commit 75a69f607310824e8bd4cc55ee28787378f6aa69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 1 09:06:12 2022 -0400
add subch2 note
CHANGES.md
commit 61c46f9e74a69fb70cc2de90f3bc4dfd2f854a2d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 30 16:41:54 2022 -0700
Mark some variables maybe_unused in Helmholtz (#676)
EOS/helmholtz/actual_eos.H
commit bac73ad3093c319d4aa9f232e20a15d8f137e5d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 30 16:40:45 2022 -0700
xn_in doesn't need to be defined in the GPU build (#920)
integration/VODE/actual_integrator.H
commit 3c4985213c5e5b1ad2602b0bba2ce164b847361a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 15 13:42:47 2022 -0400
a slightly better subch2 network (#915)
this adds Na23 + explicitly pulls in 2 rate sequences for C12+C12, C12+O16 and O16+O16, assuming fast n captures
networks/subch2/20180319default2
networks/subch2/README.md
networks/subch2/actual_network.H
networks/subch2/actual_network_data.cpp
networks/subch2/actual_rhs.H
networks/subch2/network_plot.py
networks/subch2/pynucastro.net
networks/subch2/reaclib_rate_metadata.dat
networks/subch2/reaclib_rates.H
networks/subch2/subch2.py
networks/subch2/subch_network_explore.ipynb
networks/subch2/subch_plotting.ipynb
commit 235d890ba3aa58767300d07d07c23d91fd35e34f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 15 11:41:01 2022 -0400
add a note about VODE failure with istate == 2 to the output (#919)
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
commit ef526ccd2f4bf78d248d20bf96383bfd2b94e932
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 4 14:45:50 2022 -0400
clean up the simplified SDC numerical Jacobian a bit (#917)
this eliminates a copy
integration/VODE/vode_rhs_simplified_sdc.H
integration/utils/numerical_jacobian.H
commit 4c58cebff5a604d73aadaa1ad4e697c82302a732
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 1 11:38:41 2022 -0400
update changes
CHANGES.md
commit 4f1304edcb92dd3e6711496b5437a1e07dc86591
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 29 14:30:30 2022 -0400
sync simplified SDC clean_state up with Strang (#916)
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
commit f58972c724998c3ee99ad9c42ed60ff5bc6716ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 25 13:16:10 2022 -0400
add pivoting note (#904)
sphinx_docs/source/templated_networks.rst
commit b2f7b602c0cf7efd5d5a392a2982558e8771f597
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 25 13:12:27 2022 -0400
retry_burn is no longer supported (#912)
the code that implemented this was removed a long time ago.
This just removes the parameter.
integration/_parameters
python_library/StarKiller/StarKiller/examples/BurnProfile/probin_aprox21
python_library/StarKiller/StarKiller/examples/rotating_star/probin_aprox21
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/old/inputs_reaclib_cburn.128
unit_test/test_react/old/inputs_reaclib_cburn.32
unit_test/test_react/old/inputs_reaclib_cburn.64
unit_test/test_react/old/inputs_reaclib_urca.32
unit_test/test_react/old/inputs_reaclib_urca.64
commit 198df1937f595c4006d89924c538199c21083e16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 24 17:04:24 2022 -0400
output more precision after integration failure (#914)
integration/VODE/actual_integrator_simplified_sdc.H
commit e25a9ed22075f97c099e1838150a1f1da27e8530
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 23 12:08:04 2022 -0400
for simplified-SDC, eliminate a temporary ydot_react array (#905)
since we have shifted such that the SDC VODE state is in the same
order as Strang, we no longer need a temporary. This frees up
memory and a potentially expensive copy.
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
commit 65902e187216cae6dd452ecca29e99807b793498
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 22 11:37:15 2022 -0400
add unit test inputs for ECSN (#909)
unit_test/burn_cell/inputs_ecsn
unit_test/test_react/inputs_ecsn
commit 75721f58dc170ebba6f4a316e0113cc21e5a83a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 16 20:38:41 2022 -0400
fix compilation of test_sdc_rhs_vode (#906)
unit_test/test_sdc_vode_rhs/vode_rhs_test.H
commit 5333f6dab338a00e317cd0376781e6328f179b59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 16 20:35:29 2022 -0400
remove some old Fortran network includes (#907)
integration/VODE/vode_rhs.H
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
integration/utils/numerical_jacobian.H
unit_test/test_jac/jac_zones.H
unit_test/test_rhs/rhs_zones.H
commit 41c4af200ec205a1ae16a5570ae559671a0cca8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 12 17:29:40 2022 -0500
document the EOS modes (#903)
sphinx_docs/source/eos.rst
commit b7734485e3bfc658dcf225d9785e49cde6821275
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 12 08:43:41 2022 -0800
aprox network rewrite (#802)
this switches all of the aprox/iso networks to use a templated RHS. Now meta data about the rates are provided and at compile time, through constexpr-if's we generate the entire RHS and Jacobian.
Overall, this makes these nets a lot easier to maintain and also allows for additional optimizations.
Make.Microphysics
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvnlsd.H
integration/VODE/vode_rhs.H
integration/VODE/vode_type.H
integration/VODE/vode_type_strang.H
integration/utils/numerical_jacobian.H
interfaces/Make.package
interfaces/network_initialization.cpp
interfaces/network_utilities.H
interfaces/rhs_type.H
interfaces/rhs_utilities.H
networks/Make.package
networks/aprox13/Make.package
networks/aprox13/actual_matrix.H
networks/aprox13/actual_network.H
networks/aprox13/actual_rhs.H
networks/aprox13/actual_rhs_data.cpp
networks/aprox13/aprox13.net
networks/aprox13/maskfile
networks/aprox19/Make.package
networks/aprox19/actual_network.H
networks/aprox19/actual_rhs.H
networks/aprox19/actual_rhs_data.cpp
networks/aprox19/aprox19.net
networks/aprox21/Make.package
networks/aprox21/actual_network.H
networks/aprox21/actual_network_data.cpp
networks/aprox21/actual_rhs.H
networks/aprox21/actual_rhs_data.cpp
networks/aprox21/aprox21.net
networks/iso7/Make.package
networks/iso7/actual_linear_solver.H
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
networks/iso7/actual_rhs_data.cpp
networks/rhs.H
networks/rhs.cpp
sphinx_docs/source/index.rst
sphinx_docs/source/integrators.rst
sphinx_docs/source/templated_networks.rst
unit_test/test_rhs/rhs_zones.H
commit d0440a19005889e45b2a9b62b0e7af9e2852c683
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 12 11:09:58 2022 -0500
regenerate pynucastro nets to take advantage of recent optimizations (#901)
note: subch2 will be done separately
networks/ECSN/actual_rhs.H
networks/ECSN/ecsn_network_generation.py
networks/ECSN/reaclib_rate_metadata.dat
networks/ECSN/reaclib_rates.H
networks/ignition_reaclib/C-burn-simple/actual_rhs.H
networks/ignition_reaclib/C-burn-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/C-burn-simple/reaclib_rates.H
networks/ignition_reaclib/URCA-simple/actual_rhs.H
networks/ignition_reaclib/URCA-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/URCA-simple/reaclib_rates.H
networks/nova/20180319default2
networks/nova/actual_rhs.H
networks/nova/nova.png
networks/nova/nova.py
networks/nova/reaclib_rate_metadata.dat
networks/nova/reaclib_rates.H
networks/nova2/actual_rhs.H
networks/nova2/nova.png
networks/nova2/nova2.py
networks/nova2/reaclib_rate_metadata.dat
networks/nova2/reaclib_rates.H
networks/sn160/20180319default2
networks/sn160/actual_rhs.H
networks/sn160/reaclib_rate_metadata.dat
networks/sn160/reaclib_rates.H
networks/sn160/sn160.py
networks/subch/actual_rhs.H
networks/subch/reaclib_rate_metadata.dat
networks/subch/reaclib_rates.H
networks/subch/subch.py
commit 9769f8571ac4607810cb9bce43ec0f1261e3686b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 10 20:49:40 2022 -0500
add a generic integrator_size.H (#900)
this defines the size of the ODE system we integrate and knows
about the different coupling methods.
integration/Make.package
integration/VODE/vode_type.H
integration/integrator_data.H
commit e2419c42876cf1c30973cb55060c131e6298a8a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 6 13:16:01 2022 -0500
put species at the start of the simplified-SDC vector (#894)
this makes the ordering match that of Strang. Note that there are some diffs in the output since the jacobian matrix has a different ordering and the linear algebra takes a different sequence of steps now. But the convergence tests (both reacting and NSE for SDC) show the correct behavior.
interfaces/burn_type.H
commit 967d3c2f8a56c928b0772a8aceb315276b56754d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 6 11:57:12 2022 -0500
allow burn_cell_sdc to work with more species (#899)
unit_test/burn_cell_sdc/_parameters
unit_test/burn_cell_sdc/burn_cell.H
commit 219355bde64e7efa2793e709fd89df985e0f5899
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 1 10:58:06 2022 -0500
initialize T_fixed to silence valgrind (#896)
unit_test/test_sdc/react_zones.H
commit a47a5a10cde0c7b40a0ac52aea751b9141f8de8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 28 20:24:51 2022 -0500
fix some valgrind errors in calling the jac() wrapper directly (#895)
unit_test/test_sdc_vode_rhs/vode_rhs_test.H
commit 5bd262e6f9123e1edaed348ec3fc85495904c6d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 28 11:44:37 2022 -0500
add Jacobian output to test_sdc_vode_rhs (#893)
this comes directly from the VODE jac() wrapper, so applies for
jacobian = 1 or jacobian = 3
unit_test/test_sdc_vode_rhs/vode_rhs_test.H
commit 1a114f0ab17985a8ffb0f516ae796b1a10723e0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 27 21:17:21 2022 -0500
add advective terms to test_sdc_vode_rhs (#892)
this syncs up a bit with burn_cell_sdc -- maybe eventually they
can be merged?
unit_test/test_sdc_vode_rhs/_parameters
unit_test/test_sdc_vode_rhs/inputs_aprox19
unit_test/test_sdc_vode_rhs/vode_rhs_test.H
commit 823f08af58df1eb4d7593bb63a1e9e9f5cdf95f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 27 20:50:44 2022 -0500
fix burn_cell_sdc -- we were not initializing the adv_aux terms (#891)
unit_test/burn_cell_sdc/burn_cell.H
commit a6df89c8e3b8ffc49a225a2426a9b26c2147f752
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 27 19:59:11 2022 -0500
fix compilation of test_sdc_vode_rhs (#890)
unit_test/test_sdc_vode_rhs/vode_rhs_test.H
commit 70b309c98e7cdb1ba0a4b93b954475ac75bd4aff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 27 17:46:39 2022 -0500
in the constexpr aion / zion functions, the comments were not 1-based (#885)
networks/general_null/write_network.py
commit 9715472b85baac3ff3ab32030436f733a918362c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 27 17:46:08 2022 -0500
fix some array sizes in sneut (#880)
neutrinos/sneut5.H
commit 260ac6168eaf3a2d8efebc4faa42fdd0f10f720d
Author: Eric Johnson <yut23@users.noreply.github.com>
Date: Wed Feb 23 11:46:25 2022 -0500
Improve compile action (#886)
* rework changed network detection
* run make clean between each build
* check make's return code in addition to stderr
* group each set of make output, so it can be collapsed in the github UI
.github/workflows/find_changed_files.py
commit a894d6490a56263742dd2351e14105aee879defd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 17 07:56:49 2022 -0500
clean up the docs on the ODE integration (#884)
this is prep for adding details of the templated RHS
sphinx_docs/source/integrators.rst
commit 1a131a41fdf7f08801de0cfb5401e1ed04e65bf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 16 14:41:21 2022 -0500
split the network docs across several pages (#883)
this is prep for adding details of the templated RHS
requirements.txt
sphinx_docs/source/basics.rst
sphinx_docs/source/conf.py
sphinx_docs/source/data_structures.rst
sphinx_docs/source/index.rst
sphinx_docs/source/networks-overview.rst
sphinx_docs/source/networks.rst
commit f51cc45134b27a15927303077597a16c98dc7b29
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 15 18:47:31 2022 -0500
remove some old Fortran references in the docs (#882)
sphinx_docs/source/integrators.rst
sphinx_docs/source/networks.rst
commit 11641bf5e5093c0e1d6b8ee376713e46dcf9dfbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 13 13:49:12 2022 -0500
remove some old docs and Fortran refs (#881)
sphinx_docs/source/basics.rst
sphinx_docs/source/cxx.rst
sphinx_docs/source/data_structures.rst
sphinx_docs/source/eos.rst
sphinx_docs/source/gpu.rst
sphinx_docs/source/index.rst
sphinx_docs/source/integrators.rst
sphinx_docs/source/rp_intro.rst
commit 2f059b427fb2a8082dd842ed1b83efbe36ee0211
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 1 08:19:59 2022 -0500
update changes
CHANGES.md
commit 0edf069b80564b042f6011b32d1ddc71f18c782b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 28 16:45:13 2022 -0500
update location to reflect Microphysics repo move (#879)
Microphysics is now part of AMReX-Astro
.zenodo.json
README.md
sphinx_docs/Makefile
sphinx_docs/source/conf.py
commit a81250320603a2c3d1af5a1256622d186360e508
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 27 19:40:16 2022 -0500
remove some remaining USE_FORT_MICROPHYSICS (#878)
Make.Microphysics
Make.Microphysics_extern
constants/Make.package
constants/constants_cgs.f90
networks/Make.package
networks/general_null/Make.package
unit_test/burn_cell_sdc/GNUmakefile
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_eos/GNUmakefile
unit_test/test_jac/GNUmakefile
unit_test/test_react/GNUmakefile
unit_test/test_screening/GNUmakefile
unit_test/test_sdc/GNUmakefile
commit 1a290c72e94d032efea91d3ddfacd2dc2e99987d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 15 16:55:51 2022 -0800
Initialize VODE type data (#876)
integration/VODE/vode_dvode.H
commit d89cb25ceb7e59d4dd78e2b7b0e19ad838c2cf4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 14 20:22:00 2022 -0500
fix location of MICROPHYSICS_UNUSED to silence compiler warnings (#872)
networks/general_null/network_header.template
commit 66b4954386a5115a57659103bf11840dddd3bd14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 14 20:21:36 2022 -0500
fix shadowing in 3-alpha (#874)
rates/aprox_rates.H
commit 6cc2eeccd7ad2d5ca9e8b5abba54df21abcea0f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 14 18:45:15 2022 -0500
silence some unused var warnings (#875)
screening/screen.H
commit c498d2e8c9897ddd9b239a0f452115ae3896d94a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 14 12:31:08 2022 -0500
make some if-logic clearer in sneut.H to silence compiler warnings (#873)
neutrinos/sneut5.H
commit fb7348bf9c82192b10c443e947d45b71c4628b6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 13 20:04:02 2022 -0500
silence some compiler warnings (#871)
EOS/helmholtz/actual_eos.H
integration/VODE/actual_integrator.H
interfaces/ArrayUtilities.H
rates/aprox_rates.H
commit eeef682d563d880393b84efb1606f5158bb52420
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 6 14:00:18 2022 -0500
remove support for Fortran parameters in the parser (#869)
Make.Microphysics
interfaces/extern_probin.template
util/build_scripts/runtime_parameters.py
util/build_scripts/write_probin.py
commit b4d04fb47b7082672a6d272dc0d838867279bb4c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 5 06:09:24 2022 -0800
Remove unused dT_crit parameter (#867)
integration/VODE/actual_integrator.H
integration/_parameters
sphinx_docs/source/integrators.rst
commit 934b5b9ec98755141607170c519836efa09111b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jan 5 06:08:56 2022 -0800
Remove unused do_constant_volume_burn (#868)
integration/_parameters
sphinx_docs/source/integrators.rst
commit 38d7ea0d63892904351bbe0125dabef4b2913c3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 4 17:44:59 2022 -0800
Update documentation on reaction ODE system (#866)
These changes remove references to Fortran, and update the reaction system to the one that is based on e instead of T. (Along with this, we also now point out that this e is the real internal energy instead of the tracer variable it was before.)
sphinx_docs/source/integrators.rst
commit cdae424093c8f8144746eb8eb5f09e686a64dba2
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 4 06:36:17 2022 -0800
Update network structure and requirements documentation (#864)
sphinx_docs/source/networks.rst
commit a63a341895426461770adf3188df3021b45770b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 4 06:35:19 2022 -0800
Add BL_PROFILE regions to test_react (#865)
unit_test/test_react/main.cpp
commit b5735dbb6b63d3e17d801a332ec57b277166d1d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 3 19:21:04 2022 -0800
Remove viscosity (#862)
This is currently unused and has not been ported to C++.
viscosity/constant/Make.package
viscosity/constant/_parameters
viscosity/constant/constant_viscosity.f90
commit 943d8025cc5bda4d0fb479187401ac1fb79641f0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 3 19:20:29 2022 -0800
Template EOS operator<< and use SFINAE to only operate on eos_t (#863)
This fixes #859.
interfaces/eos_type.H
commit e1bef9fd93500a5e1d628934a593c788b248cc98
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 3 15:54:00 2022 -0500
remove the last fortran bits (#861)
note: test_parameters was intended to test passing parameters from
C++ to/from Fortran, so it is no longer needed
interfaces/Make.package
interfaces/microphysics.F90
interfaces/microphysics_F.H
interfaces/network.F90
unit_test/test_parameters/GNUmakefile
unit_test/test_parameters/Make.package
unit_test/test_parameters/_parameters
unit_test/test_parameters/inputs
unit_test/test_parameters/main.cpp
unit_test/test_parameters/probin
unit_test/test_parameters/test_parameters.F90
unit_test/test_parameters/test_parameters.H
unit_test/test_parameters/test_parameters_F.H
commit 246da88939d45e3a7f8e28e200087fa4854013f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 3 09:30:22 2022 -0500
remove some Fortran unit_test stuff (#860)
also eliminate some probins
unit_test/Make.package
unit_test/burn_cell/inputs_aprox13
unit_test/burn_cell/inputs_aprox19
unit_test/burn_cell/inputs_aprox21
unit_test/burn_cell/inputs_aprox21_rot1
unit_test/burn_cell/inputs_aprox21_rot2
unit_test/burn_cell/inputs_ignition
unit_test/burn_cell/inputs_iso7
unit_test/burn_cell/inputs_rprox
unit_test/burn_cell/inputs_triple
unit_test/burn_cell/inputs_vode_example
unit_test/burn_cell/main.cpp
unit_test/burn_cell/probin
unit_test/burn_cell/probin_aprox13
unit_test/burn_cell/probin_aprox19
unit_test/burn_cell/probin_aprox21
unit_test/burn_cell/probin_aprox21_rot1
unit_test/burn_cell/probin_aprox21_rot2
unit_test/burn_cell/probin_ignition
unit_test/burn_cell/probin_iso7
unit_test/burn_cell/probin_rprox
unit_test/burn_cell/probin_triple
unit_test/burn_cell_sdc/main.cpp
unit_test/eos_cell/inputs_eos
unit_test/eos_cell/main.cpp
unit_test/eos_cell/probin
unit_test/test_aprox_rates/main.cpp
unit_test/test_conductivity/main.cpp
unit_test/test_eos/main.cpp
unit_test/test_jac/main.cpp
unit_test/test_parameters/main.cpp
unit_test/test_react/main.cpp
unit_test/test_rhs/main.cpp
unit_test/test_screening/main.cpp
unit_test/test_sdc/main.cpp
unit_test/test_sdc_vode_rhs/inputs_aprox19
unit_test/test_sdc_vode_rhs/main.cpp
unit_test/test_sdc_vode_rhs/probin.aprox19
unit_test/unit_test.F90
unit_test/unit_test.H
unit_test/unit_test_F.H
commit aba1dfe8621d5010ae660d9dc12ca7e14ba4367a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 2 19:44:43 2022 -0500
remove the Fortran implementations of the EOSes (#857)
these are no longer exercised
also remove the USE_CXX_EOS make parameter, since it is implied now
EOS/Make.package
EOS/breakout/Make.package
EOS/breakout/actual_eos.F90
EOS/composition.F90
EOS/gamma_law/Make.package
EOS/gamma_law/actual_eos.F90
EOS/helmholtz/Make.package
EOS/helmholtz/actual_eos.F90
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.F90
EOS/multigamma/composition.F90
EOS/polytrope/Make.package
EOS/polytrope/actual_eos.F90
EOS/rad_power_law/Make.package
EOS/rad_power_law/rad_power_law.F90
EOS/stellarcollapse/Make.package
EOS/stellarcollapse/README
EOS/stellarcollapse/_parameters
EOS/stellarcollapse/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
EOS/tillotson/Make.package
EOS/tillotson/actual_eos.F90
EOS/ztwd/Make.package
EOS/ztwd/actual_eos.F90
interfaces/Make.package
interfaces/eos.F90
interfaces/eos_override.F90
interfaces/eos_type.F90
rates/Make.package
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell_sdc/GNUmakefile
unit_test/eos_cell/GNUmakefile
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_conductivity/GNUmakefile
unit_test/test_eos/GNUmakefile
unit_test/test_jac/GNUmakefile
unit_test/test_react/GNUmakefile
unit_test/test_rhs/GNUmakefile
unit_test/test_screening/GNUmakefile
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc_vode_rhs/GNUmakefile
util/cj_detonation/GNUmakefile
commit ac4d84d34c64906f86f403acf7d71caa6e21b22e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 2 16:17:06 2022 -0500
get rid of the Fortran burn_type_module (#856)
interfaces/Make.package
interfaces/burn_type.F90
networks/general_null/actual_network.f90.test
networks/general_null/actual_rhs.F90
commit 52a9eab7bbae747db1817ee52bed6a5ff97b0af8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 2 16:16:46 2022 -0500
fix make typo (#858)
integration/Make.package
commit a2979b235c9b4933293e4341633da1bea848f87d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 2 15:36:47 2022 -0500
put some EOS parameters in a namespace (#855)
also fix test_react compilation for ztwd
EOS/helmholtz/actual_eos.H
interfaces/eos_type.H
unit_test/test_eos/eos_util.cpp
commit 0d9206b02bf8de1cf307d34c2db7ea924704b262
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 1 11:33:31 2022 -0500
update changes
CHANGES.md
commit 8080dc192beacbb6afb9018a65131efa1cfde40c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 31 10:46:54 2021 -0500
add density and temperature to the nonaka plot output (#853)
integration/utils/nonaka_plot.H
commit ef7b6522ed790c9a5f5bb4825ec2fc3658affa4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 31 10:46:38 2021 -0500
remove the wrapper for Fortran networks (#852)
all networks are now in C++, so this is no longer needed
interfaces/Make.package
interfaces/fortran_to_cxx_actual_rhs.F90
interfaces/fortran_to_cxx_actual_rhs.H
commit c8a32130ad62d9dc6a9052b715e5da1f81f847a8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 30 10:13:24 2021 -0800
Remove Fortran opacity modules (#851)
opacity/breakout/Make.package
opacity/breakout/opacity_table_module.F90
opacity/rad_power_law/Make.package
opacity/rad_power_law/opacity_table_module.F90
commit 4baa183833d9dffa40a8fcef7ca4d952df39ad8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 13:01:46 2021 -0500
fix the network Fortran module (#850)
this still allows us to query species properties from Fortran
this is needed by initial_models for now
interfaces/burn_type.F90
interfaces/network.F90
networks/Make.package
commit abb96a468579bedc0b095c1b28c737c62f979942
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 12:33:52 2021 -0500
remove the Fortran rate_type module (#849)
nothing uses this
networks/Make.package
networks/rate_type.f90
commit 301d94a58ffcbaaec4f737c1eebe91fe9ddc2ae8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 12:27:00 2021 -0500
remove Fortran screening (#848)
it is not used anymore
screening/Make.package
screening/screen.F90
commit 39aab28e1df737d74c517f2b311e1395228b1ebf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 12:24:25 2021 -0500
remove some Fortran integration utils (#847)
these are not used anymore
integration/utils/Make.package
integration/utils/jacobian_sparsity.F90
integration/utils/temperature_integration.F90
commit ee433a6618daf379c5c70cefeb7a334f85e9c90a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 30 08:31:05 2021 -0800
Convert ignition_chamulak to C++ (#845)
Addresses #819
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/NETWORK_PROPERTIES
networks/ignition_chamulak/actual_network.F90
networks/ignition_chamulak/actual_network.H
networks/ignition_chamulak/actual_network_data.cpp
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_chamulak/actual_rhs.H
networks/ignition_chamulak/actual_rhs_data.cpp
commit 27c9fa9eb9d3efbc4348423025e8367c6ef812e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 11:06:56 2021 -0500
remove missing Fortran file from build system (#846)
util/Make.package
commit a0273da72d81901f54842b62c21a3b61c1f42d7e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 30 07:41:22 2021 -0800
Add test_rhs inputs for ignition_chamulak (#844)
unit_test/test_rhs/inputs_chamulak
commit ff14d5cfd5e211933ce45466648429abef087db2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 30 09:42:13 2021 -0500
add strang_half to nonaka plot (#843)
integration/utils/nonaka_plot.H
interfaces/burn_type.H
commit aae8312ed86e4e4d8877efcd9f6f90c40aeb66c8
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 29 11:08:36 2021 -0800
Remove implicit d/dP terms in aprox19 and aprox21 Jacobians (#840)
In both aprox19 and aprox21 there is the reaction sequence Fe52(a,p)Co55(p,g)Ni56. Co55 is an equilibrium isotope in this reaction chain, and its equilibrium abundance depends on both this reaction sequence as well as the reaction Fe54(p,g)Co55. Since there are two contributions to the effective y(Co55), the rate ends up being somewhat complicated, but the RHS term ends up simply looking like y(Fe52) * y(He4) * y(P) * rate. The Jacobian terms consequently have a d/dP entry. However, although the proton abundance plays a role in determining the rate, the reaction sequence doesn't actually consume or produce a net proton, so it is more appropriate to think of y(P) as being part of the rate rather than part of the RHS. If the y(P) is absorbed into the rate, then this term should not appear in the Jacobian due to the same reason #686 was done: in the upcoming network rewrite, it will not be straightforward (or desirable) to represent any d(rate)/dy term. So this PR proposes removing the term on the basis that it will eventually be removed anyway, and this will make the network rewrite PR easier to evaluate when comparing test_rhs and test_react.
networks/aprox19/actual_rhs.H
networks/aprox21/actual_rhs.H
commit 79dcd89630f23a3057ca21419b7360f1cffbff81
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 29 06:34:36 2021 -0800
Disable tiling in GPU build of test_rhs (#841)
unit_test/test_rhs/main.cpp
commit cbd3e3656bd960fe99a158234383a938cfec4f5f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 28 16:42:18 2021 -0800
Fix Fe54 Jacobian terms in aprox19 (#839)
networks/aprox19/actual_rhs.H
commit 5c4a17e2cba51beb416a97e06a48af255539c1ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:37:16 2021 -0500
remove some old unused Fortran (#823)
nothing is using this
util/Make.package
util/esum.py
util/esum_module.F90
util/eval_rhs/GNUmakefile
util/eval_rhs/evaluate_rhs.f90
util/eval_rhs/inputs_reaclib_urca
util/microphysics_math.F90
util/test/GNUmakefile
util/test/bl_error.f90
util/test/bl_types.f90
util/test/test_esum.f90
commit 09741e279567a8fd5faa680ab952fdec940044d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:34:44 2021 -0500
remove the Fortran conductivities (#831)
nothing uses these anymore
conductivity/constant/Make.package
conductivity/constant/constant_conductivity.F90
conductivity/constant_opacity/Make.package
conductivity/constant_opacity/constant_conductive_opacity.F90
conductivity/powerlaw/Make.package
conductivity/powerlaw/powerlaw_conductivity.F90
conductivity/stellar/Make.package
conductivity/stellar/stellar_conductivity.F90
interfaces/Make.package
interfaces/conductivity.F90
interfaces/microphysics.F90
unit_test/test_conductivity/conductivity_util_F.F90
unit_test/test_conductivity/test_cond_F.H
unit_test/test_conductivity/variables_F.F90
commit c2140ba691a3404bedd694641c312524fe8b0780
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:34:30 2021 -0500
remove Fortran neutrino loss module (#835)
nothing is using this
neutrinos/Make.package
neutrinos/sneut5.F90
commit e297fc92892e57280c72997ddc9a9a23662ec92c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 28 10:34:15 2021 -0500
eliminate NAUX_NETWORK in favor of auto-detection (#836)
instead of hardcoding the number of aux quantities in the network, we
now determine it at compile time by parsing the .net file via the
new get_naux.py script.
This also separates some of the commonly
used network property file stuff into a separate routine.
networks/ECSN/NAUX_NETWORK
networks/Make.package
networks/aprox13/NAUX_NETWORK
networks/aprox19/NAUX_NETWORK
networks/aprox21/NAUX_NETWORK
networks/general_null/Make.package
networks/general_null/NAUX_NETWORK
networks/general_null/get_naux.py
networks/general_null/net_file.py
networks/general_null/network_param_file.py
networks/general_null/write_network.py
networks/get_naux.py
networks/ignition_chamulak/NAUX_NETWORK
networks/ignition_reaclib/C-burn-simple/NAUX_NETWORK
networks/ignition_reaclib/URCA-simple/NAUX_NETWORK
networks/ignition_simple/NAUX_NETWORK
networks/iso7/NAUX_NETWORK
networks/nova/NAUX_NETWORK
networks/nova2/NAUX_NETWORK
networks/powerlaw/NAUX_NETWORK
networks/rprox/NAUX_NETWORK
networks/sn160/NAUX_NETWORK
networks/subch/NAUX_NETWORK
networks/subch2/NAUX_NETWORK
networks/triple_alpha_plus_cago/NAUX_NETWORK
networks/vode_example/NAUX_NETWORK
commit f147628a0689826bae95af361e5f8404c13e03b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 20 10:03:33 2021 -0500
don't output state to nonaka plot file for Jacobian evaluation (#838)
we now just store the RHS evals used in the advance, and not for
computing the numerical Jacobian
integration/VODE/vode_dvjac.H
integration/VODE/vode_rhs.H
integration/VODE/vode_rhs_simplified_sdc.H
commit 999e2976018db47fad183aa86baeb8a60ae19073
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 20 10:02:32 2021 -0500
for jacobian=3, fix RHS eval counter (#837)
we need to incremement it each time we compute the numerical Jacobian
via differencing
integration/VODE/vode_rhs_simplified_sdc.H
commit 7d1ed422e6f468c4da62472b522c2522b520c554
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 16 09:50:36 2021 -0500
add the sdc iter to a column in the nonaka plot output (#834)
integration/utils/nonaka_plot.H
commit 0ca784f47d12e3d3aabb92423042b55731c85c94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 14 15:15:27 2021 -0500
add back in support for the "Nonaka plot" (#830)
this outputs the integration state each RHS evaluation into a file, for a single zone.
this can be enabled with USE_NONAKA_PLOT=TRUE
Make.Microphysics_extern
integration/VODE/vode_rhs.H
integration/VODE/vode_rhs_simplified_sdc.H
integration/_parameters
integration/utils/Make.package
integration/utils/nonaka_plot.H
integration/utils/nonaka_plot.f90
interfaces/burn_type.H
interfaces/network_initialization.cpp
unit_test/test_react/react_zones.H
unit_test/test_sdc/react_zones.H
commit e628968cdf85c68ecfe96482b305f5222419c772
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 13:04:56 2021 -0500
remove .F90 files for nets with C++ implementation (#826)
also breakout was a null net, so merge that into general_null
Make.Microphysics
networks/aprox13/Make.package
networks/aprox13/actual_network.F90
networks/aprox19/Make.package
networks/aprox19/actual_network.F90
networks/aprox19/nse_F.F90
networks/aprox19/nse_check.F90
networks/aprox21/Make.package
networks/aprox21/actual_network.F90
networks/breakout/Make.package
networks/breakout/NAUX_NETWORK
networks/breakout/NETWORK_PROPERTIES
networks/breakout/actual_network.f90
networks/breakout/actual_rhs.f90
networks/general_null/breakout.net
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_simple/Make.package
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_rhs.F90
networks/iso7/Make.package
networks/iso7/actual_network.F90
networks/powerlaw/Make.package
networks/powerlaw/actual_network.F90
networks/powerlaw/actual_rhs.F90
networks/rprox/Make.package
networks/rprox/actual_network.F90
networks/rprox/actual_rhs.F90
networks/rprox/rates_module.F90
networks/rprox/tfactors.F90
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_network.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/dydt.F90
networks/triple_alpha_plus_cago/rates_module.F90
networks/triple_alpha_plus_cago/screen_module.F90
networks/vode_example/Make.package
networks/vode_example/actual_network.F90
networks/vode_example/actual_rhs.F90
commit 49906b214410008a1a009ec6d3a58d1febe7022f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 12:53:21 2021 -0500
synchronize the strang and SDC step rejection logic (#821)
also boost the threshold
integration/VODE/_parameters
integration/VODE/vode_dvstep.H
integration/VODE/vode_type.H
commit 2e3dad4f5a726ca41f081bbf0cace5446c4b05f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 12:47:03 2021 -0500
remove xrb_simple (#827)
We never used this network and it was really originally intended for studying the convection, with approximations made for lower temperatures.
