f90
Source/Src_3d/flatten_3d.f90
commit 5db89d315aa544229cf0c8bdb27f689d54021f77
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Feb 12 16:30:22 2014 -0500
make use_flattening a parameter and get rid of the hardcoded iflaten
that was floating around. Also note that this change includes a
relaxation of the allowed values of ppm_reference (to let it be 0,1, or 2)
in the runtime checks. This is for some debugging and won't affect
anyone.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/flatten_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/meth_params.f90
commit d887fc7b30ac7b30dfc51205c391f8cdbb6864dd
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Feb 12 16:15:25 2014 -0500
separate uflaten out into its own module to sync up with 2-d
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/flatten_3d.f90
commit 56cf248afbf9293d228e67f270896646fa951400
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Feb 12 12:46:58 2014 -0500
move the flattening routine off on its own to allow for experimentation...
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/flatten_2d.f90
commit 3570406e388ffc55d26a7e6d4d2a77034bdff516
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 16:16:05 2014 -0800
better inputs
RadSlope/inputs
commit 632e33caf5065bf623f2af395317d84157155c57
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 15:32:06 2014 -0800
initial commit of RadSlope
RadSlope/GNUmakefile
RadSlope/Make.package
RadSlope/Prob_1d.f90
RadSlope/inputs
RadSlope/probdata.f90
RadSlope/probin
commit cff9d638872d707d39f61590d571fa197e939186
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 15:31:00 2014 -0800
fixed comment
RadSuOlson/inputs
commit 02d7d3ed521de0be7970cb0ad7c2872513164658
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 14:03:08 2014 -0800
new way of passing c to RadBndry and MGRadBndry
MGRadBndry.H
MGRadBndry.cpp
RadBndry.H
RadBndry.cpp
Radiation.cpp
commit c0574f49d0315b143d1e8c564206d938a7c0861c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 12:42:25 2014 -0800
set c for RadBndry and MGRadBndry
MGRadBndry.H
RadBndry.H
Radiation.cpp
commit 46addd27642d3c7cda308fd18aff7142e84da101
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 12:05:27 2014 -0800
tiny
Make.package
RadDerive_1d.f90
RadDerive_2d.f90
RadDerive_3d.f90
Rad_nd.f90
commit 336ad5c81d02f8d0853350fb5a3bfad081179037
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 10:54:25 2014 -0800
FINISHED cleanup
Rad2Tshock/inputs.M2
Rad2Tshock/inputs.M2.mg
Rad2Tshock/inputs.M5
Rad2Tshock/inputs.M5.mg
RadBreakout/inputs.1d
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadShestakovBolstad/inputs.common
RadSphere/inputs
RadSuOlson/inputs
RadSuOlsonMG/inputs.common
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
commit 973922931fd05a326b5e64d25d1e29e59c9087dc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 10:44:06 2014 -0800
cleanup
Rad2Tshock/inputs.M2.mg
Rad2Tshock/inputs.M5.mg
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadShestakovBolstad/inputs.common
RadSphere/inputs
RadSuOlsonMG/inputs.common
commit 9cc3b09bc919cbeb400817a73023ffcc46777ba1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 10:41:55 2014 -0800
cleanup
Rad2Tshock/inputs.M5.mg
RadShestakovBolstad/inputs.common
RadSphere/inputs
RadSuOlsonMG/inputs.common
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
commit f2783ef7e44ec0c2b0f2c2c113974a3d7892ea1a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 10:39:55 2014 -0800
clean up
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadCoreCollapse/probin.1d.mgfld
RadCoreCollapse/probin.2d.mgfld
RadCoreCollapse/probin.3d.mgfld
commit 8b30b2d6bdca3180f978ecbf03d47b35126296b4
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Feb 11 10:38:18 2014 -0800
clean up
RadCoreCollapse/GNUmakefile
RadCoreCollapse/Prob_1d.f90
RadCoreCollapse/Prob_2d.f90
RadCoreCollapse/Prob_3d.f90
RadCoreCollapse/probdata.f90
commit fbb950e3017b1a4af91b28df69bdb8fc16f30f2a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 21:31:11 2014 -0800
comment
RadThermalWave/inputs.2d
commit ee3f9d07060a57e2388a389bba34031f13adfa45
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 17:01:28 2014 -0800
add shock breakout
RadBreakout/GNUmakefile
RadBreakout/Make.package
RadBreakout/Prob_1d.f90
RadBreakout/filt_prim_1d.f90
RadBreakout/inputs.1d
RadBreakout/model.input.87a.23
RadBreakout/model.input.bo
RadBreakout/model.input.envel
RadBreakout/probdata.f90
RadBreakout/probin.1d
RadBreakout/probin.1d.87a.23
commit f617b6866daf8722adb0ffcc01c918c9aa3e60f0
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 16:49:15 2014 -0800
add 2T shock test
Rad2Tshock/Castro_error.cpp
Rad2Tshock/GNUmakefile
Rad2Tshock/Make.package
Rad2Tshock/Makefile.bc
Rad2Tshock/Prob_1d.f90
Rad2Tshock/bc.f90
Rad2Tshock/inputs.M2
Rad2Tshock/inputs.M2.mg
Rad2Tshock/inputs.M5
Rad2Tshock/inputs.M5.mg
Rad2Tshock/probdata.f90
Rad2Tshock/probin.M2
Rad2Tshock/probin.M5
Rad2Tshock/python/LowrieEdwardsUnits.py
Rad2Tshock/python/RadShock.py
Rad2Tshock/python/initincgs.py
Rad2Tshock/python/paper-M2-mg.py
Rad2Tshock/python/paper-M2.py
Rad2Tshock/python/paper-M5-mg.py
Rad2Tshock/python/paper-M5.py
Rad2Tshock/python/phys.py
Rad2Tshock/python/read_gnu.py
commit 4c696af0df84be32450ae2bc2390c0a356da8d74
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 16:38:11 2014 -0800
minor
RadThermalWave/Prob_2d.f90
RadThermalWave/inputs.2d
RadThermalWave/probin.3d
commit 3311e092970817b66b437470ba8d4b3e07336257
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 15:22:24 2014 -0800
minor
RadCoreCollapse/GNUmakefile
RadThermalWave/GNUmakefile
RadThermalWave/inputs.3d
RadThermalWave/probin.3d
commit 34136715d4b55747f03ff4d561e30079352bbb8f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 15:07:17 2014 -0800
add Thermal Wave test
RadThermalWave/Castro_error.cpp
RadThermalWave/GNUmakefile
RadThermalWave/Make.package
RadThermalWave/Prob_1d.f90
RadThermalWave/Prob_2d.f90
RadThermalWave/Prob_3d.f90
RadThermalWave/Tagging_1d.f90
RadThermalWave/Tagging_2d.f90
RadThermalWave/Tagging_3d.f90
RadThermalWave/inputs.1d
RadThermalWave/inputs.2d
RadThermalWave/inputs.3d
RadThermalWave/probdata.f90
RadThermalWave/probin.1d
RadThermalWave/probin.2d
RadThermalWave/probin.3d
commit 02cd9b11b946205ad4c1f68b27c4b9e758438fa2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 14:50:54 2014 -0800
Su-Olson test
RadSuOlson/GNUmakefile
RadSuOlson/Make.package
RadSuOlson/Prob_1d.f90
RadSuOlson/inputs
RadSuOlson/probdata.f90
RadSuOlson/probin
RadSuOlson/python/paper.py
commit cfba3e767ead9399cea0ad2789c8210a5e36e024
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 14:11:14 2014 -0800
rm RadStreaming test
RadStreaming/GNUmakefile
RadStreaming/Make.package
RadStreaming/Prob_1d.f90
RadStreaming/inputs
RadStreaming/probdata.f90
RadStreaming/probin
commit 13480ebc4ec3b152b7cffdba60bc038a42981702
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 14:10:46 2014 -0800
minor update
RadSphere/README
RadSphere/Tools/GNUmakefile
RadSphere/Tools/fradsphere.f90
RadSphere/inputs
commit e805f2ecd0ebff10e68a0dad14097c0162fff589
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 14:10:27 2014 -0800
minor
RadStreaming/inputs
commit 60a18307611f28c999089cf84737b928fde19a87
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 14:08:45 2014 -0800
add RadStreaming test
RadStreaming/GNUmakefile
RadStreaming/Make.package
RadStreaming/Prob_1d.f90
RadStreaming/inputs
RadStreaming/probdata.f90
RadStreaming/probin
commit 9613983c18a1a0caf1683d229dabfd3dee91073f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 13:44:55 2014 -0800
tools for RadSphere test
RadSphere/Tools/radbc.f90
RadSphere/python/RadGroup.py
RadSphere/python/paper.py
RadSphere/python/phys.py
commit 6a83258fc1c56adc2cf6553c3ec456581323394c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 13:01:05 2014 -0800
add RadSphere test
RadSphere/GNUmakefile
RadSphere/Make.package
RadSphere/Prob_1d.f90
RadSphere/README
RadSphere/Tools/GNUmakefile
RadSphere/Tools/analytic.f90
RadSphere/Tools/bc.f90
RadSphere/Tools/fradsphere.f90
RadSphere/inputs
RadSphere/probdata.f90
RadSphere/probin
commit 4f278111971f9283e2609647d67810e773cf43e6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 12:35:54 2014 -0800
cleanup
RadSuOlsonMG/python/one.py
commit 815a12c7af488a3c103d4389b733802c6ef86b11
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 12:28:38 2014 -0800
add Shestakov-Bolstad test
RadShestakovBolstad/GNUmakefile
RadShestakovBolstad/Make.package
RadShestakovBolstad/Prob_1d.f90
RadShestakovBolstad/inputs-Tf0.1
RadShestakovBolstad/inputs.Planck
RadShestakovBolstad/inputs.common
RadShestakovBolstad/probdata.f90
RadShestakovBolstad/probin.common
RadShestakovBolstad/python/initunits.py
RadShestakovBolstad/python/paper.py
RadShestakovBolstad/python/phys.py
RadShestakovBolstad/python/read_gnu.py
commit fd84570eace656b4cea48a1669177426c78bc35e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 12:12:32 2014 -0800
add RadCoreCollapse
RadCoreCollapse/Castro_error.cpp
RadCoreCollapse/GNUmakefile
RadCoreCollapse/Make.package
RadCoreCollapse/Prob_1d.f90
RadCoreCollapse/Prob_2d.f90
RadCoreCollapse/Prob_3d.f90
RadCoreCollapse/Tagging_1d.f90
RadCoreCollapse/Tagging_2d.f90
RadCoreCollapse/Tagging_3d.f90
RadCoreCollapse/bc_fill_1d.f90
RadCoreCollapse/bc_fill_2d.f90
RadCoreCollapse/bc_fill_3d.f90
RadCoreCollapse/filt_prim_1d.f90
RadCoreCollapse/inputs.1d.mgfld
RadCoreCollapse/inputs.2d.mgfld
RadCoreCollapse/inputs.3d.mgfld
RadCoreCollapse/modelInput
RadCoreCollapse/probdata.f90
RadCoreCollapse/probin.1d.mgfld
RadCoreCollapse/probin.2d.mgfld
RadCoreCollapse/probin.3d.mgfld
commit b96a6a8fb4b95c857829f2a9789322f8aba86e9c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 10:58:04 2014 -0800
added gcv back for MG Su-Olson test
MGFLD.cpp
RAD_F.H
commit 9b932d9988b4842bc481beaaa519d6949eeaf764
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 10:58:04 2014 -0800
added gcv back for MG Su-Olson test
RadSuOlsonMG/inputs.common
RadSuOlsonMG/python/paper.py
commit a4b591433640e04e6907ea386cbc0da6525b2208
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 10:56:55 2014 -0800
minor cleanup of Radiation stuff
Source/Castro_error.cpp
Source/Castro_setup.cpp
commit c3556ed9c9464118b7e3460c32d1f7be31952c5a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 10:13:55 2014 -0800
cleanup
RadSuOlsonMG/inputs.neut
commit ac3fd905b617f28f02fbc086f404f1caf03e8b27
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 10 10:07:16 2014 -0800
fixed comment
RadSuOlsonMG/inputs.common
commit 6cec1d16eeb55bf67097390536ca92f1a4cd52d2
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 7 21:44:56 2014 -0800
Initial commit
CastroRad_1d.f90
CastroRad_2d.f90
CastroRad_3d.f90
Castro_radiation.cpp
DumpModel1d.H
DumpModel1d.cpp
FLD_limiter.F
HABEC_1D.F
HABEC_2D.F
HABEC_3D.F
HABEC_F.H
HypreABec.H
HypreABec.cpp
HypreExtMultiABec.H
HypreExtMultiABec.cpp
HypreMultiABec.H
HypreMultiABec.cpp
LHH.H
MGFLD.cpp
MGFLDRadSolver.cpp
MGFLD_1d.f90
MGFLD_2d.f90
MGFLD_3d.f90
MGFLDneut_1d.f90
MGFLDneut_2d.f90
MGFLDneut_3d.f90
MGRadBndry.H
MGRadBndry.cpp
Make.package
NGBndry.H
RAD_1D.F
RAD_2D.F
RAD_3D.F
RAD_F.H
RadBndry.H
RadBndry.cpp
RadDerive_1d.f90
RadDerive_2d.f90
RadDerive_3d.f90
RadEOS_1d.f90
RadEOS_2d.f90
RadEOS_3d.f90
RadHydro_1d.f90
RadHydro_2d.f90
RadHydro_3d.f90
RadHydro_nd.f90
RadMultiGroup.cpp
RadN_1d.f90
RadN_2d.f90
RadN_3d.f90
RadSolve.H
RadSolve.cpp
RadTypes.H
Radiation.H
Radiation.cpp
SGFLD.cpp
SGFLD_1d.f90
SGFLD_2d.f90
SGFLD_3d.f90
SGRadSolver.cpp
StateLayout.H
Using.H
_CompSolver/COMPSOLVER_1D.F
_CompSolver/COMPSOLVER_2D.F
_CompSolver/COMPSOLVER_3D.F
_CompSolver/COMPSOLVER_F.H
_CompSolver/CompSolver.H
_CompSolver/CompSolver.cpp
_CompSolver/CompSolverLevel.H
_CompSolver/CompSolverLevel.cpp
_CompSolver/EDGEVAR_1D.F
_CompSolver/EDGEVAR_2D.F
_CompSolver/EDGEVAR_3D.F
_CompSolver/EDGEVAR_F.H
_CompSolver/EdgeVar.H
_CompSolver/EdgeVar.cpp
_CompSolver/Make.package
_interpbndry/DIMS.H
_interpbndry/Make.package
_interpbndry/RADINTERPBNDRYDATA_1D.F
_interpbndry/RADINTERPBNDRYDATA_2D.F
_interpbndry/RADINTERPBNDRYDATA_3D.F
_interpbndry/RADINTERPBNDRYDATA_F.H
_interpbndry/RadBndryData.H
_interpbndry/RadBndryData.cpp
_interpbndry/RadBoundCond.H
_interpbndry/RadInterpBndryData.H
_interpbndry/RadInterpBndryData.cpp
blackbody.f90
energy_diagnostics.cpp
filt_prim_1d.f90
filt_prim_2d.f90
filt_prim_3d.f90
filter.f90
fluxlimiter.f90
rad_params.f90
radhydro_params.f90
commit 1213f356388f52829ca0f564141506be6d856ef5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 7 21:44:56 2014 -0800
Initial commit
Make.Castro
Make.Radiation
RadSuOlsonMG/GNUmakefile
RadSuOlsonMG/Make.package
RadSuOlsonMG/Prob_1d.f90
RadSuOlsonMG/inputs.common
RadSuOlsonMG/inputs.neut
RadSuOlsonMG/probdata.f90
RadSuOlsonMG/probin.common
RadSuOlsonMG/python/initunits.py
RadSuOlsonMG/python/one.py
RadSuOlsonMG/python/paper.py
RadSuOlsonMG/python/phys.py
RadSuOlsonMG/python/read_gnu.py
commit 92dd380f5418a184e150da27299d06ec6aae0af3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Feb 3 11:07:53 2014 -0800
made getCPUTime() static
Source/Castro.H
commit b905833b7fd7d61551d669bd44798cd8004e967e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Feb 3 14:04:52 2014 -0500
lots of comments
Source/Src_2d/Castro_advection_2d.f90
commit cf9414cdef7eb3444b9de0ba1ba1f479e57d05cb
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Feb 3 12:36:32 2014 -0500
some comments
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
commit 7ee145360ad0fa4d6b5a1d60a642650aa5944f9c
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Jan 31 14:48:45 2014 -0500
move cmpflx into riemann
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
commit 6e64e6a5733f715016e098a7fdd633e4ba55510a
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Jan 31 14:42:11 2014 -0500
move cmpflx into riemann_2d.f90 -- it is more logical to put it there,
and this will allow for some experimentation
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/riemann_2d.f90
commit 2e65688ff766c94aefd9f857a2fee3a68fe57bd6
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Jan 31 12:46:43 2014 -0500
remove some unused energy factors in the CG RIemann solver
Source/Src_2d/riemann_2d.f90
commit 53d583072233e0aaf371e7bbc74ff15757e999c7
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Jan 24 11:53:36 2014 -0500
more flattening methods -- now we do the FLASH method of
flattening BEFORE we monotonize (ppm_flatten_before_integrals = 1),
the Miller & Colella method of flattening just after we monotonize,
but before doing the integration (ppm_flatten_before_integrals=2),
or the old CASTRO way (ppm_flatten_before_integrals=0 -- the default)
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 8fdef9cbe9e8bfbbce06764b7cd7b390dfacce87
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Jan 24 10:33:22 2014 -0500
runtime check to make sure we only try ppm_flatten_before_integrals
with ppm_type == 1
Source/Castro.cpp
commit aed6075ab3198ed85185087bc7bee5037575bb87
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Jan 23 21:37:33 2014 -0500
move flatn into the ppm() routine for upcoming changes to when
we apply flattening
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit fa2f182867bbc93699cf3032cb11d7f57b1c528a
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Jan 23 20:47:12 2014 -0500
another fun ppm parameter: ppm_flatten_before_integrals. Not used yet (but soon!). This
will select between several different variations on *when* to apply the flattening.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit ef6ceae4f27376ada2a625dd74e3c32783312b94
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 10 15:36:38 2014 -0500
Fixed bug in enforce_minimum_density where the loop would go out of bounds on uout.