Also, the 14o(ap)17f rate (from CF88) had a typo in it (and extra t943 instead of t953)
networks/xrb_simple/Make.package
networks/xrb_simple/NAUX_NETWORK
networks/xrb_simple/NETWORK_PROPERTIES
networks/xrb_simple/_parameters
networks/xrb_simple/actual_network.f90
networks/xrb_simple/actual_rhs.f90
networks/xrb_simple/xrb_simple.net
sphinx_docs/source/networks.rst
unit_test/test_react/inputs_xrb_simple
commit 5613e129116682ae56f9a59560da293f09e80818
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 13 12:37:02 2021 -0500
do a better job at cleaning up linked files (#825)
this now cleans up the pynucastro files and helm in the _extern stub
this way application codes pick up these rules automagically
Make.Microphysics
Make.Microphysics_extern
unit_test/test_jac/GNUmakefile
unit_test/test_react/GNUmakefile
unit_test/test_rhs/GNUmakefile
unit_test/test_sdc_vode_rhs/GNUmakefile
commit 30a58b2bf138893b088195dca140943eda1a4322
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 11 09:01:51 2021 -0500
don't build Fortran if USE_FORT_MICROPHYSICS is not TRUE (#828)
opacity/breakout/Make.package
opacity/rad_power_law/Make.package
commit dc771c3663743c182c8eb27ce6b646cea8f45819
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 9 09:24:46 2021 -0500
remove Fortran code paths from unit tests (#822)
these were not used and we will be removing the Fortran implementations
soon anyway.
unit_test/test_conductivity/GNUmakefile
unit_test/test_conductivity/Make.package
unit_test/test_conductivity/input_conductivity
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/probin
unit_test/test_react/main.cpp
unit_test/test_screening/GNUmakefile
unit_test/test_screening/Make.package
unit_test/test_screening/main.cpp
unit_test/test_screening/screening_util.cpp
unit_test/test_screening/screening_util_F.F90
unit_test/test_screening/test_screen_F.H
unit_test/test_screening/variables_F.F90
commit 55d1484ec93e7f57d4e0154d90960295fd0ddda7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 7 10:32:09 2021 -0500
colorize some of the failure warnings (#824)
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_dvode.H
commit 9ab6e942555adb8fd8c124ab2ceb3498526972e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 2 10:19:56 2021 -0500
turn on USE_MICROPHYSICS_DEBUG (#820)
unit_test/burn_cell_sdc/GNUmakefile
commit 92436019fdee9ecfaa47d204dc530edc1ddc7029
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 10:33:33 2021 -0500
adjust the checks for SDC step rejection (#818)
this turns on the X based checks to SDC to ensure that the mass fractions don't change too much per step. This works reasonable well now that the y_save bug was fixed. Might still need tweaking.
integration/VODE/vode_dvstep.H
commit ddcc2698b48fd26578b680bb14f99676c293a387
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 1 09:30:29 2021 -0500
update changes
CHANGES.md
commit c45dec4e4b84c22034bd674f2f66666cf431f16d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 30 09:40:46 2021 -0500
convert all pynucastro nets to C++ (#809)
this uses the latest version of pynucastro to write out Starkiller C++ networks
.gitignore
networks/ECSN/Make.package
networks/ECSN/_parameters
networks/ECSN/actual_network.F90
networks/ECSN/actual_network.H
networks/ECSN/actual_network_data.cpp
networks/ECSN/actual_rhs.F90
networks/ECSN/actual_rhs.H
networks/ECSN/ecsn_network_generation.py
networks/ECSN/inputs.burn_cell.VODE
networks/ECSN/physical_constants.f90
networks/ECSN/reaclib_rate_metadata.dat
networks/ECSN/reaclib_rates.F90
networks/ECSN/reaclib_rates.H
networks/ECSN/table_rates.F90
networks/ECSN/table_rates.H
networks/ECSN/table_rates_data.cpp
networks/ECSN/table_type.H
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/C-burn-simple/_parameters
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_network.H
networks/ignition_reaclib/C-burn-simple/actual_network_data.cpp
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.H
networks/ignition_reaclib/C-burn-simple/c.py
networks/ignition_reaclib/C-burn-simple/inputs.burn_cell.VODE
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.H
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.H
networks/ignition_reaclib/C-burn-simple/table_rates_data.cpp
networks/ignition_reaclib/C-burn-simple/table_type.H
networks/ignition_reaclib/C-test/Make.package
networks/ignition_reaclib/C-test/NAUX_NETWORK
networks/ignition_reaclib/C-test/NETWORK_PROPERTIES
networks/ignition_reaclib/C-test/_parameters
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/c.py
networks/ignition_reaclib/C-test/inputs.burn_cell.VODE
networks/ignition_reaclib/C-test/physical_constants.f90
networks/ignition_reaclib/C-test/pynucastro.net
networks/ignition_reaclib/C-test/reaclib_rate_metadata.dat
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/_parameters
networks/ignition_reaclib/URCA-simple/actual_network.H
networks/ignition_reaclib/URCA-simple/actual_network_data.cpp
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.H
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/URCA-simple/reaclib_rates.H
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.H
networks/ignition_reaclib/URCA-simple/table_rates_data.cpp
networks/ignition_reaclib/URCA-simple/table_type.H
networks/ignition_reaclib/URCA-simple/urca.py
networks/nova/20180319default2
networks/nova/Make.package
networks/nova/_parameters
networks/nova/actual_network.F90
networks/nova/actual_network.H
networks/nova/actual_network_data.cpp
networks/nova/actual_rhs.F90
networks/nova/actual_rhs.H
networks/nova/inputs.burn_cell.VODE
networks/nova/nova.png
networks/nova/nova.py
networks/nova/physical_constants.f90
networks/nova/reaclib_rate_metadata.dat
networks/nova/reaclib_rates.F90
networks/nova/reaclib_rates.H
networks/nova/table_rates.F90
networks/nova/table_rates.H
networks/nova/table_rates_data.cpp
networks/nova/table_type.H
networks/nova2/Make.package
networks/nova2/_parameters
networks/nova2/actual_network.F90
networks/nova2/actual_network.H
networks/nova2/actual_network_data.cpp
networks/nova2/actual_rhs.F90
networks/nova2/actual_rhs.H
networks/nova2/inputs.burn_cell.VODE
networks/nova2/nova.png
networks/nova2/nova2.py
networks/nova2/physical_constants.f90
networks/nova2/reaclib_rate_metadata.dat
networks/nova2/reaclib_rates.F90
networks/nova2/reaclib_rates.H
networks/nova2/table_rates.F90
networks/nova2/table_rates.H
networks/nova2/table_rates_data.cpp
networks/nova2/table_type.H
networks/sn160/20180319default2
networks/sn160/Make.package
networks/sn160/NETWORK_PROPERTIES
networks/sn160/_parameters
networks/sn160/actual_network.F90
networks/sn160/actual_network.H
networks/sn160/actual_network_data.cpp
networks/sn160/actual_rhs.F90
networks/sn160/actual_rhs.H
networks/sn160/inputs.burn_cell.VODE
networks/sn160/physical_constants.f90
networks/sn160/reaclib_rate_metadata.dat
networks/sn160/reaclib_rates.F90
networks/sn160/reaclib_rates.H
networks/sn160/sn160.py
networks/sn160/table_rates.F90
networks/sn160/table_rates.H
networks/sn160/table_rates_data.cpp
networks/sn160/table_type.H
networks/sn160/xin.pynucastro.128
networks/sn160/xin.pynucastro.16
networks/sn160/xin.pynucastro.256
networks/sn160/xin.pynucastro.32
networks/sn160/xin.pynucastro.64
networks/sn160/xin.sn160.128
networks/sn160/xin.sn160.16
networks/sn160/xin.sn160.256
networks/sn160/xin.sn160.32
networks/sn160/xin.sn160.64
networks/subch/20180319default2
networks/subch/Make.package
networks/subch/_parameters
networks/subch/actual_network.F90
networks/subch/actual_network.H
networks/subch/actual_network_data.cpp
networks/subch/actual_rhs.F90
networks/subch/actual_rhs.H
networks/subch/inputs.burn_cell.VODE
networks/subch/physical_constants.f90
networks/subch/reaclib_rate_metadata.dat
networks/subch/reaclib_rates.F90
networks/subch/reaclib_rates.H
networks/subch/subch.py
networks/subch/table_rates.F90
networks/subch/table_rates.H
networks/subch/table_rates_data.cpp
networks/subch/table_type.H
networks/subch2/20180319default2
networks/subch2/Make.package
networks/subch2/_parameters
networks/subch2/actual_network.F90
networks/subch2/actual_network.H
networks/subch2/actual_network_data.cpp
networks/subch2/actual_rhs.F90
networks/subch2/actual_rhs.H
networks/subch2/inputs.burn_cell.VODE
networks/subch2/physical_constants.f90
networks/subch2/reaclib_rate_metadata.dat
networks/subch2/reaclib_rates.F90
networks/subch2/reaclib_rates.H
networks/subch2/subch2.py
networks/subch2/table_rates.F90
networks/subch2/table_rates.H
networks/subch2/table_rates_data.cpp
networks/subch2/table_type.H
commit eadaf261e1899dd099ab79ed4fe5a12266e08186
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 22 13:43:37 2021 -0500
bail if the primary species isn't defined (#804)
unit_test/react_util.H
commit 4246ae09348b4fdbc29ce36452d7d0f1c4817ea9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 22 11:56:06 2021 -0500
store y_save before attempting any steps (#815)
we were storing it in the step trial loop, which meant if there
were successive failures, then we would use the old failed state
as the reference to check the increase in species against. This
make the species step rejection stuff not work reliably.
integration/VODE/vode_dvstep.H
commit d70fa26c5afe90e9cb0bd450d2f52093221f6d41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 22 11:29:33 2021 -0500
add inputs that causes SDC integration fail with step rejection (#814)
if we uncomment out the logic in vode_dvstep.H that rejects a step if
the change in a species from one step to the next is too large, then
this inputs fails
unit_test/burn_cell_sdc/inputs_subch2_failure_stepreject
commit 1efbad22d915ba76fb4b9a9c89fd1fd63213c4d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 22 11:29:14 2021 -0500
add USE_MICROPHYSICS_DEBUG that defines MICROPHYSICS_DEBUG (#817)
Make.Microphysics
commit ecbefd91530c6f114f6a1f0bfcd439e69b80ce0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 22 11:13:05 2021 -0500
add a new style plot of this network using latest pynucastro (#816)
networks/subch2/network_plot.py
commit e105f584217894e3e222006493af02ce5c93e9a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 16 10:50:25 2021 -0500
some burn_cell_sdc changes (#813)
these gives more flexibility in creating the inputs for burn_cell_sdc
from an integration failure
unit_test/burn_cell_sdc/_parameters
unit_test/burn_cell_sdc/burn_cell.H
unit_test/burn_cell_sdc/parse_integration_failure.py
commit b203dc8d619051580b88a3dc535c305359a452c5
Merge: 323535bb d492bc39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 6 14:00:41 2021 -0400
Merge branch 'main' into development
commit 323535bbdccb8b3137ce0dda369723de604bcdfd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 4 13:41:31 2021 -0400
Fix ecsn (#812)
regenerate ECSN so it actually works
it looks like we changed how inits are done, but never update this.
networks/ECSN/NETWORK_PROPERTIES
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/ecsn_network_generation.py
networks/ECSN/reaclib_rate_metadata.dat
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/ECSN/xin.pynucastro.128
networks/ECSN/xin.pynucastro.16
networks/ECSN/xin.pynucastro.256
networks/ECSN/xin.pynucastro.32
networks/ECSN/xin.pynucastro.64
commit f44b26902eb837642afa000ab2eda22be6b1c471
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 4 13:01:24 2021 -0400
regenerate -- now the .dat files are automatically caught by our build system (#811)
networks/ignition_reaclib/URCA-simple/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/inputs.burn_cell.VODE
networks/ignition_reaclib/URCA-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
commit bbfb0c61a259c175674aeb546cc352e96bbf6484
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 4 11:38:51 2021 -0400
add inputs for nova and ECSN (#810)
also remove tmax -- it is not used for this test
unit_test/test_rhs/_parameters
unit_test/test_rhs/inputs_aprox13
unit_test/test_rhs/inputs_aprox19
unit_test/test_rhs/inputs_aprox21
unit_test/test_rhs/inputs_ecsn
unit_test/test_rhs/inputs_ignition_simple
unit_test/test_rhs/inputs_nova
unit_test/test_rhs/inputs_powerlaw
unit_test/test_rhs/inputs_rprox
unit_test/test_rhs/inputs_triple_alpha_plus_cago
commit d492bc397beb07cf5772851b645ac7f8ee157061
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 1 09:32:25 2021 -0400
update for 21.11
CHANGES.md
commit 02a8f1ef0250df29d26cf06b6ec77033b88d0b97
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 30 15:18:20 2021 -0400
fix the Fortran Jacobian wrapper for J_E_E (#805)
we were not accessing the energy component
interfaces/fortran_to_cxx_actual_rhs.H
commit cb3629ec68e835a5dfe65606f71116f6b0491e78
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 29 17:49:18 2021 -0400
use a more general strategy for linking net tables (#803)
Make.Microphysics_extern
commit e9ec1e1a25f4ad938286d2a62e0c4472769f955c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 22 09:40:11 2021 -0400
fix the size of the Jac when zeroing (#801)
networks/powerlaw/actual_rhs.H
commit 64328b5e7521c7e2f94bc9fbeff4d2608a632750
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 22 06:11:52 2021 -0700
Abort if helm_table.dat is not found (#800)
EOS/helmholtz/actual_eos.H
commit c09d0dc285f0b109c0f9b73816753476443d0354
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 16 17:33:41 2021 -0700
Remove unused density derivatives in aprox19 (#796)
networks/aprox19/actual_rhs.H
commit 3edc8a37dbeb52511f82ce504eaa8cd7020c1cb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 16 16:35:14 2021 -0400
AMREX_USE_CUDA -> AMREX_USE_GPU (#795)
interfaces/extern_probin.template
commit 478cb168702498500de39e452326d9b35c64080e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 16 13:21:43 2021 -0700
Fix typo in header guard (#794)
rates/aprox_rates_data.H
commit b39b6643420b051cf265a76cc03ff900865fa1c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 16 13:14:08 2021 -0700
AMREX_USE_CUDA -> AMREX_USE_GPU (#793)
EOS/ztwd/actual_eos.H
integration/ForwardEuler/actual_integrator.H
integration/QSS/actual_integrator.H
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_type.H
commit d99c152c84b1bef8eaabddae005a67532b66a891
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 16 13:05:58 2021 -0700
Explicit set dedr to zero in Tillotson EOS (#792)
EOS/tillotson/actual_eos.H
commit 4570b42a2d3f367ac0adbbb477f378bc629adeb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 15 17:49:32 2021 -0400
fix the substep computation for burn_cell (#784)
we were not doing the correct thing for tfirst = 0.0 or nsteps = 1
unit_test/burn_cell/burn_cell.H
commit ba8badd4456e4ed20ab58c551cce6cd044439761
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 15 14:59:33 2021 -0400
fix logical Fortran "gets" when we build with Fortran support (#789)
we need to cast them to int before passing back to C++
the current method was working fine with GNU, but not Intel compilers
util/build_scripts/runtime_parameters.py
commit c9ba4af42f7cd19f2ae9651b2362e4d705e3650c
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 15 08:52:50 2021 -0700
Remove dratdumdy arrays from aprox19 (#785)
The functionality was removed in #686, this just removes the unnecessary dead weight memory.
This changes the Jacobian for aprox19. It turns out that in #567 I forgot to turn off many of the dratdumdy1 terms in aprox19 as I had intended. So this effectively completes what I meant to do at the time.
networks/aprox19/actual_network.H
networks/aprox19/actual_rhs.H
commit 350046b066c130481d913fb13168c34732a44491
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 15 11:51:36 2021 -0400
get simplified-SDC working with Fortran nets (#786)
integration/utils/numerical_jacobian.H
commit c7c2897fab7d30a0f7cf9f2c88b60d9b42a80e6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 8 10:15:19 2021 -0400
eliminate more empty probin files (#782)
unit_test/test_aprox_rates/input_aprox_rates
unit_test/test_aprox_rates/probin
unit_test/test_screening/inputs
unit_test/test_screening/probin
commit 5bae8e06f0cf8e477be5931800486d41f807f42f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Oct 7 07:39:46 2021 -0700
Merge extra species into species enum, appended at end (#781)
Following up on #779, the "extra" species are now appended to the end of the regular species in various places, including the species enumerator, and the aion and zion arrays. This will make it easy to write loops that do the same thing over the real and extra species by just looping from 1 to NumSpecTotal instead of 1 to NumSpec. Since these are appended at the end, existing code that uses aion and zion in various places will not break, since those loops already explicitly go from 1 to NumSpec. Pasted below is an example of what iso7's enumerator now looks like; the other networks remain unchanged. In this example we have Be8=8, Ca40=9, Ti44=10, NumberTotalSpecies=10, and NumberExtraSpecies=3, as desired.
namespace Species {
enum NetworkSpecies {
He4=1,
C12,
O16,
Ne20,
Mg24,
Si28,
Ni56,
NumberSpecies=Ni56,
Be8,
Ca40,
Ti44,
NumberExtraSpecies=Ti44-Ni56+1,
NumberTotalSpecies=Ti44
};
}
networks/general_null/network_header.template
networks/general_null/write_network.py
networks/iso7/actual_rhs.H
networks/iso7/iso7.net
commit 36953398f5ce5815d346ff06e0627e4d972a83b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 5 13:01:19 2021 -0700
Add concept of extra species that do not directly react (#779)
We can now define additional auxiliary species to the network that aren't directly reacting but are used in intermediate rate calculations (such as the Ca40 + He4 -> Ti44 intermediate rate used in iso7 which is used to construct the overall Si28 -> Ni56 rate).
networks/general_null/network_header.template
networks/general_null/write_network.py
networks/iso7/actual_rhs.H
networks/iso7/iso7.net
commit 63461bac00826169232bb9dca1fb6c1ad45270d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 2 21:48:43 2021 -0400
remove probin stub -- that was a temporary hack (#778)
we no longer read the file if it doesn't exist
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_aprox13
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_aprox19.nse_disabled
unit_test/test_react/inputs_aprox19_nse
unit_test/test_react/inputs_aprox21
unit_test/test_react/inputs_ignition
unit_test/test_react/inputs_ignition_chamulak
unit_test/test_react/inputs_iso7
unit_test/test_react/inputs_nova
unit_test/test_react/inputs_powerlaw
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_sn160
unit_test/test_react/inputs_xrb_simple
unit_test/test_react/probin
commit 679515b1a69361bcec7bf2f40884d53a9e23c68c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 2 21:43:42 2021 -0400
eliminate probin from test_rhs (#777)
unit_test/test_rhs/inputs_aprox13
unit_test/test_rhs/inputs_aprox19
unit_test/test_rhs/inputs_aprox21
unit_test/test_rhs/inputs_ignition_simple
unit_test/test_rhs/inputs_iso7
unit_test/test_rhs/inputs_iso7_table
unit_test/test_rhs/inputs_powerlaw
unit_test/test_rhs/inputs_rprox
unit_test/test_rhs/inputs_triple_alpha_plus_cago
unit_test/test_rhs/probin.aprox13
unit_test/test_rhs/probin.aprox19
unit_test/test_rhs/probin.aprox21
unit_test/test_rhs/probin.ignition_simple
unit_test/test_rhs/probin.iso7
unit_test/test_rhs/probin.powerlaw
unit_test/test_rhs/probin.rprox
unit_test/test_rhs/probin.triple_alpha_plus_cago
commit bac966a2b4e977e42d7b5fce8f1a797527421348
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 1 12:29:05 2021 -0700
Revert usage of C++17 inline variables (#776)
EOS/breakout/Make.package
EOS/breakout/actual_eos.H
EOS/breakout/actual_eos_data.H
EOS/breakout/actual_eos_data.cpp
EOS/helmholtz/Make.package
EOS/helmholtz/actual_eos.H
EOS/helmholtz/actual_eos_data.H
EOS/helmholtz/actual_eos_data.cpp
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.H
EOS/multigamma/actual_eos_data.H
EOS/multigamma/actual_eos_data.cpp
EOS/polytrope/Make.package
EOS/polytrope/actual_eos.H
EOS/polytrope/actual_eos_data.H
EOS/polytrope/actual_eos_data.cpp
interfaces/Make.package
interfaces/eos_data.H
interfaces/eos_data.cpp
screening/Make.package
screening/screen.H
screening/screen_data.H
screening/screen_data.cpp
commit 07fcd8821a712bca60a14b57e2ad1abc6085f3e3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu Sep 30 15:47:35 2021 -0700
General null gpu (#775)
* general_null on GPU. WIP.
* AMREX_FORCE_INLINE
* Fix cuda compile issue
Co-authored-by: Doreen Fan <dfan@lbl.gov>
networks/general_null/Make.package
networks/general_null/actual_network.H
networks/general_null/actual_network_data.cpp
networks/general_null/actual_rhs.H
networks/general_null/actual_rhs_data.cpp
commit 4099b681799914ca07152c72f4d43bef214eabc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 29 19:04:01 2021 -0400
add a fixed T to SDC to support drive_initial_convection (#772)
integration/VODE/vode_type_simplified_sdc.H
interfaces/burn_type.H
commit 0c1e3c3c4b03b74e836dd773b6f4857dde10d6cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 27 09:47:02 2021 -0400
don't compile powerlaw Fortran unless we ask (#774)
networks/powerlaw/Make.package
commit 11046e6d182c79615d854111d0691e8b722930b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 26 10:11:13 2021 -0700
Do density dependence of analytic rates using new function (#771)
Do density dependence of analytic rates using new function. As with #767 we aren't yet doing this with the Ca40<->Ti44 rate since that requires additional work.
networks/iso7/actual_rhs.H
commit ed4cc06a27fcf5e0041e747410556160be2bb62b
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Sep 21 17:08:49 2021 +0100
Add action to compile code when pushed to remote (#773)
This compiles the two tests burn_cell and test_eos when changes are made to the Microphysics repo.
.github/workflows/compile_action.yml
.github/workflows/find_changed_files.py
commit 919d59827ea001a44ff7d934e58eb9e3d313fe60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 15 17:26:03 2021 -0400
remove integrator_sdc.H -- it is redundant (#768)
integration/integrator.H
integration/integrator_sdc.H
interfaces/burner.H
unit_test/test_sdc/main.cpp
commit 3aeed2036de9d945856a324c9beb95a8dafaeb9f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 15 08:19:56 2021 -0700
iso7 28/∞ (#767)
Adds a function to automatically compute density dependence of tabulated rates.
The Ca40 + He4 <-> Ti44 rate is not dealt with yet since it doesn't have an entry in rhs_data().
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
commit da0dc63cba5c36276ef2958218181ed179845ef3
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Sep 15 14:28:38 2021 +0100
add css files to conf.py (#770)
sphinx_docs/source/conf.py
commit 7473574600cc56c53bfb900e248607c4a30f1dd8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 12 14:48:18 2021 -0400
remove Fortran support from test_eos (#757)
also get rid of the probin's
unit_test/test_eos/GNUmakefile
unit_test/test_eos/Make.package
unit_test/test_eos/eos_util_F.F90
unit_test/test_eos/input_eos
unit_test/test_eos/input_eos.multigamma
unit_test/test_eos/input_eos.polytrope
unit_test/test_eos/input_eos.tillotson
unit_test/test_eos/main.cpp
unit_test/test_eos/probin
unit_test/test_eos/probin.multigamma
unit_test/test_eos/probin.polytrope
unit_test/test_eos/probin.tillotson
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/variables_F.F90
commit 7cbb7f891f426360597205762a26d3cd802fcb06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 12 13:01:27 2021 -0400
test_jac only works in C++, so eliminate Fortran compilation (#759)
also get rid of the probin files
unit_test/test_jac/GNUmakefile
unit_test/test_jac/Make.package
unit_test/test_jac/inputs_aprox13
unit_test/test_jac/main.cpp
unit_test/test_jac/probin.aprox13
unit_test/test_jac/test_react_F.H
commit 52f03861573a09f4a2a901ab5f54f81f419b199d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 12 12:50:32 2021 -0400
don't bailout due to NSE if t > tout (#766)
integration/VODE/vode_dvode.H
commit e1b86481be7462849685ece53aa7c815638d367b
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Sun Sep 12 17:50:02 2021 +0100
Template the eos_type output operator (#764)
This templates the << operator for the structs in eos_type.H, adding checks to see whether variables exist in the struct so it should now work for any of the eos structs defined in that file.
This addresses #629.
interfaces/eos_type.H
commit faab9e9c3c7b1ad264eb675d50f97bec197ea0f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 10 11:41:11 2021 -0400
remove unused probin (#758)
unit_test/test_sdc/probin.aprox19.nse
commit 9bff71a294fd4c744ea8f70d187ff570b82d3046
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 9 17:54:08 2021 -0700
Move identical particle factors into rates (#583)
networks/aprox21/actual_rhs.H
commit 3fe8f9902c84c78fcda61a514881961f70b7d94a
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 9 17:47:47 2021 -0700
Use bulk multiplication interface for react_boost (#735)
integration/VODE/vode_rhs.H
integration/VODE/vode_rhs_simplified_sdc.H
commit 744e8e6d38cbcd5bf47afb2728a925ee8e227da0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Sep 2 07:49:29 2021 -0700
Convert iso7 entirely to new-style rates (#716)
iso7 is converted entirely to the new-style rates where we explicitly separate out the forward and reverse terms. To go along with this some quantities are renamed and we maintain "legacy" species_rhs and species_jac interfaces for the other networks which haven't been converted to this style yet. This should not change results.
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
networks/rate_type.H
commit 749d5d0ee02565ca8f0f1907c9f3d182b293feb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 1 08:15:16 2021 -0400
update changes for 21.09
CHANGES.md
commit b079ee86ca830cc2622d192fb9e7f21b80bcfc9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 22:38:12 2021 -0400
extend the NSE relax criteria to C and O (#754)
networks/aprox19/nse.H
commit aec977c3f02b3e7e38d408188e7e9fbce6814a20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 22:30:58 2021 -0400
if we bailout due to NSE, properly set the time (#755)
the logic there is that when we exit VODE after this bailout, in the actual_integrator_simplified_sdc.H we use vstate.t to make the state consistent. but it was not being set properly (at all?), since that is only really set at the end.
integration/VODE/vode_dvode.H
commit 5315568c118711f50a1b70efaa27d0208b0db06a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 21:29:04 2021 -0400
don't do the NSE bailout if there is no time remaining (#753)
this is a potential corner case
interfaces/burner.H
commit 739331809f000965d77fcdca70685c88462c57b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 31 11:46:41 2021 -0400
add a slightly more extensive nova network (#751)
this includes all of the nuclei that Ami and Jordi use
networks/nova2/Make.package
networks/nova2/NAUX_NETWORK
networks/nova2/NETWORK_PROPERTIES
networks/nova2/_parameters
networks/nova2/actual_network.F90
networks/nova2/actual_rhs.F90
networks/nova2/inputs.burn_cell.VODE
networks/nova2/nova.png
networks/nova2/nova2.py
networks/nova2/physical_constants.f90
networks/nova2/pynucastro.net
networks/nova2/reaclib_rate_metadata.dat
networks/nova2/reaclib_rates.F90
networks/nova2/table_rates.F90
commit 1d97ce466025490ab6a63a75831edbc48df4e580
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 30 09:32:54 2021 -0400
fix compilation with Strang + NSE (#752)
interfaces/burner.H
commit 71ae6bfac1cef1902bb94c7e4177df90559bbb8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 27 11:36:53 2021 -0400
fix mathjax rendering (#750)
sphinx_docs/source/conf.py
commit d5a72a5d3ec2f831c2bf327c39d16ff8e4472c3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 27 11:36:42 2021 -0400
sdc integration failure zone verbosity (#749)
integration/VODE/actual_integrator_simplified_sdc.H
interfaces/burner.H
commit cf60f17d87ceb781e79ce6d11844abe93058edf0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 17 10:45:56 2021 -0400
add iomanip header for std::setprecision() (#748)
interfaces/burn_type.H
commit 2bdbae7f30351c36303779ca71b24edac4150948
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 16 15:35:32 2021 -0400
make the SDC failure output easier to read (#743)
integration/VODE/actual_integrator_simplified_sdc.H
commit 684046fa0109faf99b24fc8b362ce499201c3cef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 16 15:35:16 2021 -0400
make the burn_state << output have more precision (#746)
also for SDC, label the important terms
interfaces/burn_type.H
commit 3a9725219b4ce8c461f09a2542361162aec1d3cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 16 15:34:56 2021 -0400
make some references const (#747)
integration/VODE/vode_type_simplified_sdc.H
commit a9b1dc8bcfaef0ba44828e04d44d0a9f7af2bc28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 16 15:34:36 2021 -0400
add a single zone SDC burn test (#744)
this will help investigate SDC failures
unit_test/burn_cell_sdc/GNUmakefile
unit_test/burn_cell_sdc/Make.package
unit_test/burn_cell_sdc/_parameters
unit_test/burn_cell_sdc/burn_cell.H
unit_test/burn_cell_sdc/inputs_aprox19
unit_test/burn_cell_sdc/inputs_aprox19_failure
unit_test/burn_cell_sdc/main.cpp
unit_test/burn_cell_sdc/parse_integration_failure.py
commit 9b47046a8ec4f7dd90b0495c8b53b8e0e65d3d54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 11 14:32:30 2021 -0400
add a check on the perturbed T in the numerical Jacobian (#741)
this should not be needed, but some times VODE explores things early on
and bad things can happen.
integration/utils/numerical_jacobian.H
commit 588989a0a00f43386050eed49ff3cea00e56b645
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 6 09:31:29 2021 -0400
redo the numerical Jacobian (again) (#738)
now we difference in terms of T, X_k, but convert to e, X_k
integration/utils/numerical_jacobian.H
commit 8a0983ef8c4148d5bea587ed5590578439360a03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 6 09:30:58 2021 -0400
only check for NSE bailout after 10 steps (#739)
VODE sometimes does some initial exploration that is rejected, but may
trigger the NSE bailout, resulting in a very bad state with huge NSE
energy release. Now we instead don't check for the NSE bailout until after
10 steps have been taken. The number 10 is arbitrary, but seems sufficient
for VODE to have settled down.