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit d9a251db07abbc583f17789dd7c0371e33992663
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 23 10:33:26 2013 -0500
Can now set the polytrope parameters with eos_set_polytrope_parameters.
EOS/polytrope/eos_stuff.f90
commit 0121a656715e71c4c6ef7b9d05b344bcdec8356a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 18 17:34:08 2013 -0500
If do_rotation = 0, still check to see if the user has set rotational_period.
Source/Castro.cpp
commit 639766489ab6e31bb347627652910c2b98e404b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 18 16:22:30 2013 -0500
mu_e was the inverse of what it should be, by default.
EOS/polytrope/_parameters
commit e4116b2fd61d29680aeeb7dc5b3754a7f34e0935
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 18 16:18:59 2013 -0500
Slightly updated the description of the polytrope EOS option in the user's guide.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 42a253a18e7762e423a5518688424d0fd7010e59
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 18 16:12:10 2013 -0500
Thermodynamic derivatives were relying on T derivatives but those vanish for a polytrope. They are now calculated using the density dependence only.
EOS/polytrope/eos_stuff.f90
commit 2f2c7f0556381c8dd1b7975eb616a443ccbd5437
Merge: 8537a2f3e 3f2d9d0cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 18 16:01:39 2013 -0500
Merge branch 'master' of gamera:/usr/local/gitroot/Castro into polytrope
commit 3f2d9d0cd6d0ac0ae16a10b5cf1637b7a768f570
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Nov 13 11:09:10 2013 -0800
sum_integrated_quantities() does not need to be virtual because it does not exist in AmrLevel and no classes derive from Castro.
Source/Castro.H
commit a2c627563f4c231c5f4a3ad387a2e2f0c724a63f
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Nov 7 21:42:57 2013 -0500
wrap a print in a parallel_IOProcessor()
Prob_2d.f90
commit f90d0a0d7e93cebc769959a96e47c4c9eb1e1ab8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Nov 7 18:10:06 2013 -0800
Oops -- wasn't defining rho!
ext_src_2d.f90
commit 1321853482bbef6bccc325fd0566f07d3bfdb9e2
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Nov 7 20:53:53 2013 -0500
the BCs need gravity set in probin
probin
commit 1d86d09289aa12c414893788c26048fa54e46949
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Nov 7 20:27:24 2013 -0500
need to turn off Coulomb
probin
commit dceec6827745a4dc5f084595f88fad49cb6c8ead
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Nov 7 17:14:33 2013 -0800
fixed boundary function name for radiation
Source/Castro_setup.cpp
commit 7dec4c6c222828cf236d5d0aab6e8c3cedccad79
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Nov 7 16:21:48 2013 -0800
Add new run directory -- test_convect -- designed to run the same
problem as in MAESTRO/TEST_PROBLEMS/test_convect. This is the
first convection problem in MAESTRO paper III.
GNUmakefile
Make.package
Prob_2d.f90
Problem.H
Problem_F.H
ext_src_2d.f90
inputs_2d
model.hse
probdata.f90
probin
sponge_2d.f90
sum_integrated_quantities.cpp
commit 8537a2f3e479ec68473ce54f3f6236627a253040
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 4 13:34:22 2013 -0500
Add mu_e as a parameter.
EOS/polytrope/_parameters
EOS/polytrope/eos_stuff.f90
commit 67116e5da54271ddb9fe70eb9a6437e196e2313c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Oct 30 10:43:39 2013 -0400
Added description of polytrope EOS to the User's Guide.
UsersGuide/EOSNetwork/EOSNetwork.tex
commit 4cb848e66d356308041a4a9726cc460cd7f830b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 29 23:10:58 2013 -0400
Removed gamma as a Castro parameter. For the gamma law gas, users should specify eos_gamma in the extern namelist in their probin file.
EOS/README
EOS/gamma_law_general/_parameters
EOS/gamma_law_general/eos_stuff.f90
Exec/DustCollapse/inputs_1d
Exec/DustCollapse/inputs_2d_halfstar
Exec/DustCollapse/inputs_2d_monopole_regtest
Exec/DustCollapse/inputs_2d_octant
Exec/DustCollapse/inputs_2d_poisson_regtest
Exec/DustCollapse/inputs_3d_fullstar
Exec/DustCollapse/inputs_3d_monopole_regtest
Exec/DustCollapse/inputs_3d_monopole_regtest_restart
Exec/DustCollapse/inputs_3d_octant
Exec/DustCollapse/inputs_3d_poisson_regtest
Exec/DustCollapse/probin.fullstar
Exec/DustCollapse/probin.halfstar
Exec/DustCollapse/probin.octant
Exec/Sod/Figure1/inputs-sod-1d
Exec/Sod/Figure1/probin-sod-x
Exec/Sod/Figure2/inputs-test2-1d
Exec/Sod/inputs-test2-1d
Exec/Sod/probin-test2-1d
Exec/Sod_stellar/inputs-test3-x
Exec/Sod_stellar/probin-test3-x
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
UsersGuide/Inputs/CastroInputs.tex
commit cedeaccc542375b8792fa1f896e65bc231fe3f0c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 29 18:35:50 2013 -0400
Make polytrope constants and polytrope type parameters for the extern namelist.
EOS/polytrope/_parameters
EOS/polytrope/eos_stuff.f90
commit b7b536840b6034eab6eed472f954e221e5702bec
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 29 12:49:58 2013 -0400
Added a basic polytropic EOS.
EOS/polytrope/Make.package
EOS/polytrope/_parameters
EOS/polytrope/eos_stuff.f90
commit b27d0c473ee03c709feefcdc0fdfd26a92f5c409
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Oct 23 10:48:23 2013 -0400
more vis doc cleanups
UsersGuide/CastroUserGuide.tex
UsersGuide/Visualization/CastroVisualization.tex
commit 5e707f30bc2b34a295c2a4d362909681de664cef
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Oct 23 10:38:01 2013 -0400
change the subsections to sections
UsersGuide/Visualization/CastroVisualization.tex
commit 90c13e2eaba291d63b894c7ff3f3f313f0bc2090
Merge: 1a99a346d d066f1ab5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 21 14:31:50 2013 -0400
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 1a99a346d3eb49fc61bdcf7abc1500e94b7f38c5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 21 14:31:37 2013 -0400
Sign error in user's guide momentum equation in rotating reference frame.
UsersGuide/Rotation/CastroRotation.tex
commit d066f1ab5d97175aec06c70cf6524d10e182f076
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Oct 18 12:10:57 2013 -0400
tighten things up with small stepsize for the rarefaction
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/inputs.test4.helm
Util/exact_riemann/riemann_support.f90
commit e596562b0fa2343980643542c54406e8a7a5a21a
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Oct 18 12:01:39 2013 -0400
disable Coulomb corrections for this problem
Util/exact_riemann/inputs.test4.helm
commit 1f9252b2cea8c189a43e44a00f2417d8639a8744
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Oct 18 10:49:57 2013 -0400
some minor changes that just affect roundoff behavior + we now use tau
instead of rho in determining which state we keep (only matters really
in the case of u = 0)
Source/Src_2d/riemann_2d.f90
commit 850369a021a1d4d068c35b5db937fb4c416a9155
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Oct 18 10:38:34 2013 -0400
comments
Source/Src_2d/reset_internal_energy_2d.f90
commit f9191dc2bb0327e881b22234cdff01278567d965
Author: vince <vebeckner@lbl.gov>
Date: Mon Oct 14 14:12:18 2013 -0700
added file.
Exec/HCBubble/Make.package
commit 5bef961dcc666fd432b50466c784cb647a9539ee
Author: vince <vebeckner@lbl.gov>
Date: Mon Oct 14 13:57:58 2013 -0700
cy_didem test problem.
Exec/HCBubble/GNUmakefile
Exec/HCBubble/Prob_3d.f90
Exec/HCBubble/inputs-sod-x
Exec/HCBubble/inputs.L0
Exec/HCBubble/probdata.f90
Exec/HCBubble/probin-sod-x
commit 384adab6bc5af5b3daf4e83422d6c240e6935226
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Oct 11 11:48:15 2013 -0400
commenting
Source/Src_2d/ppm_2d.f90
commit 93545021c9c57d26e16be796f93a5f00ee1997b3
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Oct 10 15:59:35 2013 -0400
new test problem at lower density -- has Coulomb issues...
Util/exact_riemann/inputs.test4.helm
commit 0fb42747f6cb78577e38ac0f43d1956aed63aa27
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Oct 9 17:29:33 2013 -0700
Fixed the test on whether level > 0 grids touch the domain boundary
in the case when we are trying to fill Dirichlet boundary conditions
for the Poisson gravity solve.
Source/Gravity.cpp
commit 28a5b06614a4b54709f1c6b9d421af1f3bf24dc9
Author: Ann Almgren <almgren@bender.astro.sunysb.edu>
Date: Wed Oct 9 17:15:49 2013 -0400
Put in a test on whether grids at level > 0 touch the domain
boundary and we're not periodic -- in this case we don't know how
to fill the boundary values using the multipole approximation.
Instead of proceding along with undefined values we now abort.
Source/Gravity.cpp
commit 725ad038acb274cf9d55c764884b8c83d87f7463
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Oct 7 21:15:19 2013 -0400
implement ppm_reference_edge_limit -- if this is on then we rely on the ppm_3d.f90
to replace I with the limit of the quadratic interpolant to the edge if the
wave doesn't move to the interface
Source/Src_3d/trace_ppm_3d.f90
commit 494ddeafddb3f243db8c2f9b6d7b084e3ee64baf
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Oct 7 20:35:52 2013 -0400
implement ppm_reference_edge_limit -- if this is on then we rely on the ppm_2d.f90
to replace I with the limit of the quadratic interpolant to the edge if the
wave doesn't move to the interface
Source/Src_2d/trace_ppm_2d.f90
commit 1e72d722aad9d6b6c12f115c8206af57a9a50e17
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon Oct 7 12:20:40 2013 -0400
why not another parameter? ppm_reference_edge_limit will be used to
determine what we do with the I's when the wave is not moving toward
the interface -- use the cell-centered value or the limit of the
parabolic interpolant to the interface
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 48c366fc4f7279023be83e45b3d1264f69d604ec
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Oct 5 15:25:35 2013 -0400
if the wave is not moving toward the interface, make I be the limit of the
parabolic interpolant to that interface.
This does not change anything yet, since we need to adjust the logic in the
trace_ppm_2d.f90 routine to have this take effect.
Source/Src_2d/ppm_2d.f90
commit 505f22ac9c1dd357d7ddecbc0a77f6c5273b84a3
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Oct 4 16:21:40 2013 -0400
change the way the I's are constructed -- now if the wave is not moving
toward the interface, we use the limit of the parabolic interpolant to that
interface for I.
This change alone should not affect anything, because we overwrite this
(for now...) in trace_ppm_3d.f90
Source/Src_3d/ppm_3d.f90
commit 8bb28c84190269fc63e73a68da28b04685174464
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Oct 1 22:34:46 2013 -0400
add a copy of the Sod problem for the stellar equation of state along with
the suite of inputs files that are used in the paper exploring temperature
Exec/Sod_stellar/GNUmakefile
Exec/Sod_stellar/Make.package
Exec/Sod_stellar/Prob_1d.f90
Exec/Sod_stellar/Prob_2d.f90
Exec/Sod_stellar/Prob_3d.f90
Exec/Sod_stellar/inputs-sod-x
Exec/Sod_stellar/inputs-test1-helm
Exec/Sod_stellar/inputs-test1-helm-y
Exec/Sod_stellar/inputs-test1-helm-z
Exec/Sod_stellar/inputs-test2-helm
Exec/Sod_stellar/inputs-test2-x
Exec/Sod_stellar/inputs-test3-helm
Exec/Sod_stellar/inputs-test3-x
Exec/Sod_stellar/probdata.f90
Exec/Sod_stellar/probin-sod-x
Exec/Sod_stellar/probin-test1-helm
Exec/Sod_stellar/probin-test1-helm-y
Exec/Sod_stellar/probin-test1-helm-z
Exec/Sod_stellar/probin-test2-helm
Exec/Sod_stellar/probin-test2-x
Exec/Sod_stellar/probin-test3-helm
Exec/Sod_stellar/probin-test3-x
Exec/Sod_stellar/runs/CW-ev/inputs-test1-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test2-helm
Exec/Sod_stellar/runs/CW-ev/inputs-test3-helm
Exec/Sod_stellar/runs/CW-ev/probin-test1-helm
Exec/Sod_stellar/runs/CW-ev/probin-test2-helm
Exec/Sod_stellar/runs/CW-ev/probin-test3-helm
Exec/Sod_stellar/runs/CW/inputs-test1-helm
Exec/Sod_stellar/runs/CW/inputs-test2-helm
Exec/Sod_stellar/runs/CW/inputs-test3-helm
Exec/Sod_stellar/runs/CW/probin-test1-helm
Exec/Sod_stellar/runs/CW/probin-test2-helm
Exec/Sod_stellar/runs/CW/probin-test3-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-I-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-II-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/inputs-test3-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test1-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test2-helm
Exec/Sod_stellar/runs/MC-ppmT-III-ev/probin-test3-helm
Exec/Sod_stellar/runs/MC/inputs-test1-helm
Exec/Sod_stellar/runs/MC/inputs-test2-helm
Exec/Sod_stellar/runs/MC/inputs-test3-helm
Exec/Sod_stellar/runs/MC/probin-test1-helm
Exec/Sod_stellar/runs/MC/probin-test2-helm
Exec/Sod_stellar/runs/MC/probin-test3-helm
Exec/Sod_stellar/runs/dataRead.py
Exec/Sod_stellar/runs/exact/test1.exact.out
Exec/Sod_stellar/runs/exact/test2.exact.out
Exec/Sod_stellar/runs/exact/test3.exact.out
Exec/Sod_stellar/runs/makePlot-MC-CW.py
Exec/Sod_stellar/runs/makePlot-MC-final.py
Exec/Sod_stellar/runs/makePlot-Tfixes.py
Exec/Sod_stellar/runs/makePlotEigenT.py
Exec/Sod_stellar/runs/makePlotZoom.py
Exec/Sod_stellar/trace_ppm_2d.f90
commit 9cb2fef5274dbb5cb45202e38f93d2b81bcf40ab
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Sep 28 15:12:58 2013 -0400
fix the y-direction for castro.ppm_use_tau_in_tracing -- had an extra Clag_ev in there
Source/Src_3d/trace_ppm_3d.f90
commit db5cab82ba57b2a03f3d14c65487877698c22717
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Sep 28 15:01:12 2013 -0400
fix uninitialize p_ev for y and z. Now z Sod problems with helmeos seem
to agree with x, but y is still off for some reason (note: only applies
with castro.ppm_tau_in_tracing=1)
Source/Src_3d/trace_ppm_3d.f90
commit 41d7049aaee8b8270a06502547118e5d4c5143a0
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 21:53:36 2013 -0400
add the ppm_tau_in_tracing option to 3-d. Tested with Sedov and it seems
to work. This is closer in spirit to the original Colella & Woodward
method.
Source/Src_3d/trace_ppm_3d.f90
commit 395ab513e78a59199f89bcd511df97ce78d04e5c
Merge: 49a8d3e99 cb05cd210
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 19:42:48 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 49a8d3e99535e4f1b1fc30f6d8889b79370c1e44
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 19:42:31 2013 -0400
more work on the tau_in_tracing
Source/Src_3d/trace_ppm_3d.f90
commit cb05cd210875f43d3a34be6ab79ae2599257df29
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 16:33:01 2013 -0400
typo bug
Source/Src_3d/trace_ppm_3d.f90
commit 28e06a10507ff203e16f50b42cc05bb95b0ea91c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 10:23:00 2013 -0400
define the tau stuff for use later with tau_in_tracing
Source/Src_3d/trace_ppm_3d.f90
commit d3246c7b540314b1fa030d31ba8ffe3321ffd25a
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 10:07:14 2013 -0400
move where the flattening is applied to sync up with 2-d. This has
no functional change, but may give roundoff level order of operation
differences.
Source/Src_3d/trace_ppm_3d.f90
commit 9f75eae112c7d8400c8f2d865321c793796f9849
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 27 09:41:28 2013 -0400
minor comment fix
Source/Src_2d/trace_ppm_2d.f90
commit 5b8c9cccc4d7f77469bbe825f9639f2b439b938e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 26 13:44:00 2013 -0700
fixed a bug in the initial setup for RT3D
Exec/RT/Prob_3d.f90
Exec/RT/inputs_3d
commit f74aa8aac49d9de35109d0c304f6b9caedc02097
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Sep 26 15:02:20 2013 -0400
fix uninitialize enth from cleaning
Source/Src_3d/trace_ppm_3d.f90
commit 65965d31689d2050bb2a5444dd5fd2bc094eae67
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 26 10:58:55 2013 -0700
added 3D RT test
Exec/RT/Prob_3d.f90
Exec/RT/inputs_3d
commit e56c57698a2c97214bd3cb8e6469bb05e3354562
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 26 10:29:35 2013 -0700
fixed some minor bugs in asserting correct boundaries
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
commit 3718e16f7d03b4404481cf087c0f1d5a48fa74d1
Merge: 9651c7a4a b3f46a0ce
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Sep 26 12:50:30 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 9651c7a4ae9645f8c38fca99fce7b197626246d9
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Sep 26 12:50:00 2013 -0400
commit the ppm_reference_eigenvectors in 3-d
Source/Src_3d/trace_ppm_3d.f90
commit b3f46a0cedaae9362a7aba2dd1509ada741d9a7d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 26 09:15:45 2013 -0700
Change 1.e-8 --> 1.e-6 in the definition of "eps" in the test on whether time is
t_old or t_new.