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_dvode.H
integration/VODE/vode_type.H
commit a46177631cb323e95c9cb855b2219d092a31b50f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 4 11:11:41 2021 -0400
if SDC integration fails, output more information about the state (#737)
integration/VODE/actual_integrator_simplified_sdc.H
commit 997f5801dce3427fd94234cf4e77d0bdd6e497c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 1 20:43:43 2021 -0400
update changes
CHANGES.md
commit edc950da91a7c94e2870d6c71b13838d833f36e4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 31 14:43:04 2021 -0700
Add option for uniform composition in unit tests (#734)
This is useful for performance testing
unit_test/react_util.H
unit_test/test_jac/_parameters
unit_test/test_jac/main.cpp
unit_test/test_react/_parameters
unit_test/test_react/main.cpp
unit_test/test_rhs/_parameters
unit_test/test_rhs/main.cpp
unit_test/test_sdc/_parameters
unit_test/test_sdc/main.cpp
commit 98024992d4ff7fe76463460fe57592b1a90e9e55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 31 10:52:17 2021 -0400
for the numerical Jacobian, fix some of the thermodynamics (#728)
in particular, when we perturb X, T changes
integration/VODE/vode_rhs_simplified_sdc.H
integration/utils/numerical_jacobian.H
commit 4b07ed851220fa525f5eac7edfdb8e00afd0649a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 31 07:38:13 2021 -0700
Fix aprox13 actual_matrix references to net_itemp (#732)
networks/aprox13/actual_matrix.H
commit 6c8b91696a4117428eb3bb57893ae4cf9d86c187
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 31 07:37:54 2021 -0700
Work around lack of long double support on Power9 (#730)
screening/screen.H
util/microphysics_math.H
commit ca26122c2f02b6b8ef462004294c8b9316eb0e52
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 31 06:51:47 2021 -0700
Turn off tiling for GPUs in test_react (#733)
unit_test/test_react/main.cpp
commit 41facbcb8a736f9aab73205fe3e7914a364a4d37
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 29 17:44:11 2021 -0700
Switch to constexpr screen factors evaluation (#727)
Switch to constexpr screen factors evaluation
networks/aprox13/actual_rhs.H
networks/aprox13/actual_rhs_data.cpp
commit f2e656f2d0a71bc3befda72529e7280ed5a1f21f
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 29 17:07:19 2021 -0700
Add a constexpr version of screen5 (#726)
An overload of screen5 is added that accepts as argument a screen_factors_t, as well as a constexpr function that can do a compile-time evaluation of these factors (depends on the new support added in #725). This allows the constant screening factors to be evaluated inline in the screening routine at compile time without needing the separate set_up_screening_factors() step.
screening/screen.H
commit 38cce7c2fa0f35bbe096e5ea8d26c47bf233ef98
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 29 09:02:41 2021 -0700
Add constexpr function versions of aion and zion (#723)
networks/general_null/network_header.template
networks/general_null/write_network.py
commit f508bbfa06e2844e2f74cdf53657a7a9187ef2ca
Merge: 7cc3525c fafd4a4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 29 10:06:26 2021 -0400
Merge pull request #725 from maxpkatz/add_gcem
Add the gcem library for compile-time math evaluation
There are some cases where we want to do compile-time evaluation of math functions (exp, pow, log) in constexpr functions. These functions are not constexpr in the C++ standard, so we need to turn to a community implementation. The gcem library here provides this:
https://github.com/kthohr/gcem
This library is added as a git subtree. A subtree is preferred to a submodule in this case because I don't expect we will need to update this dependency often and adding a submodule would result in breaking changes to the user environment. For reference here is how I added this code (from the top-level directory):
git remote add -f gcem https://github.com/kthohr/gcem.git
git subtree add --prefix util/gcem gcem master --squash
commit fafd4a4a38c7d663fd5426c79e0dcd9ed5bbe6fa
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 28 21:31:25 2021 -0700
Add gcem to Make.package
util/Make.package
commit 9843c607efdd85a8feaef557a32f907114c5c749
Merge: 7cc3525c b904ef8b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 28 21:24:00 2021 -0700
Merge commit 'b904ef8bedaa64a980aff33dce4f2a1ae9d9dd68' as 'util/gcem'
commit b904ef8bedaa64a980aff33dce4f2a1ae9d9dd68
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 28 21:24:00 2021 -0700
Squashed 'util/gcem/' content from commit 8d0e62d9
git-subtree-dir: util/gcem
git-subtree-split: 8d0e62d9c9c47dfad2cb2d800281908cf7ff16c6
.appveyor.yml
.gitignore
.lgtm.yml
.readthedocs.requirements.txt
.readthedocs.yml
.travis.yml
CMakeLists.txt
LICENSE
NOTICE.txt
README.md
binder/environment.yml
cmake_files/gcemConfig.cmake.in
contributors.txt
docs/Doxyfile
docs/Makefile
docs/environment.yml
docs/make.bat
docs/source/_static/main_stylesheet.css
docs/source/api/algorithms.rst
docs/source/api/basic_functions.rst
docs/source/api/hyperbolic_functions.rst
docs/source/api/math_index.rst
docs/source/api/special_functions.rst
docs/source/api/trigonometric_functions.rst
docs/source/conf.py
docs/source/examples.rst
docs/source/index.rst
include/gcem.hpp
include/gcem_incl/abs.hpp
include/gcem_incl/acos.hpp
include/gcem_incl/acosh.hpp
include/gcem_incl/asin.hpp
include/gcem_incl/asinh.hpp
include/gcem_incl/atan.hpp
include/gcem_incl/atan2.hpp
include/gcem_incl/atanh.hpp
include/gcem_incl/beta.hpp
include/gcem_incl/binomial_coef.hpp
include/gcem_incl/ceil.hpp
include/gcem_incl/copysign.hpp
include/gcem_incl/cos.hpp
include/gcem_incl/cosh.hpp
include/gcem_incl/erf.hpp
include/gcem_incl/erf_inv.hpp
include/gcem_incl/exp.hpp
include/gcem_incl/expm1.hpp
include/gcem_incl/factorial.hpp
include/gcem_incl/find_exponent.hpp
include/gcem_incl/find_fraction.hpp
include/gcem_incl/find_whole.hpp
include/gcem_incl/floor.hpp
include/gcem_incl/fmod.hpp
include/gcem_incl/gcd.hpp
include/gcem_incl/gcem_options.hpp
include/gcem_incl/incomplete_beta.hpp
include/gcem_incl/incomplete_beta_inv.hpp
include/gcem_incl/incomplete_gamma.hpp
include/gcem_incl/incomplete_gamma_inv.hpp
include/gcem_incl/is_even.hpp
include/gcem_incl/is_finite.hpp
include/gcem_incl/is_inf.hpp
include/gcem_incl/is_nan.hpp
include/gcem_incl/is_odd.hpp
include/gcem_incl/lbeta.hpp
include/gcem_incl/lcm.hpp
include/gcem_incl/lgamma.hpp
include/gcem_incl/lmgamma.hpp
include/gcem_incl/log.hpp
include/gcem_incl/log1p.hpp
include/gcem_incl/log2.hpp
include/gcem_incl/log_binomial_coef.hpp
include/gcem_incl/mantissa.hpp
include/gcem_incl/max.hpp
include/gcem_incl/min.hpp
include/gcem_incl/neg_zero.hpp
include/gcem_incl/pow.hpp
include/gcem_incl/pow_integral.hpp
include/gcem_incl/quadrature/gauss_legendre_30.hpp
include/gcem_incl/quadrature/gauss_legendre_50.hpp
include/gcem_incl/round.hpp
include/gcem_incl/sgn.hpp
include/gcem_incl/signbit.hpp
include/gcem_incl/sin.hpp
include/gcem_incl/sinh.hpp
include/gcem_incl/sqrt.hpp
include/gcem_incl/tan.hpp
include/gcem_incl/tanh.hpp
include/gcem_incl/tgamma.hpp
include/gcem_incl/trunc.hpp
notebooks/gcem.ipynb
tests/CMakeLists.txt
tests/Makefile
tests/abs.cpp
tests/acos.cpp
tests/acosh.cpp
tests/asin.cpp
tests/asinh.cpp
tests/atan.cpp
tests/atan2.cpp
tests/atanh.cpp
tests/binomial_coef.cpp
tests/copysign.cpp
tests/cos.cpp
tests/cosh.cpp
tests/cov_check
tests/erf.cpp
tests/erf_inv.cpp
tests/exp.cpp
tests/expm1.cpp
tests/factorial.cpp
tests/fmod.cpp
tests/gcd.cpp
tests/gcem_tests.hpp
tests/incomplete_beta.cpp
tests/incomplete_beta_inv.cpp
tests/incomplete_gamma.cpp
tests/incomplete_gamma_inv.cpp
tests/is_odd.cpp
tests/lcm.cpp
tests/lgamma.cpp
tests/log.cpp
tests/log1p.cpp
tests/log2.cpp
tests/log_binomial_coef.cpp
tests/other.cpp
tests/pow.cpp
tests/rounding.cpp
tests/run_tests
tests/signbit.cpp
tests/sin.cpp
tests/sinh.cpp
tests/sqrt.cpp
tests/tan.cpp
tests/tanh.cpp
tests/tgamma.cpp
commit 7cc3525c7f075a0d2cdd432dc1f916faa1c3cb74
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 26 21:22:26 2021 -0400
the SDC Jacobian reduces to just the reaction Jacobian in terms of X, e (#717)
integration/VODE/vode_jac_util_simplified_sdc.cpp
commit 7d917866f49cc02d71959398d2a4ded86f1fb8b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 26 21:21:40 2021 -0400
fix the case of an immediate NSE bailout (#722)
if we bailout after the first step, then t = 0 and we generate
an Inf if we try to compate an energy generation rate. Now we
protect against this.
integration/VODE/actual_integrator_simplified_sdc.H
commit b9a5ab1222999753aaacf9e4ee3446c9cacfdd2e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 25 15:00:50 2021 -0400
Use auto species_rhs for d(rate)/dT in Jacobian (#721)
Use auto species_rhs for d(rate)/dT in Jacobian
This will cause a test suite diff. The reason is that there was a bug in #699: I didn't remember that this part of aprox13 hadn't yet been converted to the generic species_rhs functionality, so I didn't remove the identical particle factor from this rhs() function in aprox13 to compensate. As a result that did actually substantially change the d/dE terms in the Jacobian for aprox13 as indicated in test_rhs, I just didn't notice it at the time: http://groot.astro.sunysb.edu/Microphysics/test-suite/gfortran/2021-07-22-002/test_rhs_aprox13.html. This change gets the identical particle factor right automatically.
networks/aprox13/actual_rhs.H
commit 6dbd4d09f88694018e93c80d6bc4ac2f0da60c17
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 24 20:40:52 2021 -0400
Add intermediate links to NumRatesFR (#720)
networks/aprox13/actual_network.H
commit d404b301b9e06d0294a211813ab3a8c0a2507503
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 24 20:20:46 2021 -0400
fix test_sdc compilation (#719)
burn_state.T_from_eden no longer exists
unit_test/test_sdc/react_zones.H
commit d1932ac91b0b7d996cf23868e04aa4c9d143abb7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 24 20:15:03 2021 -0400
Give more descriptive names to intermediate reaction links (#718)
networks/aprox13/actual_network.H
networks/aprox13/actual_rhs.H
commit c8d4cbdf88e260971df50d5cdf2d958d2475688e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 23 11:19:26 2021 -0400
eliminate (rho E) from the simplified-SDC integration system (#712)
We now only integrate (rho X) and (rho e) directly. At the end of integration, (rho E) is updated conservatively. This also greatly simplifies the form of the Jacobian.
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_dvstep.H
integration/VODE/vode_jac_util_simplified_sdc.cpp
integration/VODE/vode_type_simplified_sdc.H
interfaces/burn_type.H
commit 7149613002ccf2abbe1e52e2917679b867e4a141
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 22 13:50:52 2021 -0400
Move identical particle factor out of rate (#699)
This is now computed automatically based on the reaction properties.
interfaces/rhs_utilities.H
networks/aprox13/actual_rhs.H
networks/iso7/actual_rhs.H
commit 476be7d4e91584985cabe0746d55fd53621fbeb6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 22 10:33:13 2021 -0400
Store unused reverse rates (#693)
Store unused reverse rates in the rates array -- this will end up happening automatically in a subsequent change anyway. This change has no effect since these rates are set to zero in the rate routines.
networks/iso7/actual_rhs.H
commit db6b44397a4bf2ab36f6ca221c4623900ffbf484
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 22 10:28:02 2021 -0400
regenerate Urca with latest pynucastro (#713)
networks/ignition_reaclib/URCA-simple/23Na-23Ne_electroncapture.network.dat
networks/ignition_reaclib/URCA-simple/23Ne-23Na_betadecay.network.dat
networks/ignition_reaclib/URCA-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/URCA-simple/README.md
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/inputs.burn_cell.VODE
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_reaclib/URCA-simple/xin.urca.128
networks/ignition_reaclib/URCA-simple/xin.urca.16
networks/ignition_reaclib/URCA-simple/xin.urca.256
networks/ignition_reaclib/URCA-simple/xin.urca.32
networks/ignition_reaclib/URCA-simple/xin.urca.64
commit ad19a7f780d0e0eb6698c1c88d860382ea7c3e8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 22 10:27:43 2021 -0400
remove the unused run_prefix parameter (#714)
unit_test/test_jac/_parameters
unit_test/test_react/_parameters
unit_test/test_rhs/_parameters
unit_test/test_sdc_vode_rhs/_parameters
unit_test/test_sdc_vode_rhs/probin.aprox19
commit dac0763ca7da7bcf0a21d3f0625e040f4a301494
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 22 08:32:05 2021 -0400
iso7 25/∞ (#625)
Convert tabulated rates to new rate indexing scheme
networks/iso7/actual_rhs.H
networks/iso7/actual_rhs_data.cpp
commit 2579d35057c86bc5d9536874c8b778f8be6fecaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 21 15:05:23 2021 -0400
remove fortran from test_sdc (#715)
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/inputs_aprox13
unit_test/test_sdc/inputs_aprox19.no_nse
unit_test/test_sdc/inputs_aprox19.nse
unit_test/test_sdc/probin
commit f1bbcfca84d0a1a8856eb93484697c0e5cd975f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 18 22:05:30 2021 -0400
make the numerical Jacobian more robust (#660)
we now use the algorithm from LSODE / VODE. In particular, you can find the description of this implementation in Radhakrishnan and Hindmarsh, "Description and Use of LSODE, the Livermore Solver for Ordinary Differential Equations", section 3.4.5
integration/VODE/vode_rhs_simplified_sdc.H
integration/_parameters
integration/utils/numerical_jacobian.H
unit_test/test_jac/jac_zones.H
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_aprox19.nse_disabled
unit_test/test_react/inputs_aprox21
unit_test/test_react/inputs_rprox
unit_test/test_react/old/inputs_aprox19.BS
unit_test/test_react/test_network_combinations.py
commit 18f87313ecd9ebde183b5a49077ec1bbc373c160
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 18 12:53:53 2021 -0400
some clean-ups of the simplified-SDC code paths (#688)
in particular, this now zeros the rates if the temperature is out of bounds.
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
commit cd347c7941765d72e2ff8c02d5d758f6dfb54bfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 18 12:53:19 2021 -0400
add an NSE relax factor, network.nse_relax_factor (#702)
if the burn fails and we are close to NSE, we relax the NSE check
by this factor (< 1) to allow us to enter NSE.
interfaces/burner.H
networks/aprox19/_parameters
networks/aprox19/nse.H
commit b73b6f8c2ec62db3d776da697c3ea8859d65e947
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 12 09:48:49 2021 -0400
fix the scaling of species before the EOS call for SDC (#707)
this fixes an issue with #663
integration/VODE/vode_type_simplified_sdc.H
commit adb6b405e38654199edf47106d83db17ba118ac6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 8 11:29:25 2021 -0400
for SDC+NSE, after the renormalize of X, we need to update aux (#663)
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
commit 9fa4eb789393948b3fdc9dfe1601171e6b63406c
Merge: 7f332d21 f2da8cec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 1 09:15:53 2021 -0400
Merge branch 'development'
commit 7f332d214b11445a92674187974ba496d8b05a7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 1 09:15:42 2021 -0400
21.07 changes
CHANGES.md
commit f2da8cec7b2037a224811bc580a706ed63d48829
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 29 10:22:12 2021 -0400
add amrex:: prefix to Real (#704)
interfaces/microphysics_F.H
commit 0f336e49b71110f3dadd35f29347a0ae7bc8c3e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 24 08:02:32 2021 -0700
Use automatic analytic Jacobian functionality (#700)
We now use the automatic analytic Jacobian functionality.
networks/aprox13/actual_rhs.H
commit e78e537e395eea91609cfeeb07f7d8f7690b608f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 22 17:16:29 2021 -0400
fix some uninitialized variables with Fortran nets from C++ (#698)
interfaces/fortran_to_cxx_actual_rhs.F90
commit 9dd68fc0556e116a3044094798ca16c988895acf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 12:48:23 2021 -0400
implement the abort_on_failure functionality (#697)
we lost this in the F90 -> C++ port
this closes #667
integration/integrator.H
integration/integrator_sdc.H
interfaces/burner.H
commit 47e588d112e0d41ca594a6e50abcd59f80774327
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 11:08:48 2021 -0400
since we've merged the c12ag rates, modify the test_aprox_rates function calls (#695)
this also now builds C++ only
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/aprox_rates_util.cpp
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates.H
commit 97e1c0c8b38d260b5adcb15828dfb0adb5f4219c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 20 11:08:25 2021 -0400
have runtime_init bind to C so we can call it directly (#694)
interfaces/extern_probin.template
unit_test/unit_test.F90
unit_test/unit_test.H
util/build_scripts/write_probin.py
commit c70a6eb4325267a3e51a903028f1dceaf032563d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 11 21:22:55 2021 -0400
test_react now builds 0 Fortran (#692)
Make.Microphysics
constants/Make.package
networks/Make.package
unit_test/test_react/GNUmakefile
commit 521d83ac3e08f97ac4eab4cbbc1ea5b375d284f6
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 11 16:28:02 2021 -0700
Merge C12(a,g)O16 rate functions (#687)
networks/aprox13/actual_rhs.H
networks/aprox19/actual_rhs.H
networks/aprox21/actual_rhs.H
networks/iso7/actual_rhs.H
rates/aprox_rates.H
commit bbc16e10aa4d221477d34763d4ca0319edaed4d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 11 11:51:55 2021 -0400
more work on skipping Fortran build (#691)
Now test_react doesn't build any of the Fortran Microphysics by default, including the runtime parameter support.
conductivity/constant/Make.package
conductivity/constant_opacity/Make.package
conductivity/stellar/Make.package
constants/Make.package
integration/utils/Make.package
networks/Make.package
networks/aprox13/Make.package
networks/aprox19/Make.package
networks/aprox21/Make.package
networks/breakout/Make.package
networks/ignition_simple/Make.package
networks/iso7/Make.package
networks/rprox/Make.package
networks/triple_alpha_plus_cago/Make.package
networks/update_headers.py
networks/vode_example/Make.package
networks/xrb_simple/Make.package
neutrinos/Make.package
screening/Make.package
unit_test/Make.package
unit_test/test_react/GNUmakefile
unit_test/unit_test.H
unit_test/write_job_info.cpp
util/Make.package
util/build_scripts/write_probin.py
commit 40745b5fd450d5f71c48d72e35f69514bf002450
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 10 21:27:22 2021 -0400
optionally eliminate the Fortran extern.F90 (#690)
Make.Microphysics
util/build_scripts/write_probin.py
commit 1b28f911b1b5652a60ed778a6b4ba04e47a2a0d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 10 20:17:53 2021 -0400
create USE_FORT_MICROPHYSICS to enable/disable the Fortran network build (#689)
EOS/Make.package
EOS/breakout/Make.package
EOS/gamma_law/Make.package
EOS/helmholtz/Make.package
EOS/multigamma/Make.package
EOS/polytrope/Make.package
EOS/rad_power_law/Make.package
EOS/stellarcollapse/Make.package
EOS/tillotson/Make.package
EOS/ztwd/Make.package
Make.Microphysics_extern
interfaces/Make.package
interfaces/microphysics.F90
networks/Make.package
networks/general_null/Make.package
networks/general_null/write_network.py
unit_test/test_eos/Make.package
unit_test/test_eos/main.cpp
commit 2b3d75bc482bd5b2f858774b8a2e60a54a722fa3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 10 07:05:15 2021 -0700
Remove Jacobian infrastructure for d(rate)/dY (#686)
Now that #567 is done, we can remove the custom infrastructure for the Jacobian. Now in iso7, both the RHS and the Jacobian are automatically constructed from a single source of truth in actual_network.H.
interfaces/network_utilities.H
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 91d22a0e2091a8f0e26b5fa3d322f7f5f1c08ef1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 10:14:40 2021 -0400
fix the unit test compilation after the pretty_print conversion (#685)
unit_test/write_job_info.cpp
commit 324091798062f06a48f782dc25312990a3700388
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 9 09:23:33 2021 -0400
convert the job_info param tests for extern to a C++ include file (#684)
interfaces/extern_probin.template
util/build_scripts/write_probin.py
commit f80a2894a664465a6d41697f385c2fe2ff9de060
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 8 15:45:35 2021 -0700
Remove Jacobian terms that depend on d(rate)/dY (#567)
From experimentation, these don't seem to be especially helpful for most networks, and they will get in the way of the automated infrastructure for building a Jacobian from the RHS. We may be able to add them back later after all of the networks have been refactored, if needed.
networks/aprox19/actual_rhs.H
networks/aprox21/actual_rhs.H
networks/iso7/actual_rhs.H
commit 2d172fa69a774f7e58faeb248a722383a3d516e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 8 14:45:20 2021 -0400
remove some unneeded functions (#683)
update_thermodynamics already ensures that the burn_t is valid, so we don't need a vode_to_burn (or later burn_to_vode) call in vode_rhs.
integration/VODE/vode_rhs.H
commit ab110f9ce55c8aa363a0031a7bb87aff19d6b186
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 8 13:01:14 2021 -0400
move the check that the temperature is reasonable after we update thermo (#681)
previously, we were checking on the old T, not the T corresponding to the
current e that we are trying to integrate with.
integration/VODE/vode_rhs.H
commit 48a1f1c5fe1aff7db53fe26d796d7d46903883d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 7 22:10:22 2021 -0400
allow for runtime parameter arrays to be read at runtime (#680)
this adds the C++ queryarr logic to support specifying values for array
runtime parameters in an inputs file or on the commandline
util/build_scripts/runtime_parameters.py
commit 309980937ec731a1a22492185a33abd5de62b6ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 1 10:14:41 2021 -0400
highlight major changes
CHANGES.md
commit 243e667582683658c23f6995befe1c4a27dea516
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 1 06:49:48 2021 -0700
Remove make flags to use system BLAS (#675)
Make.Microphysics
README.md
networks/Make.package
util/BLAS/Make.package
util/BLAS/daxpy.f
util/BLAS/dcopy.f
util/BLAS/ddot.f
util/BLAS/dgemm.f
util/BLAS/dscal.f
util/BLAS/idamax.f
util/BLAS/license.txt
commit b67de15138b47a3c718cf92dd0bbe06f6a94f811
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 31 21:57:48 2021 -0400
for C++, replace "d" with "e" in numbers (#679)
util/build_scripts/runtime_parameters.py
commit a9051a3a150c82985bf578c670037174844ba240
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 31 20:57:09 2021 -0400
another runtime param fix for bool fortran params in C++ (#678)
util/build_scripts/runtime_parameters.py
commit fb28901b9aaf97ef162bce956e7ee9906acb255b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 30 20:48:59 2021 -0400
for C++, we need to change logical to integer for the job_info test (#677)
util/build_scripts/runtime_parameters.py
commit d988edd7b45a69362ed724ffbd119cad102d09d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat May 29 18:31:46 2021 -0400
remove the F90 rates_module (#672)
we only use the C++ version now
interfaces/microphysics.F90
networks/aprox13/Make.package
networks/aprox13/actual_rhs.F90
networks/aprox19/Make.package
networks/aprox19/actual_rhs.F90
networks/aprox21/Make.package
networks/aprox21/actual_rhs.F90
networks/iso7/Make.package
networks/iso7/actual_rhs.F90
rates/Make.package
rates/aprox_rates.F90
rates/tfactors.F90
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/aprox_rates_util_F.F90
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/variables_F.F90
unit_test/test_screening/main.cpp
commit d0b33feb85a86f39d1d3e5b423cefd1904f73e96
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon May 24 19:14:55 2021 -0700
Add Tillotson EOS for hypervelocity impacts (#654)
EOS/tillotson/Make.package
EOS/tillotson/README.md
EOS/tillotson/_parameters
EOS/tillotson/actual_eos.F90
EOS/tillotson/actual_eos.H
unit_test/test_eos/input_eos.tillotson
unit_test/test_eos/probin.tillotson
commit 185adac3a9bf0998aead4f61d43c86f4dd48710a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 24 21:49:28 2021 -0400
don't try to read probin if it doesn't exist (#674)
interfaces/extern_probin.template
commit f6a4ebb89938ce0f8eafeb56b3621e0754a7cf6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 21 16:28:24 2021 -0700
kappa_floor should only be applied to Rosseland opacity (#673)
In Castro originally the floor on kappa was only applied to the Rosseland opacity for numerical stability reasons. This change reverts to that previous behavior. This error in the port explains AMReX-Astro/Castro#1539; in that problem setup we had kappa_floor = 1.e-5, which is larger than the actual constant kappa for the Planck mean. We could still have separate floors for kappa_r and kappa_p but that would be done in a separate change.
opacity/rad_power_law/actual_opacity.H
opacity/rad_power_law/opacity_table_module.F90
commit 4d475218d09cceef441134d51d9b03a08972b0c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 16 03:57:23 2021 -0700
Remove GPU pragma ifdefs (#671)
EOS/breakout/actual_eos.F90
EOS/gamma_law/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
EOS/rad_power_law/rad_power_law.F90
integration/utils/temperature_integration.F90
interfaces/eos.F90
interfaces/eos_type.F90
networks/ECSN/actual_network.F90
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_network.F90
networks/aprox19/nse_F.F90
networks/aprox21/actual_network.F90
networks/general_null/network.template
networks/general_null/network_properties.template
networks/ignition_chamulak/actual_network.F90
networks/ignition_simple/actual_network.F90
networks/iso7/actual_network.F90
networks/iso7/actual_rhs.F90
networks/powerlaw/actual_network.F90
networks/rprox/actual_network.F90
networks/sn160/actual_network.F90
networks/sn160/reaclib_rates.F90
networks/triple_alpha_plus_cago/actual_network.F90
rates/aprox_rates.F90
screening/screen.F90
unit_test/test_aprox_rates/variables_F.F90
unit_test/test_conductivity/variables_F.F90
unit_test/test_eos/variables_F.F90
unit_test/test_screening/variables_F.F90
commit 87bc88e7e999336c343a0c38f09a406b69995811
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 15 06:18:13 2021 -0700
Remove custom GPU directives (#670)
EOS/breakout/actual_eos.F90
EOS/composition.F90
EOS/gamma_law/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/multigamma/composition.F90
EOS/polytrope/actual_eos.F90
EOS/rad_power_law/rad_power_law.F90
EOS/stellarcollapse/actual_eos.F90
EOS/ztwd/actual_eos.F90
conductivity/constant/constant_conductivity.F90
conductivity/constant_opacity/constant_conductive_opacity.F90
conductivity/powerlaw/powerlaw_conductivity.F90
conductivity/stellar/stellar_conductivity.F90
integration/utils/jacobian_sparsity.F90
integration/utils/temperature_integration.F90
interfaces/burn_type.F90
interfaces/conductivity.F90
interfaces/eos.F90
interfaces/eos_override.F90
interfaces/eos_type.F90
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_rhs.F90
networks/aprox19/nse_F.F90
networks/aprox19/nse_check.F90
networks/aprox21/actual_rhs.F90
networks/general_null/actual_rhs.F90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_simple/actual_rhs.F90
networks/iso7/actual_rhs.F90
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/reaclib_rates.F90
networks/nova/table_rates.F90
networks/powerlaw/actual_rhs.F90
networks/rprox/actual_rhs.F90
networks/rprox/rates_module.F90
networks/rprox/tfactors.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/sn160/reaclib_rates.F90
networks/sn160/table_rates.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/reaclib_rates.F90
networks/subch2/table_rates.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/dydt.F90
networks/triple_alpha_plus_cago/rates_module.F90
networks/triple_alpha_plus_cago/screen_module.F90
neutrinos/sneut5.F90
opacity/breakout/opacity_table_module.F90
opacity/rad_power_law/opacity_table_module.F90
rates/aprox_rates.F90
rates/tfactors.F90
screening/screen.F90
unit_test/test_aprox_rates/aprox_rates_util_F.F90
unit_test/test_conductivity/conductivity_util_F.F90
unit_test/test_eos/eos_util_F.F90
unit_test/test_parameters/test_parameters.F90
unit_test/test_screening/screening_util_F.F90
util/esum.py
util/esum_module.F90
commit 63858b032af5ba2a415318ae5524640f1f40c61f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 15 06:07:56 2021 -0700
Remove remaining OpenACC directives (#669)
EOS/gamma_law/actual_eos.F90
EOS/helmholtz/actual_eos.F90
integration/utils/jacobian_sparsity.F90
integration/utils/temperature_integration.F90
interfaces/burn_type.F90
interfaces/eos.F90
interfaces/eos_override.F90
interfaces/eos_type.F90
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/nse_F.F90
networks/general_null/network.template
networks/general_null/network_properties.template
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_rhs.F90
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/reaclib_rates.F90
networks/nova/table_rates.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/sn160/reaclib_rates.F90
networks/sn160/table_rates.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/reaclib_rates.F90
networks/subch2/table_rates.F90
networks/triple_alpha_plus_cago/actual_network.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/dydt.F90
networks/triple_alpha_plus_cago/rates_module.F90
networks/triple_alpha_plus_cago/screen_module.F90
rates/aprox_rates.F90
screening/screen.F90
commit 0e12c71ac1553962af4a1d9d1b46e979b87739f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat May 8 10:17:32 2021 -0700
Deal with unused variable warnings in breakout (#668)
EOS/breakout/actual_eos.H
commit fceddf7e5cd142d4954fb72d6a0b463e4a9943ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 4 10:52:12 2021 -0400
remove the Fortran numerical Jacobian -- it is not used (#666)
integration/utils/Make.package
integration/utils/numerical_jacobian.F90
integration/utils/numerical_jacobian_sdc.f90
unit_test/test_jac/Make.package
unit_test/test_jac/jac_zones.F90
unit_test/test_jac/main.cpp
unit_test/test_jac/probin.aprox13
unit_test/test_jac/variables_F.F90
commit 563e56ed57f43f76671bc1a1e60cc675c73c41ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 3 12:26:54 2021 -0400
we no longer use rtol_temp and atol_temp, so remove them (#665)
note: any application probin's that use these need to be updated
integration/_parameters
networks/ECSN/inputs.burn_cell.VODE
networks/ignition_reaclib/C-burn-simple/inputs.burn_cell.VODE
networks/ignition_reaclib/C-test/inputs.burn_cell.VODE
networks/ignition_reaclib/URCA-simple/inputs.burn_cell.VODE
networks/nova/inputs.burn_cell.VODE
networks/rprox/_parameters
networks/sn160/inputs.burn_cell.VODE
networks/subch/inputs.burn_cell.VODE
networks/subch2/inputs.burn_cell.VODE
networks/triple_alpha_plus_cago/_parameters
networks/xrb_simple/_parameters
python_library/StarKiller/StarKiller/examples/BurnProfile/probin_aprox21
python_library/StarKiller/StarKiller/examples/ECSN/probin_ecsn
python_library/StarKiller/StarKiller/examples/probin_aprox13
python_library/StarKiller/StarKiller/examples/probin_burn_subch
python_library/StarKiller/StarKiller/examples/rotating_star/probin_aprox21
sphinx_docs/source/integrators.rst
unit_test/burn_cell/inputs_aprox13_mott
unit_test/burn_cell/probin_aprox13
unit_test/burn_cell/probin_aprox19
unit_test/burn_cell/probin_aprox21
unit_test/burn_cell/probin_aprox21_rot1
unit_test/burn_cell/probin_aprox21_rot2
unit_test/burn_cell/probin_ignition
unit_test/burn_cell/probin_iso7
unit_test/burn_cell/probin_rprox
unit_test/burn_cell/probin_triple
unit_test/burn_cell_python/probin_aprox13
unit_test/burn_cell_python/probin_burn_subch
unit_test/burn_cell_python/probin_ecsn
unit_test/test_react/inputs_iso7
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/old/inputs_reaclib_cburn.128
unit_test/test_react/old/inputs_reaclib_cburn.32
unit_test/test_react/old/inputs_reaclib_cburn.64
unit_test/test_react/old/inputs_reaclib_urca.32
unit_test/test_react/old/inputs_reaclib_urca.64
unit_test/test_sdc_vode_rhs/probin.aprox19
commit 6665176b4093b04ebd3cda0ad13ab7358345ec54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 3 10:12:15 2021 -0400
fix a comment in the numerical Jacobian (#664)
integration/utils/numerical_jacobian.H
commit b7f104ad1b818c0ec671f89ea52fabf53510500d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 2 14:19:28 2021 -0400
for jacobian == 3, we don't need to scale by aion (#662)
the numerical Jacobian is already in terms of X, so we were doing unnecessary
scalings by aion
integration/VODE/vode_jac_util_simplified_sdc.cpp
integration/VODE/vode_rhs_simplified_sdc.H
commit d3e8855d6e19457ed72a86f133553a32959f9bbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 2 09:55:34 2021 -0400
update changes
CHANGES.md
commit 89320520a8e4d44e4926fc346f83d7c15a93d877
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 30 13:36:23 2021 -0400
these test results are very out of date (#661)
unit_test/test_react/param_testing/aprox13-BS-test-results.txt
unit_test/test_react/param_testing/aprox13-VBDF-test-results.txt
unit_test/test_react/param_testing/aprox13-VODE-test-results.txt
unit_test/test_react/param_testing/aprox19-BS-test-results.txt
unit_test/test_react/param_testing/aprox19-VODE-test-results.txt
unit_test/test_react/param_testing/rprox-BS-test-results.txt
unit_test/test_react/param_testing/rprox-VBDF-test-results.txt
unit_test/test_react/param_testing/rprox-VODE-test-results.txt
commit dee960c69752b7ebf56ed96eca1e7f9eac9840db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 30 13:26:46 2021 -0400
update subch2 to the latest pynucastro (#635)
this fixes the 3-alpha screening
networks/subch2/NETWORK_PROPERTIES
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/reaclib_rates.F90
networks/subch2/xin.pynucastro.128
networks/subch2/xin.pynucastro.16
networks/subch2/xin.pynucastro.256
networks/subch2/xin.pynucastro.32
networks/subch2/xin.pynucastro.64
commit 19bbe2d092d53aa4933a591e4f71e4366bcd21f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 30 13:24:19 2021 -0400
regenerate subch with pynucastro 3-alpha screening fix (#634)
networks/subch/NETWORK_PROPERTIES
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/reaclib_rates.F90
commit b0c5e20e03a79d4610d2abe5bb4e1b231fc9f6ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 30 13:23:43 2021 -0400
update nova with pynucastro so it builds again (#627)
this also fixed 3-alpha screening
networks/nova/NETWORK_PROPERTIES
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/nova.py
networks/nova/reaclib_rates.F90
commit f0b532fe53714dbdacf9ade5cab9efac0941a04d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 30 13:23:08 2021 -0400
bail out of integration if we hit NSE (#658)
this changes the behavor of VODE to detect if we hit NSE during
the course of integration, and if so, we return a new error code
and we will catch that and finish the burn via NSE
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_dvode.H
interfaces/burner.H
commit 7fb05e43fa4621927f16d3665afef7f6440d40b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 28 08:16:49 2021 -0400
simplify the guess for T in vode_to_burn for SDC (#659)
integration/VODE/vode_type_simplified_sdc.H
commit 0ee6681fa0fd111081c541ac6050f4a3562251d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 27 10:16:48 2021 -0400
store the integration time achieved in the burn_t (#657)
this can be used to recover from failed burns, e.g., the NSE bailout
integration/ForwardEuler/actual_integrator.H
integration/QSS/actual_integrator.H
integration/VODE/vode_type_simplified_sdc.H
integration/VODE/vode_type_strang.H
interfaces/burn_type.H
commit d328ebf42b98dfbba60d4c960ca3c435b8d3479a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 26 20:30:29 2021 -0400
remove the lagged reaction terms from simplified-SDC (#656)
we no longer require these for the update
interfaces/burn_type.H
unit_test/test_sdc/react_zones.H
commit fdd238b1729fa677ac2e107af55d2d6169c88116
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 24 08:30:04 2021 -0400
change the NSE-SDC update (#655)
We now do the NSE SDC update by iteratively constructing the source terms to the aux data. This no longer requires the lagged source terms from the previous iteration and seems to converge better than what we were doing.
networks/aprox19/nse.H
commit 9ee7915250313f613e2a6fdb444b1cde3a56b08c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 18 18:08:29 2021 -0400
convert the CJ detonation code to C++ (#646)
util/cj_detonation/GNUmakefile
util/cj_detonation/Make.package
util/cj_detonation/_parameters
util/cj_detonation/cj_det.H
util/cj_detonation/cj_det.f90
util/cj_detonation/inputs
util/cj_detonation/main.cpp
util/cj_detonation/main.f90
util/cj_detonation/probin
commit a70b4bafb8ef45c877d6d3b1c942081d3c94964c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 20:23:17 2021 -0400
remove the gamma_law EOS and rename gamma_law_general to gamma_law (#653)
we no longer need the simpler version of this EOS since we have templated EOSes
and can define types that carry a reduced set of information.
CHANGES.md
EOS/gamma_law/Make.package
EOS/gamma_law/actual_eos.F90
EOS/gamma_law/actual_eos.H
EOS/gamma_law/gamma_law.F90
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/_parameters
EOS/gamma_law_general/actual_eos.H
Make.Microphysics_extern
networks/Make.package
sphinx_docs/source/eos.rst
sphinx_docs/source/networks.rst
commit b0b238fdf79b887f854304902e1693dec3de32f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 19:15:02 2021 -0400
add comments to vode_type.H and remove some unused ones (#649)
integration/VODE/vode_dvode.H
integration/VODE/vode_dvstep.H
integration/VODE/vode_type.H
commit d252f78d4a73f36a620832713211ff0978851bb1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 16:23:16 2021 -0400
eos_rep_t needs dpdZ and dpdA for SDC (#652)
interfaces/eos_type.H
commit 156353aabbc6a9c5deb247248b831636f971b8ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 14 14:36:49 2021 -0400
add a new EOS types (#650)
eos_rep_t has everything needed for p and e
interfaces/eos_type.H
commit a1e47a0c07e1909186d113f4ba8c8a10ec7df406
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 13 09:47:30 2021 -0400
add a jacobian = 3 option for simplified SDC (#642)
We compute the Jacobian as J = dR/dw dw/dU
this will construct dw/dU analytically but dR/dw numerically
integration/VODE/vode_dvjac.H
integration/VODE/vode_rhs_simplified_sdc.H
integration/_parameters
commit 33a4d0fe6c115ee92d906186a8208c184c47f0d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 5 18:53:33 2021 -0400
fix scaling of rtol for species in SDC (#643)
we were scaling rtol for SDC by rho
it should be left unscaled. only atol gets scaled
integration/VODE/actual_integrator_simplified_sdc.H
commit bd5f51ec88e7ce82a766074ba83e499862913079
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 1 09:32:34 2021 -0400
update changes
CHANGES.md
commit e12a253e23a20f783aa92619545342954ec4a3e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 30 08:24:25 2021 -0700
Don't use changes in e to set the QSS timestep (#638)
integration/QSS/actual_integrator.H
commit 7a9abf1988e14c8972dc8f8f919b367356bf7630
Author: doreenfan <35239173+doreenfan@users.noreply.github.com>
Date: Thu Mar 25 15:43:20 2021 -0700
Fix compile errors seen with SDC_EVOLVE_ENTHALPY (#636)
Currently, SDC_EVOLVE_ENTHALPY requires pressure or enthalpy input instead of energy. Hence, eos_t should be used instead of eos_re_t.
integration/VODE/vode_dvstep.H
integration/VODE/vode_jac_util_simplified_sdc.cpp
integration/VODE/vode_type_simplified_sdc.H
commit 2aa03ee2defe55eeccdf3235913fa346c7d5fb47
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Mar 24 10:02:11 2021 -0400
fix call to nse_burn for SDC (#633)
Make sure that sdc_nse_burn is called if using simplified SDC
interfaces/burner.H
commit 49c70ef277924fc650b8f44498e37c3533e9fd9e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 24 09:30:37 2021 -0400
if Strang burn fails b/c it wants to be in NSE, be in NSE (#628)
* if Strang burn fails b/c it wants to be in NSE, be in NSE
* Only trigger nse_burn if the burn fails
Co-authored-by: Alice Harpole <aliceharpole@gmail.com>
integration/VODE/actual_integrator.H
interfaces/burner.H
commit 7c7d1caa87625a5ea6160c4ef5f1583ebc99870b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 23 06:01:09 2021 -0700
Rename two QSS parameters to more closely match Mott (#631)
integration/QSS/_parameters
integration/QSS/actual_integrator.H
commit 09a542053b8b26c448d640454887c24ab7af34ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 23 06:00:34 2021 -0700
Add burn_cell test problem for Mott aprox13 problem (#632)
This is the test problem from section 6.3 of Mott's thesis and section 9 of the third Guidry paper. Temperature is held constant for this problem (though Mott does show results for the version where temperature is allowed to update).
unit_test/burn_cell/inputs_aprox13_mott
commit 3c4b8a2138f397efc6c1be3d4adf3a2b66b7cdcf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 22 18:15:28 2021 -0400
add <fstream> include (#630)
unit_test/write_job_info.cpp
commit 08faa5782ae6d778b07646b09cf449edd42bb5a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 17 13:50:22 2021 -0400
add VODE step rejection for simplified and true SDC based on rho X (#619)
this also ensure that in simplified-SDC the density is positive (VODE can take big dt's perhaps for interpolation that make the advective term evacuate a cell, crashing the density).
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_dvstep.H
integration/VODE/vode_type_simplified_sdc.H
commit 1f826c5661ca61a31829fe2cfa8d5e974d38f1d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 14 11:12:56 2021 -0700
Get QSS compiling using new RHS scheme (#626)
integration/QSS/actual_integrator.H
commit 8e8f9e5048e65aa2c3d0811117d8c721adec5dd5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 13 17:20:07 2021 -0800
Move generic species Jacobian into utilities header (#624)
Move generic species Jacobian into utilities header
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
commit 544ad8f73b4e2b061ba21d69094586799495b3cd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 12 17:23:58 2021 -0800
Do normal sum in the new RHS scheme (#620)
interfaces/rhs_utilities.H
commit 5421972ed685ed6984638eb8131a002441bef7d7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 12 17:23:21 2021 -0800
Use normal sum in iso7 Jacobian (#622)
Use normal sum in iso7 Jacobian
networks/iso7/actual_rhs.H
commit 13df7a4e44d0ba912554787ed62291519f90bf6b
Author: doreenfan <35239173+doreenfan@users.noreply.github.com>
Date: Thu Mar 11 10:57:35 2021 -0800
Fix ignition_simple after moving legacy constants into fundamental_constants header (#623)
networks/ignition_simple/actual_network.H
networks/ignition_simple/actual_network_data.cpp
commit 54ec4200a62f1af26ed91e492a3d2e0fb74b53ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 11 06:24:00 2021 -0800
Move ener_rhs into utilities header (#621)
interfaces/rhs_utilities.H
networks/aprox13/actual_rhs.H
networks/iso7/actual_rhs.H
commit e63518b4c356be097d6646873be1b13fbaf5b0ba
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 10 11:19:28 2021 -0800
Move legacy constants into fundamental_constants header (#618)
constants/fundamental_constants.H
networks/aprox13/actual_network.H
networks/aprox19/actual_network.H
networks/aprox21/actual_network.H
networks/ignition_simple/actual_network.H
networks/iso7/actual_network.H
networks/rprox/actual_network.H
networks/rprox/actual_network_data.cpp
commit 8f8a74b6d35421f30cbcff14f40bb9d35ef3ed3b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 7 11:54:27 2021 -0800
Compute Jacobian terms automatically based on RHS (#617)
For all Jacobian terms of the form d(f) / d(Y), we can compute these automatically based on RHS, since we know how to compute the derivative of a term like (N * Y_1**e_1 * Y_2**e_2 * rate) analytically (multiply by the exponent, then decrement the exponent). This means we do not need to explicitly hand-write these terms to construct the network.
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 8e3aee32bb4d35427f752e16247ef2ce76dcefe9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 7 08:08:36 2021 -0800
Move mion and bion to generic network namespace (#616)
This will be helpful later for building a generic energy RHS function that just assumes the network supplies mion, so we can reduce redundancy.
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox13/actual_rhs.H
networks/aprox19/actual_network.H
networks/aprox19/actual_network_data.cpp
networks/aprox19/actual_rhs.H
networks/aprox19/nse.H
networks/aprox21/actual_network.H
networks/aprox21/actual_network_data.cpp
networks/aprox21/actual_rhs.H
networks/ignition_simple/actual_network.H
networks/ignition_simple/actual_network_data.cpp
networks/ignition_simple/actual_rhs.H
networks/iso7/actual_network.H
networks/iso7/actual_network_data.cpp
networks/iso7/actual_rhs.H
networks/rprox/actual_network.H
networks/rprox/actual_network_data.cpp
networks/rprox/actual_rhs.H
networks/triple_alpha_plus_cago/actual_network.H
networks/triple_alpha_plus_cago/actual_network_data.cpp
networks/triple_alpha_plus_cago/actual_rhs.H
commit 01328f29744e9bba59a584e04f13a96db2418b49
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 6 11:12:22 2021 -0800
aprox13 14/∞ (#615)
Create RHS-specific version of energy RHS
networks/aprox13/actual_rhs.H
commit f5cfebe26957333e19631d5213c309b4e3f623f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 6 09:17:00 2021 -0800
Add some utilities for partial equilibrium (#614)
interfaces/rhs_utilities.H
commit 3fe56c23b7e84c84597db6957126f3c477e540f3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Mar 6 09:09:19 2021 -0800
Move aprox13 over to new RHS scheme (#613)
Move aprox13 over to new RHS scheme
networks/aprox13/actual_network.H
networks/aprox13/actual_rhs.H
commit 327caf7041fbcd9fefa8ca63a0f33e2f1551f16c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 4 07:14:47 2021 -0800
Move intermediate rates to the end of the rates list (#611)
networks/aprox13/actual_network.H
commit c5fd3ec2a729cd44fe8b2470b950a2cf7dd3b1d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 4 06:30:30 2021 -0800
Move RHS eval to separate function in ForwardEuler (#612)
integration/ForwardEuler/actual_integrator.H
commit 720b13c5f62796ce77d84e5277b6d06e7b21abc0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 4 09:29:33 2021 -0500
remove some unused parameters (#607)
integration/_parameters
sphinx_docs/source/integrators.rst
commit fd74e68f9fabf69cb5deb80bc3674390d16e475e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 4 09:27:51 2021 -0500
implement the example stiff system from VODE (#605)
This implements the example ODE system from the VODE documentation. It also changes burn_cell to divide
the time domain into log spaced intervals, so we can better see trends. There is a new tfirst optional parameter
that sets the first output time.
networks/vode_example/Make.package
networks/vode_example/NAUX_NETWORK
networks/vode_example/NETWORK_PROPERTIES
networks/vode_example/README.md
networks/vode_example/actual_network.F90
networks/vode_example/actual_network.H
networks/vode_example/actual_rhs.F90
networks/vode_example/actual_rhs.H
networks/vode_example/vode_example.net
unit_test/burn_cell/_parameters
unit_test/burn_cell/burn_cell.H
unit_test/burn_cell/inputs_vode_example
unit_test/burn_cell/probin
commit fc359ea1937759b6440e6ee7b86d7ac5fb0847a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 3 13:11:03 2021 -0800
iso7 20/∞ (#563)
The general form of a reaction is
n_a A + n_b B + n_c C <-> n_d D + n_e E + n_f F
for species A, B, C, D, E, and F, where n_a particles of A, n_b particles of B, and n_C particles of C are consumed in the forward reaction and produced in the reverse reaction, and the analogous statement holds for particles D, E, and F.
For a given species, such as species A, the forward reaction term is of the form
-n_A * Y(A)**a * Y(B)**b * Y(C)**c * forward_rate
and the reverse reaction term is of the form
n_A * Y(D)**d * Y(E)**e * Y(F)**f * reverse_rate
Here a, b, and c are reaction-specific exponents which usually, but not always, are equal to n_a, n_b, and n_c respectively.
For example, in C12 + He4 <-> O16, species A is C12, species B is He4, species D is O16 (the other species are unused). Then n_a = n_b = n_d = 1, and a = b = d = 1. In the triple alpha forward reaction we have A = He4, D = C12, n_a = 3, a = 3, and n_d = 1.
In order to do this, we add a rate_fr_t which explicitly holds both forward and reverse contributions, and we take the shortcut (for now) that it should have half as many rates as the "real" network rates (which separate out the forward and reverse terms). After the Jacobian is converted over to this new scheme, we can make things a little clearer.
By writing it in this way, it becomes possible to explicitly identify reaction pairs that are in equilibrium and then take some action in response (this will be the focus of a later PR in this series).
interfaces/network_utilities.H
interfaces/rhs_utilities.H
networks/iso7/actual_network.H
networks/rate_type.H
commit 0ad103c6591f9de41405d94a59ee94abf32180a2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 3 11:52:07 2021 -0800
Merge proton links into main reaction channels (#603)
Merge proton links into main reaction channels
networks/aprox19/actual_rhs.H
commit 96125d677df87bf9d0c25fe8c4abd4cb2c3e87c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 3 14:11:08 2021 -0500
remove carbon as a primary species so we hit the special Si28 rate (#610)
unit_test/test_rhs/probin.iso7
commit 86fc6a5d077a88e2d29793fdb121687e46ef7304
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 3 10:58:11 2021 -0800
Convert remaining EOS data to inline (#549)
EOS/breakout/Make.package
EOS/breakout/actual_eos.H
EOS/breakout/actual_eos_data.H
EOS/breakout/actual_eos_data.cpp
EOS/gamma_law/Make.package
EOS/gamma_law/actual_eos.H
EOS/gamma_law/actual_eos_data.H
EOS/gamma_law/actual_eos_data.cpp
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.H
EOS/multigamma/actual_eos_data.H
EOS/multigamma/actual_eos_data.cpp
EOS/polytrope/Make.package
EOS/polytrope/actual_eos.H
EOS/polytrope/actual_eos_data.H
EOS/polytrope/actual_eos_data.cpp
interfaces/Make.package
interfaces/eos_data.H
interfaces/eos_data.cpp
commit 933a3aa3e5dad5aec040030acbe86c0358cff5d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 2 18:28:21 2021 -0800
iso7 21/∞ (#571)
Calculate density dependence in tabulated rates inline. This will help in a future step where we can query iso7tab a rate at a time instead of computing all the (unscreened) rates at once.
networks/iso7/actual_rhs.H
commit 466ad1b5898b4ce721ceb8790082d2ad59a95a87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 1 19:10:58 2021 -0500
fix scaling of species in numerical Jacobian (#609)
integration/utils/numerical_jacobian.H
commit 60f8e44bb3092a812d4bb951919c0609cf2e9321
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 28 12:05:55 2021 -0500
revert a debugging hack (#608)
unit_test/react_util.H
commit 46fcc130da061a1e4875e164acca6696e08797f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 27 17:59:53 2021 -0500
fix forward Euler integration (#606)
integration/ForwardEuler/actual_integrator.H
commit d1bf7bc64ff8741fb4ad3cb3eecabb649b15311d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 27 12:36:07 2021 -0800
Remove proton links from rates list (#601)
Remove proton links from rates list
networks/aprox13/actual_network.H
networks/aprox13/actual_rhs.H
commit 0ec1c65c7a409a4d9c676d1962b1d8d6297e56e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 26 13:18:41 2021 -0500
update burn_cell (#604)
this updates burn_cell to the new (e, X_k) integration strategy and greatly simplifies the output.
unit_test/burn_cell/burn_cell.H
unit_test/burn_cell/burn_cell_F.H
unit_test/burn_cell/main.cpp
unit_test/burn_cell/probin_triple
unit_test/react_util.H
commit c4704201d400e22f153236489700946a60998fb8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 25 12:58:10 2021 -0800
Heavy ion reactions (#598)
Split up the heavy ion reactions, covering the same scope as #566 and #574 did for aprox13.
networks/aprox19/actual_network.H
networks/aprox19/actual_rhs.H
commit b3430fa9dafd37cb00c15c268b17998a2c82d19e
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 25 12:12:26 2021 -0800
Re-enable call_eos_in_rhs option (#597)
For now, this is done for Strang only.
Note: in principle this could break a setup that was previously explicitly setting call_eos_in_rhs = F. However, I think this is pretty unlikely to have happened, I only found one setup (Castro xrb_mixed) that is doing it.
integration/ForwardEuler/actual_integrator.H
integration/QSS/actual_integrator.H
integration/VODE/vode_type_strang.H
integration/_parameters
commit 827747c9843248f9b31242444b51620da0615142
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 22 19:50:23 2021 -0500
fix true SDC compilation (#596)
interfaces/burn_type.H
commit c915a578477228a17b0bd5987849de4b62cf2bc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 22 12:23:31 2021 -0500
add discussions (#595)
README.md
commit 606836398c107213b7ad817203ebdce336e6729e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 22 05:48:32 2021 -0800
Call EOS using burn_t (#593)
For now, only the Strang paths are updated.
integration/ForwardEuler/actual_integrator.H
integration/QSS/actual_integrator.H
integration/VODE/actual_integrator.H
integration/VODE/vode_type_strang.H
integration/utils/numerical_jacobian.H
interfaces/burn_type.H
commit ec2d7a48c893a23d3e2206831ac50fe74aa65d1e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 17:18:13 2021 -0800
Use eos_re_t in integration (#592)
EOS/eos_composition.H
integration/ForwardEuler/actual_integrator.H
integration/QSS/actual_integrator.H
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_jac_util_simplified_sdc.cpp
integration/VODE/vode_type_simplified_sdc.H
integration/VODE/vode_type_strang.H
integration/utils/numerical_jacobian.H
interfaces/burn_type.H
networks/aprox19/nse.H
commit dd53a18b3d167316fb464720a1528c1f81d68f33
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 21 10:39:26 2021 -0800
Remove constant pressure burn code path in C++ (#591)
This will need to be replaced later with a correct solution for integrating enthalpy
integration/utils/jacobian_utilities.H
commit 1647596c03ac24f7acc71a0b4479a3faaeb62167
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 20 18:04:54 2021 -0500
fix test_react compilation on GPU (#589)
unit_test/test_react/main.cpp
commit e40ee330ff0f170a0bf2cb0f8ede3f046242556c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 20 10:24:50 2021 -0800
Rename alpha chain rates (#588)
networks/aprox19/actual_network.H
networks/aprox19/actual_rhs.H
commit 3b15748709ce15b6cb8a1436552ee74a9905ea51
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 09:23:32 2021 -0800
Remove for_jacobian_tderiv (#580)
networks/aprox13/actual_rhs.H
commit dacd8ef0ce03b590c014eab61637831cc1527171
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 09:00:38 2021 -0800
Move identical particle factors into rates (#582)
Move identical particle factors into rates
networks/aprox19/actual_rhs.H
commit 53033dd76e951314a976ba51a61f913204972ffc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 18 11:53:37 2021 -0500
make H1 a primary species for aprox21 test_rhs (#587)
unit_test/test_rhs/probin.aprox21
commit ea98f03dcdfe579d01f4bb472242a388d2d71dec
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 08:11:35 2021 -0800
Remove unused rate names (#586)
The string names of the rates aren't actually used anywhere, and since we're in the middle of refactors involving lots of rate removals/additions and name changes, these will just get in the way.
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox19/actual_network.H
networks/aprox19/actual_network_data.cpp
networks/aprox21/actual_network.H
networks/aprox21/actual_network_data.cpp
networks/iso7/actual_network.H
networks/iso7/actual_network_data.cpp
networks/rprox/actual_network.H
networks/rprox/actual_network_data.cpp
networks/triple_alpha_plus_cago/actual_network.H
networks/triple_alpha_plus_cago/actual_network_data.cpp
commit 834a867d494fd074090aa475e6def409773cd9b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 07:50:29 2021 -0800
Remove network_rhs.F90 which is no longer used (#585)
integration/utils/Make.package
integration/utils/network_rhs.F90
commit 46160b57cdab8c370fff73bf4e707e69709da763
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 18 07:03:35 2021 -0800
ifdef out Fortran RHS wrapper if C++ implementation exists (#584)
interfaces/fortran_to_cxx_actual_rhs.F90
commit fca93f61fbec3d2df0db526ea2267677ae42f162
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 18:18:07 2021 -0800
Remove deriva (#579)
networks/aprox13/actual_rhs.H
commit 590861dad0800c5e9003b6269e218d00a4983ca6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 17 20:37:44 2021 -0500
remove the Fortran code path for test_rhs + fix Jac names (#578)
now we test the RHS for a network with a Fortran RHS through the C++ wrappers
this also updates the names of the Jacobian elements now that we integrate e
unit_test/test_rhs/Make.package
unit_test/test_rhs/main.cpp
unit_test/test_rhs/rhs_zones.F90
unit_test/test_rhs/test_react_F.H
unit_test/test_rhs/variables.cpp
unit_test/test_rhs/variables_F.F90
commit 90eb0c157f3802203a0bff5efec0a2d4ed256057
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 16:00:35 2021 -0800
Move identical particle factor into triple alpha rate (#575)
Move identical particle factor into triple alpha rate
networks/aprox13/actual_rhs.H
commit 17f40cf63ef0e8bedbf8da47e6ec18237813b603
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 17 15:14:35 2021 -0800
aprox13 7/∞ (#574)
This change splits the heavy ion reactions C12 + O16 and O16 + O16 into their respective endpoints. The former can end up with both Si28 and Mg24 + He4 with equal probability (same as iso7), while the latter can end in Si28 + He4 or S32, with an intermediate state of P31 + proton.
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox13/actual_rhs.H
commit b7a19fecf7a5981f9e240e65dbbfdb366652e1ca
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 15 18:51:17 2021 -0800
Fold more proton links into the alpha chain (#573)
networks/aprox13/actual_rhs.H
commit 35642a70cb71ce728e71804746bf0dc15458c5c2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 15 16:59:12 2021 -0800
Update aprox21 for new integration scheme (#576)
networks/aprox21/actual_rhs.H
commit c90f523fb5fa468dc65ab625cf5daf8e470ec86e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 15 16:13:01 2021 -0800
Do not integrate T; get it from e (#496)
We now integrate (X_k, e) instead of (X_k, T) for Strang split coupling. Closes #471
Note: we always assume a constant volume burn now -- later we can extend this to enthalpy
for constant pressure burns.
To deal with Fortran, our wrapper is going to have to create temporary RHS and Jacobian arrays to pass to actual_rhs that have the temperature component, then strip the temperature component (for the RHS) or convert it to the energy component (for the analytic Jacobian).
CHANGES.md
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_dvstep.H
integration/VODE/vode_jac_util_simplified_sdc.cpp
integration/VODE/vode_rhs.H
integration/VODE/vode_type.H
integration/VODE/vode_type_simplified_sdc.H
integration/VODE/vode_type_strang.H
integration/_parameters
integration/utils/Make.package
integration/utils/jacobian_utilities.H
integration/utils/numerical_jacobian.H
integration/utils/temperature_integration.H
interfaces/burn_type.H
interfaces/fortran_to_cxx_actual_rhs.F90
interfaces/fortran_to_cxx_actual_rhs.H
networks/aprox13/actual_rhs.H
networks/aprox19/actual_rhs.H
networks/ignition_simple/actual_rhs.H
networks/iso7/actual_rhs.H
networks/powerlaw/actual_rhs.H
networks/rprox/_parameters
networks/rprox/actual_rhs.H
networks/triple_alpha_plus_cago/_parameters
networks/triple_alpha_plus_cago/actual_rhs.H
networks/xrb_simple/_parameters
unit_test/test_react/inputs_aprox21
unit_test/test_react/inputs_iso7
unit_test/test_rhs/probin.iso7
unit_test/test_rhs/rhs_zones.F90
unit_test/test_rhs/rhs_zones.H
unit_test/test_rhs/variables.H
unit_test/test_rhs/variables.cpp
unit_test/test_rhs/variables_F.F90
commit 25fbb379bb1798cc70280bdeac85efb785b10a73
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 15 15:09:42 2021 -0800
Convert aprox21 to C++ (#321)
networks/aprox21/Make.package
networks/aprox21/actual_network.H
networks/aprox21/actual_network_data.cpp
networks/aprox21/actual_rhs.H
networks/aprox21/actual_rhs_data.cpp
unit_test/test_rhs/inputs_aprox21
unit_test/test_rhs/probin.aprox21
commit a08d9926618dc8c2f7a61d3fa45efb7193c00107
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 16:37:13 2021 -0800
Fold more proton links into the alpha chain (#572)
Fold more proton links into the alpha chain
networks/aprox13/actual_rhs.H
commit d5872d0994199e2a953330f224af27da69b77156
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 10:18:11 2021 -0800
Calculate density dependence in tabulated rates inline (#570)
Calculate density dependence in tabulated rates inline. This will help in a future step where we can query aprox13tab a rate at a time instead of computing all the (unscreened) rates at once.
networks/aprox13/actual_rhs.H
commit 5f2ddff2a7efcded5ec27255bb069ad1b611af31
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 14 09:24:20 2021 -0800
aprox13 3/∞ (#569)
This change folds the reaction pairs (irmgap, irr1), which did Mg24 -> Al27 -> Si28, and (irsigp, irr1), which did Si28 -> Al27 -> Mg24, into the effective Mg24 <-> Si28 rates. This allows us to remove irr1 from the rate list. More importantly it works toward the goal where every "reaction" known to the network connects an actual pair of species in the network, while any intermediate rates connecting the two can be considered implementation details, which will be helpful for methods looking at microscopic equilibria. This change will be followed by removing the rest of the intermediate proton links.
Note: irmgap, the rate for Mg24(a,p)Al27, is still in the list of rates known to the network. A requirement of the target scheme is that this no longer be true, and it would just be calculated inline while calculating the effective Mg24(a,g)Si28 rate. However it is not straightforward to do this yet -- at the moment, we calculate at once all of the raw (unscreened) rates in the aprox13rat or aprox13 tab routine, and we don't have a way to select a specific raw rate for calculation, which is what would be needed here. So a later change will be to convert the raw rate routines to calculate rates one-by-one (see also #568, which would be needed for calculating the fully screened rates one-by-one), and then we can do that second piece of cleanup.
This causes no harm though; both in the current scheme and the new scheme for iso7, this rate will be calculated but then never explicitly enter into the RHS (only implicitly in the updated Mg24 <-> Si28 rates).
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox13/actual_rhs.H
commit 19e591f2946f5d64993cec6f2ecc2a5439f582c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 11 06:40:06 2021 -0800
Move identical particle factor into C12+C12 rate (#566)
Move identical particle factor into C12+C12 rate. Also add an entry for the reverse rate which will be zero always.
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox13/actual_rhs.H
commit 1a0dd59e8336eb8f237e5de28db9c1eafbdfb75c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 10 17:19:53 2021 -0800
iso7 19/∞ (#554)
Move y(Si28) into the RHS instead of the rate. This will be important later for calculating the equilibrium state.