Source/Gravity.cpp
commit e9e72ab85f7c12edc2faf774f02d478ee58dd901
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Sep 26 10:12:20 2013 -0400
lots of comments
Source/Src_3d/trace_ppm_3d.f90
commit f225ed7dd3482d81e9de82d6e5e7c03abb89e9ef
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Sep 26 09:18:03 2013 -0400
construct parabolic interpolants of gamma_1 and pass them through to the tracing
routine
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit b209464ff8e4750a48a0b94b29f9002a5b86fdca
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 25 20:37:19 2013 -0400
sync up with the changes from Sod_stellar to get a reference value
of Gamma_1
Source/Src_2d/trace_ppm_2d.f90
commit a93405cd8ae8278c9a7b4e93a42268ccfa731e57
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 25 18:10:20 2013 -0400
pass gamc into the ppm tracing routines to allow us to start using reference states
for the eigenvectors
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit e6fb800e8f28e02f2a57ab4ffd8cc90b91378c20
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 25 18:02:52 2013 -0400
change the order of lo and hi to match gamc to grav
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit d84bac8dcb2bb6b62d479e9b72798befb11de0cf
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 25 17:54:44 2013 -0400
sync ppm_temp_fix=2 up to the new method
Source/Src_3d/Castro_advection_3d.f90
commit 1065083d5dd331c9a8e36dee1554801b7978f0cc
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 24 21:03:04 2013 -0400
eos_input_rp -> eos_input_re for ppm_temp_fix=2 -- this seems much better
Source/Src_2d/Castro_advection_2d.f90
commit 9b3f84dfe76a0363f70a148b6b5e44a37fc2cec7
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon Sep 23 14:47:53 2013 -0400
bring gamc into trace_ppm_2d for fun things!
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 50453f4fd7ee2391ec5876bdc2666ba2cd5655fb
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Sep 20 21:51:06 2013 -0400
add the ppm_reference_eigenvectors stuff -- seems to improve
some tests
Source/Src_2d/trace_ppm_2d.f90
commit 90dcc4178c5f8506485ec8e673504ebaadaa521c
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Sep 20 12:09:13 2013 -0400
add ppm_reference_eigenvectors -- this flag will allow you to set
whether you want to use the reference state in the computation
of the eigenvectors used in the tracing or whether you use the time n
state
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 04f2ec19a4a8a8f8e932747995cdf5da34e57aab
Merge: db56158e9 1abbf75b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 17 13:26:56 2013 -0400
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit db56158e91d07cde3a7313cc0b4f3b63527c9a91
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Sep 17 13:26:42 2013 -0400
We now do the old and new state data swaps at all levels at the beginning of the coarse timestep.
Source/Castro_advance.cpp
commit 1abbf75b271518028a4917be1c238bc1626c33bc
Merge: ffe62a4b9 f97ae00a0
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Sep 13 13:30:17 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit ffe62a4b975d9676ebad2aa868b5f38dae0bb14e
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Sep 13 13:29:18 2013 -0400
fix the ppm_tau_in_tracing stuff -- there was a sign error. Now the
general EOS stuff looks good with it.
Note: this also switches to using e not (rho e) in the eigensystem
for the characteristic tracing.
Source/Src_2d/trace_ppm_2d.f90
commit f97ae00a051673fa2f1056e07a52b08d2bb5e59b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 13 13:27:28 2013 -0400
Switched variables from rotational_frequency to rotational_period for the rotation source terms.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_2d/Rotate_2d.f90
Source/Src_3d/Rotate_3d.f90
Source/meth_params.f90
UsersGuide/Inputs/CastroInputs.tex
UsersGuide/Rotation/CastroRotation.tex
commit aa359fcbde6c4dd38b3501710a6bdd14b43552c1
Author: Chris Malone <cmalone@lanl.gov>
Date: Thu Sep 12 10:58:48 2013 -0700
mock up 3d version and more comments
Exec/KH/GNUmakefile
Exec/KH/Prob_3d.f90
Exec/KH/README
Exec/KH/inputs.2d
Exec/KH/inputs.3d
commit 80007175e67ca951eb9224d4c1f7dff0141d639a
Author: Chris Malone <cmalone@lanl.gov>
Date: Wed Sep 11 16:19:22 2013 -0700
sync with new parameterization
Exec/KH/inputs.2d
Exec/KH/probin
commit 53b3ce004c8f818033a436daf95be9d0fae1ac5b
Author: Chris Malone <cmalone@lanl.gov>
Date: Wed Sep 11 16:17:18 2013 -0700
revamped model based on McNally+ 2012
Exec/KH/Prob_2d.f90
Exec/KH/README
Exec/KH/probdata.f90
commit 441aa29d6a38ffea2345a1a6fe97d4ae105bf994
Author: Chris Malone <cmalone@lanl.gov>
Date: Wed Sep 11 11:14:08 2013 -0700
fix typo
EOS/gamma_law_general/eos_stuff.f90
commit 75b15bc61617af1d25fb3add941cb1b1190c0d4a
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Sep 9 10:09:45 2013 -0700
fix incorrect species initialization
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
commit 911498034ebc128e58eb5d12008b60903656c943
Merge: 8cccbb6e3 013f2cd3d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Sep 4 09:43:40 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 8cccbb6e30f72a1a87adc97a9de1d36e5f5baf95
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Sep 4 09:42:06 2013 -0400
add the ppm_tau_in_tracing option -- this uses tau = 1/rho in the
characteristic projections, which is what the original CW PPM
paper did.
Note that I changed when the flattening coefficients are applied --
this should save on some operations, but might make roundoff level
differences in the output.
This option seems to work (as tested with Sedov in 2-d).
Source/Src_2d/trace_ppm_2d.f90
commit 013f2cd3d8f2d4ce939e773c08f5d1e2e140d83c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Sep 3 14:42:20 2013 -0700
option to do pure hydro using the radiation hyperbolic solver
Source/Castro_advance.cpp
commit d73927f89f59c98a13282ef8967bbef81bbf117f
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 15:48:35 2013 -0400
add ppm_tau_in_tracing parameter -- not yet implemented in the guts (stay tuned...)
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit ffa48b7b9d66487dfde582b115d4e552e35f9fd5
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 14:31:15 2013 -0400
deallocate Ip_g and Im_g (shouldn't matter for F95)
Source/Src_2d/trace_ppm_2d.f90
commit cd4edda222bb5d61486531b3100fa97b07946bc1
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 14:22:23 2013 -0400
lots o' commenting to make things clearer
Source/Src_2d/trace_ppm_2d.f90
commit 3b6b5b9b6f0113866a98cfd39cd781f77cfec062
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 13:39:27 2013 -0400
had the order of idim and iwave reversed in ppm_temp_fix = 1 -- no
harm done though, since both were loops from 1 to 3
Source/Src_3d/Castro_advection_3d.f90
commit 2e593c22a7b28bd659fa2f7e80b0318395566bba
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 13:37:37 2013 -0400
fix the loop over dim -- had it backwards
Source/Src_2d/trace_ppm_2d.f90
commit 04e228b81ebba8cd9e8d45263939bd519fc87c7d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 13:22:14 2013 -0400
add ppm_temp_fix = 1 to 2-d. Note that we need to do this
in the trace routine, since we never have the Ip/Im stuff at a
higher level in 2-d (unlike 3-d)
Source/Src_2d/trace_ppm_2d.f90
commit 2789ba210f078324338fe008dc7e5983a8c986b7
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Sep 3 13:06:14 2013 -0400
add ppm_temp_fix = 2 here. Note we need to be careful about the
loop indices, since the 2-d differs from 3-d. Also we can't mirror
the ppm_temp_fix = 1 stuff from 3-d here -- that will need to go
into the tracing routine.
Also make the indenting nicer
Source/Src_2d/Castro_advection_2d.f90
commit c274f9b2fdf6437f63d3fcfe10665a9cfe89dc33
Author: vince <vebeckner@lbl.gov>
Date: Tue Aug 27 13:54:20 2013 -0700
added more profiling.
Source/Castro.cpp
Source/CastroParticles.cpp
Source/Castro_advance.cpp
Source/Castro_react.cpp
Source/Diffusion.cpp
Source/Gravity.cpp
Source/main.cpp
Source/sum_utils.cpp
commit e894b18d2ea134cb621f3f0970f97387a671cd0a
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Aug 27 16:00:58 2013 -0400
sync up with 3-d
Source/Src_2d/riemann_2d.f90
commit db5c6f1b0ee966c0f7e332c6c18b165afa1bce15
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Aug 23 21:47:53 2013 -0400
when checking for p < small_pres or rhoe < 0, reset both
(and gam1) to make sure that we are thermodynamically consistent
Source/Src_3d/riemann_3d.f90
commit bcd96c75394a0cb575b8d7843db677ec4d47223e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Aug 23 12:19:54 2013 -0700
Some cleanup of stuff, and add extern.f90, network.f90, plt* and chk*
to the .gitignore file.
.gitignore
Source/Castro.cpp
Source/Castro_nd.f90
Source/Gravity.cpp
commit 655559be8413c52aa062eff523bdfbca193f5815
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Aug 23 11:36:54 2013 -0400
update docs with ppm parameters
UsersGuide/Inputs/CastroInputs.tex
commit 9be9f6515db8603e1d98983945a54025b715f8dc
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 23 10:55:42 2013 -0400
Added the new CG inputs to the 2D Riemann solver.
Source/Src_2d/riemann_2d.f90
commit bb0cb8dd3d7d75510d76cd5adcc25763fdd5d8dd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 23 10:49:47 2013 -0400
Added cg_maxiter and cg_tol as runtime parameters for the Colella/Glaz Riemann solver.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/riemann_3d.f90
Source/meth_params.f90
UsersGuide/Inputs/CastroInputs.tex
commit 8c3f7cfa910ae7c78ebcfd0234805c47b5c1acb8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Aug 23 10:31:17 2013 -0400
fix OMP issue
Source/Src_3d/riemann_3d.f90
commit ac7f84fac574e440edba84dfe3b6c9d8c1f1457c
Merge: 6e4c53016 7d7a7ba06
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Aug 23 10:30:34 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 6e4c530165360f3cdca527ae81f8fed14302291d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Aug 23 10:29:58 2013 -0400
call the EOS if we come in with (rho e)_{l,r} < 0
Source/Src_3d/riemann_3d.f90
commit 7d7a7ba068053adbcface48ead545f9577f194bc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Aug 23 06:58:16 2013 -0700
fixed an OMP problem
Source/Src_3d/riemann_3d.f90
commit 02b87e0688f4fe9909163f515296cce076389a12
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 23 09:42:48 2013 -0400
warn on negative energy
Source/Src_3d/riemann_3d.f90
commit b98a423ca09b6e00e847be5fbb63c9f1313ffe93
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Aug 22 22:01:55 2013 -0400
sync up with the 3-d CG solver
Source/Src_2d/riemann_2d.f90
commit e736f05e2eb3699b857de40f4894ee2b16d8dc2c
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Aug 22 21:46:55 2013 -0400
up the iterations from 8 to 12
print out the states when we don't converge
Source/Src_3d/riemann_3d.f90
commit 1b166042d801e8061033e5fe7309eed1ecaa9c30
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 22 20:48:40 2013 -0400
some double precisioning of constants + tighted up smlp1, used to
set wsq = csq when pstar - p_s is small
Source/Src_3d/riemann_3d.f90
commit b1f8804d748727c3917a393956fc43340ad7f89d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 22 20:03:43 2013 -0400
bug fix: we were doing iter_max-1 not iter_max iterations.
Also, store a history of the pstar guesses from the iteration
and print out the history when we barf from non-convergence
Source/Src_3d/riemann_3d.f90
commit e54e967e2e0ba5fffca01a17167bcf87df3c9ef1
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Aug 21 13:37:54 2013 -0400
formatting
Source/Src_2d/trace_ppm_2d.f90
commit 8bc36d06d09d3a647fe41a77ed5ff043ddad45fc
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Tue Aug 20 10:09:41 2013 -0400
restore
Exec/Sod/inputs-test1-helm
commit 02378064ee0c5d01a48402cb1da9e81ec2d98478
Merge: 6bbb9dbd5 b35021644
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Tue Aug 20 10:08:46 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
Conflicts:
UsersGuide/Visualization/CastroVisualization.tex
commit 6bbb9dbd5358e919f2741ecd54e82ba48e165130
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Tue Aug 20 10:07:28 2013 -0400
add subsection
UsersGuide/Visualization/CastroVisualization.tex
commit b350216448f91e6e2e8a8b80386c9837b1a3984c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 9 11:46:21 2013 -0400
loosen tolerances on the shock solve to 1.e-6
Util/exact_riemann/inputs.bug6
Util/exact_riemann/riemann_support.f90
commit 6e4e2a1dfa55ad2fcb666c5e730dbd072f58305e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 9 10:23:12 2013 -0400
better fix -- if pstar - p_l ~ roundoff, then don't go into the
shock routines -- it is hard to converge there.
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit 3411c7833356e9e794478de101efced7b7151ffc
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Fri Aug 9 09:09:29 2013 -0400
new test
Util/exact_riemann/inputs.bug5
commit a574e579ee713bb1e08d2b82d8673740248dabd4
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 20:32:39 2013 -0400
another pathalogical test case
Util/exact_riemann/inputs.bug4
commit c443938a8b523446dfd22979a8d5421e2ba7e074
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 20:31:58 2013 -0400
there is a pathalogical case when p_l - p_r ~ 0 (to roundoff). In this case,
we use the limit for the W**2 expression in the shock solution
Util/exact_riemann/riemann_support.f90
commit 3a95535c135d3640d35896a910fc1fdc0560ecfd
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 19:46:42 2013 -0400
another nasty test case
Util/exact_riemann/inputs.bug3
commit afad129fb2f5ced9a15dc7475f7c18072c3785f5
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 19:46:27 2013 -0400
even more robustness
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit 642893907cc3cee31444fa7bca453c9e64762e64
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 18:34:44 2013 -0400
remove a print + stop
Source/Castro_nd.f90
commit 0f43985059b4533275aa2bd23fb3c5915d5a1736
Merge: 5007a725e 66b154ef0
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 18:29:17 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 5007a725e72b7f3e834736dffbcb33101cd98dd7
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 18:28:23 2013 -0400
sometimes the Newton-Raphson solve in the shock function fails to converge
because we hit a cycle. If that's the case, try to bisect around the
last known W_s to find the value.
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit 66b154ef036bfe792b570dcd7f05c86518e86631
Merge: 61873ef9f f065a74ba
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Aug 8 14:59:16 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 61873ef9f589f0084484c84edfe99eb8f1af2b63
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Aug 8 14:58:58 2013 -0700
Fix latest changes re enforcing no-flow ...
Source/Src_3d/riemann_3d.f90
commit f065a74ba0871df522869ea78e3562f1ffa08773
Merge: a6331245a a8165437d
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 17:57:44 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit a6331245aa146df922ddf3f2417af6de34513c71
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 17:57:15 2013 -0400
move the shock jump conditions into a function to make it easier to switch
root-finding methods
Util/exact_riemann/riemann_support.f90
commit a8165437d0e39afea1632e874d3ab7eca819474a
Merge: 2746353f3 71005c2a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Aug 8 14:45:27 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 2746353f349b39727bc6d70afd3065047e7228c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Aug 8 14:45:09 2013 -0700
Oops -- left in the print statement -- now gone
Source/Src_2d/riemann_2d.f90
commit 71005c2a870f78e967fcba36c5885d43040c5c04
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Aug 8 17:41:38 2013 -0400
some hard test cases
Util/exact_riemann/inputs.bug
Util/exact_riemann/inputs.bug2
commit bf8c43e8cf72dacf00ee6e16f52e5523115d2770
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Aug 8 14:15:28 2013 -0700
We now pass domlo and domhi to the Riemann solver so we can enforce hard no-flow
through walls as well as symmetry boundaries.
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/riemann_3d.f90
Source/prob_params.f90
commit 2700d30886543d52e802fa3e3424cc0f38ffa35f
Merge: 3e384de4d fc4a93dc6
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 15:29:07 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 3e384de4d6ce04ad82e3a500cee41f2a0ac03ff7
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 15:28:49 2013 -0400
add print and some convergence history
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit fc4a93dc62aa7c5f4a2d2e19ab71198da6ce5cf0
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Aug 8 15:26:28 2013 -0400
robustness for the case when q_l = q_r -- the shock solution doesn't
like this
Util/exact_riemann/riemann_star_state.f90
commit 132e8ec7516d086e9d69673d7bacd532d1901f24
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 13:04:30 2013 -0400
make things quiet by default -- also modularize some things
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.f90
Util/exact_riemann/riemann_support.f90
commit 8bde616c9fa7eb80488d9fe0aa4fdca20ace1266
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 12:46:54 2013 -0400
turn off debugging
Util/exact_riemann/riemann_star_state.f90
commit 629f49a7e7a91df8cbc09b329a5364bb343b6033
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 12:30:01 2013 -0400
in case we want to hook Castro into this
Util/exact_riemann/Make.package
commit b98285296d539626e06dd3ebfb74ff031599d7e5
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Aug 8 11:23:07 2013 -0400
slight change to the use_colglaz logic to allow for offline hacking
-- no functionality change
Source/Src_2d/Castro_advection_2d.f90
commit 426d596f90abbee8a7185182ce94f3c56e5eea36
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Aug 7 11:14:32 2013 -0400
remove unused variables
Util/exact_riemann/exact_riemann.f90
commit c1a19384cf5cb92d0bbaac47eaf3e62cfaab97b7
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Aug 7 11:09:57 2013 -0400
break things into subroutines to make it easier to reuse
Util/exact_riemann/riemann_sample.f90
Util/exact_riemann/riemann_star_state.f90
commit 1514097bb1eccea2130b6eea93a7503029e82888
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Aug 7 11:02:59 2013 -0400
put this back in
Util/exact_riemann/GPackage.mak
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/inputs.test1.helm
commit 7422faafbdefaf6d8fea0e7472b4d505bb3b77e6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Aug 6 16:28:15 2013 -0400
new setup
Exec/Sod/inputs-test2-helm
Exec/Sod/inputs-test3-helm
Exec/Sod/probin-test2-helm
Exec/Sod/probin-test3-helm
commit 0d72dc0a743129d7ec9831a43a25a7796345c761
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Aug 6 16:23:34 2013 -0400
rename test -> test1
change stop time for test3
Util/exact_riemann/inputs.test.helm
Util/exact_riemann/inputs.test3.helm
commit 04ec8119a8a32424167e22ed3192d0579955dd4d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Aug 6 16:10:26 2013 -0400
rename
Exec/Sod/inputs-test1-helm
Exec/Sod/probin-test1-helm
commit 562fd39f27b706eb2b14929bd673c9f5d0a21a9f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Aug 6 15:26:02 2013 -0400
play with setting CASTRO_TOP_DIR
Util/exact_riemann/GNUmakefile
commit c2390d6eb2d71f2d995c00571deaab59af3d2ba9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Aug 6 15:09:36 2013 -0400
add README
Util/exact_riemann/README
commit 89f1c6e4650e4e7b182ce96530d4ee9417b397d6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Aug 6 15:06:42 2013 -0400
fix table linking
Util/exact_riemann/GNUmakefile
commit bbd758ee5be5c689f5948c5c7b1deb5218759fab
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Aug 6 15:04:55 2013 -0400
forgot a file
Util/exact_riemann/riemann_support.f90
commit d1498b1ee9aac707f8c942bc26ddd28edc96830f
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Tue Aug 6 15:03:21 2013 -0400
add an exact Riemann solver for a general equation of state, based
on CG 1985. This is not for running in the code directly, but instead
for generating exact solutions to the Riemann problem for comparison
to Castro output. This will be used in a forthcoming paper looking
at temperature behavior with helmeos.