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 8f95d690e132732aedf651e3236900923cc836b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Feb 10 14:23:03 2021 -0800
Convert some rate names to mirror iso7 (#564)
Convert some rate names to mirror iso7 (just the alpha chain for now)
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox13/actual_rhs.H
commit e8f2875267b87f261f82c7be5be4720b5993abd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 10 17:21:17 2021 -0500
add checks on O and Si to the NSE check (#565)
this allows us to better capture the regions where NSE should hold
networks/aprox19/_parameters
networks/aprox19/nse.H
networks/aprox19/nse_check.F90
commit bb7e85552524985041d8e411e7d0b2861bc2bdb5
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 4 07:13:48 2021 -0800
Set ForwardEuler integrator to integrate e but not T (#562)
Applies the approach from #471 and #496 to the ForwardEuler integrator. (The QSS integrator already does this.)
integration/ForwardEuler/actual_integrator.H
commit 7df52cf1e1592a073ec84347e8a790ea0e9fce26
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 4 06:58:58 2021 -0800
Remove Fortran burner and integrator interfaces (#561)
Also remove some tests which no longer make sense
integration/Make.package
integration/VODE/Make.package
integration/VODE/vode_integrator.F90
integration/integration_data.f90
integration/integrator.F90
integration/integrator_scaling.F90
interfaces/Make.package
interfaces/burner.F90
interfaces/microphysics.F90
networks/ECSN/Make.package
networks/ECSN/actual_burner.F90
networks/aprox13/Make.package
networks/aprox13/actual_burner.F90
networks/aprox13/test-cpp/GNUmakefile
networks/aprox13/test-cpp/Make.package
networks/aprox13/test-cpp/do_initialization.f90
networks/aprox13/test-cpp/main.cpp
networks/aprox13/test-cpp/probin
networks/aprox13/test-cpp/testburn.f90
networks/aprox13/test-cpp/testjacobian.f90
networks/aprox13/test/GNUmakefile
networks/aprox13/test/testburn.f90
networks/aprox19/Make.package
networks/aprox19/actual_burner.F90
networks/aprox19/test-cpp/GNUmakefile
networks/aprox19/test-cpp/Make.package
networks/aprox19/test-cpp/do_initialization.f90
networks/aprox19/test-cpp/main.cpp
networks/aprox19/test-cpp/probin
networks/aprox19/test-cpp/testnse.cpp
networks/aprox19/test-cpp/testnse_F.F90
networks/aprox19/test-net-cpp/GNUmakefile
networks/aprox19/test-net-cpp/Make.package
networks/aprox19/test-net-cpp/do_initialization.f90
networks/aprox19/test-net-cpp/main.cpp
networks/aprox19/test-net-cpp/probin
networks/aprox19/test-net-cpp/testburn.f90
networks/aprox19/test-net-cpp/testjacobian.f90
networks/aprox21/Make.package
networks/aprox21/actual_burner.F90
networks/aprox21/test-cpp/GNUmakefile
networks/aprox21/test-cpp/Make.package
networks/aprox21/test-cpp/do_initialization.f90
networks/aprox21/test-cpp/main.cpp
networks/aprox21/test-cpp/probin
networks/aprox21/test-cpp/testburn.f90
networks/aprox21/test-cpp/testjacobian.f90
networks/breakout/Make.package
networks/breakout/actual_burner.f90
networks/general_null/Make.package
networks/general_null/actual_burner.F90
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_burner.F90
networks/ignition_chamulak/test/GNUmakefile
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/actual_burner.F90
networks/ignition_reaclib/C-test/Make.package
networks/ignition_reaclib/C-test/actual_burner.F90
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_simple/Make.package
networks/ignition_simple/actual_burner.F90
networks/ignition_simple/test-cpp/GNUmakefile
networks/ignition_simple/test-cpp/main.cpp
networks/ignition_simple/test-cpp/probin
networks/ignition_simple/test-cpp/testburn.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/iso7/Make.package
networks/iso7/actual_burner.F90
networks/iso7/test-cpp/GNUmakefile
networks/iso7/test-cpp/Make.package
networks/iso7/test-cpp/do_initialization.f90
networks/iso7/test-cpp/main.cpp
networks/iso7/test-cpp/probin
networks/iso7/test-cpp/testburn.f90
networks/iso7/test-cpp/testjacobian.f90
networks/nova/Make.package
networks/nova/actual_burner.F90
networks/powerlaw/Make.package
networks/powerlaw/actual_burner.F90
networks/rprox/Make.package
networks/rprox/actual_burner.F90
networks/rprox/test/GNUmakefile
networks/rprox/test/README
networks/rprox/test/eval.f90
networks/rprox/test/testburn.f90
networks/sn160/Make.package
networks/sn160/actual_burner.F90
networks/subch/Make.package
networks/subch/actual_burner.F90
networks/subch2/Make.package
networks/subch2/actual_burner.F90
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_burner.F90
networks/triple_alpha_plus_cago/test/GNUmakefile
networks/triple_alpha_plus_cago/test/eval.f90
networks/triple_alpha_plus_cago/test/testburn.f90
networks/triple_alpha_plus_cago/test/testjacobian.f90
networks/xrb_simple/Make.package
networks/xrb_simple/actual_burner.f90
networks/xrb_simple/test/GNUmakefile
networks/xrb_simple/test/testburn.f90
unit_test/burn_cell/Make.package
unit_test/burn_cell/burn_cell.F90
unit_test/burn_cell/main.cpp
unit_test/test_reaclib_rates/GNUmakefile
unit_test/test_reaclib_rates/_parameters
unit_test/test_reaclib_rates/inputs_urca
unit_test/test_reaclib_rates/main.f90
unit_test/test_reaclib_rates/matplotlibrc
commit 936bc6bbb811f3352e4e1a1e23022b3643ceac32
Author: doreenfan <35239173+doreenfan@users.noreply.github.com>
Date: Wed Feb 3 17:46:09 2021 -0800
Fix maestro::use_tfromp (#560)
This PR fixes some bugs seen with simplified SDC and SDC_EVOLVE_ENTHALPY on.
integration/VODE/vode_dvstep.H
integration/VODE/vode_type_simplified_sdc.H
commit 2791ed3f42496dda236e8de4267f5c0e34f7e3dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 20:30:46 2021 -0500
fix an asset on the GPU (#557)
screening/screen.H
commit 57238ba6b075d670213014f319a3294aa148e314
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 12:45:33 2021 -0500
true SDC does not use the burner interface (#559)
interfaces/burner.H
commit 3440f8be743eed9b9fdaa71b8df6a9c7ed16e8cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 09:47:28 2021 -0500
extract out the Jacobian into a normal .cpp (#558)
The CUDA build with simplified SDC was taking a long time (> 2 hours). By extracting the Jacobian bits into a .cpp file instead of inlining them, the build time is greatly reduced. This addresses Castro issue: AMReX-Astro/Castro#1567
integration/VODE/Make.package
integration/VODE/vode_jac_util_simplified_sdc.H
integration/VODE/vode_jac_util_simplified_sdc.cpp
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
commit 12122dde5e2aa42f582154b62297f550ce42a09b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 09:34:22 2021 -0500
SDC+NSE part II (#497)
This builds on #423 and completes the coupling of NSE and the simplified-SDC integration. Previously we updated the SDC integrator code path to use the aux data for the thermodynamics. Now we do the test on whether we are in NSE and if so, do a predictor-corrector update of the state to capture the advection + NSE changes.
CHANGES.md
interfaces/burn_type.H
interfaces/burner.H
networks/aprox19/actual_network_data.cpp
networks/aprox19/nse.H
unit_test/test_sdc/inputs_aprox19.nse
unit_test/test_sdc/probin.aprox19.nse
unit_test/test_sdc/react_zones.H
commit f96b40cd4c2e47b0bce6aadea9a7f6cd129d603e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 2 16:55:02 2021 -0800
Decrease tmax for aprox13 burn (#556)
1e-3 seconds is a little hard to achieve for the burns that already burn to NSE
unit_test/test_react/inputs_aprox13
commit 098d55c563c12c636c7bf2d299526d7d0f35a7ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 1 11:14:30 2021 -0500
fix create_release action (#555)
we were not sending the release text for the environment
.github/workflows/create_release.yml
commit a2ce66d26359c2545b98f33715dbf438c01d559e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 30 12:41:28 2021 -0800
iso7 18/∞ (#553)
Three reactions in iso7 include reactions of identical particles. At the moment, the factor of 1/2 implied by this is not included in the reaction rate, but rather applied in the RHS directly.
To continue the RHS generalization process we're doing, it will be useful if we don't have to worry about this factor, so this PR moves the term directly into the reaction rate, multiplying the RHS by the inverse factor.
For example, the C12 + C12 term currently looks like
dydt(He4) = (1/2) * Y(C12) * Y(C12) * rate(ir1212)
dydt(C12) = -Y(C12) * Y(C12) * rate(ir1212)
dydt(Ne20) = (1/2) * Y(C12) * Y(C12) * rate(ir1212)
and it will now look like
rate(ir1212) *= 1/2;
dydt(He4) = Y(C12) * Y(C12) * rate(ir1212)
dydt(C12) = -2 * Y(C12) * Y(C12) * rate(ir1212)
dydt(Ne20) = Y(C12) * Y(C12) * rate(ir1212)
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 900a7efd8d8521080085861107bc02c951671f1b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 30 06:38:22 2021 -0800
Add EXTRA_THERMO to eos_re_t (#552)
interfaces/eos_type.H
commit ef23ae62326432c20067a6036ab54009f2fc5b91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 30 09:37:15 2021 -0500
fix the docs building badge (#551)
it is no longer travis, but now a github action
README.md
commit 4e0db43ca58f2ceb964f7b2e8cec57d005fe76e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 29 16:57:33 2021 -0800
Add an EOS type that only has rho, T, e (#518)
interfaces/eos_type.H
commit cce8edfbabc180dcf012419c4dbbfbd79b45b838
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jan 26 08:04:41 2021 -0800
iso7 part 17 (#547)
networks/iso7/actual_network.H
networks/iso7/actual_network_data.cpp
networks/iso7/actual_rhs.H
commit 6211e2001acf700c57f60649acb6ba0c473ef93d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 14:53:34 2021 -0500
remove Fortran support in test_react (#540)
unit_test/test_react/Make.package
unit_test/test_react/main.cpp
unit_test/test_react/react_zones.F90
unit_test/test_react/test_react_F.H
unit_test/test_react/variables_F.F90
commit a2ef8eba729faf994098c0b7af7d9211ac394e49
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 23 11:27:16 2021 -0800
Make Helmholtz data inline instead of extern (#548)
EOS/helmholtz/Make.package
EOS/helmholtz/actual_eos.H
EOS/helmholtz/actual_eos_data.H
EOS/helmholtz/actual_eos_data.cpp
commit fdb402e8e637c31e3d673fac632e448624146938
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 13:47:06 2021 -0500
add assets to MathArray and template linear algebra (#534)
interfaces/ArrayUtilities.H
commit 09ead9162a1667694336ed4c97658faea1b2867a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 23 13:46:43 2021 -0500
remove the Fortran VODE (#538)
We no longer support the Fortran VODE since we did the port to C++ and all networks, including those with Fortran implementations, can be run from the C++ VODE. Further the Fortran VODE no longer supports GPUs (since we switch to a C++ lambda-capture approach).
CHANGES.md
integration/VODE/Make.package
integration/VODE/cuVODE/Make.cuVODE
integration/VODE/cuVODE/README
integration/VODE/cuVODE/docs/Makefile
integration/VODE/cuVODE/docs/NOTES.md
integration/VODE/cuVODE/docs/doxyfile_vode
integration/VODE/cuVODE/license.txt
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/source/linpack_module.F90
integration/VODE/cuVODE/source/rpar.F90.template
integration/VODE/cuVODE/test/GNUmakefile
integration/VODE/cuVODE/test/Make.package
integration/VODE/cuVODE/test/README.md
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/extern_probin.template
integration/VODE/cuVODE/test/inputs
integration/VODE/cuVODE/test/main.cpp
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuVODE/test/test_react.H
integration/VODE/cuVODE/test/test_react_F.H
integration/VODE/cuVODE/test/vode_rhs.F90
integration/VODE/cuVODE/test/vode_rpar.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_true_sdc.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs_true_sdc.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type.F90
integration/VODE/vode_type_true_sdc.F90
commit 26f4c8e9e2a98240e8f9a34c7e96b6a57d1fd6bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 22 20:15:39 2021 -0500
don't print nse table read on all procs (#546)
networks/aprox19/nse.H
commit 26e0ae0787c305a9658a8c1b6cd7729c3dcd76ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 18:55:21 2021 -0500
allow us to enable jacobian caching even on the GPU (#545)
integration/VODE/Make.package
integration/VODE/vode_dvjac.H
integration/VODE/vode_type.H
commit cd099605a241b169644a344a7b199a5cac08a72d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 21 18:47:05 2021 -0500
add missing files for test_jac (#543)
unit_test/test_jac/jac_zones.F90
unit_test/test_jac/variables_F.F90
commit 7bce3329aa7b08b2e88340cd8cf0332dc24a5cb2
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 21 15:42:25 2021 -0800
iso7 part 16 (#479)
Rename rate indices to be more descriptive.
networks/iso7/actual_network.H
networks/iso7/actual_network_data.cpp
networks/iso7/actual_rhs.H
commit 924aff6497dd818a696a3063b2c60b19f423e081
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jan 21 09:14:50 2021 -0800
iso7 15 (#478)
Size the RHS array to be exactly the number of non-zero terms. This finally returns the actual work done to the original implementation.
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
commit 98f4b5ef5fb748a56aed7bdd15896933dc288de2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 20 14:14:38 2021 -0500
fix rprox GPU / C++ (#542)
networks/rprox/Make.package
networks/rprox/actual_rhs.H
commit 407ed3af166c669e0926263dfbf357d24ec5ce91
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 18 14:37:15 2021 -0800
Convert rprox to C++ (#326)
networks/rprox/Make.package
networks/rprox/NETWORK_PROPERTIES
networks/rprox/actual_network.H
networks/rprox/actual_network_data.cpp
networks/rprox/actual_rhs.H
networks/rprox/rprox_rates.H
networks/rprox/rprox_tfactors.H
unit_test/test_rhs/inputs_rprox
unit_test/test_rhs/probin.rprox
commit a346f5857c8b6d698db45f601be4a8afc4086d0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 18 13:56:28 2021 -0500
remove the Fortran CVODE integrator (#539)
* remove the Fortran CVODE integrator
we never use it and we are not supporting Fortran integrators anymore
* remove test_cvode_react
* remove Make.CVODE
* remove CVODE option from GPU documentation
* remove CVODE from Make.Microphysics.
Co-authored-by: Donald E. Willcox <eugene.willcox@gmail.com>
Make.CVODE
Make.Microphysics
integration/CVODE/Make.package
integration/CVODE/_parameters
integration/CVODE/actual_integrator.F90
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_rpar.F90
integration/CVODE/cvode_type.F90
sphinx_docs/source/gpu.rst
unit_test/test_cvode_react/GNUmakefile
unit_test/test_cvode_react/Make.package
unit_test/test_cvode_react/README.md
unit_test/test_cvode_react/_parameters
unit_test/test_cvode_react/inputs_aprox13
unit_test/test_cvode_react/inputs_aprox13_uniform
unit_test/test_cvode_react/inputs_ignition
unit_test/test_cvode_react/inputs_reaclib_urca
unit_test/test_cvode_react/inputs_sn160
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/make_aprox13_cusolver.sh
unit_test/test_cvode_react/probin.aprox13
unit_test/test_cvode_react/probin.aprox13.uniform
unit_test/test_cvode_react/probin.ignition
unit_test/test_cvode_react/probin.reaclib_urca
unit_test/test_cvode_react/probin.sn160
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_serial.cpp
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react.H
unit_test/test_cvode_react/test_react_F.H
unit_test/test_cvode_react/util.f90
unit_test/test_cvode_react/variables.F90
unit_test/test_cvode_react/xin.aprox13
unit_test/test_cvode_react/xin.aprox13.128
unit_test/test_cvode_react/xin.aprox13.256
unit_test/test_cvode_react/xin.aprox13.32
unit_test/test_cvode_react/xin.aprox13.64
unit_test/test_cvode_react/xin.ignition
unit_test/test_cvode_react/xin.sn160.16
commit 909c4dc28bff1e1b020ada939ee7bc162ab06bde
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 17 10:59:54 2021 -0500
update doc pointer (#537)
README.md
commit 1dafd2e6849935987c117b9835f2cec6f6007973
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 16 20:00:10 2021 -0500
change the if logic for the RHS include in C++ VODE (#535)
in particular, this will allow Castro's true-SDC C++ port work
integration/Make.package
integration/VODE/Make.package
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/vode_dvhin.H
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvode.H
integration/VODE/vode_type.H
integration/utils/Make.package
integration/utils/jacobian_sparsity.F90
integration/utils/numerical_jacobian.H
integration/utils/temperature_integration.H
interfaces/Make.package
interfaces/burn_type.H
interfaces/burner.H
interfaces/microphysics.F90
networks/aprox13/Make.package
networks/aprox19/Make.package
networks/aprox21/Make.package
networks/breakout/Make.package
networks/general_null/Make.package
networks/ignition_chamulak/Make.package
networks/ignition_simple/Make.package
networks/iso7/Make.package
networks/powerlaw/Make.package
networks/rprox/Make.package
networks/triple_alpha_plus_cago/Make.package
networks/xrb_simple/Make.package
commit 1f0c666f18c0418a3ab0aa817de00f8fd52ebac7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jan 16 10:45:22 2021 -0800
Start moving towards zero-based indexing with linpack (#536)
RArray1D and RArray2D are one-based arrays, and that causes friction with the zero-based indexing of xn and other arrays. So we want to move everything to zero-based indexing.
The strategy will be to suffix function parameters with "1", e.g. a -> a1, and then do
auto& a = reinterpret_cast<Array2D<Real, 0, num_eqs-1, 0, num_eqs-1>&>(a1)
Then, in the function, we can convert all the calculations to zero-based indexing. When all of the conversions have been done, we can do one final sweep to convert RArray1D and RArray2D to be zero-based and then remove all the reinterpret_cast statements and rename the function parameters to their original names. This will allow us to do an incremental conversion.
util/linpack.H
commit e43200d778dde9d7cc01bfc1702090302bb42ce9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 11 15:08:47 2021 -0500
move more stuff into the build scripts (#533)
now the Fortran "get" routines are part of runtime_parameters.py. This also adds array support. This will help with porting the Castro problem parameters over.
util/build_scripts/runtime_parameters.py
util/build_scripts/write_probin.py
commit 401a434306a229bbe397a6176843efc677a855b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 10 09:40:02 2021 -0800
Mark screening data inline (#529)
screening/Make.package
screening/screen.H
screening/screen_data.H
screening/screen_data.cpp
unit_test/test_screening/main.cpp
unit_test/test_screening/screening_util.cpp
commit ce5836614734d45dd7c921040845b162980d7722
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 12:14:58 2021 -0500
fix runtime parameter parsing and some doc formatting (#532)
sphinx_docs/rp.py
sphinx_docs/source/nse.rst
commit 55ff256949f531300c2fb280fb543eaea1860f1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 11:31:40 2021 -0500
fix typo in opacity namespace (#531)
opacity/rad_power_law/_parameters
commit 8bc56d5b451d885b07683c4636557bda935399a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 10:26:21 2021 -0500
remove errant semi-colons (#530)
util/build_scripts/write_probin.py
commit 82908138593b280e478df0404ceb517d7403f0f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 09:03:45 2021 -0500
convert some unit test parameters to C++ (#526)
this converts test_screening, test_aprox_rates, and test_sdc.
commit bca31fc3887ffbbb126ed6cd371bcdfbaab3158b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 10 09:03:08 2021 -0500
convert test_react to C++ parameters (#527)
unit_test/test_aprox_rates/input_aprox_rates
unit_test/test_aprox_rates/probin
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_3alpha.VBDF
unit_test/test_react/inputs_aprox13
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_aprox19.nse_disabled
unit_test/test_react/inputs_aprox19_nse
unit_test/test_react/inputs_aprox21
unit_test/test_react/inputs_ignition
unit_test/test_react/inputs_ignition_chamulak
unit_test/test_react/inputs_iso7
unit_test/test_react/inputs_nova
unit_test/test_react/inputs_powerlaw
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_sn160
unit_test/test_react/inputs_xrb_simple
unit_test/test_react/probin
unit_test/test_react/probin.3alpha
unit_test/test_react/probin.3alpha.VBDF
unit_test/test_react/probin.aprox13
unit_test/test_react/probin.aprox13.cvode_compare
unit_test/test_react/probin.aprox19
unit_test/test_react/probin.aprox19.nse_disabled
unit_test/test_react/probin.aprox19_nse
unit_test/test_react/probin.aprox21
unit_test/test_react/probin.ignition
unit_test/test_react/probin.ignition_chamulak
unit_test/test_react/probin.iso7
unit_test/test_react/probin.nova
unit_test/test_react/probin.powerlaw
unit_test/test_react/probin.reaclib_cburn
unit_test/test_react/probin.reaclib_ctest
unit_test/test_react/probin.reaclib_urca
unit_test/test_react/probin.reaclib_urca_cfcvode
unit_test/test_react/probin.rprox
unit_test/test_react/probin.sn160
unit_test/test_react/probin.xrb_simple
unit_test/test_screening/inputs
unit_test/test_screening/probin
unit_test/test_sdc/inputs_aprox13
unit_test/test_sdc/inputs_aprox19.no_nse
unit_test/test_sdc/probin
unit_test/test_sdc/probin.aprox13
unit_test/test_sdc/probin.aprox19.no_nse
commit 17699cd8fd106d1e0b6d345b65117e3bfeaeb267
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 10 06:02:42 2021 -0800
jacobian override needs correct namespace (#528)
networks/powerlaw/_parameters
commit 6279aacf181aea76fae527335531dd47a7161190
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 9 20:18:13 2021 -0500
make the Microphysics parameters optionally managed by C++ (#505)
as part of this change, each parameter now has a namespace. You can set them in your probin as before with no changes. But you can also now set them in the inputs file, which means that they are read in by C++. Here you would use the namespace for the parameter (like eos.use_coulomb = 1). Note: if a parameter is set both in the probin and the inputs, then the inputs value is used.
This can be tested using the test_parameters unit test.
CHANGES.md
EOS/breakout/_parameters
EOS/gamma_law/_parameters
EOS/gamma_law_general/_parameters
EOS/helmholtz/_parameters
EOS/multigamma/_parameters
EOS/polytrope/_parameters
EOS/rad_power_law/_parameters
EOS/stellarcollapse/_parameters
EOS/ztwd/_parameters
conductivity/constant/_parameters
conductivity/constant_opacity/_parameters
conductivity/powerlaw/_parameters
integration/CVODE/_parameters
integration/ForwardEuler/_parameters
integration/QSS/_parameters
integration/VODE/_parameters
integration/_parameters
interfaces/extern_probin.template
networks/ECSN/_parameters
networks/_parameters
networks/aprox13/_parameters
networks/aprox19/_parameters
networks/aprox21/_parameters
networks/ignition_reaclib/C-burn-simple/_parameters
networks/ignition_reaclib/C-test/_parameters
networks/ignition_reaclib/URCA-simple/_parameters
networks/nova/_parameters
networks/powerlaw/_parameters
networks/rprox/_parameters
networks/sn160/_parameters
networks/subch/_parameters
networks/subch2/_parameters
networks/triple_alpha_plus_cago/_parameters
networks/xrb_simple/_parameters
opacity/rad_power_law/_parameters
unit_test/burn_cell/_parameters
unit_test/burn_cell/main.cpp
unit_test/eos_cell/_parameters
unit_test/eos_cell/main.cpp
unit_test/test_aprox_rates/_parameters
unit_test/test_aprox_rates/main.cpp
unit_test/test_conductivity/_parameters
unit_test/test_conductivity/main.cpp
unit_test/test_cvode_react/_parameters
unit_test/test_eos/_parameters
unit_test/test_eos/main.cpp
unit_test/test_jac/_parameters
unit_test/test_jac/main.cpp
unit_test/test_parameters/GNUmakefile
unit_test/test_parameters/_parameters
unit_test/test_parameters/inputs
unit_test/test_parameters/main.cpp
unit_test/test_parameters/test_parameters.F90
unit_test/test_reaclib_rates/_parameters
unit_test/test_react/_parameters
unit_test/test_react/main.cpp
unit_test/test_rhs/_parameters
unit_test/test_rhs/main.cpp
unit_test/test_screening/_parameters
unit_test/test_screening/main.cpp
unit_test/test_sdc/_parameters
unit_test/test_sdc/main.cpp
unit_test/test_sdc_vode_rhs/_parameters
unit_test/test_sdc_vode_rhs/main.cpp
unit_test/unit_test.F90
unit_test/unit_test.H
unit_test/unit_test_F.H
unit_test/write_job_info.cpp
util/build_scripts/runtime_parameters.py
util/build_scripts/write_probin.py
viscosity/constant/_parameters
commit c441fe9bae811a2781c3485536980b41ec0763f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 9 14:40:16 2021 -0500
remove util/LINPACK (#493)
this does not seem to be used by anything anymore
networks/Make.package
util/LINPACK/Make.package
util/LINPACK/dgbfa.f
util/LINPACK/dgbsl.f
util/LINPACK/dgefa.f
util/LINPACK/dgesl.f
util/LINPACK/license.txt
util/LINPACK/vddot.f
commit 26a4c9c1fa1fb1c46916552b9d8a7d791640fbb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 9 13:18:16 2021 -0500
clean up strings in runtime_parameters.py (#525)
now they are all allocated in Fortran the same regardless if
we are coming in from Fortran or C++. This requires changes
on the application code side.
util/build_scripts/runtime_parameters.py
commit 90ac18df551d3fc277d39c5d01a6a08af4247d2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 8 17:38:58 2021 -0500
centralize the init_unit_test functionality (#524)
unit_test/Make.package
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/Make.package
unit_test/burn_cell/burn_cell_F.H
unit_test/burn_cell/main.cpp
unit_test/eos_cell/GNUmakefile
unit_test/eos_cell/Make.package
unit_test/eos_cell/eos_cell_F.H
unit_test/eos_cell/main.cpp
unit_test/eos_cell/unit_test.F90
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/unit_test.f90
unit_test/test_conductivity/Make.package
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/test_cond_F.H
unit_test/test_conductivity/unit_test.f90
unit_test/test_cvode_react/unit_test.f90
unit_test/test_eos/Make.package
unit_test/test_eos/main.cpp
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/unit_test.f90
unit_test/test_jac/Make.package
unit_test/test_jac/main.cpp
unit_test/test_jac/test_react_F.H
unit_test/test_jac/unit_test.f90
unit_test/test_parameters/GNUmakefile
unit_test/test_parameters/Make.package
unit_test/test_parameters/main.cpp
unit_test/test_parameters/test_parameters_F.H
unit_test/test_parameters/unit_test.f90
unit_test/test_react/Make.package
unit_test/test_react/main.cpp
unit_test/test_react/test_react_F.H
unit_test/test_react/unit_test.f90
unit_test/test_rhs/Make.package
unit_test/test_rhs/main.cpp
unit_test/test_rhs/test_react_F.H
unit_test/test_rhs/unit_test.f90
unit_test/test_screening/Make.package
unit_test/test_screening/main.cpp
unit_test/test_screening/test_screen_F.H
unit_test/test_screening/unit_test.f90
unit_test/test_sdc/Make.package
unit_test/test_sdc/main.cpp
unit_test/test_sdc/unit_test.f90
unit_test/test_sdc_vode_rhs/Make.package
unit_test/test_sdc_vode_rhs/main.cpp
unit_test/test_sdc_vode_rhs/test_react_F.H
unit_test/test_sdc_vode_rhs/unit_test.f90
unit_test/unit_test.F90
unit_test/unit_test_F.H
commit d25ead38ef1717be7174373d1074da21b85afb33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 8 11:07:05 2021 -0500
more param tweaks for MAESTROeX (#523)
util/build_scripts/runtime_parameters.py
commit 25acfa284d156574a08fe65f1f108780e680cc3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 7 19:02:28 2021 -0500
fix a few issues with runtime_parameters.py (#522)
util/build_scripts/runtime_parameters.py
commit eb0ee41f5134193b44b7e97926895dfdffa90fdb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 11:01:37 2021 -0500
fix breakout EOS compilation (#521)
EOS/breakout/actual_eos.H
commit 20c2e2711b2587a0f7d79c635971557fdb5bb57d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 10:39:37 2021 -0500
start reusing some code for runtime parameters (#510)
This creates a centralized Params class in runtime_paramerters.py that eventually will be used by the application codes and Microphysics for managing runtime parameters. It has all of the necessary methods to write the C++ and Fortran needed for when Fortran manages the runtime parameters (as currently is the case in Microphysics) and for when C++ manages them (like we do in Castro for the main parameters).
interfaces/extern_probin.template
util/build_scripts/runtime_parameters.py
util/build_scripts/write_probin.py
commit b62fb17cad952c85ca2b2a542fd6c17c3461e76f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 08:52:48 2021 -0500
remove support for F90 simplified SDC with VODE (#492)
We are transitioning to C++ in the application codes that use SDC,
so the F90 simplified SDC interface is unused and will not get new
features.
CHANGES.md
integration/Make.package
integration/VODE/Make.package
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_rhs_simplified_sdc.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type_simplified_sdc.F90
integration/integrator_sdc.F90
interfaces/Make.package
interfaces/burner.F90
interfaces/sdc_type.F90
unit_test/test_sdc/Make.package
unit_test/test_sdc/main.cpp
unit_test/test_sdc/react_zones.F90
unit_test/test_sdc/test_react_F.H
unit_test/test_sdc/variables_F.F90
commit d097ff33f296d62f477128aeb7af6b45f5de749d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 5 14:09:30 2021 -0500
fix CUDA compilation (#520)
unit_test/write_job_info.cpp
commit 305901c0376fcd03ad35d44e0e35af8707c3c28e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 4 15:55:20 2021 -0500
only do the temperature RHS and Jac for Strang (#519)
in particular, this is now safe for true SDC
networks/aprox13/actual_rhs.H
networks/aprox19/actual_rhs.H
networks/ignition_simple/actual_rhs.H
networks/iso7/actual_rhs.H
networks/powerlaw/actual_rhs.H
networks/triple_alpha_plus_cago/actual_rhs.H
commit 99f89547c00353aa4bc20b6055171ef3228570da
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 11:07:49 2021 -0800
Only access variables in the state in breakout (#516)
EOS/breakout/actual_eos.H
commit 3b30c72a0ca76e61da267464ef22f26d59a16d03
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 11:05:42 2021 -0800
Only access variables in the state in ztwd (#515)
EOS/ztwd/actual_eos.H
commit 44c8760fea902c7a59dd0d719cebea0b89938a03
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 11:04:06 2021 -0800
Only access variables in the state in rad_power_law (#514)
EOS/rad_power_law/actual_eos.H
commit 7d0973c48c5afcfbca77d3b51e036efd40cfa006
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 08:40:01 2021 -0800
Only access variables in the state in multigamma (#513)
EOS/multigamma/actual_eos.H
commit 08719be654db3b27f26c8bf9369e5e1e6e4ac452
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 07:47:38 2021 -0800
Only access variables in the state in polytrope (#512)
EOS/polytrope/actual_eos.H
commit 72687a97260b122f7f6297f00fc95ae11ba1fefe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 07:46:02 2021 -0800
Only access variables in the state in gamma_law (#511)
EOS/gamma_law/actual_eos.H
commit 53f6cf65ec3ef142d51cda3ecab58cc4fb026ec9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 4 06:49:37 2021 -0800
Some updates to the README (#517)
README.md
commit e6a784c6f0dc2b41c3cde4ca3ee8a1d58ca3388e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 3 15:30:23 2021 -0800
Only access variables in the state in gamma_law_general (#509)
EOS/gamma_law_general/actual_eos.H
commit bea1033e6f405f54156fc26e4d1fef879e10f745
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 3 18:29:24 2021 -0500
remove Fortran OpenACC and CUDA managed memory (#508)
util/build_scripts/write_probin.py
commit c526e797285cfa5770d6c5c08cc0a395797ead68
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 3 13:51:11 2021 -0800
Only accesses variables in the state in Helmholtz (#507)
Continues #470 by compiling out accesses to members of the struct sent to the EOS that are invalid. This will allow us later to, for example, send a type to the EOS that doesn't have entropy or enthalpy.
We don't explicitly compile out all intermediate expressions that led up to the quantities in question. That could be done, but compilers should be able to recognize that as dead code and compile it out for us.
EOS/helmholtz/actual_eos.H
commit baf2f42f19a5b17b213494780f4e666b40343b71
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jan 3 13:09:38 2021 -0800
Skip EOS reset if eos_t doesn't have relevant quantities (#506)
This is a first demonstration of how we can use C++17 if constexpr to template out unnecessary logic.
interfaces/eos.H
commit 3f754b8088f9e36dd2248e72c4a5867cccbcfdb1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 3 12:56:02 2021 -0500
adjust VODE validity checks for simplfied-SDC (#498)
integration/VODE/vode_dvstep.H
commit 0ec314c4e7518114a3ad508ef7e545af7defedda
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 1 18:13:19 2021 -0800
Generalize linpack and move to util (#503)
Closes #502
integration/VODE/Make.package
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvnlsd.H
util/Make.package
util/linpack.H
commit 3244390007f3c7feba922f0f58b4f7563bd64f16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 1 21:08:11 2021 -0500
sync the release script with Castro (#501)
this will hopefully fix the release notes
.github/workflows/get_release_txt.py
commit 6f28333d40c9e15fdfbb1c4dc208e887fb5549c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jan 1 14:20:40 2021 -0800
Fix variable names in eos_init (#500)
This fixes an issue in #495 that was avoiding some global variable shadowing, but didn't change all the variable names correctly.
interfaces/eos.H
commit ad6f2f0dad6543aca040f3d45605e08ba5933804
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jan 1 15:16:31 2021 -0500
define STRANG if we are not doing an SDC variant (#499)
Make.Microphysics
Make.Microphysics_extern
commit 9a9ca8960bc70c9d3d39f661c384dc5ac840922e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 30 09:02:40 2020 -0800
Update to C++17 as minimum standard (#485)
CHANGES.md
Make.Microphysics
commit 888598c3f270c094875d509c862f6c1174df8260
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 29 14:57:44 2020 -0500
remove the BS integrator (#488)
BS was Fortran only, so we couldn't use it in our codes anyway
it also was not very good. We also now have a C++ ForwardEuler if
we want to generate a reference solution (with really small timesteps)
for testing. This change also removes the integrator switch logic
in the Fortran driver.
CHANGES.md
integration/BS/LAPACK/LICENSE.txt
integration/BS/Make.package
integration/BS/_parameters
integration/BS/bs_integrator.F90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type.F90
integration/BS/stiff_ode.F90
integration/BS/test/GNUmakefile
integration/BS/test/f_rhs.f90
integration/BS/test/test.f90
integration/Make.package
integration/integrator.F90
sphinx_docs/source/integrators.rst
sphinx_docs/source/sdc.rst
sphinx_docs/source/unit_tests.rst
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_ignition.BS
unit_test/test_react/inputs_ignition_chamulak.BS
unit_test/test_react/inputs_reaclib_cburn.BS
unit_test/test_react/inputs_reaclib_ctest.BS
unit_test/test_react/inputs_reaclib_urca.BS
unit_test/test_react/probin.3alpha.BS
unit_test/test_react/probin.ignition.BS
unit_test/test_react/probin.ignition_chamulak.BS
unit_test/test_react/probin.reaclib_cburn.BS
unit_test/test_react/probin.reaclib_ctest.BS
unit_test/test_react/probin.reaclib_urca.BS
commit 554722a22ebb7e8cb4877c74c04e072b69fddc9c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 29 10:15:24 2020 -0800
Address various compiler warnings (#495)
Use of single argument static_assert without a message is C++17-only
One usage of static_assert in helmeos was prematurely implemented at compile time instead of runtime
Shadowing of small_dens and small_temp in eos.H
Unknown compiler pragmas (pragma gpu)
Invalid use of compound literals in eos_type.H (C99 only)
slen is unused in extern_parameters.cpp if there are no string parameters
EOS/breakout/actual_eos.H
EOS/gamma_law/actual_eos.H
EOS/gamma_law_general/actual_eos.H
EOS/helmholtz/actual_eos.H
EOS/multigamma/actual_eos.H
EOS/polytrope/actual_eos.H
EOS/rad_power_law/actual_eos.H
EOS/ztwd/actual_eos.H
integration/VODE/cuVODE/test/main.cpp
interfaces/eos.H
interfaces/eos_type.H
unit_test/test_aprox_rates/main.cpp
unit_test/test_conductivity/main.cpp
unit_test/test_eos/main.cpp
unit_test/test_react/main.cpp
unit_test/test_rhs/main.cpp
unit_test/test_screening/main.cpp
unit_test/test_sdc/main.cpp
util/build_scripts/write_probin.py
commit 04c51a8555727ef66a6d4bd0d48e899489d06247
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 29 09:59:44 2020 -0500
start porting NSE to SDC (#423)
This puts the auxiliary data into the SDC code path and syncs it up with the mass fractions as needed. This will allow us to get the thermodynamic information from aux instead of X.
This gives O(1.e-8) agreement with the Castro reacting_convergence test, comparing the output for the 64^2 run with and without USE_NSE.
integration/VODE/actual_integrator_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
interfaces/burn_type.H
interfaces/burner.H
networks/aprox19/nse.H
unit_test/test_sdc/react_zones.H
unit_test/test_sdc/variables.H
unit_test/test_sdc/variables.cpp
unit_test/test_sdc/variables_F.F90
unit_test/test_sdc_vode_rhs/GNUmakefile
unit_test/test_sdc_vode_rhs/Make.package
unit_test/test_sdc_vode_rhs/README.md
unit_test/test_sdc_vode_rhs/_parameters
unit_test/test_sdc_vode_rhs/inputs_aprox19
unit_test/test_sdc_vode_rhs/main.cpp
unit_test/test_sdc_vode_rhs/probin.aprox19
unit_test/test_sdc_vode_rhs/test_react.H
unit_test/test_sdc_vode_rhs/test_react_F.H
unit_test/test_sdc_vode_rhs/unit_test.f90
unit_test/test_sdc_vode_rhs/vode_rhs_test.H
commit aadfa7f51e09df35629e99e97eb3501c816c5f11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 28 20:03:00 2020 -0500
rmeove unused variables (#494)
unit_test/test_aprox_rates/main.cpp
unit_test/test_conductivity/main.cpp
unit_test/test_cvode_react/main.cpp
unit_test/test_screening/main.cpp
unit_test/test_sdc/main.cpp
commit 28df5d8db577a98e95e38afdd3bca277e0484582
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Dec 27 13:34:01 2020 -0500
eliminate some divides in the EOS composition (#491)
EOS/eos_composition.H
commit 899dd8f006b1f8156a4881ee821f795775cc0f63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 26 21:41:40 2020 -0500
we don't need the travis encrypted key anymore (#490)
we use github actions
id_rsa_travis.enc
commit 747e017d427715bf757cb891e05084d4d332c74f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 26 18:09:45 2020 -0800
Initialize n_rhs in ForwardEuler (#489)
integration/ForwardEuler/actual_integrator.H
commit e92ebd0b7e04a93cf8d6f1813e224ce6b5cc512f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 25 10:10:36 2020 -0800
Various improvements to the QSS integrator (#487)
* Initialize n_rhs to 0
* If any X goes sufficiently negative or > 1, reject the timestep immediately and cut by a factor of 2
* Fix predictor for e
* The predictor needs to be evaluated inside the timestep loop, not before it, since it depends on dt
integration/QSS/_parameters
integration/QSS/actual_integrator.H
commit 82b28c2198db939cc7fe25e3a6cdc5737bd5b080
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 25 06:30:24 2020 -0800
Choose a better initial dt for the QSS integrator (#486)
integration/QSS/_parameters
integration/QSS/actual_integrator.H
commit 0afe1c1344433b803fcf669d96a3d417606ae9c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 24 07:20:43 2020 -0800
Fix iso7 Fortran finalization (#484)
networks/iso7/actual_network.F90
commit 6f97814076988c00a3cba5cdc9c5d2bcef5c599f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 15:19:28 2020 -0800
Add types to determine if an EOS type has given members (#481)
To do #470 we will need to be able to determine at compile time if a given template type has certain member data. This adds a few structs for that purpose. The idea is that they can be used like
if constexpr (has_xne_xnp<T>::value) {
state.xne = xnefer;
state.xnp = 0.0e0_rt;
}
The intended usage above requires C++17, but this PR does not yet require that.
interfaces/eos_type.H
commit dd3eb0701248c4b61c2eaaaf905fe8f9086af11c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 12:22:33 2020 -0800
Template on eos_input_t (#483)
This will be necessary for some compile-time evaluation we want to do for #470.
EOS/breakout/actual_eos.H
EOS/gamma_law/actual_eos.H
EOS/gamma_law_general/actual_eos.H
EOS/helmholtz/actual_eos.H
EOS/multigamma/actual_eos.H
EOS/polytrope/actual_eos.H
EOS/rad_power_law/actual_eos.H
EOS/ztwd/actual_eos.H
interfaces/eos.H
commit cd6494d94ffa33e0db0db53f13f90c03716401bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 23 11:02:53 2020 -0800
Template functions which accept an eos_t (#480)
Starts #470 by making all functions which previously accepted an eos_t be templated.
EOS/breakout/actual_eos.H
EOS/eos_composition.H
EOS/gamma_law/actual_eos.H
EOS/gamma_law_general/actual_eos.H
EOS/helmholtz/actual_eos.H
EOS/multigamma/actual_eos.H
EOS/multigamma/eos_composition.H
EOS/polytrope/actual_eos.H
EOS/rad_power_law/actual_eos.H
EOS/ztwd/actual_eos.H
conductivity/constant/actual_conductivity.H
conductivity/constant_opacity/actual_conductivity.H
conductivity/powerlaw/actual_conductivity.H
conductivity/stellar/actual_conductivity.H
integration/VODE/vode_type_simplified_sdc.H
interfaces/burn_type.H
interfaces/conductivity.H
interfaces/eos.H
interfaces/eos_override.H
commit b4fd1176b06c2f05485827765f5aebe6e138542b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Dec 22 08:45:39 2020 -0800
Update explicit integrator to use QSS method (#472)
integration/ExplicitAsymptotic/README.md
integration/ExplicitAsymptotic/_parameters
integration/ExplicitAsymptotic/actual_integrator.H
integration/QSS/Make.package
integration/QSS/README.md
integration/QSS/_parameters
integration/QSS/actual_integrator.H
commit 14e6cf977dcde984c1f04c89ce76825773b69a72
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 18:22:29 2020 -0800
Add an option to set a maximum burning timestep (#473)
integration/ExplicitAsymptotic/actual_integrator.H
integration/ForwardEuler/actual_integrator.H
integration/VODE/actual_integrator.H
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/vode_dvstep.H
integration/VODE/vode_integrator.F90
integration/VODE/vode_type.H
integration/_parameters
commit 2909d10b33135b6d01d7f292ca838063e25c5344
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 17:45:35 2020 -0800
iso7 14/∞ (#467)
Evaluate as much of the RHS as possible at compile time. Specifically we do not waste memory or flops on contributions to each RHS from rates that don't actually contribute.
To make this simpler to review I am retaining the old behavior that the esum is over NumRates terms even though most of them are zero. I will do the piece that skips the zero terms in a later PR.
interfaces/rhs_utilities.H
commit 618cbf60bdbf647f359f72bf6f264a37ea893985
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 21 20:07:11 2020 -0500
create a C++ numerical Jacobian (#468)
This is not needed by VODE, since VODE internally does its own thing, but this could be useful for other integrators and also for the SDC implementations where we just do Newton iterations instead of an ODE solve.
This PR also introduces a unit test to test the C++ numerical Jacobian.
integration/utils/numerical_jacobian.H
interfaces/burn_type.H
unit_test/test_jac/GNUmakefile
unit_test/test_jac/Make.package
unit_test/test_jac/README.md
unit_test/test_jac/_parameters
unit_test/test_jac/inputs_aprox13
unit_test/test_jac/jac_zones.H
unit_test/test_jac/main.cpp
unit_test/test_jac/probin.aprox13
unit_test/test_jac/test_react.H
unit_test/test_jac/test_react_F.H
unit_test/test_jac/unit_test.f90
unit_test/test_jac/variables.H
unit_test/test_jac/variables.cpp
unit_test/test_rhs/main.cpp
commit 76bbe84064ada22d573610ce4bb8377ae6ab68fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 16:57:27 2020 -0800
Make ForwardEuler respect burner_verbose and ode_max_steps (#477)
integration/ForwardEuler/actual_integrator.H
commit 3e1910f3b88f5438760d635f6c3d313ade53483d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 15:38:26 2020 -0800
Fix iso7 Jacobian bug from #457 (#476)
networks/iso7/actual_network.H
commit 765057da7335a1c5237d7196b3f4176e0f4b60a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Dec 21 14:50:49 2020 -0800
Fix order of arguments in C++ wrapper to Fortran RHS (#475)
interfaces/fortran_to_cxx_actual_rhs.F90
commit e3fe087b19601f0e1a711319f0dd2d89568545fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 19 12:07:34 2020 -0800
Test iso7 RHS more comprehensively (#469)
Since we're just evaluating the RHS we can afford to do it over more zones and still have the test complete within a few seconds. Also, since the critical piece of this network is the silicon burning, I made that one of the primary species.
unit_test/test_rhs/inputs_iso7
unit_test/test_rhs/probin.iso7
commit 338a4cea5b04c14cfe85d4d4459639a537a579d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 15:38:00 2020 -0800
Add explicit integrator with asymptotic approximation (#466)
The explicit integration method of Guidry et al. (2013) (paper 1 of 3) is implemented. In this approach we detect which terms in the species RHS would equilibrate within the current integration timestep and then use the asymptotic approximation to update that term instead of normal explicit integration.
This seems to work OK for "easy" burns at low temperature -- the answer is fairly inaccurate for the default choice of parameters, presumably due to the first order method, but if we are very restrictive on the timestep then the answer converges to what VODE provides. Near NSE we just run into the same problems as the simple forward Euler integrator, which will require the "partial equilibrium" method that detects which specific rates are in approximate detailed balance and removes them from the integration.
To do:
* Use a higher-order integration method for both the explicit and asymptotic terms (the paper describes a predictor-corrector scheme)
 * Add the partial equilibrium method from paper 3 of that series
integration/ExplicitAsymptotic/Make.package
integration/ExplicitAsymptotic/README.md
integration/ExplicitAsymptotic/_parameters
integration/ExplicitAsymptotic/actual_integrator.H
commit ca022d871cb9575cc7eeb9161f32839a52c32700
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 15:11:57 2020 -0800
iso7 part 13 (#465)
species_rhs and ener_rhs return their values.
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
commit f4f9172c4d62f1d601097431890d301b65df7bc1
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 18 08:45:09 2020 -0800
iso7 12/∞ (#461)
temperature_rhs returns its value rather than filling ydot.
integration/utils/temperature_integration.H
networks/aprox13/actual_rhs.H
networks/aprox19/actual_rhs.H
networks/ignition_simple/actual_rhs.H
networks/iso7/actual_rhs.H
networks/powerlaw/actual_rhs.H
networks/triple_alpha_plus_cago/actual_rhs.H
commit 643a0bdf2171b4c674ee708f9f5146bf0f3ce7f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 17 22:21:53 2020 -0500
some documentation updates (#397)
sphinx_docs/source/basics.rst
sphinx_docs/source/integrators.rst
commit 9667db0105961e473e6d71267f559f9fe781fc9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 17 22:20:58 2020 -0500
fix doc builds (#463)
sphinx_docs/source/conf.py
commit 0bbd91c02f5cd6770baa8200cac7179441763d43
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Dec 17 05:59:27 2020 -0800
Replace AMREX_MFITER_REDUCE macro with AsyncArray (#464)
unit_test/test_react/main.cpp
unit_test/test_sdc/main.cpp
commit 187b580ee98a8c00b15720a0b4892c11f4c5021e
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 16 15:27:18 2020 -0800
iso7 11/∞ (#457)
Convert remaining Jacobian terms to new scheme
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 8fbcb21207f649e3a2fe0654705c3a9c540d4b94
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 16 10:29:21 2020 -0800
Shorten iso7 integration time (#462)
unit_test/test_react/probin.iso7
commit c02d5ef1ace7e07fb9f53846dbc343af66ed2e72
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 17:30:56 2020 -0800
iso7 10/∞ (#456)
Extend to all components of the He4 Jacobian
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 61a3272896646de523d43fdae6419959ac466101
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Dec 9 09:41:31 2020 -0800
iso7 9/∞ (#455)
Now we start applying the same approach to the Jacobian that we did for the RHS. We assert that the Jacobian terms have the same form as the RHS terms, K * rate * Y1 * Y2 * Y3 (although I think there cannot be any three-body terms). A complicating factor is that the rate derivative d(rate) / dY may be non-zero since many of the rates in the aprox networks have hidden contributions from equilibrium sequences that depend on Y. So in addition the Jacobian have a term from K * drate/dY * Y1 * Y2 * Y3.
interfaces/network_utilities.H
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit a541fe2227a9c2d4f7dfc8b6c1a4456fd97f7493
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 9 12:37:51 2020 -0500
setup_composition does not need to be on the GPU (#460)
this fixes GPU compilation
unit_test/react_util.H
commit 2af71bdfe8cb54a6edeff18a73c40cd92c866d51
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Dec 6 12:50:44 2020 -0800
Pass small_temp and small_dens into eos_init (#459)
This is needed because the downstream codes do not make these variables available as globals without a namespace.
interfaces/eos.H
unit_test/burn_cell/main.cpp
unit_test/eos_cell/main.cpp
unit_test/test_aprox_rates/main.cpp
unit_test/test_conductivity/main.cpp
unit_test/test_eos/main.cpp
unit_test/test_react/main.cpp
unit_test/test_rhs/main.cpp
unit_test/test_screening/main.cpp
unit_test/test_sdc/main.cpp
commit f1aa3e9c62c6ca8306683cf2803b5dc6cd738108
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 5 20:22:43 2020 -0500
allow the EOS to be turned off by setting USE_FORT_EOS=FALSE (#458)
By default, we set USE_FORT_EOS ?= TRUE in the Make.Microphysics_extern, so no codes will need to be changed.
This addresses part of #453
EOS/Make.package
EOS/breakout/Make.package
EOS/gamma_law/Make.package
EOS/gamma_law_general/Make.package
EOS/helmholtz/Make.package
EOS/multigamma/Make.package
EOS/polytrope/Make.package
EOS/rad_power_law/Make.package
EOS/stellarcollapse/Make.package
EOS/ztwd/Make.package
Make.Microphysics_extern
interfaces/Make.package
interfaces/microphysics.F90
unit_test/test_eos/Make.package
unit_test/test_eos/main.cpp
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/unit_test.f90
commit 32103c9c31d7e69021b545c7985436f683cf9d89
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 5 10:47:00 2020 -0800
iso7 part 8 (#449)
iso7 has a rate dependence on Y since the (7*He4 + Si28 -> Ni56) effective rate (both forward and reverse) depends on Y. The forward rate is given by k(rho, T) * Y(He)^3 * Y(Si28), so several Jacobian elements need to have d(rate)/dY terms to be computed correctly. (A similar thing is true for the reverse rate.) The current code knows exactly which d(rate)/dY terms are computed and stores them in rate arrays dratedy1 and dratedy2. But if we want to generalize this we need to be agnostic to which specific rates and which specific species have the dependence. A solution is to allow the Jacobian to generally be a function of the derivatives of the rates with respect to Y in addition to the derivatives of Y itself in the RHS. To effect this generally we need to have a dratedY container which has NumSpec species and NumRates rates, and this change enables that. The vast majority of these entries will be empty, so this temporarily increases the storage requirements and adds some redundant calculations. But the change we'll be doing later is to detect the nonzero ones and only add them in at compile time.
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit fbcfffb35e6a5797e95317a631767fc5ad2c58b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Dec 5 08:44:36 2020 -0800
Remove C++ interface to Fortran small_dens/small_temp (#454)
This interface is unnecessary because the C++ EOS initialization duplicates what the Fortran does regarding mintemp/mindens, and this is one of the blockers for #453.
interfaces/Make.package
interfaces/eos.H
interfaces/eos_F.H
commit 235de0ce4dc0d4004fae5cd9356bca51c4b9c0be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 19:49:49 2020 -0500
have test_sdc use C++ initialization (#452)
unit_test/test_sdc/Make.package
unit_test/test_sdc/main.cpp
unit_test/test_sdc/react_zones.F90
unit_test/test_sdc/test_react_F.H
unit_test/test_sdc/util.f90
commit 5e351e0bc61b737aee022c3586ebe0c1de76b11e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 4 19:32:38 2020 -0500
switch more unit_test stuff off to C++ (#450)
unit_test/Make.package
unit_test/react_util.H
unit_test/test_react/Make.package
unit_test/test_react/react_zones.F90
unit_test/test_react/util.f90
unit_test/test_rhs/GNUmakefile
unit_test/test_rhs/Make.package
unit_test/test_rhs/main.cpp
unit_test/test_rhs/rhs_zones.F90
unit_test/test_rhs/rhs_zones.H
unit_test/test_rhs/test_react_F.H
unit_test/test_rhs/util.f90
unit_test/test_rhs/variables.F90
unit_test/test_rhs/variables.H
unit_test/test_rhs/variables.cpp
unit_test/test_rhs/variables_F.F90
commit ce9754f8819d43e29c4a1b3e5cb131a12c8db36d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 16:20:36 2020 -0800
iso7 part 7 (#442)
Directly inline species_rhs into actual_rhs and actual_jac
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
commit 611a5ff154d9e925636172b1650b4952c1c961fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 15:12:22 2020 -0800
iso7 part 6 (#441)
A version of the energy equation is created just for the RHS (directly includes the neutrino term).
networks/iso7/actual_rhs.H
commit a660fb478dab2468d76eeb06f8362e0652447894
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 13:22:50 2020 -0800
iso7 part 5 (#439)
A version of the rate evaluation is added which works only on a single rate group (so only makes sense to call from actual_rhs).
networks/iso7/actual_rhs.H
commit c7824d8d3775b3b97ea8c54863af5a1c88c66c65
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 12:29:43 2020 -0800
iso7 part 4 (#435)
Continues #434 by moving the construction of the species RHS terms to a standalone header.
interfaces/Make.package
interfaces/rhs_utilities.H
networks/iso7/actual_rhs.H
commit 8340dd1ac8ce57a479463a8e106126588800e981
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 11:45:01 2020 -0800
iso7 part 3 (#434)
Continues #433 by looping over species in addition to looping over rates. In order to make the loop work we resize the esum array to the number of total rates (since Array1D's size needs to be known at compile time). This means that esum will have some redundant work -- this de-optimization will eventually be recovered.
networks/iso7/actual_rhs.H
commit 05ea57f295d545664dad3a1f8052626a65fb4efb
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Dec 4 08:32:53 2020 -0800
iso7 part 2 (#433)
Continues #413 by extending the approach to all species
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit 60b04065f4290b47be65883e3b21f2c6dc51d248
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 12:45:33 2020 -0500
fix more github-linguist stuff (#451)
.gitattributes
commit 76599f9f6d44d25729a7cc26f6061140b964a3e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 09:54:33 2020 -0500
switch the test_react init to C++ (#448)
unit_test/test_eos/main.cpp
unit_test/test_react/GNUmakefile
unit_test/test_react/Make.package
unit_test/test_react/main.cpp
unit_test/test_react/react_util.H
unit_test/test_react/react_zones.F90
unit_test/test_react/test_react_F.H
commit ab65f3350274fc784ad95d81dbfc8b7db214a0e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 09:47:41 2020 -0500
this is an inputs that can be used for testing the SDC code path with USE_NSE (#443)
this disables calling the NSE table, but will do the thermodyanics via aux
unit_test/test_sdc/inputs_aprox19.no_nse
unit_test/test_sdc/probin.aprox19.no_nse
commit 5ff81cef88f80f82433e8038c82a3c331bfe46aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 3 07:33:53 2020 -0500
switch more unit tests over to using C++ for variable info (#447)
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/test_cond_F.H
unit_test/test_conductivity/variables_F.F90
unit_test/test_screening/main.cpp
unit_test/test_screening/test_screen_F.H
unit_test/test_screening/variables_F.F90
unit_test/test_sdc/main.cpp
unit_test/test_sdc/test_react_F.H
unit_test/test_sdc/variables_F.F90
commit f2b3c12d8845953169287f2e71aa292b26403efb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 2 18:13:07 2020 -0500
use C++ for getting the main variable info (#446)
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/variables_F.F90
unit_test/test_eos/main.cpp
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/variables_F.F90
unit_test/test_react/main.cpp
unit_test/test_react/test_react_F.H
unit_test/test_react/variables.H
unit_test/test_react/variables.cpp
unit_test/test_react/variables_F.F90
commit e7f51a8a0c4986766cdc01a6afcd25e675b293d3
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Dec 1 10:15:06 2020 -0500
fix release python script (#445)
.github/workflows/get_release_txt.py
commit 44f773aa8ef9524e6aeceb7fcff32fa0a69ebfe6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 29 18:50:54 2020 -0500
ignore Jupyter and TeX in language stats (#444)
.gitattributes
commit ac5ed9a09b49065bab82d993c1b14d4e9eaece3d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 22 05:24:01 2020 -0800
Add include (#440)
EOS/helmholtz/actual_eos.H
commit bf864ef7fd5cb31bf74445298de538e73cbfb40a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 17:29:05 2020 -0500
template set_nse_aux_from_X (#438)
networks/aprox19/nse.H
commit 330482b360d015742743b3350e3a95e125018245
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 21 13:38:55 2020 -0500
make in_nse a templated function (#437)
now we can pass in an eos_t or a burn_t
networks/aprox19/nse.H
commit 5f314a79ca40cff715dba076b3e7628d325b581b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Nov 19 10:10:38 2020 -0800
Implement iso7 RHS terms in a standardized form using data from a constexpr function (#413)
This PR is the start of a series of refactors so that iso7's RHS is re-implemented by moving all of the RHS data to the header in a function called rhs_data that returns an rhs_t struct. Every term in an RHS is a multiplicative combination of up to five terms: a prefactor, Y(i), Y(j), Y(k), and rate(l). Most reactions have two Y factors, like C12 + C12 -> Mg24; some have only one Y factor, like C12 + gamma -> 3He4; and the three-body reactions (triple alpha) can have three. If the species index is -1, we know to ignore it. If the compiler can optimize this suitably well by evaluating these terms at compile time, this should add no additional runtime cost. This initial change will do the evaluation at run time and incur a performance cost, but that will be resolved in a future PR.
The motivation for this change is that we want the flexibility to experiment with integrators that can directly utilize information about the form of the RHS. Right now the RHS is a black box to the integrator, but if we implement every RHS in a standard form like this, then we can write general integrators that can perform more sophisticated integration algorithms (but that can still construct the standard form of the RHS if needed, since they have all the terms ready to do so).
From the implementation perspective, I'm constructing the RHS by looping over rates, identifying the rates that contribute to the RHS for each species, and then filling the array which we then pass to esum.
With this infrastructure in place, and because we now fully construct the RHS behind the scenes, we should be able to do any number of things to experiment with integration schemes. For example, we could look into the idea I mentioned of constructing the RHS as a running esum rather than explicitly constructing the array and only then applying esum to it. We could also experiment with constructing the rates one by one and filling the RHS as we go, rather than explicitly constructing the full rate array. More generally I want to experiment with other integration strategies which require access to direct information about the structure of the RHS terms.
For this first PR, I've only applied it to one term in iso7 -- the Ni56 RHS -- and for now we're doing the evaluation at run time, not compile time. This will temporarily slow down iso7 but I have been able to demonstrate that when the changes are done, the performance will be recovered.
interfaces/Make.package
interfaces/network_utilities.H
networks/iso7/actual_network.H
networks/iso7/actual_rhs.H
commit d4b5b0f47fc70d24d41553177e940ec889df80c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 12:53:51 2020 -0800
Fix capitalization (#432)
opacity/breakout/actual_opacity.H
commit 3069e855717602fa11b66220767e978a36a43c55
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 11:23:00 2020 -0800
Fix exponential notation in C++ (#431)
opacity/breakout/actual_opacity.H
commit 3c20d202efd9d1ef011510625a214f48e4719093
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 10:09:39 2020 -0800
Convert opacity to C++ (#428)
Make.Microphysics_extern
opacity/Make.package
opacity/breakout/Make.package
opacity/breakout/actual_opacity.H
opacity/opacity.H
opacity/rad_power_law/Make.package
opacity/rad_power_law/actual_opacity.H
commit e2e7adb8bc3ee0efe9bf2a8ae81c9f59d93f4d7c
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Nov 18 09:47:16 2020 -0500
Fix create_release action (#430)
set_env is no longer supported in GitHub actions, so this fixes the create_release action so that it no longer includes that command.
.github/workflows/create_release.yml
commit f03eae34db4f54cb258567627e39fe051aa33813
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 18 05:29:16 2020 -0800
Add includes (#429)
constants/fundamental_constants.H
commit 7d6a60abdec3cfbc60064207aabd442349619c9b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 17 18:06:36 2020 -0800
Add templated esum implementation (#427)
util/esum.H
util/esum_cxx.py
commit 403a17bef19da09f48e74384eb704097d8bf7468
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 16 12:51:16 2020 -0500
remove the string names from the plot_t object
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/variables.H
unit_test/test_aprox_rates/variables.cpp
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/variables.H
unit_test/test_conductivity/variables.cpp
unit_test/test_eos/main.cpp
unit_test/test_eos/variables.H
unit_test/test_eos/variables.cpp
unit_test/test_screening/main.cpp
unit_test/test_screening/variables.H
unit_test/test_screening/variables.cpp
unit_test/test_sdc/variables.H
unit_test/test_sdc/variables.cpp
commit 1c1567c89e0fafe679ef1122bdb87034bdb502a1
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 08:10:36 2020 -0800
Add a simple forward Euler integrator (#426)
This will be useful for testing purposes going forward as we experiment with new integration schemes.
The timestepping scheme is not sophisticated right now and so the integrator has trouble in the NSE regime -- this should be fixed later.
Only Strang is provided for now.
integration/ForwardEuler/Make.package
integration/ForwardEuler/README.md
integration/ForwardEuler/_parameters
integration/ForwardEuler/actual_integrator.H
commit 73b7b2ba6b6cc2db961fac921dd57562495bb9f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 07:10:09 2020 -0800
Allow other C++ integrators (#424)
integration/VODE/Make.package
integration/VODE/actual_integrator.H
integration/VODE/actual_integrator_simplified_sdc.H
integration/integrator.H
integration/integrator_sdc.H
commit acef57cf95bbe82da07a526ee114b4ebe3f0928c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 14 06:28:44 2020 -0800
Allow integrator to have only a C++ implementation (#425)
In this case, we just make integrator.F90 a no-op.
integration/BS/Make.package
integration/CVODE/Make.package
integration/VODE/Make.package
integration/integrator.F90
commit 40cafe8862008cad91fa72feca68987c0bdb4132
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Nov 10 11:38:37 2020 -0800
Increase atol_spec to 1e-8 (#422)
CHANGES.md
integration/_parameters
commit ae3c29619fe849ca7fccd8218210651089a537fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 9 15:22:52 2020 -0800
Raise atol_spec to 1e-10 (#421)
CHANGES.md
integration/_parameters
commit b8c6f729d7bf222808147ea7ba7178307ba413ef
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 8 16:20:05 2020 -0800
Enable standard burn_to_eos for SDC (#420)
interfaces/burn_type.H
commit 84e497baea7157884f40a0b10f978e965a5a4081
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 7 14:17:32 2020 -0500
make the Strang NSE update more thermodynamically consistent (#404)
This uses a method slightly different than the Ma et al. 2013 update for the NSE. Instead of just taking Ye from the first call to the NSE table, we instead predict what the new Ye will be and re-call the table to get consistent composition and energy release from the table.
networks/aprox19/_parameters
networks/aprox19/actual_burner.F90
networks/aprox19/nse.H
commit 6e15c6a02f3f76c31bbd174dc48fc08b806fe5e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 1 13:50:47 2020 -0800
Add interface for C++ integrator to use Fortran RHS (#419)
If a network has a C++ RHS implementation, it should set DEFINES += -DNETWORK_HAS_CXX_IMPLEMENTATION in its Make.package, and the C++ integrator will continue to use it. Otherwise, we default to the Fortran RHS, and we add a wrapper script that translates between the C++ RHS/Jac and the Fortran RHS/Jac.