Util/exact_riemann/GNUmakefile
Util/exact_riemann/GPackage.mak
Util/exact_riemann/_parameters
Util/exact_riemann/dummy.probin.template
Util/exact_riemann/exact_riemann.f90
Util/exact_riemann/inputs.sod-minus.gamma
Util/exact_riemann/inputs.sod.gamma
Util/exact_riemann/inputs.test.helm
Util/exact_riemann/inputs.test2.helm
Util/exact_riemann/inputs.test3.helm
commit ba5797d4456e194405966fe60caf0314ced33375
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Mon Aug 5 14:58:55 2013 -0400
sync the gravity source stuff up with 3-d -- previously there was no option `2', and we
hardcoded in gravity_source_type = 1
Source/Src_2d/Castro_grav_sources_2d.f90
commit 2e4991cae6f47cf03e203f4acbb9c6edb6f3808b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Aug 5 11:13:44 2013 -0700
The default grav_source_type is 2 now.
Source/Castro.cpp
commit 585cae6d058debe74bcf8b3a9160c41551ae63bf
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Aug 4 16:56:58 2013 -0400
OMP the CG Riemann solver
Source/Src_3d/riemann_3d.f90
commit 14005ce7e267eafcf02d7b37f04fe4d7ff238b3c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Aug 3 21:57:12 2013 -0400
get the CG Riemann solver working -- we do not include pgdnv in the
velocity fluxes in 2-d, since we need to worry about different geometries
and the difference between the div and grad when area factors come
into play. This seems to work well now.
Source/Src_2d/riemann_2d.f90
commit 68d7ba313e3daac8bd6d35da60bf4a9409436a62
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Aug 3 21:02:10 2013 -0400
add comment
Source/Src_3d/riemann_3d.f90
commit db33b7dfd088752b0a84635e1126604318088a63
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Aug 3 19:42:14 2013 -0400
some cleaning -- still doesn't seem to work right. Hmm....
Source/Src_2d/riemann_2d.f90
commit ab7ada01615c4186c0f982a01385af4c0fa14066
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Aug 3 19:14:16 2013 -0400
remove unused variables
Source/Src_2d/Castro_advection_2d.f90
commit cbc5d8fbb501860961d65b8b777e57519e33702f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Aug 3 16:22:53 2013 -0400
visualization info with yt from Noel
UsersGuide/Visualization/CastroVisualization.tex
UsersGuide/Visualization/LineQueryPlot_0_t_magvel.eps
UsersGuide/Visualization/LineQueryPlot_0_t_magvel.png
UsersGuide/Visualization/OffAxisProjection_density.eps
UsersGuide/Visualization/OffAxisProjection_density.png
UsersGuide/Visualization/Profile2D_1_Density_magvel_kineng.eps
UsersGuide/Visualization/Profile2D_1_Density_magvel_kineng.png
UsersGuide/Visualization/Slice_z_pressure.eps
UsersGuide/Visualization/Slice_z_pressure.png
UsersGuide/Visualization/isocontours.eps
UsersGuide/Visualization/isocontours.png
UsersGuide/Visualization/volume.eps
UsersGuide/Visualization/volume.png
UsersGuide/Visualization/yt_images.tar.gz
commit 4cf68dd235a437bc345daee3587304e437df92bf
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Aug 3 13:47:06 2013 -0400
start of getting the CG Riemann solver into 2-d. Doesn't seem to work
correctly yet, but want to get it in there.
Source/Castro.cpp
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/riemann_2d.f90
commit 20ab8091df731003e5f1168e1f2db55b6cc56ab4
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 2 21:22:51 2013 -0400
add comment
Source/Src_3d/ppm_3d.f90
commit c73f5f0fda00ba5325bc3d14a1aaf97c2dfa034f
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Jul 25 11:13:44 2013 -0400
forgot to check this in yesterday -- this removed k3d from the
interface (unused) + more comments
Source/Src_3d/riemann_3d.f90
commit dd1abd8ab13f36158ea5637be631f301a93007d6
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Jul 24 12:49:49 2013 -0400
add the ppm_temp_fix = 2 -- you don't want to use this!
Source/Src_3d/Castro_advection_3d.f90
commit 74c9f623b6408317b10766060323602766018d4e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Jul 24 10:43:56 2013 -0400
add ppm_temp_fix parameter -- this is EXPERIMENTAL -- DO NOT USE
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/estdt_burning_1d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/meth_params.f90
commit 5c4083b77bd3f9db208284a6275e677d51ec86f2
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Jul 23 11:05:27 2013 -0400
add tracing of the gravity under parabolas to the 2-d stuff. This is
for ppm_types = 1, 2 only
Source/Src_2d/trace_ppm_2d.f90
Source/Src_2d/trans_2d.f90
commit 6be2e89e2c5ca61d681e5d430a5ffa48f52162b6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Jul 23 09:44:17 2013 -0400
modify the interface of ppm_2d() to take separate index ranges for
s, the variable we are parabolizing, and u,c, the speeds for the
tracing. This will allow for gravitational tracing. This change
brings the code in sync with 3-d
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit 1352ee7f5ba7e54b7dc7f19d9de59537ba210710
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Jul 23 09:26:07 2013 -0400
bring grav into trace_ppm
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/trace_ppm_2d.f90
commit b59431fd293219cbdc5e7b44d5c116cf9e10d8f9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Jul 22 16:04:30 2013 -0400
fix the flattening with the new ppm reference state stuff -- this syncs us up with
the 3-d code.
Source/Src_2d/trace_ppm_2d.f90
commit 36b86bcb6af7c0bed0d9918bc6ec568f3d48a56d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Jul 22 15:29:07 2013 -0400
add a convergence check for the Colella & Glaz Riemann solver
Source/Src_3d/riemann_3d.f90
commit a83d46c0967607f5dc55f2ef397581e854779a4d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Jul 22 15:10:53 2013 -0400
mostly comments, some simplifications and commenting out of unused stuff
Source/Src_3d/riemann_3d.f90
commit 8a21cd689e01701ec209dd9deddd8fd29138f388
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Jul 21 11:17:57 2013 -0400
sync up 2-d with the recent changes
Exec/Sod/Prob_2d.f90
commit eac1fc2507f5fa98b9a3ea10add315109f4193d9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Jul 21 11:07:14 2013 -0400
sync up with 3-d
Exec/Sod/Prob_1d.f90
commit afb87e164f7ce0483d512815a89a6c24ce07b4d7
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Jul 21 10:56:49 2013 -0400
add the ability for T, not p, to be specified as input
Exec/Sod/Prob_3d.f90
Exec/Sod/probdata.f90
Exec/Sod/probin-test-helm
commit a607d1efda1512d05c3f4cc3b941d44532375eb0
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 21:16:01 2013 -0400
again -- make it gamma_law_general
Exec/Sod/GNUmakefile
commit ba44f839b361da1d4e75c374adf51626320eb8e9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 19:37:29 2013 -0400
update 3-d to work with a general equation of state
Exec/Sod/Prob_3d.f90
Exec/Sod/inputs-test-helm
commit eaf95b15a0f4405b6aebef4d79e5475dc2cf3333
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 18:51:36 2013 -0400
switch back to gammalaw.net for the test suite
Exec/Sod/GNUmakefile
commit e007736d2395b81a57fc362be675f2179ef45a0f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 18:51:16 2013 -0400
initialize all species
Exec/Sod/Prob_1d.f90
commit 70cf2809745c1f892e880999784334fff3913fe9
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 18:13:12 2013 -0400
switch back to gamma_law_general for the test suite
Exec/Sod/GNUmakefile
commit 4ad7d5b5f25c486a4162fadac46f5152849690e7
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 16:56:04 2013 -0400
inputs file for the helmholtz "Sod" problem
Exec/Sod/GNUmakefile
Exec/Sod/inputs-test-helm
Exec/Sod/probdata.f90
Exec/Sod/probin-test-helm
commit 5599b37438ce2eb69ae98e20869f8ed886ff0f8f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Jul 20 16:55:05 2013 -0400
convert this to allow for a general (non-gammalaw) EOS.
Exec/Sod/Prob_1d.f90
commit aeb2994f5977ea90520376017a6ad8c45e0d2a50
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Thu Jul 18 12:54:52 2013 -0400
add a check on whether we are running with ppm_trace_grav = 1 and
ppm_type = 0 -- that doesn't do what you'd think it would do.
Source/Castro.cpp
commit 8eb96b1bc17f183b797cde6f235a6d3bbc200b67
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jul 8 15:47:56 2013 -0700
In deriving vorticity, abs function is unnecessary
Source/Src_3d/Derive_3d.f90
commit 3d83b3012b427d0aa8e64340428529e3223e10cd
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Jun 27 16:03:28 2013 -0700
Radiation solvers need one ghost in state data
Source/Castro_setup.cpp
commit ccc0818f9f3b574c50d02ef483cd0efca47f2e80
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date: Wed Jun 26 11:05:55 2013 -0700
Removed some trim() calls on string comparisons.
Networks/general_null/network.template
Networks/ignition_simple/network.f90
Util/model_parser/model_parser.f90
commit dc580e32131de2d257baaba27666886cfdba76fa
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 24 16:23:14 2013 -0700
avoid filling non-valid cells in the initial setup
Exec/Sedov/Prob_2d.f90
commit 463135b5df1d38c8c0cce94c3aa9f2557bbd95cb
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Jun 24 15:58:56 2013 -0700
no ghost cells are needed for StateData
Source/Castro_setup.cpp
commit ad1af7c4b17c544934a0ae99b1505cc2cd03b845
Author: Chris Malone <malone@ucolick.org>
Date: Wed Jun 19 10:49:25 2013 -0700
intel didn't like array passing to IntVect, so just pass the values
Source/Gravity.cpp
commit 0f6aaf2dab7d22b6c537fd9914d66358926ba67c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 17 16:52:55 2013 -0400
Included a description of the direct sum option for the Poisson boundary conditions.
UsersGuide/Gravity/CastroGravity.tex
UsersGuide/Inputs/CastroInputs.tex
commit 052f77f6335c2d1d568a7a346b71252a9eb39e98
Merge: a5a056b7b bad428964
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jun 17 12:07:12 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit a5a056b7bd57c536c7ab94d02ce408b318f95c70
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jun 17 12:06:58 2013 -0700
Latest multipole / direct sum files from Max.
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
commit bad428964d96b6400a29f7d98ddee23c7e80457f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 13 18:38:28 2013 -0400
Added a description of the multipole boundary conditions now being used for the 3D Poisson solves.
UsersGuide/Gravity/CastroGravity.tex
commit 6338808d63a83b071048c821a86a187d69bf0348
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Jun 6 14:54:32 2013 -0700
Need to set mg_bc when Inflow face -- before this wasn't set.
Source/Diffusion.cpp
commit 7fc70fad807208cf2bac29821e8b42ed0e2fd240
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Jun 4 11:45:05 2013 -0700
Modified gravity routines that now use fill_multipole_BCs instead of
make_radial_phi in 3D only.
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
commit e72ecd0b14fe4a596845aba22edbafc19cd4b1cd
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed May 29 12:18:58 2013 -0700
Fix problem when BL_SPACEDIM != 3
Source/Gravity.cpp
commit 7be326c3184eeeb22548fa534cd486f9314d1cd8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 29 15:13:01 2013 -0400
Don't do multipole if we're in an octant/half-star geometry. This is determined by whether the problem center is near any of the domain corners.
Source/Gravity.cpp
commit 672ea0825d630c00970c2b4e10aca36a6e467ca6
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed May 29 10:11:39 2013 -0700
Put back in missing semicolon for BL_SPACEDIM < 3.
Source/Gravity.cpp
commit 05be5100748f8341bd6130aa63e70f50ee0c30f5
Merge: ad1d5ea83 56dc0c9f2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 29 12:08:52 2013 -0400
Merge branch 'multipoleBCs'
commit ad1d5ea83aaa76f65ea287ead6bfc007c27aad8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 29 11:48:23 2013 -0400
Forgot to include a file in that last update.
Source/Src_3d/prescribe_grav_3d.f90
commit d0f133ac099a78857a3d197c0272ec206cf435c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 29 11:44:36 2013 -0400
Removed instances where pi was typed explicitly and replaced with calls to bl_constants_module.
Source/Src_1d/Castro_sums_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Rotate_2d.f90
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_3d/Rotate_3d.f90
commit 91216413e6109e41afa5c2a9f1d7aa8881e960ce
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 28 17:49:58 2013 -0400
Fixed a bug where volProductSum was zeroing out phi.
Source/sum_utils.cpp
commit 56dc0c9f2adb89f13317a71a0211f10085d007df
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 24 13:50:54 2013 -0400
Added OMP to multipole loops.
Source/Src_3d/Gravity_3d.f90
commit 3c51e820ba0c3f7aced5c3ba0fc42a3a21a2cb33
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 24 11:45:09 2013 -0400
Generalize for arbitrary multipole orders using the recurrence relations for the Legendre polynomials. Hard-coded maximum is l = 50.
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
commit 310cdb6954f91c30d4678f94c6f91cd732615902
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 23 18:24:35 2013 -0400
Added multipole boundary conditions for Poisson gravity. This is a generalization of the previous monopole boundary conditions, and by default it reduces to a monopole calculation. This is changed by setting gravity.max_multipole_order to some integer in your inputs file, where the integer determines the maximum value of l that is used in the multipole expansion. Currently the limit is hardcoded at lmax = 5. This commit only includes the version for 3D Cartesian coordinates.
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_3d/Gravity_3d.f90
commit 58015b5bb57217d340ce76155dfc26fd25e93ffc
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Tue May 21 12:32:54 2013 -0400
more informative error messages (some had copy/paste errors)
EOS/helmeos/eos_stuff.f90
commit 2ef68633f992f597e5db15ba5cf2384d024c5700
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Mon May 20 16:26:41 2013 -0400
also bump up numpts_1d in 2-d
Source/Castro.cpp
commit 8f49b2f354e601d0b416117249b8c5595205c560
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Mon May 20 16:25:04 2013 -0400
add a ghost cell to grav_vec (now 4). This allows for the tracing to work,
and brings us in line with the original PPM paper. Note that I also
needed to bump up numpts_1d from int(sqrt(ndiagsq))+6 to int(sqrt(ndiagsq))+8
Source/Castro.cpp
Source/Castro_advance.cpp
commit 9391c4fd485fda6970042962be6757d6013ca1c3
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Mon May 20 16:11:48 2013 -0400
remove debug print
Source/Src_3d/ppm_3d.f90
commit 2705f94962f9ab987ac7adda472b8307e4245792
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun May 19 20:48:20 2013 -0400
start of the tracing of the gravity after doing a parabolic reconstruction. This is enabled via ppm_trace_grav.
3-d only so far, and .... it doesn't work right now because of a ghost cell issue. By default, this shouldn't
change anything, so it's in here for sharing.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
Source/meth_params.f90
commit b813b843bbde1a8107fb57e76328cc7352258314
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 14 08:30:18 2013 -0400
Fixed an issue where the energy diagnostics were falsely reporting a small negative density correction when OpeMP is enabled.
Source/Src_3d/Castro_advection_3d.f90
commit f0f16d2f3979c2f58ea7b035fe50d04374859b00
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon May 6 19:40:26 2013 -0400
use ppm_reference = 1 as the default now
Source/Castro.cpp
commit 30bf9e45c2b1c466944f0ee0a1b2e98a49dd3f12
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sat Apr 20 22:05:09 2013 -0400
add rho_K_contrib to the OMP private stuff -- only affects things
with OMP and SGS
Source/Src_3d/riemann_3d.f90
commit 960da15ec17e550e386ea6f33fc087da58d8223b
Merge: 662db0861 fb458a449
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Apr 18 14:23:52 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit fb458a449a52f9fef0e8ce061c4afe8bd52d9b9f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 18 13:41:58 2013 -0700
Fix interface to subroutine ppm in 3d.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/ppm_3d.f90
commit 662db086144194e6b1f21e02403d21ff2f6ab5ea
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Apr 16 10:09:41 2013 -0700
option to save both lambda and flux for SGFLD
Source/Castro_setup.cpp
commit a189018ca5c66940c2721723399b7e2a864b4f44
Merge: 6c156a9c6 090e6b33d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Apr 12 13:57:39 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 6c156a9c6825053e81355bf704b351c6705d5317
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Apr 12 13:55:59 2013 -0700
Forgot to add xi,xi1 to the OMP directives.
Source/Src_3d/trace_ppm_3d.f90
commit 090e6b33d8243f84d885a33b9dbd56d0094768d6
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Apr 12 14:43:25 2013 -0400
rmeove unneeded params
Source/Src_2d/compute_temp_2d.f90
commit fba0070339a4071083fb0880b60645fea512dd4e
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Apr 12 14:28:27 2013 -0400
add a comment`
Source/Src_2d/Castro_advection_2d.f90
commit 374cefe16278165cf469bd872ddd566db6d13c18
Merge: 100a3af44 7421f0de0
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Apr 12 10:53:00 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 100a3af4485514f9a1385523461eab0e404bcc88
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Apr 12 10:52:45 2013 -0700
Fix the reference state stuff so it is now correct.
Source/Src_3d/trace_ppm_3d.f90
commit 7421f0de01b0aa8e57f89db383c49ba979492f86
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Apr 12 11:13:32 2013 -0400
if we are 2-d, rotating, with axisymmetry, then carry along an
advected variable for the velocity through the plane
Source/Castro_setup.cpp
commit eada4bed3cc69417603c6349eb57124de4157b4d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Apr 11 22:47:11 2013 -0400
remove unneeded ivar argument
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/ppm_3d.f90
commit a9a435143c03c5ab8e3d0496230a33a362ae32ac
Merge: c41418648 a1b171734
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Apr 11 20:24:45 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit c414186480cf0d21dcbfb41aaeae95625c902a6c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Apr 11 20:24:26 2013 -0400
add a tracing option for debugging
Exec/Make.Castro
commit a1b171734cea4e1ce388b310050ae29fc220122e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 11 15:34:12 2013 -0700
More cosmetic clean-up so it looks more like Nyx.
Source/Src_3d/trace_ppm_3d.f90
commit cc2efb87ad7c64497bbddd3202d9aaa7d7331c09
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 11 14:57:00 2013 -0700
Add more comments.
Source/Src_3d/trace_ppm_3d.f90
commit 933c482ec147d08a4356d7f655330ba696157ee6
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 11 14:13:54 2013 -0700
Clean up of trace_ppm and trans routines so that the Castro and Nyx routines
look much more similar.
Source/Src_3d/trace_ppm_3d.f90
Source/Src_3d/trans_3d.f90
commit 728ae70791263e261d092441c59ead99afcceea3
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 11 13:43:32 2013 -0700
Clean up trans routines in the same way Nyx has been cleaned up,
i.e. put all the passively advected quantities together ...
Source/Castro_setup.cpp
Source/Src_3d/trans_3d.f90
commit 918c7b81f2cae2a497d66303f38ce35a35720c66
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 11 11:32:04 2013 -0700
Move trans* subroutines into a separate file.
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/trans_2d.f90
commit 0fbfefd1e869fb4e5b242a0d2345dc6753d2f6a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 11 11:30:32 2013 -0700
Move the trans* subroutines into a separate file (trans_3d.f90).
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/trans_3d.f90
commit d81ceea0080856f045596ad16d245db3b2775f9b
Merge: 6ff77833e a3a91eb67
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 4 12:47:58 2013 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 6ff77833ea0696e410f32ecebc201e9f18d3c04a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Apr 4 12:47:41 2013 -0700
Fix comments about sphericity for Poisson ...
UsersGuide/Gravity/CastroGravity.tex
commit a3a91eb6744d042bdd4015ebd049c29e62ec01f1
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Mar 15 16:37:22 2013 -0400
some cleanup on the way NumSpec, NumAux, and NumAdv are handled. Previously,
the assumed that there were NumX >= 2. Now it works more generally. Also,
remove the LastX pointers -- they were never used. The incrementing
of cnt is now also much cleaner.
Source/Castro.H
Source/Castro.cpp
Source/Castro_setup.cpp
commit ec4ef5099db5553aeece5522eac9e3346e60718e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Mar 15 15:39:28 2013 -0400
fix a comment
Source/Castro_setup.cpp
commit d0ee24fe466291f1d15a3ee6b855c505bf2a134e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Feb 22 20:28:17 2013 -0500
we were aborting if const_grav was set with RZ -- but this should be
fine -- by default the constant gravity direction is in the last
dimension, which is z -- this is an axisymmetric domain with vertical
gravity. This works well for plane-parallel geometries.
Source/Gravity.cpp
commit 31ea8e307695956d3642f1006799366aea5f13e5
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Feb 22 20:24:49 2013 -0500
add const_grav to meth_params_module -- often we want the constant
gravitation acceleration when setting up BCs or initial models in
Prob_?d.f90 -- this makes it so...
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit dc17f08f36c06ccfe8a3131df85ea6b225a95a75
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Feb 15 15:01:10 2013 -0800
Add castro.allow_negative_energy to all inputs files that use
gamma_law_general.
Exec/KH/inputs.2d
Exec/KH/inputs.3d
Exec/RT/inputs_2d
commit 471832d00d8bb85df91b1f8a996f94c06e839f60
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Feb 15 14:59:12 2013 -0800
Add castro.allow_negative_energy = 0 to all inputs files in Sod.
Exec/Sod/inputs-sod-rt1
Exec/Sod/inputs-sod-rt2
Exec/Sod/inputs-sod-rt3
Exec/Sod/inputs-sod-x
Exec/Sod/inputs-sod-y
Exec/Sod/inputs-sod-z
Exec/Sod/inputs-test2-1d
Exec/Sod/inputs-test2-x
Exec/Sod/inputs-test2-y
Exec/Sod/inputs-test2-z
Exec/Sod/inputs-test3-x
Exec/Sod/inputs-test3-y
Exec/Sod/inputs-test3-z
commit bc2c27e47ddcb6fffdd0edf8787e217b114d0222
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Feb 15 14:56:21 2013 -0800
Add castro.allow_negative_energy = 0 to all the inputs files.
Exec/Sedov/inputs.1d.cyl
Exec/Sedov/inputs.1d.sph
Exec/Sedov/inputs.2d.cyl_in_cartcoords
Exec/Sedov/inputs.2d.cyl_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.3d.cyl
Exec/Sedov/inputs.3d.sph
commit b9a5235c586c3e59fab9635f6f9ca297c15602ea
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Feb 14 13:19:38 2013 -0800
Remove file that should never have been committed.
Source/Src_2d/Gravity_2d.f90.new
commit 707717f6495e9e6e993ce8c5f9b9210970d08f10
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Feb 14 13:09:03 2013 -0800
We now do the best of both worlds for monopole gravity -- for
radii at which the mass (at that radius) is entirely contained
in the domain, we sum the mass of the cells. For radii at which
some of the mass is outside the domain, we switch to computing
the average density and then multiply that by what the volume
of the spherical shell should be.
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Gravity_nd.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90.new
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
commit 7f283eec98cb5670ce93890821637951bd3cca0c
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Feb 13 13:43:45 2013 -0800
Fix case when level == 0.
Source/Gravity.cpp
commit 158a96502e0eefb17e2e3429ba1bbaede508eb9b
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Feb 13 13:28:05 2013 -0800
New way of computing the monopole gravity so that we correctly account
for the mass near the coarse-fine interface. This version also retains
all the mass, but doesn't count in the monopole approximation any mass
which is outside the domain but "might" count if you were computing density
as a function of radius.
Source/Castro.H
Source/Castro.cpp
Source/Castro_io.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
commit e7467a359c0e0a03dc80edc75a4b4539ed769d2a
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Feb 11 10:38:19 2013 -0500
add a .gitignore
.gitignore
commit d4830eda32562c2c8cab4fec409acd003304d3b8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Feb 1 13:27:54 2013 -0800
#include <ctime> in Castro_io
Source/Castro_io.cpp
commit 71adbaaae4875f4cb269f5c5ed81f34645f1b751
Merge: f2944ba39 66706329d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Jan 24 14:20:38 2013 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit f2944ba3909ab261387c4fa13d2c20e62bcf7c47
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Jan 24 14:20:16 2013 -0500
add comments + some formatting changes
Source/Src_1d/ext_src_1d.f90
Source/Src_2d/ext_src_2d.f90
Source/Src_3d/ext_src_3d.f90
commit 66706329d5aff926f51ef9699e5c17d715a85df4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 24 12:11:18 2013 -0500
Adjusted some functions in sum_utils.cpp to be useable in 2D in addition to 3D, including sumlocmass2d.
Source/Castro_F.H
Source/Src_2d/Castro_sums_2d.f90
Source/sum_utils.cpp
commit 2af1126e2346e1d0932d80c79c3ebc2a7b2dd4b9
Merge: 5ba7fef3d f88f10182
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 23 16:06:37 2013 -0800
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 5ba7fef3d9479e8dc30b08f8edd23b9c40e91785
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 23 16:05:51 2013 -0800
Fixed a string in a bl_error call.
Source/Src_3d/trace_ppm_3d.f90
commit 3408a005b323fbdc60dfed6972cd9ae05a07a12e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jan 23 16:04:19 2013 -0800
Fixed a minor bug when #ifdef RADIATION is true and do_radiation is false.
Source/Castro.cpp
commit f88f10182b913eadf124ee392e2b3795732795f4
Author: Chris Malone <cmalone@lanl.gov>
Date: Wed Jan 23 10:04:09 2013 -0800
updated compiler information for cray 8.1.2
UsersGuide/Suggestions/Suggestions.tex
commit a21d3d0906c0c7f7ba2f46ca908b2a1ee66bfc71
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 8 12:30:59 2013 -0800
minor
Source/Castro_advance.cpp
commit e94924cd24a852ba2ae87e3f2e5fbfdf104859dc
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 8 12:28:55 2013 -0800
Fixed a minor bug in nan detection
Source/Castro_advance.cpp
commit de646df3a34f14552c40b787c1e7ebfc33ea15c6
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Jan 8 09:48:02 2013 -0800
Changed the way to make sure dx = dy = dz.
Source/Castro.cpp
commit aebb403389f2e71b0b8bceb754e1f69cc4d6c33c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 4 13:07:52 2013 -0500
Added locWgtSum2D function to sum_utils; this is useful for calculating a sum weighted in two directions in a 3D space, e.g. angular momentum. Added corresponding routine in Castro_sums_3d.f90.
Source/Castro.H
Source/Castro_F.H
Source/Src_3d/Castro_sums_3d.f90
Source/sum_utils.cpp
commit c188dfd086f5ccae5d6fba36a50c43f969549511
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 31 14:32:36 2012 -0500
and problem_restart now has the dir
Source/Castro_io.cpp
Source/Problem.f90
Source/Problem_F.H
commit 7c5a3f7979998d18b76b618e4a3d07a99f34da64
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 31 14:27:08 2012 -0500
more problem_checkpoint() stuff -- successfully pass through the checkpoint dir name
Source/Castro_io.cpp
Source/Problem.f90
Source/Problem_F.H
commit cc593a13623672ae20b8d338f9de60244aad6977
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 31 13:40:21 2012 -0500
add a problem_checkpoint() and problem_restart() routine that
is called from Castro_io.cpp at checkpoint and restart. This allows
problems to store problem-specific information needed for restart.
Note: checkpoint is called by the IO Processor only but restart
is called by all processors.
Source/Castro_io.cpp
Source/Make.package
Source/Problem.f90
Source/Problem_F.H
commit e0da422423fe21962c760e1f812a98909dc75c57
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Dec 21 18:48:42 2012 -0500
move the checkpoint, restart, and plotfile stuff into Castro_io.cpp -- starting to clean-up
Source/Castro.cpp
Source/Castro_io.cpp
Source/Make.package
commit a88f51979592faffbf7fe7d5ac66ddf2d61d6920
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Thu Dec 20 22:34:26 2012 -0500
add the elapsed CPU time since the start of the simulation to the
job_info file -- this is like in Maestro. The current elapsed
time is stored in chkXXXXX/CPUtime. It is calculated in the
code as numCores * (time since start of current run) + (time from restart file).
where numCores is the number of MPI * OMP, and the time from restart file
is what is read in from the chkpoint CPUtime file if we restarted.
This keeps the time cumulative between restarts.
Source/Castro.H
Source/Castro.cpp
Source/Castro_setup.cpp
commit 918d07d494de55e488b3a276a5e9980c38be434a
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Thu Dec 20 18:51:31 2012 -0500
comment
Source/Castro_setup.cpp
commit c3b342366b4da3a1d45aad8837e03dd8117991d8
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Thu Dec 20 14:49:22 2012 -0500
more job_info stuff -- now species info
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
commit e96b7f1fea60e6d14e23e369edc5f9e122679de3
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Thu Dec 20 13:37:35 2012 -0500
more job_info syncing with Maestro -- now output the grid info
Source/Castro.cpp
commit 1f71234ec50d40db5fc296b243b8522f2b986532
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Dec 12 10:36:44 2012 -0500
sync up with the 3-d tracing -- max the pressure edge state with small_pres
Source/Src_2d/trace_ppm_2d.f90
commit da5d76bcb9cf0be2a4d2650cce9dc793db9a0f19
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Dec 12 10:15:54 2012 -0500
add the ppm_reference stuff to 2-d
Source/Src_2d/trace_ppm_2d.f90
commit f936498d8f24816a280dbe69c52fc61d13c68d34
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Dec 11 14:25:10 2012 -0500
remove unneeded modules
Source/Src_3d/Castro_grav_sources_3d.f90
commit 19b4143122feea75c7d34f43cb896d5810812978
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Dec 11 13:26:20 2012 -0500
the colglaz logic was wrong -- there was a hardcoded parmeter that overrode
the value of use_colglaz_in
Source/Castro_nd.f90
commit 98b8990fc2bcf9a3b9e1368bee7672d3f70a9363
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Dec 11 13:22:54 2012 -0500
fix prototype
Source/Castro_F.H
commit 00b653cbcf0af7607b647f250a557b822e08edaa
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Dec 11 13:19:03 2012 -0500
make rot_freq a meth_param. Remove rot_freq from the argument list
in the Rotate_?d.f90 routines.
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_rotation.cpp
Source/Castro_setup.cpp
Source/Src_2d/Rotate_2d.f90
Source/Src_3d/Rotate_3d.f90
Source/meth_params.f90
commit 2547e19fcbccb0ad6f5d1b7c7a90eafdf5bc5aac
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Dec 7 13:55:14 2012 -0800
Made some subroutines public for radiation codes
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_advection_3d.f90
commit 6c5029fcaaae310d46ccb678c0c94ec45dcada05
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Dec 7 13:21:20 2012 -0800
Nothing has really changed except that all Fortran 90 procedures that
are not called from C++ live in modules now.
Exec/DustCollapse/sponge_3d.f90
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/Castro_grav_sources_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/ppm_1d.f90
Source/Src_1d/reset_internal_energy_1d.f90
Source/Src_1d/riemann_1d.f90
Source/Src_1d/slope_1d.f90
Source/Src_1d/sponge_1d.f90
Source/Src_1d/trace_1d.f90
Source/Src_1d/trace_ppm_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/ppm_2d.f90
Source/Src_2d/reset_internal_energy_2d.f90
Source/Src_2d/riemann_2d.f90
Source/Src_2d/slope_2d.f90
Source/Src_2d/sponge_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/ppm_3d.f90
Source/Src_3d/riemann_3d.f90
Source/Src_3d/slope_3d.f90
Source/Src_3d/sponge_3d.f90
Source/Src_3d/trace_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit b32162a9159a88d2cf43fa354e7029d0d56e50f5
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Dec 7 14:42:23 2012 -0500
fix the check on use_colglaz. Also put in a sanity check on ppm_reference
Source/Castro.cpp
commit 969c9777fdbb836ae04d5cfc460b2a1d809983e9
Merge: 56cec7f05 feb60e145
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Dec 7 14:39:13 2012 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 56cec7f05f0392a37450e5d9615187d3dd759033
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Dec 7 14:14:02 2012 -0500
comments + remove the jumps that are not actually used (like the transverse velocities
carried by the u-c and u+c waves). Also make ppm_reference = 2 -> 1.
Source/Src_3d/trace_ppm_3d.f90
commit feb60e145cf92c22545788c152467eba3a3612ad
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 6 15:22:51 2012 -0800
Fixed more mistaching argument bugs
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/sponge_1d.f90
commit 8ec35dbef0dc8f4e3ec83dfa8a546d9812950c5c
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 6 15:10:29 2012 -0800
Fixed a bug. An actual argument was missing
Source/Src_2d/Castro_advection_2d.f90
commit 085245b71a96b50fbada6e4439a9449cd6cf1236
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 6 14:54:27 2012 -0800
Fixed the intent of an argment. It should be inout instead of out.
EOS/gamma_law_general/eos_stuff.f90
commit 09480f325995438f77c8d9c4f338ffdf50c8fa37
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Dec 6 14:51:51 2012 -0800
Fixed a bug
Source/Src_1d/CastroCG_1d.f90
commit 5931a9fe3162bb8f2492f5aa39b125250de76bbe
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date: Thu Dec 6 13:20:15 2012 -0800
Calls to sponge() weren't matching the declaration. domlo & domhi are integers.
Changed the definition of sponge() to match.
Exec/DustCollapse/sponge_3d.f90
Source/Src_1d/sponge_1d.f90
Source/Src_2d/sponge_2d.f90
Source/Src_3d/sponge_3d.f90
commit 81dfb4cdef4cd8eea389f3e0c25d48e5e1a731f0
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Dec 4 13:12:46 2012 -0500
ppm_reference = 2 -- this is like 1, but it only sets the reference state
to the jump carried by the fastest moving wave IF that wave is actually moving
toward the interface. Doesn't seem to make a difference, but this should be
more correct.
Source/Src_3d/trace_ppm_3d.f90
commit 4a508354d94659d07a9db4770b67b1ed334396cf
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Dec 3 11:22:28 2012 -0800
Add one more OMP line.