With this change, any downstream application can use USE_CXX_REACTIONS = TRUE everywhere and still use any network. The only catch is that there is no CUDA implementation right now in this PR, so the legacy Fortran networks won't run on GPUs. If we need to fix that later, it should be possible.
CHANGES.md
integration/VODE/vode_rhs.H
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type_simplified_sdc.H
interfaces/Make.package
interfaces/fortran_to_cxx_actual_rhs.F90
interfaces/fortran_to_cxx_actual_rhs.H
interfaces/network_initialization.cpp
networks/aprox13/Make.package
networks/aprox19/Make.package
networks/ignition_simple/Make.package
networks/iso7/Make.package
networks/powerlaw/Make.package
networks/triple_alpha_plus_cago/Make.package
unit_test/test_rhs/rhs_zones.H
commit ccd82d1e962b79e15d19fd77575b69e536550553
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 1 05:33:25 2020 -0800
Guard against pulling in actual_network (#417)
We pull in this file if USE_CXX_REACTIONS = TRUE, but if that is set without USE_REACT = TRUE, we will attempt to pull in actual_network.H, which only exists for some networks.
interfaces/network_initialization.cpp
commit 7952b11254b947c3975bf343c69454ffbf72647a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 05:58:54 2020 -0700
Remove array over NumGroups from rate_t (#416)
In every place in the networks where we are using rate_t, it works just as well to have an array of rate_t, where the size of the array is the number of rate groups, as it does to have the rate_t be a 2D array. Making this change has two benefits: we can clean up some of the RHS code later, because the RHS (unlike the Jacobian) typically does not actually need to fill all the rate groups (so this will save work and memory), and also this will support the change in #413.
networks/aprox13/actual_rhs.H
networks/aprox19/actual_rhs.H
networks/ignition_simple/actual_rhs.H
networks/iso7/actual_rhs.H
networks/rate_type.H
networks/triple_alpha_plus_cago/actual_rhs.H
commit c32823dcdd7041f80f5a42507f8f2bc85b8eb533
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 05:20:17 2020 -0700
Remove T_eval from rate_t (#414)
This is not used anywhere.
networks/aprox13/actual_rhs.F90
networks/aprox13/actual_rhs.H
networks/aprox19/actual_rhs.F90
networks/aprox19/actual_rhs.H
networks/aprox21/actual_rhs.F90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_simple/actual_rhs.F90
networks/ignition_simple/actual_rhs.H
networks/iso7/actual_rhs.F90
networks/iso7/actual_rhs.H
networks/rate_type.H
networks/rate_type.f90
networks/rprox/actual_rhs.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/actual_rhs.H
networks/xrb_simple/actual_rhs.f90
commit 6e0594e14022d0d26d3cc3aecf4a953fed8cf2c3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Oct 31 05:16:50 2020 -0700
Template powerlaw Jacobian to get it compiling again (#415)
networks/powerlaw/actual_rhs.H
commit 77553d1548b0308fcc0910a3029370d1ba38a564
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 11:11:36 2020 -0700
Guard some more attributes(managed) with USE_GPU_PRAGMA (#412)
interfaces/eos.F90
unit_test/test_react/variables_F.F90
unit_test/test_rhs/variables.F90
unit_test/test_screening/variables_F.F90
commit b69b86756271d186e30f7b67ac0363d9ddc12c2a
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 10:59:13 2020 -0700
Remove attributes(device) from cuVODE (#411)
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/linpack_module.F90
commit 8e5a5a4fb2c7a4c0cedbba9f15759a58e3af2af9
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 05:59:15 2020 -0700
Remove attributes(managed) when USE_GPU_PRAGMA = FALSE (#409)
EOS/breakout/actual_eos.F90
EOS/gamma_law/gamma_law.F90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
EOS/rad_power_law/rad_power_law.F90
integration/integrator_scaling.F90
integration/utils/temperature_integration.F90
interfaces/eos_type.F90
networks/ECSN/actual_network.F90
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_network.F90
networks/aprox19/nse_F.F90
networks/aprox21/actual_network.F90
networks/general_null/network.template
networks/general_null/network_properties.template
networks/ignition_chamulak/actual_network.F90
networks/ignition_simple/actual_network.F90
networks/iso7/actual_network.F90
networks/iso7/actual_rhs.F90
networks/nova/actual_network.F90
networks/powerlaw/actual_network.F90
networks/rprox/actual_network.F90
networks/sn160/actual_network.F90
networks/sn160/reaclib_rates.F90
networks/subch/actual_network.F90
networks/subch/reaclib_rates.F90
networks/subch2/actual_network.F90
networks/subch2/reaclib_rates.F90
networks/triple_alpha_plus_cago/actual_network.F90
rates/aprox_rates.F90
screening/screen.F90
unit_test/test_aprox_rates/variables_F.F90
unit_test/test_conductivity/variables_F.F90
unit_test/test_cvode_react/variables.F90
unit_test/test_eos/variables_F.F90
util/build_scripts/write_probin.py
commit 77b5f6972cbd4adefe6027e0ac0c851505a3a58b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 05:32:30 2020 -0700
Wrap EOS CUDA interfaces with AMREX_USE_GPU_PRAGMA (#408)
interfaces/eos.F90
interfaces/eos_type.F90
commit d9a60a05d9ce896368a2dccc2f08abec79722a22
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 30 05:20:41 2020 -0700
Remove aprox13 CUDA when USE_GPU_PRAGMA = FALSE (#410)
networks/aprox13/actual_rhs.F90
commit 13518a467a2bc654a569ae025ee54fae704dd42d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 27 13:22:19 2020 -0400
fix compilation of C++ aprox19 w/o NSE (#407)
networks/aprox19/actual_network_data.cpp
commit 0d6779e431dccff6824574cc7b8e7e6261115a5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 27 12:43:47 2020 -0400
fix #if -> #ifdef (#406)
integration/VODE/vode_type.F90
commit 789ba2f010fab83664eae92af3e9045f99a87576
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 26 09:55:33 2020 -0400
Create a C++ version of aprox19 + NSE (#362)
This mirrors the Fortran aprox19 + NSE network
CHANGES.md
integration/VODE/vode_type_strang.H
interfaces/burner.H
networks/Make.package
networks/aprox19/Make.package
networks/aprox19/_parameters
networks/aprox19/actual_network.F90
networks/aprox19/actual_network.H
networks/aprox19/actual_network_data.cpp
networks/aprox19/nse.H
networks/aprox19/nse19.tbl
networks/aprox19/nse_F.F90
networks/aprox19/table_preprocess/nse19.tbl.orig
networks/aprox19/table_preprocess/rewrite.f90
networks/aprox19/test-cpp/GNUmakefile
networks/aprox19/test-cpp/Make.package
networks/aprox19/test-cpp/main.cpp
networks/aprox19/test-cpp/testnse.cpp
networks/aprox19/test-cpp/testnse_F.F90
networks/aprox19/test-net-cpp/GNUmakefile
networks/aprox19/test-net-cpp/Make.package
networks/aprox19/test-net-cpp/do_initialization.f90
networks/aprox19/test-net-cpp/main.cpp
networks/aprox19/test-net-cpp/probin
networks/aprox19/test-net-cpp/testburn.f90
networks/aprox19/test-net-cpp/testjacobian.f90
unit_test/test_react/variables.F90
commit cf504e8bdbc7666640ed93d18009ddd27f1c52c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 21 10:18:30 2020 -0400
port the simplified SDC code paths to C++ (#389)
The main thing to keep in mind here is that in VODE, we use 1-based indexing (so for the dvode_t), but in burn state we use 0-based indexing.
Co-authored-by: Alice Harpole <harpolea@users.noreply.github.com>
CHANGES.md
integration/VODE/Make.package
integration/VODE/vode_dvhin.H
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvode.H
integration/VODE/vode_dvstep.H
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_integrator_simplified_sdc.H
integration/VODE/vode_rhs_simplified_sdc.H
integration/VODE/vode_type.H
integration/VODE/vode_type_simplified_sdc.H
integration/VODE/vode_type_strang.H
integration/integrator_sdc.H
integration/utils/Make.package
integration/utils/temperature_integration.H
interfaces/burn_type.H
interfaces/burner.H
interfaces/sdc_type.F90
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/Make.package
unit_test/test_sdc/_parameters
unit_test/test_sdc/main.cpp
unit_test/test_sdc/react_zones.F90
unit_test/test_sdc/react_zones.H
unit_test/test_sdc/test_react_F.H
unit_test/test_sdc/variables.H
unit_test/test_sdc/variables.cpp
unit_test/test_sdc/variables_F.F90
commit 05c5462625215aed382cac0f27a4975308cef404
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Oct 9 09:42:50 2020 -0400
Move screening directly into ignition_simple rates (#403)
networks/ignition_simple/actual_network.H
networks/ignition_simple/actual_rhs.H
commit 668ec0be7750ceb44cd527ea284097b55951ee38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 1 07:48:07 2020 -0400
update changes
CHANGES.md
commit ee0b99f301693ad98ed7183faa08cff3f32de452
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 25 12:37:40 2020 -0400
update changes
CHANGES.md
commit 08b5d9de0e57166ace2328afb25342ed5d67cf8c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 20 10:22:23 2020 -0400
cs and dx were removed from the burn_t (#400)
this fixes the compilation
unit_test/burn_cell/burn_cell.F90
commit a1c0346fe0287a816724f3f5bfe1f6569970ace5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 19 21:44:13 2020 -0400
switch to use the same C++ variables class as other tests (#398)
unit_test/test_react/Make.package
unit_test/test_react/main.cpp
unit_test/test_react/react_zones.H
unit_test/test_react/test_react_F.H
unit_test/test_react/variables.H
unit_test/test_react/variables.cpp
unit_test/test_react/variables_F.F90
commit b523b0afe7c68b84ac3b87d46d078c55a5735c63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 19 20:40:01 2020 -0400
add some C++ files missing in Make.package (#399)
networks/aprox19/Make.package
commit 4c1657ba14cced601c870c3da87b8ebb590475ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 19 14:43:55 2020 -0400
switch to using bion instead of ebin (#354)
this is consistent with the aprox nets and eliminates a multiply on the sum over dY/dt
eventually we should sync the binding energies up across networks.
networks/triple_alpha_plus_cago/actual_burner.F90
networks/triple_alpha_plus_cago/actual_network.F90
networks/triple_alpha_plus_cago/actual_network.H
networks/triple_alpha_plus_cago/actual_network_data.cpp
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/actual_rhs.H
commit 993d7f50ff789f7421690d94714e7a6ba6a83dfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 19 11:51:24 2020 -0400
sync up with the Castro overrides
sphinx_docs/source/_static/theme_overrides.css
commit fc6b9e5fb29c4f6c41ec06ea32176f162ed6b180
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 18 18:38:09 2020 -0400
add a hybrid aprox19 + NSE network (#332)
This will use an NSE table at high densities and temperature to provide the energy generation and composition variables.
CHANGES.md
EOS/composition.F90
EOS/eos_composition.H
Make.Microphysics
Make.Microphysics_extern
integration/VODE/vode_rpar.F90
integration/VODE/vode_type.F90
interfaces/burn_type.H
networks/Make.package
networks/README
networks/aprox13/README.md
networks/aprox19/Make.package
networks/aprox19/NAUX_NETWORK
networks/aprox19/README
networks/aprox19/README.md
networks/aprox19/_parameters
networks/aprox19/actual_burner.F90
networks/aprox19/actual_network.F90
networks/aprox19/actual_network.H
networks/aprox19/aprox19.net
networks/aprox19/nse.F90
networks/aprox19/nse19.tbl
networks/aprox19/nse_check.F90
networks/general_null/network_header.template
networks/general_null/write_network.py
sphinx_docs/source/index.rst
sphinx_docs/source/integrators.rst
sphinx_docs/source/nse.rst
sphinx_docs/source/refs.bib
unit_test/test_react/inputs_aprox19.nse_disabled
unit_test/test_react/inputs_aprox19_nse
unit_test/test_react/probin.aprox19.nse_disabled
unit_test/test_react/probin.aprox19_nse
unit_test/test_react/react_zones.F90
unit_test/test_react/variables.F90
commit 23c217daa0e5f13551b1db626167210ebcb7ae30
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 18 12:01:34 2020 -0400
fix make bug (= instead of +=) (#395)
integration/VODE/cuVODE/test/Make.package
unit_test/burn_cell/Make.package
unit_test/test_cvode_react/Make.package
unit_test/test_react/Make.package
unit_test/test_rhs/Make.package
unit_test/test_sdc/Make.package
commit 2717b044924f5b9d433d9d6624d4d251f9deeadb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 14 07:59:06 2020 -0400
remove simplified-SDC evolution from the BS integrator (#393)
this is not tested, not maintained, and not used
it also doesn't have a GPU path
integration/BS/Make.package
integration/BS/bs_integrator_sdc.F90
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type_sdc.F90
integration/BS/numerical_jacobian_sdc.f90
integration/BS/stiff_ode.F90
integration/Make.package
integration/integrator_sdc.F90
commit 3bd742ae21c1ce527fe68aa97b2c226a399ed444
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 10 13:48:38 2020 -0400
switch includes from "" to <> (#392)
done via:
for i in `git grep -l "#include \""`; do sed -r -i -E "s/#include \"(\w+\.\w+)\"/#include <\1>/g" $i; done
conductivity/constant/actual_conductivity.H
conductivity/constant_opacity/actual_conductivity.H
conductivity/powerlaw/actual_conductivity.H
conductivity/stellar/actual_conductivity.H
integration/VODE/cuVODE/test/main.cpp
networks/ignition_simple/test-cpp/main.cpp
unit_test/burn_cell/main.cpp
unit_test/eos_cell/main.cpp
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates.H
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/test_cond.H
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_serial.cpp
unit_test/test_eos/main.cpp
unit_test/test_eos/test_eos.H
unit_test/test_parameters/main.cpp
unit_test/test_react/main.cpp
unit_test/test_rhs/main.cpp
unit_test/test_screening/main.cpp
unit_test/test_screening/test_screen.H
unit_test/test_sdc/main.cpp
unit_test/write_job_info.cpp
commit 6ebb1d3df87532578a549d01881f33abbef195f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 6 12:56:01 2020 -0400
fix compilation
interfaces/microphysics.F90
commit acf72fade7b0722d9c31fa0068ae51c9059adb29
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 5 21:40:13 2020 -0400
add versions of the init / finalize callable from C++ (#391)
interfaces/Make.package
interfaces/microphysics.F90
interfaces/microphysics_F.H
commit a669e78bbf9ea4f63afdd3ff0594788216a9cf41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 2 21:09:49 2020 -0400
microphysics_math / esum is only needed for reactions (#390)
util/Make.package
commit 9da8f5b261f44d6e62f9f74bdafed6180d962132
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 2 15:40:14 2020 -0400
we were not copying p0 in the copy_burn_t routine (#387)
interfaces/burn_type.F90
commit 10ddacaef4e28c3be293fc0858ee9110d351157f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 2 14:02:43 2020 -0400
remove some unused parameters (#388)
these (cs, dx, t_sound) were all used for the different burning modes
integration/BS/bs_integrator.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type.F90
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_rpar.F90
integration/CVODE/cvode_type.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type.F90
interfaces/burn_type.F90
interfaces/burn_type.H
commit 171db565736a1ae0f6772d114bc8084585ca5da6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 20:10:53 2020 -0400
remove burning mode -- we always assume we are burning_mode = 1 (#340)
this addresses #300 and greatly simplifies the integrators.
integration/BS/bs_integrator.F90
integration/CVODE/cvode_type.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator.H
integration/VODE/vode_integrator_simplified_sdc.F90
integration/_parameters
integration/utils/temperature_integration.F90
networks/aprox13/test-cpp/probin
networks/aprox19/test-cpp/probin
networks/aprox21/test-cpp/probin
networks/ignition_simple/test-cpp/probin
networks/iso7/test-cpp/probin
networks/powerlaw/_parameters
networks/rprox/_parameters
networks/rprox/test/README
networks/rprox/test/testburn.f90
networks/triple_alpha_plus_cago/_parameters
networks/xrb_simple/_parameters
sphinx_docs/source/integrators.rst
unit_test/test_react/inputs_aprox19.burning_mode_0
unit_test/test_react/probin.aprox13.burning_mode_0
unit_test/test_react/probin.aprox19.burning_mode_0
commit 79520fe3fd26e3889fbb8be682b046038b275163
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 20:03:48 2020 -0400
remove the burn_to_vode in jac() -- it appears unnecessary (#381)
closes #364
integration/VODE/vode_rhs.H
commit f80002e89f6528eae8fdb3001fffd0ecca647f85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 13:53:10 2020 -0400
switch to local copies of the build scripts (#386)
Make.Microphysics
util/build_scripts/findparams.py
commit 0fbd83936e00301f7eb90636a68926a50c18475b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 10:04:04 2020 -0400
update changes
CHANGES.md
commit 4b73a5293031916a5301cbb2d7689f8a008d9f42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 10:02:10 2020 -0400
add a job_info file to the unit tests (#383)
This adds a job_info file to all of the unit tests that produce a plotfile.
Closes #139
unit_test/Make.package
unit_test/Make.unit_test
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/main.cpp
unit_test/test_conductivity/GNUmakefile
unit_test/test_conductivity/main.cpp
unit_test/test_eos/GNUmakefile
unit_test/test_eos/main.cpp
unit_test/test_react/GNUmakefile
unit_test/test_react/main.cpp
unit_test/test_rhs/GNUmakefile
unit_test/test_rhs/main.cpp
unit_test/test_screening/GNUmakefile
unit_test/test_screening/main.cpp
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/main.cpp
unit_test/unit_test.H
unit_test/write_job_info.cpp
commit e71390a463bb003364729d0d1a779916c83f2926
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 09:43:58 2020 -0400
update the extern_probin.template (#380)
this adds the ability to output the runtime parameters to a job_info
and deletes an unused template
interfaces/extern_probin.template
unit_test/dummy.probin.template
commit 6527d9deeb9fcbc803bf454303f9bd0b7203d85c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 09:42:46 2020 -0400
update the gitigore to ignore Jupyter, old plotfiles, + build stuff (#384)
.gitignore
commit 6c432b2a437a1e7679dc1622f76bcf1cc93a71cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 1 09:42:23 2020 -0400
create a routine to call any of the EOSes with a single thermodynamics state (#382)
This adds the eos_cell unit test which simply calls the (C++) EOS on a single zone and outputs the information. To do the output, this creates a << operator for an eos_t. We also fix a bug in the burn_t << for aux data.
interfaces/burn_type.H
interfaces/eos_type.H
unit_test/eos_cell/GNUmakefile
unit_test/eos_cell/Make.package
unit_test/eos_cell/_parameters
unit_test/eos_cell/eos_cell.H
unit_test/eos_cell/eos_cell_F.H
unit_test/eos_cell/inputs_eos
unit_test/eos_cell/main.cpp
unit_test/eos_cell/probin
unit_test/eos_cell/unit_test.F90
commit de7095c55f2c8be4ac78c123adf17e5580dd4841
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 28 19:53:24 2020 -0400
update changes
CHANGES.md
commit e6ed3f2f6259d2d67b70c97f4839015f3945d42b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 28 17:36:08 2020 -0400
fill in more of the gamma law state (#374)
for some inputs, we were not defining the sound speed or derivatives
EOS/gamma_law/actual_eos.H
commit 5eccc0232e8c7d2c2e560c71e89a2a556456011c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 28 17:28:43 2020 -0400
this gets burn_cell compiling with USE_CXX_EOS=FALSE (#378)
(we also need USE_CXX_REACTIONS=FALSE)
EOS/Make.package
interfaces/Make.package
unit_test/burn_cell/main.cpp
commit e325aa7dca47b89dbbe31d2a5f25c242c8d4ba1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 28 16:37:30 2020 -0400
update README (#375)
* update README
* update screening
networks/rprox/README.md
commit 09a73947a4afea01b67c97c04114023da3d4b07c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 28 16:35:08 2020 -0400
add screening to the rprox network (#377)
rprox now does screening.
In addtion, this fixes the aion argument for add_screening_factor for Si26(a,p)P29 which was using A=28 for Si-26 instead of A=26.
Co-authored-by: Donald E. Willcox <eugene.willcox@gmail.com>
networks/rprox/Make.package
networks/rprox/actual_network.F90
networks/rprox/actual_rhs.F90
commit 69d63ffd267714f0c72c3f46ae995e323aa0bde2
Author: shardi2 <56055254+shardi2@users.noreply.github.com>
Date: Fri Aug 28 14:29:22 2020 -0400
Changed the script for the comparisons (#351)
this outputs the time instead of the steps and also adds some inputs/probins for other networks
unit_test/burn_cell/probin_aprox19
unit_test/burn_cell/probin_triple
commit f002d397f35458dc56613e1b16ac43d87697196b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 24 14:12:23 2020 -0400
Warning fixes (#373)
The static variables in network_properties.H are warned as unused with GCC everywhere we include the header and don't use them all. This uses the [[gnu::unused]] attribute to silence these warnings.
interfaces/network.H
networks/general_null/network_header.template
commit f6befed2c9d2a1e14d2c44de6e8f6da1c14b9b04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 23 13:13:32 2020 -0400
fix some compiler warnings (#372)
EOS/composition.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_rhs.H
networks/aprox13/actual_network.H
networks/aprox13/actual_rhs.H
networks/aprox19/actual_network.H
networks/iso7/actual_network.H
neutrinos/sneut5.F90
rates/aprox_rates.H
screening/screen.H
screening/screen_data.H
unit_test/test_react/main.cpp
unit_test/test_react/react_zones.F90
unit_test/test_react/util.f90
commit 2b36a6d593ca45450df431ae2a8704b071ce4d16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 18 23:46:08 2020 -0400
get some of the scattered unit tests building again (#368)
* get this building again
* switch to not depend on Castro
* get this building again
* get this compiling again
* get this building again
* block off C++
Make.Microphysics
networks/aprox13/test-cpp/GNUmakefile
networks/aprox13/test-cpp/Make.package
networks/aprox13/test-cpp/do_initialization.f90
networks/aprox13/test-cpp/main.cpp
networks/aprox13/test-cpp/testburn.f90
networks/aprox13/test-cpp/testjacobian.f90
networks/aprox19/test-cpp/GNUmakefile
networks/aprox19/test-cpp/Make.package
networks/aprox19/test-cpp/do_initialization.f90
networks/aprox19/test-cpp/main.cpp
networks/aprox19/test-cpp/testburn.f90
networks/aprox19/test-cpp/testjacobian.f90
networks/aprox21/test-cpp/GNUmakefile
networks/aprox21/test-cpp/Make.package
networks/aprox21/test-cpp/do_initialization.f90
networks/aprox21/test-cpp/main.cpp
networks/aprox21/test-cpp/testburn.f90
networks/aprox21/test-cpp/testjacobian.f90
networks/iso7/Make.package
networks/iso7/test-cpp/GNUmakefile
networks/iso7/test-cpp/Make.package
networks/iso7/test-cpp/do_initialization.f90
networks/iso7/test-cpp/main.cpp
networks/iso7/test-cpp/testburn.f90
networks/iso7/test-cpp/testjacobian.f90
commit 0b68c83746259ca71f89f2d13044a1a8bf711771
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 7 10:57:12 2020 -0400
move the naux info into a separate include file (#370)
this will allow us to do make logic, like checking on whether USE_NSE is set.
CHANGES.md
networks/ECSN/NAUX_NETWORK
networks/ECSN/NETWORK_PROPERTIES
networks/Make.package
networks/aprox13/NAUX_NETWORK
networks/aprox13/NETWORK_PROPERTIES
networks/aprox19/NAUX_NETWORK
networks/aprox19/NETWORK_PROPERTIES
networks/aprox21/NAUX_NETWORK
networks/aprox21/NETWORK_PROPERTIES
networks/breakout/NAUX_NETWORK
networks/breakout/NETWORK_PROPERTIES
networks/general_null/Make.package
networks/general_null/NAUX_NETWORK
networks/general_null/NETWORK_PROPERTIES
networks/general_null/network_header.template
networks/general_null/write_network.py
networks/ignition_chamulak/NAUX_NETWORK
networks/ignition_chamulak/NETWORK_PROPERTIES
networks/ignition_reaclib/C-burn-simple/NAUX_NETWORK
networks/ignition_reaclib/C-burn-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/C-test/NAUX_NETWORK
networks/ignition_reaclib/C-test/NETWORK_PROPERTIES
networks/ignition_reaclib/URCA-simple/NAUX_NETWORK
networks/ignition_reaclib/URCA-simple/NETWORK_PROPERTIES
networks/ignition_simple/NAUX_NETWORK
networks/ignition_simple/NETWORK_PROPERTIES
networks/iso7/NAUX_NETWORK
networks/iso7/NETWORK_PROPERTIES
networks/nova/NAUX_NETWORK
networks/nova/NETWORK_PROPERTIES
networks/powerlaw/NAUX_NETWORK
networks/powerlaw/NETWORK_PROPERTIES
networks/rprox/NAUX_NETWORK
networks/rprox/NETWORK_PROPERTIES
networks/sn160/NAUX_NETWORK
networks/sn160/NETWORK_PROPERTIES
networks/subch/NAUX_NETWORK
networks/subch/NETWORK_PROPERTIES
networks/subch2/NAUX_NETWORK
networks/subch2/NETWORK_PROPERTIES
networks/triple_alpha_plus_cago/NAUX_NETWORK
networks/triple_alpha_plus_cago/NETWORK_PROPERTIES
networks/update_headers.py
networks/xrb_simple/NAUX_NETWORK
networks/xrb_simple/NETWORK_PROPERTIES
commit 6efc0419c92f9c38cf80f53d9619a9941d109cc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 6 11:23:34 2020 -0400
split the integrators off into their own docs (#363)
sphinx_docs/source/index.rst
sphinx_docs/source/integrators.rst
sphinx_docs/source/networks.rst
commit 126fcc76e29850b87a52db3839bdb56f3417d51b
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Mon Aug 3 10:12:37 2020 -0400
Github action for building docs (#367)
This removes the travis workflow for building the docs, and replaces it with a Github action which builds docs for the development and main branches (as done in Castro and MAESTROeX).
.github/workflows/gh-pages.yml
.travis.yml
deploy_docs.sh
deploy_docs_action.sh
interfaces/burn_type.H
sphinx_docs/source/_templates/dev_layout.html
sphinx_docs/source/_templates/layout.html
commit 61dd9dbf3aa46b25a3cd7dde78be9b473860f926
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 31 11:00:34 2020 -0400
update the changelog
CHANGES.md
commit ca01493910f41cc7efe89cb40af5f86fca2a2471
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 26 18:18:49 2020 -0400
fix some more compiler warnings (#359)
EOS/eos_composition.H
EOS/helmholtz/actual_eos.H
EOS/multigamma/eos_composition.H
interfaces/eos_override.H
interfaces/network.H
networks/general_null/network_header.template
commit 0cc507b47f889f8424297e517cb38a99da655148
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 26 17:29:26 2020 -0400
fix NAUX for this network (#360)
networks/breakout/NETWORK_PROPERTIES
commit 5bc24e1fb43b3f540c46e995a34fca3795d76c53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 05:30:11 2020 -0400
C++ doesn't like 0-length arrays, so don't include aux in the eos_t if naux = 0 (#358)
interfaces/eos_type.H
commit 73efb413c33366c545e5cdb057f73f377b70d164
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 05:29:35 2020 -0400
warn_all gives a pedantic warning for a ; closing a namespace (#357)
constants/fundamental_constants.H
networks/general_null/network_header.template
commit ce898c7b106e154ffd77d359af766323e662ad7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 05:29:11 2020 -0400
remove has_been_reset from reset_rho and reset_T (#356)
they never used it
interfaces/eos.H
commit 818f4dbbd7dbc92a5b112177c56569ede693596b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 01:12:35 2020 -0400
update the docs on the unit tests (#346)
sphinx_docs/source/unit_tests.rst
commit 3c539e55de5b3c9526d48fb12ccc4950af5275a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 01:11:04 2020 -0400
unify the conductivity unit tests (C++ and Fortran) into a single test (#345)
unit_test/test_conductivity/GNUmakefile
unit_test/test_conductivity/Make.package
unit_test/test_conductivity/README
unit_test/test_conductivity/_parameters
unit_test/test_conductivity/conductivity_util.cpp
unit_test/test_conductivity/conductivity_util_F.F90
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/test_cond.H
unit_test/test_conductivity/test_cond_F.H
unit_test/test_conductivity/test_conductivity.H
unit_test/test_conductivity/variables.H
unit_test/test_conductivity/variables.cpp
unit_test/test_conductivity/variables_F.F90
unit_test/test_conductivity_C/GNUmakefile
unit_test/test_conductivity_C/Make.package
unit_test/test_conductivity_C/_parameters
unit_test/test_conductivity_C/input_conductivity
unit_test/test_conductivity_C/main.cpp
unit_test/test_conductivity_C/probin
unit_test/test_conductivity_C/test_cond.H
unit_test/test_conductivity_C/test_cond_F.H
unit_test/test_conductivity_C/unit_test.f90
commit 72bd591a23b401fa124c5cdbe22b39f5bdbbc64c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 24 01:08:55 2020 -0400
some better initial species abundances for aprox19 (#352)
unit_test/burn_cell/probin_aprox19
commit 0fe55169822fa0dcd4948c280cf7f13b0328fc6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 23 14:13:31 2020 -0400
ifdef out unused var unless EXTRA_THERMO is set (#355)
EOS/helmholtz/actual_eos.H
commit b8f06934a18ab33681212af3c8e43f4379abedf6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 22 09:14:53 2020 -0700
Convert aprox19 to C++ (#320)
I've tested this on both test_rhs and test_react. For test_rhs, the maximum relative difference between the Fortran and C++ is O(1e-15) for the RHS, and O(1e-13) for the Jacobian. For test_react, the maximum relative difference is 1e-11 for the CPU build and 1e-4 for the GPU build. (The difference for the GPU build is of comparable magnitude to what we see for the other networks.)
networks/aprox19/Make.package
networks/aprox19/actual_network.H
networks/aprox19/actual_network_data.cpp
networks/aprox19/actual_rhs.H
networks/aprox19/actual_rhs_data.cpp
unit_test/test_rhs/inputs_aprox19
unit_test/test_rhs/probin.aprox19
commit 9dda345d6c21e4c39a09e507e4950a7861cfad22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 22 08:37:13 2020 -0400
unify the C++ and Fortran test_aprox_rates unit tests (#344)
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/README
unit_test/test_aprox_rates/README.md
unit_test/test_aprox_rates/aprox_rates_util.cpp
unit_test/test_aprox_rates/aprox_rates_util_F.F90
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates.H
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/variables.H
unit_test/test_aprox_rates/variables.cpp
unit_test/test_aprox_rates/variables_F.F90
unit_test/test_aprox_rates_C/GNUmakefile
unit_test/test_aprox_rates_C/Make.package
unit_test/test_aprox_rates_C/README
unit_test/test_aprox_rates_C/_parameters
unit_test/test_aprox_rates_C/input_aprox_rates
unit_test/test_aprox_rates_C/main.cpp
unit_test/test_aprox_rates_C/probin
unit_test/test_aprox_rates_C/test_aprox_rates.H
unit_test/test_aprox_rates_C/test_aprox_rates_F.H
unit_test/test_aprox_rates_C/unit_test.f90
commit ac980184d08c88c14eae21c4bc1d51a9f538ff57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 22 08:36:47 2020 -0400
unify the C++ and Fortran screening unit tests (#343)
Previously we had test_screening and test_screening_C, but now the implementations are merged under test_screening.
unit_test/test_screening/GNUmakefile
unit_test/test_screening/Make.package
unit_test/test_screening/README
unit_test/test_screening/_parameters
unit_test/test_screening/main.cpp
unit_test/test_screening/screening_util.cpp
unit_test/test_screening/screening_util_F.F90
unit_test/test_screening/test_screen.H
unit_test/test_screening/test_screen_F.H
unit_test/test_screening/test_screening.H
unit_test/test_screening/unit_test.f90
unit_test/test_screening/variables.H
unit_test/test_screening/variables.cpp
unit_test/test_screening/variables_F.F90
unit_test/test_screening_C/GNUmakefile
unit_test/test_screening_C/Make.package
unit_test/test_screening_C/README
unit_test/test_screening_C/_parameters
unit_test/test_screening_C/inputs
unit_test/test_screening_C/main.cpp
unit_test/test_screening_C/probin
unit_test/test_screening_C/test_screen.H
unit_test/test_screening_C/test_screen_F.H
unit_test/test_screening_C/unit_test.f90
commit a09055d4248674d1dc298f1303ad8ad671b65179
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 21 08:31:26 2020 -0400
remove VBDF -- it is unmaintained. (#348)
It lives on in the git history if anyone wants to revive it
closes #208
CHANGES.md
integration/Make.package
integration/VBDF/Make.package
integration/VBDF/NOTES
integration/VBDF/_parameters
integration/VBDF/bdf.f90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VBDF/vbdf_rpar.F90
sphinx_docs/source/networks.rst
unit_test/test_react/README.md
commit 520b7ca7c08a09e80ba743a53f2992a576cc5905
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 20 18:38:12 2020 -0700
VODE steps fail if the state is not valid (#350)
Commit 9d3ddb1 added intentional failure modes to the VODE integrator to prevent VODE from giving us a state where the integrator believed it was successful but the state was not physically valid. Specifically, we checked on T < 0 and X < -0.01 or X > 1.01. Although this gave us the opportunity to then retry the burn, retries are expensive and we'd like to avoid them if possible (#106). One way we can significantly mitigate this is by preventing these failure modes from occurring at the end of each step rather than only at the end of the burn. We can then rely on the integrator's built-in step retry mechanism (which decreases dt or changes the integration order).