Source/Src_3d/trace_ppm_3d.f90
commit ec35c10fa5d36532d13d2773fc01bd89fe60bb92
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 14:08:41 2012 -0500
make grav_source_type a runtime parameter. Also fix type = 2 so that
in the prediction, it does the same as type 1.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
Source/meth_params.f90
commit 2aff6e8b13ceac0b8fc979bfd58ebcab81d9ee92
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 14:01:07 2012 -0500
OMP fix
Source/Src_3d/trace_ppm_3d.f90
commit c07314b3a7ba1b12cb10fdb32b3f1053bef1137d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:42:47 2012 -0500
mainlined
Source/Src_3d/trace_ppm_3d.f90.new
commit e2a3501f11668b7c2da6d01a35aa799d911904dd
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:41:37 2012 -0500
if use_colglaz = 1, we now use the Colella & Glaz Riemann solver.
if ppm_reference = 1, we now use the jump carried by the fastest wave speed
as the reference state.
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit ff9c6dbfaed1d86834bf31d037c2918af47bc385
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:32:39 2012 -0500
use_colglaz now in 3-d!
Source/Castro.cpp
commit 201e115678446a712f0ab9962c505962ddd27c2f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:22:04 2012 -0500
add ppm_reference to allow us to play around with the ppm reference states
Source/Castro.H
commit e4d5503fca19e41c7e4b67e9bab67fe420f482c2
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:20:48 2012 -0500
add ppm_reference to allow us to play around with the ppm reference states
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/meth_params.f90
commit 335d0ed54f06e6d9fbb40c3d8f7c70810529cc57
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:13:28 2012 -0500
some bug fixes:
gamgdnv was defined wrong -- it should be based on game not gamc.
the eflux that was commented out is probably what we want, but it
had an extra rho factor.
one of the ustar states had the wrong wave speed (wl instead of wr)
Source/Src_1d/CastroCG_1d.f90
commit c5bab14e89d8e433b48892ad8e1454ef532c0607
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 13:03:04 2012 -0500
move riemannus into riemann_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/riemann_3d.f90
commit 63383b45ddb2910caa888f96302c37475289676c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 11:56:02 2012 -0500
a version of the PPM characteristic tracing that uses the largest
wave jump as the reference state
Source/Src_3d/trace_ppm_3d.f90.new
commit b0ea1cbc35549c27bdfb8a3a27339d99e548fa4f
Merge: 15c896e87 298ac0b05
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 11:55:06 2012 -0500
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 15c896e870e53916fbfa826d1b6a9ed62aeb707b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Dec 3 11:53:29 2012 -0500
a version of the Colella & Glaz Riemann solver. This is based
on CastroCG_1d.f90 in the Src_1d directory, but has a few bug fixes
and also don't rely on the gamma_e equation from C&G, but instead
computed gamma_e from the predicted rhoe. This seems to work, but
is not very well tested. Also, a better job needs to be done in
gmin and gmax.
Source/Src_3d/riemann_3d.f90
commit 298ac0b058910fdea074f0c4c4c671ac96dc97d2
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Dec 3 07:03:38 2012 -0800
Two small fixes to get the code to compile again.
Source/Castro_advance.cpp
Source/Src_1d/Castro_advection_1d.f90
commit 40e9721bdb4db2eef7f4c56ed019cf15fa47cfd8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 30 11:42:05 2012 -0800
Clean up energy diagnostic print statements.
Source/Castro.cpp
commit d645717eeed6d2726dc5f05c3052e6a42ce2d242
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 30 11:28:16 2012 -0800
Clean up energy diagnostics.
Source/Castro_advance.cpp
commit 6994345bed7a34fbcceb8ec024acca3988044f9d
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 30 11:13:43 2012 -0800
Add use_pslope as an option and split out the tracing routines into
separate files.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/ppm_2d.f90
Source/Src_2d/trace_2d.f90
Source/Src_2d/trace_ppm_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/trace_3d.f90
Source/meth_params.f90
commit 2f6c9179e8251a2688bbe43ea66ce377a703844f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 30 10:00:24 2012 -0800
Clean up cout statements re energy added, and add another option to
correct_gsrc.
Source/Castro.cpp
Source/Castro_advance.cpp
Source/Src_3d/Castro_grav_sources_3d.f90
commit a9de48462c68fcf8b58f99ac047c3524117a3197
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Nov 29 15:08:12 2012 -0800
Added diagnostic to print mass/eint/eden added in enforce_minimum_density routine.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
commit f3d32090b30b6257f3eacc0e7cd787f08868cd95
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 13 12:11:44 2012 -0800
inputs file for regression test
Exec/DustCollapse/inputs_3d_monopole_regtest_restart
commit f3f18163460bff687e2ac829c86ea181a7a941e3
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Tue Nov 13 12:08:44 2012 -0800
CASTRO_DIR is now set in GNUmakefile in each Exec/* directory. If it is not set in the GNUmakefile, the CASTRO_DIR environment variable will be used.
Exec/DustCollapse/GNUmakefile
Exec/KH/GNUmakefile
Exec/Make.Castro
Exec/RT/GNUmakefile
Exec/Sedov/GNUmakefile
Exec/Sod/GNUmakefile
commit b753d33b7e68bd6ee0239e7b2de5540628102604
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Nov 12 11:56:29 2012 -0800
Wrap the cout statements in test for IOProcessor
Source/Castro_advance.cpp
commit f7e06ef41d892cefa47870704a268560f8dc0bd8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Nov 10 14:30:38 2012 -0800
Updated so that everything now compiles (I think)
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Src_1d/Castro_sums_1d.f90
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Make.package
Source/sum_utils.cpp
commit 0caef3687f881873cf73e9a230e7e6cd7f943fd1
Merge: 1742b5398 4cc31c264
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 9 17:58:59 2012 -0800
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 1742b539825c5bf6038f745ad648bf20e5cbf552
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 9 17:58:44 2012 -0800
Make everything compile with DIM = 1, 2 or 3.
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_1d/Castro_advection_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/sum_utils.cpp
commit 4cc31c2647d2563a6b7115ec447910c11309551c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Nov 9 20:02:53 2012 -0500
Changed tags so that volProductSum can still be used even without gravity enabled.
Source/sum_utils.cpp
commit e2068afc6de138019a726c5af111fd26d6e0ab16
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 9 16:33:35 2012 -0800
Update to strip gravity source term routines out of Castro_advection_*d.f90
and put into separate file. Also pass E_added out of several routines.
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Src_2d/Castro_grav_sources_2d.f90
Source/Src_2d/Make.package
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_grav_sources_3d.f90
Source/Src_3d/Make.package
commit 3263358efeb490dc91eb94f0a1211ddc649186d4
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 9 16:08:32 2012 -0800
1) Fix the volWgtSumMF to actually use the component we pass in.
2) Use volWgtSumMF to compute the total energy change due to reset_internal_energy.
Source/Castro.cpp
Source/sum_utils.cpp
commit 766dda7cf48d4e79a91f81140adcb2c1af1cf55f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Nov 9 15:47:03 2012 -0800
Strip routines out of sum_integrated_quantities.cpp and put into
sum_util.cpp
Source/Castro.H
Source/Make.package
Source/sum_integrated_quantities.cpp
Source/sum_utils.cpp
commit 651027e9ed55c152d2abebab1b1236157319fb7d
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Fri Nov 9 17:35:14 2012 -0500
missing end directive
Source/Src_3d/Castro_sums_3d.f90
commit 80e4c3b769be2428515af8b15c29438adf9f7aaf
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 5 14:36:13 2012 -0800
The default for tolerance of Poisson gravity solver will depend on the
type of coordinates.
Source/Gravity.cpp
commit f757ca8b25c16c6fe8152ef7960c1f4da1284f33
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Nov 5 14:01:01 2012 -0800
Change the default tolerance for Poisson gravity solver from 1e-12 to
1e-9 because of the change in BoxLib MG solver.
Source/Gravity.cpp
commit 85b41d26b75ff51e91ced19f912ad763e036f1a3
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Oct 29 14:23:43 2012 -0700
Need this to go with new routines in Castro_sums_3d.f90
Source/Castro_F.H
commit f0b18cd1a8e54ee0661e9e70d32fd795f15918b9
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Oct 29 14:01:27 2012 -0700
1) Max tweaked Gravity_nd.f90 to get bc's for phi right in outermost cell.
2) Added two new functions to Castro_sums_3d.f90
Source/Gravity_nd.f90
Source/Src_3d/Castro_sums_3d.f90
commit 185f15eaed139d6168c6171ea95ae416ed848991
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 26 14:43:34 2012 -0700
include ctime in order to compile on Hopper (with PGI?)
Source/Castro.cpp
commit 563144b54f4219c02c703efdf764eee4099e15ca
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Oct 26 13:49:31 2012 -0400
fix up sponge interface
Exec/DustCollapse/sponge_3d.f90
commit 5c10b54c65f518204efa2ae9c6b537ab3e96e4c8
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Oct 26 13:44:08 2012 -0400
add time to the sponge argument lists -- now everyone should be happy
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/sponge_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/sponge_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/sponge_3d.f90
commit b631f1f3b9eb69dfb1cca1f4356faa7eb53232b1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 26 10:13:52 2012 -0700
More precision for XGraph1d files
Util/plot1d/XGraph1d.cpp
commit b9047b555a3cab365fc566bd4c50dd6aed74a725
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Oct 26 10:13:35 2012 -0700
Fix argument list
Exec/DustCollapse/sponge_3d.f90
commit 1f6361d44fce88c3db1e5d96afbe169009126883
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Oct 26 09:43:09 2012 -0400
fix argument list
Exec/DustCollapse/sponge_3d.f90
commit e1939410b5f90023fefc29d400a190261e67d656
Merge: bf7178c74 6e7b8b47f
Author: Michael Zingale <zingale@hopper08.(none)>
Date: Thu Oct 25 18:19:47 2012 -0700
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit bf7178c74cb42160db4ce7da5db0318e05db024f
Author: Michael Zingale <zingale@hopper08.(none)>
Date: Thu Oct 25 18:19:16 2012 -0700
pass dx and domlo/hi into the sponge so we can sponge based on coordinate
info
Source/Src_1d/Castro_advection_1d.f90
Source/Src_1d/sponge_1d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/sponge_2d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/sponge_3d.f90
commit 6e7b8b47f10b03cceae6871244bc26692c1280c0
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Oct 25 12:07:22 2012 -0700
This fix to Gravity_nd.f90 by Max Katz ensures that the gravitational potential,
phi, has the right absolute magnitude. This should not change the values
of g, but will result in an offset of previously computed values of phi.
Source/Gravity_nd.f90
commit 99d0a03786f1f3e97675f221404d53fb66d67221
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Oct 17 10:31:41 2012 -0700
Make difmag an input parameter. The default value is still 0.1.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
commit f6137f1ce6673f6b35b08f626e405e13bb23d26e
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Tue Oct 16 13:59:46 2012 -0400
switch this over to approx8 and set it up so we seem to get a decent
detonation going.
GNUmakefile
inputs-det-x
commit 01016e714f031f490acd2e4902020f5839364e4f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Thu Oct 11 18:17:07 2012 -0400
safety -- enforce dx = dy = dz
Source/Castro.cpp
commit b5cd13377151a588671ddffeae55ff36110c046a
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Oct 1 14:15:24 2012 -0700
When USE_RAD, allow a test to have network inputs in its own directory
Exec/Make.Castro
commit fecaef11b296fcf899d608c91685788e1556661c
Author: vince <vebeckner@lbl.gov>
Date: Mon Oct 1 14:09:12 2012 -0700
remote permissions test 1 for automatic battra update.
ConvertCheckpoint/README
commit 38029449bc98035864bc6408b1d59d5a1e08cfac
Author: vince <vebeckner@lbl.gov>
Date: Mon Oct 1 14:05:50 2012 -0700
remote permissions test for automatic battra update.
ConvertCheckpoint/README
commit eecaea54eef4058b008ac46bd7936a8011646909
Author: vince <vebeckner@lbl.gov>
Date: Mon Oct 1 13:49:35 2012 -0700
test 1 for automatic battra update.
ConvertCheckpoint/README
commit da2893196b52a6f5d45d3f077d7bc840f6ee8f81
Author: vince <vebeckner@lbl.gov>
Date: Mon Oct 1 13:43:22 2012 -0700
test 0 for automatic battra update.
ConvertCheckpoint/README
commit 3ff47d4bb8e37bc6d9de64dd5e39c3e9675f9d25
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 27 08:34:44 2012 -0700
Move diagnostic routines from AmrPostprocessing/F_Src/CASTRO_hydro
to Castro/Diagnostics/Sedov
Diagnostics/Sedov/GNUmakefile
Diagnostics/Sedov/fsedov1d.f90
Diagnostics/Sedov/fsedov2d_cart.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cartcoords.f90
Diagnostics/Sedov/fsedov2d_cyl_in_cylcoords.f90
Diagnostics/Sedov/fsedov2d_sph_in_cylcoords.f90
Diagnostics/Sedov/fsedov3d_cyl.f90
Diagnostics/Sedov/fsedov3d_sph.f90
commit 97882a720a781fff8eca820db7f49cba824d196a
Merge: c42a8d18d 5af66b3e4
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 27 08:33:28 2012 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit c42a8d18d1ee0d14784de2aa9b1f251dc91118aa
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 27 08:33:01 2012 -0700
New inputs files for regression testing.
Exec/DustCollapse/inputs_2d_monopole_regtest
Exec/DustCollapse/inputs_2d_poisson_regtest
Exec/DustCollapse/inputs_3d_monopole_regtest
Exec/DustCollapse/inputs_3d_poisson_regtest
commit 5af66b3e45ece980a9a2dfb5def32823ee3d29c5
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Mon Sep 24 17:42:01 2012 -0700
Fix Make.Castro for radiation
Exec/Make.Castro
commit 74edb9a752dbb38f0fbd174e59d8c95c5120ef14
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Sep 24 11:45:29 2012 -0400
clean up
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
commit 1a5d78e873733bb5b2b51849e7f018d43958afcc
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Sep 24 08:32:03 2012 -0400
another gamma issue. Also clean up formatting
Exec/RT/Prob_2d.f90
commit f80a4c2ba8ab0791d1b5869f2f658d93207f7fb2
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:49:29 2012 -0400
burner.f90 is for Maestro -- not needed here
Networks/general_null/burner.f90
commit 47615adb5c3b334b3184f4930b3abe096c5ee156
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:45:42 2012 -0400
remove null -- we should use general_null instead
Networks/null/Make.package
Networks/null/README
Networks/null/burner.f90
Networks/null/castro_burner.f90
Networks/null/network.f90
commit 8ab0d95484a48b9409dff857b22931841b293fad
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:45:18 2012 -0400
null -> general_null
Exec/DustCollapse/GNUmakefile
commit 34d9c5271a8fa11f28d6a1ce319c359d7e8167a2
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:37:52 2012 -0400
remove -- we should use general_null/gammalaw.net in its place
Networks/gammalaw/Make.package
Networks/gammalaw/burner.f90
Networks/gammalaw/castro_burner.f90
Networks/gammalaw/network.f90
commit e6e318c09f9ba990472b47243947d54c5b3f7af9
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:36:49 2012 -0400
gammalaw -> general_null
Exec/Sod/GNUmakefile
commit 1a764ffe21705f44ceca80b81d4bd0e6e6ce64b7
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:33:29 2012 -0400
gammalaw -> general_null
Exec/Sedov/GNUmakefile
commit 69e1c01de7925fa812f9121098ba2051993bb1d4
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 21:30:58 2012 -0400
remove gammalaw in factor of general_null
Exec/KH/GNUmakefile
commit 284da729016e54fb8e394a24bcf84d3f4547b7de
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 20:50:29 2012 -0400
use general_null network
Exec/RT/GNUmakefile
commit ee26ac51f2a6826c3b59a7dc4ec4a08a860181db
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 20:26:37 2012 -0400
a little more cleaning
Exec/RT/Prob_2d.f90
commit 259c4a2a1ede5a0b5e1f9630495cdbcb7daca7ec
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Sun Sep 23 20:17:44 2012 -0400
clean-up -- gamma was being used incorrectly
Exec/RT/Prob_2d.f90
Exec/RT/probdata.f90
commit cc601c49cb17e819f0616b6116abf1fe95566c1c
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date: Fri Sep 21 18:02:05 2012 -0400
Cleaned up some warnings from g++ and gfortran.
EOS/helmeos/helmeos.f90
Networks/ignition_simple/castro_burner.f90
Networks/ignition_simple/f_rhs.f90
Source/Castro_advance.cpp
Source/Gravity.cpp
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/trace_ppm_3d.f90
commit a7084a3032255023c881549be19a40f7acf005a8
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Thu Sep 20 17:28:07 2012 -0700
Please ignore this commit! Just a test
Exec/Make.Castro
commit e5bd437ab807c62e6100949755c4b4ffd867b5ee
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 20 12:38:01 2012 -0700
Finish the x_ctr --> center_x modification.
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/probdata.f90
Exec/DustCollapse/sponge_3d.f90
commit 3b56435ddcd165bd1da3c0167849104059220b8e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 20 11:11:40 2012 -0700
We forgot to multiply by cell volume when accumulating the mass for monopole gravity.
Source/Src_3d/Gravity_3d.f90
commit 1427ac4bfc61103175694d1ac5d2f8e2d9c9b0d6
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 20 10:24:59 2012 -0700
Forgot to use octant_factor after defining it in 3d monopole.
Source/Src_3d/Gravity_3d.f90
commit de9a1f94dba5ae10c7c31707d40262101eb71671
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Sep 20 09:27:31 2012 -0700
Didn't mean to have USE_GR = TRUE in the GNUmakefile, that was just
for testing.
Exec/DustCollapse/GNUmakefile
commit 345b00e9a62d9173ef30d2e386495fbdb032e44f
Author: Regression Tester account <regtester@battra.(none)>
Date: Wed Sep 19 18:16:51 2012 -0700
Use relative path to Castro dir in GNUmakefile
Exec/DustCollapse/GNUmakefile
Exec/DustCollapse/inputs_2d_regtest
commit 9f0c6670d3b2d1f79c14e6e2e1d8426ce041d444
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 19 15:00:31 2012 -0700
Move RT problem from Castro_Exec to the release version of Castro.
Exec/RT/GNUmakefile
Exec/RT/Make.package
Exec/RT/Prob_2d.f90
Exec/RT/inputs_2d
Exec/RT/probdata.f90
Exec/RT/probin
commit 0f70e1ba97f18ad07d23c981fc3f09a98e4c7e65
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 19 14:42:46 2012 -0700
We are changing the way we do the monopole gravity -- we now sum the mass
into bins rather than summing mass, creating a density profile, then
multiplying by the volumes of the spherical shells. In the previous case
we could lose mass when the mass was highly concentrated. This new form
guarantees we account for all the enclosed mass.
Source/Gravity.cpp
Source/Gravity_F.H
Source/Gravity_nd.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_3d/Castro_sums_3d.f90
Source/Src_3d/Gravity_3d.f90
commit ec82d56bf7024e3e554bc5e969da3daae6ffc5cf
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 19 14:41:58 2012 -0700
Clean up the new DustCollapse problem and diagnostics.
Diagnostics/DustCollapse/README
Diagnostics/DustCollapse/analytic.txt
Diagnostics/DustCollapse/fdustcollapse1d.f90
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Exec/DustCollapse/GNUmakefile
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/inputs_1d
Exec/DustCollapse/inputs_2d_octant
Exec/DustCollapse/inputs_3d_fullstar
Exec/DustCollapse/inputs_3d_octant
Exec/DustCollapse/inputs_3d_regtest
Exec/DustCollapse/make_1d_results
Exec/DustCollapse/make_2d_halfstar_results
Exec/DustCollapse/make_2d_octant_results
Exec/DustCollapse/make_3d_fullstar_results
Exec/DustCollapse/make_3d_octant_results
Exec/DustCollapse/results_1d.txt
Exec/DustCollapse/results_2d.txt
Exec/DustCollapse/results_3d.txt
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_3d/GR_Gravity_3d.f90
commit 66eb9005fbccb25bcd50ab731e02b6e7b7a4a682
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Wed Sep 19 13:11:38 2012 -0700
Add Exec/DustCollapse as new sample directory, and add Diagnostics/DustCollapse as
the tools needed to analyze the plotfiles in Exec/DustCollapse.
Diagnostics/DustCollapse/DustCollapse.gp
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Exec/DustCollapse/GNUmakefile
Exec/DustCollapse/Make.package
Exec/DustCollapse/Prob_1d.f90
Exec/DustCollapse/Prob_2d.f90
Exec/DustCollapse/Prob_3d.f90
Exec/DustCollapse/README
Exec/DustCollapse/inputs_1d
Exec/DustCollapse/inputs_2d_fullstar
Exec/DustCollapse/inputs_2d_halfstar
Exec/DustCollapse/inputs_3d_fullstar
Exec/DustCollapse/inputs_3d_octant
Exec/DustCollapse/probdata.f90
Exec/DustCollapse/probin.fullstar
Exec/DustCollapse/probin.halfstar
Exec/DustCollapse/probin.octant
Exec/DustCollapse/results_1d.txt
Exec/DustCollapse/results_2d.txt
Exec/DustCollapse/results_3d.txt
Exec/DustCollapse/sponge_3d.f90
commit 8fa2b82d3753e2533bc631640038b8133522df75
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 18 15:18:54 2012 -0700
Adding Diagnostics directory, with subdirectory DustCollapse. This
moves code out of AmrPostprocessing/F_Src/CASTRO_gravity. The change
to Diffusion.cpp only eliminates the print statement for the amount
of time spent in parmparse.
Diagnostics/DustCollapse/GNUmakefile
Diagnostics/DustCollapse/README
Diagnostics/DustCollapse/analytic.f90
Diagnostics/DustCollapse/fdustcollapse1d.f90
Diagnostics/DustCollapse/fdustcollapse2d.f90
Diagnostics/DustCollapse/fdustcollapse3d.f90
Source/Diffusion.cpp
commit 9706797ba678ce7ce98cbeeb4097c115ac9086df
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Sep 17 14:50:28 2012 -0400
add a note about the grav?fill routines
UsersGuide/Software/CastroSoftware.tex
commit fbf64d535cf29696b5a3cdc328f78e233412f19a
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Sep 13 16:34:04 2012 -0400
need the Problem(_F).H files in <>, not ""
Source/Castro.H
Source/Castro_F.H
commit 70f42e89dbfb76cfdb0a7936667d283f470dc31c
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Thu Sep 13 16:29:49 2012 -0400
add debugging capabilities
Exec/Make.Castro
commit 4c593ccf2336dc9d32e310f033bf4ae666750a54
Merge: 17a24dce3 d82df7775
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 12 15:05:46 2012 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 17a24dce31509ee7d9fe0226c02d5832bf4c29f3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 12 15:05:20 2012 -0400
wrap extern read output in IO processor
Source/Castro.cpp
commit d82df77753b3efee765968cc839cfb5b447ce299
Author: Marc Day <MSDay@lbl.gov>
Date: Wed Sep 12 10:50:07 2012 -0700
Move last writes to main
Source/main.cpp
commit 4024fcf66d30ffa0d8c95ba89b01effc1ac6c36e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 12 13:39:22 2012 -0400
make use_eos_coulomb a runtime parameter controlled by the extern namelist
in probin
EOS/helmeos/_parameters
EOS/helmeos/eos_stuff.f90
commit 7c506e3648ee42173e3641b0bdc296cc6076ab1c
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 12 12:36:13 2012 -0400
make eos_assume_neutral a runtime parameter instead of a hardcoded
parameter in eos_stuff.f90
EOS/gamma_law_general/_parameters
EOS/gamma_law_general/eos_stuff.f90
commit 170cfea63c7b22d760b6ed39bf01a8f87ea4bdf1
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 12 12:27:16 2012 -0400
gamma_law_general does not need use_eos_coulomb
EOS/gamma_law_general/eos_stuff.f90
commit 6ad55af82d5c0f59838e35417b3521955d0ff4e0
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Wed Sep 12 11:51:50 2012 -0400
hook in the extern runtime parameters.
Now if you put an _parameters file in any of the EOS, network, or
other microphysics directories (anything in EXTERN_CORE in Make.Castro)
then it will be added to extern_probin_module. This change now actually
calls the runtime_init() routine in extern.f90 to initialize the
runtime parameters. You can override the default values by adding
an &extern namelist section to your probin file -- if you don't do
this then we just stay with the defaults.
Source/Castro.H
Source/Castro.cpp
Source/Castro_F.H
Source/Castro_nd.f90
Source/Castro_setup.cpp
commit 3d8eddafb8d3856e52d27efcf92c5967e3559fa2
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Sep 11 14:25:16 2012 -0400
remote extranneous network_init() call -- it is already called
by Castro_setup.cpp
Prob_1d.f90
Prob_2d.f90
commit f15e83b731400d1b35c2f52e6eb49c74c694b7fd
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Sep 11 14:19:05 2012 -0400
network_init() was being called twice -- once in Castro_setup.cpp
and once in probinit. Remove the probinit version -- it is not
needed.
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
Exec/Sod/Prob_1d.f90
Exec/Sod/Prob_2d.f90
Exec/Sod/Prob_3d.f90
commit abd11dc7b38ee1d761dba923a3b5116347e4d5b9
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Sep 11 13:30:44 2012 -0400
Problem_F.H is a problem-specific header included in Castro_F.H
Source/Castro_F.H
Source/Make.package
Source/Problem_F.H
commit 6fa5fbb3c30d14c50966b5c9185c41872c8a433a
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Sep 11 12:48:12 2012 -0400
add a mechanism to allow problems to add to Castro.H without having
to drop a complete copy of Castro.H into the problem directory
Source/Castro.H
Source/Make.package
Source/Problem.H
commit 580f98cef1a96f216dceb9aefe8b5f049ce71194
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Sep 10 12:40:30 2012 -0400
fix sign convention on poisson equation to match what is in the code
-- add a note saying that it is the opposite convention from astro
UsersGuide/Gravity/CastroGravity.tex
commit 8294f312ff37ab390d3f67cf0b44ba8bc04b3093
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date: Fri Sep 7 15:48:09 2012 -0400
add castro.job_name runtime parameter -- this is a descriptive
string that will be output to the pltXXXXX/job_info file. Useful
for keeping things straight in parameter studies.
Source/Castro.H
Source/Castro.cpp
commit 6f479901f52a825fa4dc4d0a380509097498ffe2
Merge: 1da6eef23 cc7cfb3c1
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 4 12:54:15 2012 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 1da6eef23977e47f92412f81d531d6c24fb3eb76
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 4 12:53:50 2012 -0700
Remove print statement about subtracting mass_offset if is zero due to bc's.
Source/Gravity.cpp
commit cc7cfb3c1252284a917cfffba7ffb28d2a3d6b6d
Merge: 898b849ab 5cd3954c8
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Sep 4 15:41:04 2012 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 898b849abbc10077131e46f7513cb629616284b3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Sep 4 15:40:37 2012 -0400
styling -- may need to 'make clean' first.
UsersGuide/CastroUserGuide.tex
commit 5cd3954c8d43756f6dfa62722f582d033d8d3f2b
Merge: db59f7f97 183563d74
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 4 12:39:39 2012 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit db59f7f978fcf6a441a7bc7b209f68ebafc78ad7
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 4 12:39:17 2012 -0700
Fix ngrow in copyFrom call from extent_rad --> CPhi.nGrow()
Source/Gravity.cpp
commit 183563d7482bff6a21aca81e4c22415cba38d3f3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Sep 4 12:37:29 2012 -0400
some notes of the *fill routines
UsersGuide/CastroUserGuide.tex
UsersGuide/Software/CastroSoftware.tex
commit c30bb7add860725c354386b07edd925e8967f0a8
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Sep 4 11:48:10 2012 -0400
add stubs for describing adding a new problem -- need to figure some stuff
out first
UsersGuide/Software/CastroSoftware.tex
commit 24adcec66c4ce321f031a767b6d8bbbaef4ca1d3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 31 15:00:56 2012 -0400
add a close_model_file() function to clean up -- needed if we need to
read in multiple model files
Util/model_parser/model_parser.f90
commit 4fb66b5275038df977e9ca046c38847ac6d655d2
Merge: 8631099e6 48f728c37
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 31 13:02:03 2012 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit 8631099e632bae656e32243b1dc6727eb72bce85
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Aug 31 13:01:45 2012 -0400
needed for toy_convect
Networks/general_null/hotcno.net
commit 48f728c378271cf307b6375dad6bcc5702aa9f3f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Aug 29 14:13:49 2012 -0700
deleted old
Exec/Sedov/amrvis.defaults
Exec/Sod/amrvis.defaults
commit 2b38b93bde117f2db56b2fea17b531223c0cac98
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Aug 29 14:11:29 2012 -0700
renname
Exec/Sedov/amrvis.defaults.sample
Exec/Sod/amrvis.defaults.sample
commit 4790e837ce5f2c7dbd40ab7561a3de1561701f49
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Aug 13 14:36:15 2012 -0700
FPI needs to include NUM_GROW in define_tau
Source/Castro.cpp
commit 021a93caf40e695eb7f92b15b0f124e0e4d96405
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Aug 13 14:34:35 2012 -0700
tau needs NUM_GROW ghost cells for proper usage in react_first_half_dt
Source/Castro_advance.cpp
commit 66577874544315a0fe243f3623007615e7841755
Author: Chris Malone <malone@ucolick.org>
Date: Fri Aug 10 19:41:09 2012 -0700
after Ann's keen eyes looked at the code, she realized the calling sequence for react_first_half_dt was in conflict with its signature
Source/Castro_advance.cpp
commit 07d9a24d135d5fb542205aafe7d466dcb4a3a63d
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Aug 7 09:54:00 2012 -0400
add some comments
Source/Src_3d/Rotate_3d.f90
commit 26aef9113ef4a2ce108d73c406db3f5e6645c127
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Tue Aug 7 09:46:22 2012 -0400
fix typo in bl_error comment
Source/Src_3d/Rotate_3d.f90
commit 62ba0bf6efbde60408a7e1c50c2848108bdcab38
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Aug 1 21:07:33 2012 -0400
FillPatchIterator
UsersGuide/Software/CastroSoftware.tex
commit 30f1570b4f463e9c4954e318befb8599c1abefd9
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Aug 1 20:40:11 2012 -0400
add some notes about Castro data structures
UsersGuide/Software/CastroSoftware.tex
commit 3498147d485c01ba84967d160ffc1ebc2f3516ea
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Jul 30 15:33:08 2012 -0700
Add a static stencil_type to Gravity objects
Source/Gravity.H
Source/Gravity.cpp
commit 26f6fc9cc6b7015f6dd1fafa0e191779a86b8632
Author: Chris Malone <cmalone@lanl.gov>
Date: Mon Jul 30 13:30:26 2012 -0700
Give a stencil_type to a diffusion object
Source/Diffusion.H
Source/Diffusion.cpp
commit 9e1c0e7fa1d8077b7d8689f425d5540261c2a7f4
Merge: 908c78e4d 4891df06f
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jul 27 23:07:00 2012 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 908c78e4da67413b4c01c8f6eb482e8ad1672814
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jul 27 16:33:40 2012 -0700
Add git hashes to job_info file in plotfiles
Exec/Make.Castro
Source/Castro.cpp
commit 4891df06fd8275cbe68d52866c0c180cb05409df
Merge: 2379494e7 42df14321
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jul 27 14:31:10 2012 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 2379494e78878fe3e44ce4ab47f3ad3178dfb608
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jul 27 14:30:40 2012 -0700
Must now explicitly specify the stencil to be used in the multigrid solve.
Source/Gravity.cpp
commit 42df14321375acf872e7adbcf62eac412f334b51
Author: Regression Tester account <regtester@battra.(none)>
Date: Tue Jul 24 12:12:55 2012 -0700
inputs files for regression tests
Exec/Sod/inputs-sod-rt1
Exec/Sod/inputs-sod-rt2
Exec/Sod/inputs-sod-rt3
commit 5deeabacecca5abdb20dfdf205bbe5e59db23316
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Fri Jul 20 08:02:09 2012 -0700
change unistd.H to unistd.h so that it works on Linux
Source/Castro.cpp
commit 740c5f9b11856eb272a577fdb4cdf520b6dd88dc
Author: Chris Malone <malone@ucolick.org>
Date: Thu Jul 19 17:40:37 2012 -0700
added the unistd.h file; this was needed for the getcwd command on OSX
Source/Castro.cpp
commit c84be2f754090ec8cf5256eea08ab4c9085109a4
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 23:54:39 2012 -0400
store the EOS and network in job_info via aux{1,2}
Exec/Make.Castro
Source/Castro.cpp
commit 47e3d8b9a16e353867b48bec6137ba8123f16dee
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 23:39:10 2012 -0400
add COMP and FCOMP to the job_info file
Source/Castro.cpp
commit 92a9bbdfa213e493d68ee9919b6e7c7c3b323882
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 22:14:53 2012 -0400
if we are successful, then remove buildInfo.f90 -- this forces it
to be regenerated at the next build, to ensure that the build
information is always up to date
Exec/Make.Castro
commit 837bcd2ae7aeef54dd326efc9c82e33ab9e871ef
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 19:48:25 2012 -0400
remove buildInfo.cpp for 'make clean'
Exec/Make.Castro
commit c1c19fff5b9ad67cf16570585398026d3c01a1d3
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 19:40:25 2012 -0400
add build information to the job_info file -- note: buildInfo.cpp is
written at compile-time. You need to update your BoxLib for this to
work
Exec/Make.Castro
Source/Castro.cpp
commit 412ed9ba48872259f19e3e2282bedf2e01968af6
Merge: d17c3ce35 0dabe8780
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 17:12:13 2012 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/Castro
commit d17c3ce35b84ed8f14ecbcaf50e4c3e89324c8b0
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Wed Jul 18 17:11:29 2012 -0400
start of a job_info file a la MAESTRO. So far it has # of proc info,
output time and dir, and inputs parameters
Source/Castro.cpp
commit 0dabe87805221becac2544aa6dfddb85b4c7e61c
Author: Chris Malone <malone@ucolick.org>
Date: Mon Jul 16 10:08:47 2012 -0500
fpi --> Sfpi
Source/Castro_react.cpp
commit 7f1e88aabc252faf6a1f9097cca63e026c94f515
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jul 16 07:00:15 2012 -0700
Fix Castro_react.cpp
Source/Castro_react.cpp
commit da3032137fa7cb1b77e374a2eb028e5c356ac1c2
Author: Chris Malone <cmalone@lanl.gov>
Date: Wed Jul 11 12:28:59 2012 -0700
remove spurious parenthesis to get TAU-related code to compile
Source/Castro_advance.cpp
commit 10aa81a3fe25391f3b4974fc6a429f70805b0594
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jul 9 20:37:08 2012 -0700
Ok, this version seems to actually work with Strang-split reactions.
Source/Castro_advance.cpp
Source/Castro_react.cpp
Source/Src_1d/React_1d.f90
Source/Src_2d/React_2d.f90
Source/Src_3d/React_3d.f90
commit 1c4f7f52678e3b0b1e7e72aebff18b8385c7cd8a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jul 9 15:12:12 2012 -0700
Fix another oops in advance_no_hydro.
Source/Castro_advance.cpp
commit 288f2d3f67813c7730405a014efb0635bac98039
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jul 9 14:48:21 2012 -0700
Need to define ReactMF in advance_no_hydro.
Source/Castro_advance.cpp
commit 2476e0da4b15fd1a370dab7d60837d657b3ecc2a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Mon Jul 9 09:48:38 2012 -0700
Fix the calls to react_first_half_dt.
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 8d05dd32e6e2f22e040bb8d5f10ecd6d0b2d1945
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jul 6 13:11:26 2012 -0700
More fixing of the Strang splitting.
Exec/Make.Castro
Source/Castro.H
Source/Castro_react.cpp
commit e603677ed68ff69b74935d3666d1261da7aa76a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jul 6 12:39:08 2012 -0700
Fix the Strang splitting -- we must react the ghost cells as well as the
valid region in the first half-step.
Source/Castro.H
Source/Castro_advance.cpp
Source/Castro_react.cpp
commit 125986c903d4012f84fe15cd3539f3af4f3d4e09
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Jun 28 09:34:29 2012 -0700
Get the UserGuide to build again.
UsersGuide/CastroVerification/Verification.tex
UsersGuide/MAESTRO_restart/MAESTRO_restart.tex
UsersGuide/ManagingJobs/managingjobs.tex
UsersGuide/Software/CastroSoftware.tex
commit b847efcad4140910420087e01adc55210f78820a
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Jun 28 09:30:40 2012 -0700
Updated documentation to reflect new code structure.
UsersGuide/CastroVerification/Verification.tex
UsersGuide/ConvertCheckpoint/ConvertCheckpoint.tex
UsersGuide/MAESTRO_restart/MAESTRO_restart.tex
UsersGuide/ManagingJobs/managingjobs.tex
UsersGuide/Software/CastroSoftware.tex
UsersGuide/Visualization/CastroVisualization.tex
commit 97deeb1413519d279b78aa7b1a71b0b4a8fac8ca
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu Jun 28 09:22:00 2012 -0700
Updated UserGuide to reflect new code structure and the fact we get it from git
not from battra.
UsersGuide/GettingStarted/CastroGettingStarted.tex
UsersGuide/Software/CastroSoftware.tex
commit f0f1021ae6876079a7306b78c726018242dd0de4
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Jun 26 16:18:50 2012 -0700
Add CastroParticles.cpp and Castro_rotation.cpp and update Make.package.
Source/CastroParticles.cpp
Source/Castro_rotation.cpp
Source/Make.package
commit 447e17d3ac0ade6a17a3c264686cf9eea2a13f11
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jun 22 16:36:45 2012 -0700
Moved ConvertCheckpoint from CVS repo to git repo.
ConvertCheckpoint/Embiggen.cpp
ConvertCheckpoint/GNUmakefile
ConvertCheckpoint/Make.package
ConvertCheckpoint/README
ConvertCheckpoint/probinit.f90
commit 3b105ca2cb9e58e1c4ba895fcade5da6bb87693b
Merge: 4e4ffd26e 5ca3c4fb7
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jun 22 12:52:17 2012 -0700
Merge branch 'master' of gamera:/usr/local/gitroot/Castro
commit 4e4ffd26e571fe96c18906b73ef1cf360e30286f
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jun 22 12:52:06 2012 -0700
Define CASTRO_DIR...
Exec/Make.Castro
commit 5ca3c4fb735fcf75828434b762d8402e9d0d2e36
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Fri Jun 22 13:42:50 2012 -0400
triple alpha composition
Networks/general_null/triple_alpha_plus_o.net
commit afd1993387778dc996791bd43e76224e8fdefd64
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Fri Jun 22 13:15:09 2012 -0400
make it work with CASTRO_DIR
Networks/general_null/Make.package
commit 2f0ba250ad1460ddf4fdd8aec7217247f5da9c0c
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Fri Jun 22 16:59:52 2012 +0000
Fix up paths using CASTRO_DIR, EOS_HOME and NETWORK_HOME.
GNUmakefile
commit 05644825232176b20243fd24ba2d06b4a1440301
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date: Fri Jun 22 12:11:01 2012 -0400
fix loctions to use Castro tree
Networks/general_null/Make.package
commit 413d21ca86161535e2c0833da64b7d424fd5542b
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jun 20 15:50:13 2012 -0700
Minor update to test post-receive-email
UsersGuide/GettingStarted/CastroGettingStarted.tex
commit bd46480cdd6e2da18e887317ebe23fc5aa838cd1
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jun 20 15:12:24 2012 -0700
Fix comments for Network_dir
Exec/KH/GNUmakefile
Exec/Sedov/GNUmakefile
Exec/Sod/GNUmakefile
commit 203272c26289aa8f590e7b0d9f6ef78b1c259a4e
Author: WeiqunZhang <weiqunzhang@lbl.gov>
Date: Wed Jun 20 10:55:14 2012 -0700
Initial commit
EOS/Make.package
EOS/README
EOS/eos_type.f90
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/eos_stuff.f90
EOS/gamma_law_general/test/GNUmakefile
EOS/gamma_law_general/test/testeos.f90
EOS/helmeos/Make.package
EOS/helmeos/README
EOS/helmeos/eos_stuff.f90
EOS/helmeos/helm_table.dat
EOS/helmeos/helmeos.f90
EOS/helmeos/test/GNUmakefile
EOS/helmeos/test/testeos.f90
EOS/helmeos/vector_eos_f90.dek
Exec/KH/Castro_error.cpp
Exec/KH/GNUmakefile
Exec/KH/Make.package
Exec/KH/Prob_2d.f90
Exec/KH/Prob_3d.f90
Exec/KH/Tagging_2d.f90
Exec/KH/Tagging_3d.f90
Exec/KH/inputs.2d
Exec/KH/inputs.3d
Exec/KH/probdata.f90
Exec/KH/probin
Exec/Make.Castro
Exec/Sedov/GNUmakefile
Exec/Sedov/Make.package
Exec/Sedov/Prob_1d.f90
Exec/Sedov/Prob_2d.f90
Exec/Sedov/Prob_3d.f90
Exec/Sedov/Verification/Readme
Exec/Sedov/Verification/analytic/sedov3.f
Exec/Sedov/Verification/cylindrical_sedov.dat
Exec/Sedov/Verification/sedov.gp
Exec/Sedov/Verification/sedov2d.gp
Exec/Sedov/Verification/sedov_sph.gp
Exec/Sedov/Verification/spherical_sedov.dat
Exec/Sedov/amrvis.defaults
Exec/Sedov/inputs.1d.cyl
Exec/Sedov/inputs.1d.sph
Exec/Sedov/inputs.2d.cyl_in_cartcoords
Exec/Sedov/inputs.2d.cyl_in_cylcoords
Exec/Sedov/inputs.2d.sph_in_cylcoords
Exec/Sedov/inputs.3d.cyl
Exec/Sedov/inputs.3d.sph
Exec/Sedov/probdata.f90
Exec/Sedov/probin.1d.cyl
Exec/Sedov/probin.1d.sph
Exec/Sedov/probin.2d.cyl_in_cartcoords
Exec/Sedov/probin.2d.cyl_in_cylcoords
Exec/Sedov/probin.2d.sph_in_cylcoords
Exec/Sedov/probin.3d.cyl
Exec/Sedov/probin.3d.sph
Exec/Sod/ColellaGlaz/Castro_2d.f
Exec/Sod/ColellaGlaz/TODO
Exec/Sod/Figure1/128/den_0034.pla
Exec/Sod/Figure1/128/eint_0034.pla
Exec/Sod/Figure1/128/grdlog
Exec/Sod/Figure1/128/pres_0034.pla
Exec/Sod/Figure1/128/vel_0034.pla
Exec/Sod/Figure1/inputs-sod-1d
Exec/Sod/Figure1/paper_sod.gp
Exec/Sod/Figure1/probin-sod-x
Exec/Sod/Figure1/sod-exact.out
Exec/Sod/Figure1/todo_paper
Exec/Sod/Figure2/128/den_0015.pla
Exec/Sod/Figure2/128/eint_0015.pla
Exec/Sod/Figure2/128/grdlog
Exec/Sod/Figure2/128/pres_0015.pla
Exec/Sod/Figure2/128/vel_0015.pla
Exec/Sod/Figure2/2048/den_0015.pla
Exec/Sod/Figure2/2048/eint_0015.pla
Exec/Sod/Figure2/2048/grdlog
Exec/Sod/Figure2/2048/pres_0015.pla
Exec/Sod/Figure2/2048/vel_0015.pla
Exec/Sod/Figure2/512/den_0015.pla
Exec/Sod/Figure2/512/eint_0015.pla
Exec/Sod/Figure2/512/grdlog
Exec/Sod/Figure2/512/pres_0015.pla
Exec/Sod/Figure2/512/vel_0015.pla
Exec/Sod/Figure2/inputs-test2-1d
Exec/Sod/Figure2/paper_double_rarefaction.gp
Exec/Sod/Figure2/test2-exact.out
Exec/Sod/Figure2/todo_paper
Exec/Sod/Figure3/128/den_0046.pla
Exec/Sod/Figure3/128/eint_0046.pla
Exec/Sod/Figure3/128/grdlog
Exec/Sod/Figure3/128/pres_0046.pla
Exec/Sod/Figure3/128/vel_0046.pla
Exec/Sod/Figure3/inputs-test3-1d
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Networks/gammalaw/Make.package
Networks/gammalaw/burner.f90
Networks/gammalaw/castro_burner.f90
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Networks/general_null/H_core.net
Networks/general_null/Make.package
Networks/general_null/README
Networks/general_null/burner.f90
Networks/general_null/castro_burner.f90
Networks/general_null/gammalaw.net
Networks/general_null/ignition.net
Networks/general_null/network.template
Networks/general_null/simple.net
Networks/general_null/write_network.py
Networks/ignition_simple/Make.package
Networks/ignition_simple/burner.f90
Networks/ignition_simple/burner_aux.f90
Networks/ignition_simple/castro_burner.f90
Networks/ignition_simple/f_rhs.f90
Networks/ignition_simple/network.f90
Networks/ignition_simple/test/GNUmakefile
Networks/ignition_simple/test/eval.f90
Networks/ignition_simple/test/testburn.f90
Networks/ignition_simple/test/testjacobian.f90
Networks/null/Make.package
Networks/null/README
Networks/null/burner.f90
Networks/null/castro_burner.f90
Networks/null/network.f90
Networks/screen.f
Source/Castro.H
Source/Castro.cpp
Source/CastroBld.cpp
Source/Castro_F.H
Source/Castro_advance.cpp
Source/Castro_diffusion.cpp
Source/Castro_error.cpp
Source/Castro_error_F.H
Source/Castro_nd.f90
Source/Castro_react.cpp
Source/Castro_setup.cpp
Source/Derive_F.H
Source/Diffusion.H
Source/Diffusion.cpp
Source/Gravity.H
Source/Gravity.cpp
Source/Gravity_F.H
Source/Gravity_nd.f90
Source/Make.package
Source/Src_1d/CastroCG_1d.f90
Source/Src_1d/Castro_1d.f90
Source/Src_1d/Castro_advection_1d.f90
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Source/Src_1d/Derive_1d.f90
Source/Src_1d/EstDt_1d.f90
Source/Src_1d/GR_Gravity_1d.f90
Source/Src_1d/Gravity_1d.f90
Source/Src_1d/MGutils_1d.f90
Source/Src_1d/Make.package
Source/Src_1d/React_1d.f90
Source/Src_1d/Tagging_1d.f90
Source/Src_1d/compute_temp_1d.f90
Source/Src_1d/enforce_consistent_e_1d.f90
Source/Src_1d/estdt_burning_1d.f90
Source/Src_1d/ext_src_1d.f90
Source/Src_1d/pointmass_1d.f90
Source/Src_1d/ppm_1d.f90
Source/Src_1d/sponge_1d.f90
Source/Src_2d/Castro_2d.f90
Source/Src_2d/Castro_advection_2d.f90
Source/Src_2d/Castro_sums_2d.f90
Source/Src_2d/Derive_2d.f90
Source/Src_2d/EstDt_2d.f90
Source/Src_2d/GR_Gravity_2d.f90
Source/Src_2d/Gravity_2d.f90
Source/Src_2d/LevelSet_2d.f90
Source/Src_2d/MGutils_2d.f90
Source/Src_2d/Make.package
Source/Src_2d/React_2d.f90
Source/Src_2d/Rotate_2d.f90
Source/Src_2d/Tagging_2d.f90
Source/Src_2d/compute_temp_2d.f90
Source/Src_2d/enforce_consistent_e_2d.f90
Source/Src_2d/estdt_burning_2d.f90
Source/Src_2d/ext_src_2d.f90
Source/Src_2d/pointmass_2d.f90
Source/Src_2d/ppm_2d.f90
Source/Src_2d/prescribe_grav_2d.f90
Source/Src_2d/sponge_2d.f90
Source/Src_3d/Castro_3d.f90
Source/Src_3d/Castro_advection_3d.f90
Source/Src_3d/Castro_sums_3d.f90
Source/Src_3d/Derive_3d.f90
Source/Src_3d/EstDt_3d.f90
Source/Src_3d/GR_Gravity_3d.f90
Source/Src_3d/Gravity_3d.f90
Source/Src_3d/LevelSet_3d.f90
Source/Src_3d/Make.package
Source/Src_3d/React_3d.f90
Source/Src_3d/Rotate_3d.f90
Source/Src_3d/Tagging_3d.f90
Source/Src_3d/compute_temp_3d.f90
Source/Src_3d/enforce_consistent_e_3d.f90
Source/Src_3d/estdt_burning_3d.f90
Source/Src_3d/ext_src_3d.f90
Source/Src_3d/pointmass_3d.f90
Source/Src_3d/ppm_3d.f90
Source/Src_3d/prescribe_grav_3d.f90
Source/Src_3d/reset_internal_energy_3d.f90
Source/Src_3d/sponge_3d.f90
Source/Src_3d/trace_ppm_3d.f90
Source/extern_probin.template
Source/interpolate.f90
Source/main.cpp
Source/meth_params.f90
Source/prob_params.f90
Source/sum_integrated_quantities.cpp
UsersGuide/AMR/AMR.tex
UsersGuide/CastroUserGuide.tex
UsersGuide/CastroVerification/RT_ppm_type.eps
UsersGuide/CastroVerification/Verification.tex
UsersGuide/CastroVerification/radiating_source.eps
UsersGuide/CastroVerification/radiating_sphere.eps
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UsersGuide/CastroVerification/sod_3d_ppm0.eps
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UsersGuide/CastroVerification/test_suite_day.eps
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UsersGuide/CastroVerification/verification.bib
UsersGuide/ConvertCheckpoint/ConvertCheckpoint.tex
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UsersGuide/ConvertCheckpoint/grown_corner_3.eps
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UsersGuide/ConvertCheckpoint/orig_corner.eps
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UsersGuide/Equations/Equations.tex
UsersGuide/FlowChart/FlowChart.tex
UsersGuide/GNUmakefile
UsersGuide/GettingStarted/CastroGettingStarted.tex
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UsersGuide/Gravity/gr.bib
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UsersGuide/Introduction/CastroIntroduction.tex
UsersGuide/LevelSet/LevelSet.tex
UsersGuide/LevelSet/levelset.bib
UsersGuide/MAESTRO_restart/MAESTRO_restart.tex
UsersGuide/ManagingJobs/managingjobs.tex
UsersGuide/Particles/Particles.tex
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UsersGuide/Scaling/Scaling.tex
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UsersGuide/Scaling/Sod_scaling.eps
UsersGuide/Scaling/scaling_jaguarpf.eps
UsersGuide/Software/CastroSoftware.tex
UsersGuide/Suggestions/Suggestions.tex
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UsersGuide/Visualization/CastroVisualization.tex
Util/BLAS/GPackage.mak
Util/BLAS/Make.package
Util/BLAS/daxpy.f
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Util/BLAS/ddot.f
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Util/BLAS/idamax.f
Util/VODE/GPackage.mak
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Util/VODE/dacopy.f
Util/VODE/dewset.f
Util/VODE/dgbfa.f
Util/VODE/dgbsl.f
Util/VODE/dgefa.f
Util/VODE/dgesl.f
Util/VODE/dumach.f
Util/VODE/dvhin.f
Util/VODE/dvindy.f
Util/VODE/dvjac.f
Util/VODE/dvjust.f
Util/VODE/dvnlsd.f
Util/VODE/dvnorm.f
Util/VODE/dvode.f
Util/VODE/dvset.f
Util/VODE/dvsol.f
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Util/VODE/iumach.f
Util/VODE/ixsav.f
Util/VODE/test/GNUmakefile
Util/VODE/test/tvode.f
Util/VODE/vode.H
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Util/VODE/xsetun.f
Util/model_parser/GPackage.mak
Util/model_parser/Make.package
Util/model_parser/model_parser.f90
Util/plot1d/Make.package
Util/plot1d/Misc.H
Util/plot1d/XGraph1d.H
Util/plot1d/XGraph1d.cpp
Util/random/GPackage.mak
Util/random/Make.package
Util/random/mt19937ar.f90
constants/Make.package
constants/constants_cgs.f90
commit adef7d9e16843258dcd7c41d991d2ec701c7e11e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Thu May 31 22:22:19 2012 +0000
Fix EOS.
GNUmakefile
commit 5a956a04264ef02a25a15693dff9b0646f8692b1
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Tue Sep 6 21:59:08 2011 +0000
Move to new BoxLib format.
GNUmakefile
commit e0fc7176f8449868fffa15f330df7bcba57e57fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 15:42:01 2010 +0000
notes on the detonation
README
commit 06f6f42acc2a252c42a74335239996f914afea61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 05:35:06 2010 +0000
this detonates
inputs-det-x
commit ac976385ee85a4f83f646c7d26433e4d95574b6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 05:21:00 2010 +0000
rho eint, not eint
Prob_1d.f90
Prob_2d.f90
commit cb8f2f96e2cabc698fe19a152d69593981be7055
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 05:20:45 2010 +0000
need higher temp for a detonation
probin-det-x
commit daafafee2b9dc3f853a29d5e72610cf9cc6c6cd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 05:00:45 2010 +0000
2-d
GNUmakefile
inputs-det-x
commit bba00a5392c209734eeb4feb81cb1c5179348ac0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 04:32:26 2010 +0000
get it closer to a detonation
inputs-det-x
probin-det-x
commit bdbfd34f8326fc27069d90d15fe03192f0371897
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 21 04:23:54 2010 +0000
first cut at the detonation
GNUmakefile
Make.package
Prob_1d.f90
Prob_2d.f90
inputs-det-x
probdata.f90
probin-det-x