I chose to use the same failure modes as the one at the end of the burn. Additionally, I added a failure mode if any X changes by more than a factor of 2. The abundance never changes that much in a single step in a typical burn, but I have witnessed some extreme cases where the abundance floors in a single integration step and VODE doesn't reject the update. (I am not sure why.)
CHANGES.md
integration/VODE/vode_dvstep.H
integration/VODE/vode_integrator.H
integration/VODE/vode_type.H
commit 622b799cc33ed8a482d67cf745179a68c0e59e7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 20 15:01:24 2020 -0400
add an ostream for a burn_t so we can use << (#349)
interfaces/burn_type.H
commit 119fc41d8a161140ec30fceabe54e2a52ce54e80
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 19 10:55:42 2020 -0700
Convert ignition_simple to C++ (#324)
networks/ignition_simple/Make.package
networks/ignition_simple/NETWORK_PROPERTIES
networks/ignition_simple/actual_network.H
networks/ignition_simple/actual_network_data.cpp
networks/ignition_simple/actual_rhs.H
networks/ignition_simple/actual_rhs_data.cpp
unit_test/test_rhs/inputs_ignition_simple
unit_test/test_rhs/probin.ignition_simple
commit c78eeaed58b4a0348a3f392d4101e1d64188e9e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 19 13:30:04 2020 -0400
store the same output in the F90 and C++ output files (#347)
unit_test/burn_cell/burn_cell.F90
unit_test/burn_cell/probin_triple
commit b930280551f943fbd6f933f3721f7b19fa72dd1f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jul 19 10:25:48 2020 -0700
Convert triple_alpha_plus_cago to C++ (#325)
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/NETWORK_PROPERTIES
networks/triple_alpha_plus_cago/actual_network.H
networks/triple_alpha_plus_cago/actual_network_data.cpp
networks/triple_alpha_plus_cago/actual_rhs.H
networks/triple_alpha_plus_cago/actual_rhs_data.cpp
unit_test/test_rhs/inputs_triple_alpha_plus_cago
unit_test/test_rhs/probin.triple_alpha_plus_cago
commit febfe824cb2a61052465001fcb46c0c8db9251ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 15 21:07:57 2020 -0400
eliminate some divides (#342)
EOS/composition.F90
commit 710ddb8f8b101283e188c27be07ab184199395a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 15 21:03:27 2020 -0400
remove prints (#341)
the F90 one in particular gets printed by each GPU thread
unit_test/test_eos/eos_util.cpp
unit_test/test_eos/eos_util_F.F90
commit 32d9c2036cbb6d3cc1d4a8485219bf26a76919cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 11 19:32:39 2020 -0400
merge C++ and Fortran unit tests (#292)
The merges the test_eos unit tests
unit_test/test_eos/GNUmakefile
unit_test/test_eos/Make.package
unit_test/test_eos/README.md
unit_test/test_eos/eos_util.cpp
unit_test/test_eos/eos_util_F.F90
unit_test/test_eos/main.cpp
unit_test/test_eos/test_eos.H
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/variables.H
unit_test/test_eos/variables.cpp
unit_test/test_eos/variables_F.F90
unit_test/test_eos_C/GNUmakefile
unit_test/test_eos_C/Make.package
unit_test/test_eos_C/README
unit_test/test_eos_C/_parameters
unit_test/test_eos_C/input_eos
unit_test/test_eos_C/input_eos.multigamma
unit_test/test_eos_C/main.cpp
unit_test/test_eos_C/probin
unit_test/test_eos_C/probin.multigamma
unit_test/test_eos_C/test_eos.H
unit_test/test_eos_C/test_eos_F.H
unit_test/test_eos_C/unit_test.f90
commit cfae851114e2f1213a3bbecedd91eb149cfc8a4d
Author: shardi2 <56055254+shardi2@users.noreply.github.com>
Date: Wed Jul 8 15:52:21 2020 -0400
Input and Probin files for PRs (#337)
unit_test/burn_cell/burn_cell.H
unit_test/burn_cell/inputs_aprox19
unit_test/burn_cell/inputs_ignition
unit_test/burn_cell/inputs_rprox
unit_test/burn_cell/inputs_triple
unit_test/burn_cell/probin_aprox19
unit_test/burn_cell/probin_aprox21
unit_test/burn_cell/probin_ignition
unit_test/burn_cell/probin_rprox
unit_test/burn_cell/probin_triple
commit a51ae03e8bb055010d0d43b1edd750a2e2bfa458
Merge: ea9007c7 5fd40cce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 8 11:01:38 2020 -0400
Merge branch 'main' into development
commit ea9007c7ea75b7d522ea742e4cb66ba870cb2114
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 4 08:06:57 2020 -0700
Fix indexing that accidentally used a real as an int (#338)
The bit at the end of this routine that did the actual Jacobian conversion used k as a loop index and this was actually being treated as the K that was used to measure kinetic energy (since Fortran is case insensitive).
integration/VODE/vode_type_simplified_sdc.F90
commit 414d960308b2183445e8a1d8eb4fe561b6b2a6d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 3 00:31:58 2020 -0400
move the write_probin.py script from amrex to Microphysics (#336)
also do some cleaning
util/build_scripts/write_probin.py
commit afb1f340fcc6a85c184ad5c3b76734467b4b1bcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 2 13:41:29 2020 -0400
add get routines for aux (#329)
This adds "get" routines for the auxillary indices in both Fortran and C++
interfaces/network.F90
interfaces/network.H
commit 316428400b5bae14230f31ea92f33ae8315f022f
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Jul 2 08:45:23 2020 -0400
add action to automatically create a release whenever a tag of the form xx.xx is created (#335)
This adds a github action which automatically creates a release whenever a tag of the form xx.xx is created. The release text is scraped from CHANGES.md.
.github/workflows/create_release.yml
.github/workflows/get_release_txt.py
commit 98a8f137b9b1579616dff5a7b4865bcd621024d2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 1 12:24:39 2020 -0700
Restore approximate value of pi in ecapnuc (#323)
Although in the long term it would be good to sync up mathematical and physical constants with more accurate values, our immediate concern is making the C++ port match the Fortran code, and restoring the approximate value of pi hardcoded in the Fortran is necessary to do that (otherwise we get differences at the 1e-9 level for the rates depending on the output of ecapnuc, such as jac(He3, H1)).
rates/aprox_rates.H
commit bca4e98a473541462434831ce41fc75f72caab49
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 1 12:13:39 2020 -0700
Fix indexing errors in Langanke C++ implementation (#322)
I think the Langanke implementation in C++ wasn't quite right due to possible off-by-one indexing errors in the arrays as they were converted from 1-indexing to 0-indexing. Rather than sort it out, I just replaced GpuArrays with Array1D and used 1-indexing everywhere, and this now matches the Fortran output for aprox21 for the rates that depend on it (e.g. d(Cr56)/dt).
rates/aprox_rates.H
rates/aprox_rates_data.H
rates/aprox_rates_data.cpp
commit 1c2c13db0263b255e1e9c1e89a0c2f342eba826b
Author: shardi2 <56055254+shardi2@users.noreply.github.com>
Date: Wed Jul 1 15:10:04 2020 -0400
New C++ and Fortran Comparison (#334)
Add the ability to take multiple substeps to see the evolution of the burn in a zone.
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/Mass_Fractions_C++.ipynb
unit_test/burn_cell/_parameters
unit_test/burn_cell/burn_cell.F90
unit_test/burn_cell/burn_cell.H
unit_test/burn_cell/inputs_aprox13
unit_test/burn_cell/inputs_iso7
unit_test/burn_cell/probin_aprox13
unit_test/burn_cell/probin_iso7
commit 5fd40ccef9ded0ec806dd41c6718ef07d8b28cc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 1 08:52:08 2020 -0400
update changes
CHANGES.md
commit 8cadd69dd4fc7f9201dc28d7cf80b5341b1ae72c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 30 12:31:29 2020 -0400
master -> main (#333)
.travis.yml
README.md
sphinx_docs/source/conf.py
sphinx_docs/source/index.rst
commit a69e478cbd396e3a05775783fe033bc5c45d32d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 27 09:54:53 2020 -0400
add naux to NETWORK_PROPERTIES (#330)
interfaces/burn_type.F90
interfaces/burn_type.H
networks/ECSN/NETWORK_PROPERTIES
networks/Make.package
networks/aprox13/NETWORK_PROPERTIES
networks/aprox19/NETWORK_PROPERTIES
networks/aprox21/NETWORK_PROPERTIES
networks/breakout/NETWORK_PROPERTIES
networks/general_null/NETWORK_PROPERTIES
networks/ignition_chamulak/NETWORK_PROPERTIES
networks/ignition_reaclib/C-burn-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/C-test/NETWORK_PROPERTIES
networks/ignition_reaclib/URCA-simple/NETWORK_PROPERTIES
networks/ignition_simple/NETWORK_PROPERTIES
networks/iso7/NETWORK_PROPERTIES
networks/nova/NETWORK_PROPERTIES
networks/powerlaw/NETWORK_PROPERTIES
networks/rprox/NETWORK_PROPERTIES
networks/sn160/NETWORK_PROPERTIES
networks/subch/NETWORK_PROPERTIES
networks/subch2/NETWORK_PROPERTIES
networks/triple_alpha_plus_cago/NETWORK_PROPERTIES
networks/xrb_simple/NETWORK_PROPERTIES
commit 31d615ca83f8f2ef2f6c32ed7eee8516a97db654
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 27 08:42:32 2020 -0400
remove NETWORK_REQUIRES -- these are not used anymore (#331)
networks/ECSN/NETWORK_REQUIRES
networks/aprox13/NETWORK_REQUIRES
networks/aprox19/NETWORK_REQUIRES
networks/aprox21/NETWORK_REQUIRES
networks/breakout/NETWORK_REQUIRES
networks/general_null/NETWORK_REQUIRES
networks/ignition_chamulak/NETWORK_REQUIRES
networks/ignition_reaclib/C-burn-simple/NETWORK_REQUIRES
networks/ignition_reaclib/C-test/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple/NETWORK_REQUIRES
networks/ignition_simple/NETWORK_REQUIRES
networks/iso7/NETWORK_REQUIRES
networks/nova/NETWORK_REQUIRES
networks/powerlaw/NETWORK_REQUIRES
networks/rprox/NETWORK_REQUIRES
networks/sn160/NETWORK_REQUIRES
networks/subch/NETWORK_REQUIRES
networks/subch2/NETWORK_REQUIRES
networks/triple_alpha_plus_cago/NETWORK_REQUIRES
networks/xrb_simple/NETWORK_REQUIRES
commit 7d39b27dc53226cb6ed7f552fe4bf92e6b7c35d1
Merge: 946c111d da809779
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 31 12:08:42 2020 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 946c111d8e43014648d36ec787b25cafaa2ce7b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun May 31 12:08:33 2020 -0400
update changes
CHANGES.md
commit da80977954ce38820ed7135a868b5c2bee130488
Author: doreenfan <35239173+doreenfan@users.noreply.github.com>
Date: Sun May 31 09:05:50 2020 -0700
bug fix for SDC_EVOLVE_ENTHALPY (#317)
integration/VODE/vode_type_simplified_sdc.F90
interfaces/burn_type.F90
commit b8f832b3cb65074c0669791d1836ca531b859224
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 28 13:57:53 2020 -0400
add some more getting started
sphinx_docs/source/basics.rst
sphinx_docs/source/networks.rst
commit e50e4d0e8718356affbf1f5ab087ec801aa6ffae
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue May 26 14:47:52 2020 -0400
include extern_parameters.H in actual_conductivity headers (#319)
conductivity/constant/actual_conductivity.H
conductivity/constant_opacity/actual_conductivity.H
conductivity/powerlaw/actual_conductivity.H
commit c904ffd1ce3a9394f390ac0df6ac14845c987139
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Fri May 22 13:16:28 2020 -0400
add amrex namespace to stellar conductivity header (#318)
The stellar conductivity actual_conductivity.H header file needs a using namespace amrex statement so that the compiler can resolve the Real variable types.
conductivity/stellar/actual_conductivity.H
commit ed3faa8b4df660a8410bbe03c21ceadc609c860a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 17 11:43:12 2020 -0700
Delete old burn_cell, replace with burn_cell_C (#316)
We don't use the BoxLib Fortran build system anymore, so we shouldn't keep this around.
CHANGES.md
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/Make.package
unit_test/burn_cell/README.md
unit_test/burn_cell/README.txt
unit_test/burn_cell/_parameters
unit_test/burn_cell/burn_cell.F90
unit_test/burn_cell/burn_cell.H
unit_test/burn_cell/burn_cell.py
unit_test/burn_cell/burn_cell_F.H
unit_test/burn_cell/burn_cell_compare_2tests.py
unit_test/burn_cell/burn_cell_compare_abs.py
unit_test/burn_cell/burn_cell_compare_ordinate.py
unit_test/burn_cell/burn_cell_compare_rel.py
unit_test/burn_cell/burn_cell_nl.py
unit_test/burn_cell/burn_cell_testing.py
unit_test/burn_cell/inputs_ECSN_burn
unit_test/burn_cell/inputs_ECSN_burn_Case-1
unit_test/burn_cell/inputs_aprox13
unit_test/burn_cell/inputs_aprox21
unit_test/burn_cell/inputs_aprox21_rot1
unit_test/burn_cell/inputs_aprox21_rot2
unit_test/burn_cell/inputs_burn_aprox13
unit_test/burn_cell/inputs_burn_aprox19_bad
unit_test/burn_cell/inputs_burn_subch.VODE
unit_test/burn_cell/inputs_burn_urca
unit_test/burn_cell/inputs_burn_urca.BS
unit_test/burn_cell/inputs_burn_urca.VODE
unit_test/burn_cell/inputs_burn_xrb.VODE
unit_test/burn_cell/inputs_cburn.VODE
unit_test/burn_cell/inputs_ctest.BS
unit_test/burn_cell/main.cpp
unit_test/burn_cell/main.f90
unit_test/burn_cell/probin_aprox13
unit_test/burn_cell/probin_aprox21
unit_test/burn_cell/probin_aprox21_rot1
unit_test/burn_cell/probin_aprox21_rot2
unit_test/burn_cell/unit_test.F90
unit_test/burn_cell_C/GNUmakefile
unit_test/burn_cell_C/_parameters
unit_test/burn_cell_C/matplotlibrc
commit 97216c3c0027fe749139567ce9d910e30de588b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 17 11:23:01 2020 -0700
Add some more verbose output when C++ burn fails (#312)
integration/VODE/vode_integrator.H
commit 60654fa82d971bfbf4a0e75d24de662b66f3019b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 17 11:22:32 2020 -0700
Add C++ reactions to burn_cell_C (#313)
CHANGES.md
unit_test/burn_cell_C/GNUmakefile
unit_test/burn_cell_C/Make.package
unit_test/burn_cell_C/burn_cell.F90
unit_test/burn_cell_C/burn_cell.H
unit_test/burn_cell_C/burn_cell_F.H
unit_test/burn_cell_C/main.cpp
unit_test/burn_cell_C/unit_test.F90
commit cfedc7fd0c4211bcbf7f0ca90dc90f0c89aa547c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 17 08:59:21 2020 -0700
Zero out rates if temperature hits the floor or ceiling (#314)
This allows us to hit the floor or ceiling and then just ride that to the final integration time.
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs.H
commit 7a3795cd88b4ee5ff4ee21541c43d374580448f2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 7 18:20:49 2020 -0700
For simplified SDC, scale the absolute tolerances by the minimum of the old & new densities. (#311)
Absolute tolerances for rho*X, rho*E, or rho*h are set to the absolute tolerances in the inputs file for species and enuc, respectively, scaled by density rho_min.
The density scale rho_min is:
rho_min = min(rho(0), rho(0) + rho_advective_source * dt)
For SDC_EVOLVE_ENERGY, rho_advective_source is the density advective source in the sdc_t passed to the integrator.
For SDC_EVOLVE_ENTHALPY, rho_advective_source is the sum of the advective sources for the partial densities rho * Xi for the species.
integration/VODE/vode_integrator_simplified_sdc.F90
commit 8279112486a10dcebe5ee923654005e6d37f6f04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 6 14:10:24 2020 -0400
fix the Jacobian for the simplified-SDC system (#228)
For simplified SDC we need to convert from the reaction system Jacobian (in terms of X, T, e) to the system for the conserved variables. This does that transformation.
.gitignore
integration/VODE/vode_type_simplified_sdc.F90
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/probin.aprox13
unit_test/test_sdc/react_zones.F90
commit 5c7c203ef113daf9d187e9822840b2cc5ea120fa
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 2 06:31:35 2020 -0700
Modify simplified SDC tolerances with SDC iteration number (#309)
This PR adds the number of total SDC iterations to the sdc_t derived type for simplified SDC and adds an extern parameter sdc_burn_tol_factor for VODE (defaulted to 1.0 for no effect).
If the user wishes to adjust the ODE tolerances with the SDC iteration number, sdc_burn_tol_factor is accounted for in VODE for simplified SDC as follows:
sdc_tol_fac = sdc_burn_tol_factor**(state_in % num_sdc_iters - state_in % sdc_iter - 1)
Then the integrator absolute and relative tolerances are scaled by sdc_tol_fac.
integration/VODE/_parameters
integration/VODE/vode_integrator_simplified_sdc.F90
interfaces/sdc_type.F90
commit bbfabaae0a98af32dbf353a7747a8ca787710ac6
Merge: 6acbe6fb 55ce324e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 08:48:31 2020 -0400
Merge branch 'development'
commit 6acbe6fbb86a72df9fec9796f0898a3ea315688a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri May 1 08:47:19 2020 -0400
some updates
CHANGES.md
commit 55ce324ed87f5a3feabd834294acc868f7e9710f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 30 09:16:37 2020 -0400
update ymass to 1-based Array1d
unit_test/test_screening_C/main.cpp
commit 8b12d23f4443db303a883dce972a5e4d9cafa520
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 29 15:27:16 2020 -0400
exclude C++ stuff if we are not building with C++ support
networks/aprox13/Make.package
commit a8b34e3a2f4624073ca237143df5ca11781dd0a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 24 02:44:47 2020 -0700
Remove unused variables
neutrinos/sneut5.H
rates/aprox_rates.H
commit 5d868e82a6752981dced341685896859dbbf6d24
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 19 22:23:26 2020 -0700
Only include RHS if using reactions
interfaces/network_initialization.cpp
commit 30689493db963614860f61bbc39f729a7e73578f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 17 00:19:51 2020 -0700
Use sparse storage & operations in C++ VODE for aprox13 (#307)
This PR adds a sparse linear system storage and arithmetic to C++ VODE for aprox13.
The basic idea is to create sparse and dense matrix data structures for the Jacobian so the rhs and integrator can interact with it through provided functions agnostic to the underlying storage.
- Adds a sparse jacobian struct for aprox13 that handles 2D->1D indexing for access and arithmetic at compile time.
- Adds a dense jacobian struct (MathArray2D) that includes the equivalent arithmetic operations we need to supply for a consistent interface between sparse & dense jacobian data structures.
- Modifies rhs, temperature rhs, and integrator to be agnostic to the storage type
- Modifies test_rhs to use the sparse or dense jacobians to call actual_jac depending on USE_NETWORK_SOLVER.
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvnlsd.H
integration/VODE/vode_rhs.H
integration/VODE/vode_type.H
integration/utils/temperature_integration.H
interfaces/ArrayUtilities.H
networks/aprox13/Make.package
networks/aprox13/actual_matrix.H
networks/aprox13/actual_rhs.H
networks/aprox13/maskfile
networks/iso7/actual_rhs.H
neutrinos/sneut5.H
unit_test/test_rhs/rhs_zones.H
commit f9823e0f65d75a00afe62f3b0d60e8425d867d42
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Apr 16 21:47:51 2020 -0700
Move aprox13 to C++ (#305)
This PR ports aprox13 to C++ using the same strategy as for iso7 in #303.
This PR also adds input files for test_rhs for aprox13 based on test_react inputs, except with call_eos_in_rhs=T.
To avoid completely refactoring the rhs in aprox13, passing arbitrary size Array1D arrays to all esum functions is now enabled by making esums templated functions.
networks/aprox13/Make.package
networks/aprox13/actual_network.H
networks/aprox13/actual_network_data.cpp
networks/aprox13/actual_rhs.H
networks/aprox13/actual_rhs_data.cpp
unit_test/test_rhs/inputs_aprox13
unit_test/test_rhs/probin.aprox13
util/esum.H
util/esum_cxx.py
commit 71214435eb30f8ad4329c475e731a82f1865b734
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 11:26:50 2020 -0400
remove .fortran
unit_test/test_react/main.cpp
commit 428cc54a0ffdba19c97e0248354a03fa399189c3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Apr 16 08:22:23 2020 -0700
Screen compile fix (#306)
include NETWORK_PROPERTIES in the build to add NUMSCREEN to the DEFINES.
This allows us to do compile-time checks on NUMSCREEN to determine whether or not to declare the screening factors array.
networks/ECSN/NETWORK_PROPERTIES
networks/Make.package
networks/aprox13/NETWORK_PROPERTIES
networks/aprox19/NETWORK_PROPERTIES
networks/aprox21/NETWORK_PROPERTIES
networks/breakout/NETWORK_PROPERTIES
networks/general_null/NETWORK_PROPERTIES
networks/general_null/write_network.py
networks/ignition_chamulak/NETWORK_PROPERTIES
networks/ignition_reaclib/C-burn-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/C-test/NETWORK_PROPERTIES
networks/ignition_reaclib/URCA-simple/NETWORK_PROPERTIES
networks/ignition_simple/NETWORK_PROPERTIES
networks/iso7/NETWORK_PROPERTIES
networks/nova/NETWORK_PROPERTIES
networks/powerlaw/NETWORK_PROPERTIES
networks/rprox/NETWORK_PROPERTIES
networks/sn160/NETWORK_PROPERTIES
networks/subch/NETWORK_PROPERTIES
networks/subch2/NETWORK_PROPERTIES
networks/triple_alpha_plus_cago/NETWORK_PROPERTIES
networks/xrb_simple/NETWORK_PROPERTIES
screening/screen_data.H
screening/screen_data.cpp
commit 751fd854c04e0d0fda0ab8229ec6ffe0314b6fd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 10:48:31 2020 -0400
fix compilation
EOS/breakout/actual_eos.H
commit 6deceb4f129a9190f56e409e7b9ac6372a16a811
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 10:31:46 2020 -0400
fix some constants
EOS/gamma_law_general/actual_eos.H
EOS/multigamma/actual_eos.H
commit dd0ac4b0bbd7ed820fdf97b726fb8a6db88ef530
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 16 09:39:11 2020 -0400
fix constants namespace
EOS/gamma_law/actual_eos.H
commit 2e98bde19674024dafaae5e7c93a73124587d970
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 15 12:28:13 2020 -0700
Opt in to new network interface
interfaces/Make.package
commit 76bbd7f5ff4e3198a5801a57f899663bf8c42593
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 15 12:07:23 2020 -0700
Fix namespace issues in conductivity
conductivity/stellar/actual_conductivity.H
commit 34b3a2fc4210cd17151b40916f76e64ee0b2932b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 15 14:53:04 2020 -0400
update changes
CHANGES.md
commit 2686629e2b5cc35a1bc219ebf1eaf46c05dd59d9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 15 11:31:43 2020 -0700
Move iso7 to C++ (#303)
Port the iso7 network to C++ as well as other parts of Microphysics the network depends on.
This includes a C++ version of sneut5 as well as the esumN code generator script.
A test is added in unit_test/test_rhs that calls the RHS and Jacobian for a network and saves the output into a plotfile using either the C++ or Fortran network to make comparisons easy.
This PR also rearranges the screening API a bit to require zion and aion for all screened nuclei for convenience.
Right now the interfaces like burn_type and eos_type as well as aion, aion_inv, and zion still use 0-based indexing. The C++ iso7 liberally uses amrex::Array1D with 1-based indexing to make comparisons & porting from Fortran much easier.
In the future we can standardize this, but that's probably best saved for another PR.
Make.Microphysics
constants/fundamental_constants.H
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvnlsd.H
integration/VODE/vode_rhs.H
interfaces/ArrayUtilities.H
interfaces/Make.package
interfaces/burn_type.H
interfaces/network.H
interfaces/network_initialization.cpp
networks/Make.package
networks/iso7/Make.package
networks/iso7/actual_linear_solver.H
networks/iso7/actual_network.H
networks/iso7/actual_network_data.cpp
networks/iso7/actual_rhs.H
networks/iso7/actual_rhs_data.cpp
networks/powerlaw/Make.package
networks/powerlaw/actual_network.H
networks/powerlaw/actual_network_data.cpp
networks/powerlaw/actual_rhs.H
networks/powerlaw/actual_rhs_data.cpp
networks/rate_type.H
neutrinos/Make.package
neutrinos/sneut5.H
rates/tfactors.H
screening/screen.H
screening/screen_data.H
screening/screen_data.cpp
unit_test/test_react/main.cpp
unit_test/test_rhs/GNUmakefile
unit_test/test_rhs/Make.package
unit_test/test_rhs/README.md
unit_test/test_rhs/_parameters
unit_test/test_rhs/inputs_iso7
unit_test/test_rhs/inputs_powerlaw
unit_test/test_rhs/main.cpp
unit_test/test_rhs/probin.iso7
unit_test/test_rhs/probin.powerlaw
unit_test/test_rhs/rhs_zones.F90
unit_test/test_rhs/rhs_zones.H
unit_test/test_rhs/test_react.H
unit_test/test_rhs/test_react_F.H
unit_test/test_rhs/unit_test.f90
unit_test/test_rhs/util.f90
unit_test/test_rhs/variables.F90
unit_test/test_rhs/variables.H
unit_test/test_screening_C/main.cpp
util/Make.package
util/esum.H
util/esum_cxx.py
util/microphysics_math.H
commit 4236eaa81a40359eb7ce2aea8a25cf96ec25a3e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 14 22:59:08 2020 -0400
add a species name enum to network_properties.H (#304)
This adds an enum like
namespace Species {
enum NetworkSpecies {
He4=1,
C12,
O16,
Ne20,
Mg24,
Si28,
S32,
Ar36,
Ca40,
Ti44,
Cr48,
Fe52,
Ni56,
NumberSpecies=Ni56
};
};
to the network_properties.H file.
To test this, in test_react (or any unit test), do:
make net_prop_debug
and then look in tmp_build_dir for the network_properties.H
networks/general_null/network_header.template
networks/general_null/write_network.py
commit babc837c04ebd3ec8b8fef55cc9cae6957141ad9
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 14 15:45:46 2020 -0700
Inline some constants
screening/screen.H
commit d0acf80b97b022c35598ae470ef9a1ffae6fdb2e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 14 08:31:15 2020 -0400
update changes
CHANGES.md
commit 5b020c3af34809444f438e7e362cecdc40813528
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 13 22:07:19 2020 -0400
fix O16+O16 screening setup (#302)
this was caught by the C++ assert
networks/iso7/actual_rhs.F90
commit b877290b82f01088b17bec3c77669fa2e7b92733
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 13 21:35:54 2020 -0400
add a comment
integration/VODE/vode_dvjust.H
commit 0de426bf7be9052ea2120d3815b7c91c4d4f95ab
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 13 00:23:07 2020 -0700
ifdef out C++ reactions if not ported yet
unit_test/test_react/GNUmakefile
unit_test/test_react/main.cpp
commit 2c51345519b5e69765dcde2a793fa5f0c28fc941
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Apr 12 17:37:16 2020 -0700
Convert VODE integrator to C++ (#299)
- A header-only implementation of VODE in C++ is added, as well as `burner` and `integrator` generic interfaces to access it. The new .H files are all located in `integration/VODE`. The C++ code is a direct port of cuVODE with some simplifications made and cleanup done. In particular, the `dvode_t` is much simpler and doesn't contain the `rpar` data. Any data that was stored in `rpar` is now just stored in the `burn_t` instead, and we directly pass the `burn_t` into VODE so that it can be passed into the RHS and Jacobian.
- Some interfaces are different. In particular, note that the integrator accepts a single `burn_t` which it modifies in place (rather than the Fortran input and ouput implementation). Also, note the new interfaces to the RHS and Jacobian which use `amrex::Array1D`.
- The `powerlaw` network is converted to C++ as a demonstration. Note that there's a single file, `actual_network.H`, which includes the RHS and Jacobian in this case. The `actual_burner` interface has been removed; `burner` now directly calls the integrator without going through the network. This simplifies the software design so that the EOS and network are building blocks that the integrator strictly builds on top of.
- test_react is updated to implement the C++ burn as an option, and an `inputs_powerlaw` test case has been added.
- Things that are not currently done:
- burning_mode = 2 and 3 are not implemented
- A couple components like `i,j,k` and `dx` have been left out of the burn_t -- we can always add them back if we want
- Simplified SDC is not yet supported
- Sparse linear algebra is not yet supported (this will be handled in a future PR)
- A numerical Jacobian has not yet been implemented (VODE provides its own)
- Stateful implementations (integrator_init, network_init) are not implemented.
- The retry logic is not implemented, and the burner does not abort if the burn failed, it just sets the `success` flag of `burn_t`.
Co-authored-by: Donald E. Willcox <eugene.willcox@gmail.com>
integration/Make.package
integration/VODE/Make.package
integration/VODE/vode_dvhin.H
integration/VODE/vode_dvjac.H
integration/VODE/vode_dvjust.H
integration/VODE/vode_dvnlsd.H
integration/VODE/vode_dvode.H
integration/VODE/vode_dvset.H
integration/VODE/vode_dvstep.H
integration/VODE/vode_integrator.H
integration/VODE/vode_linpack.H
integration/VODE/vode_rhs.H
integration/VODE/vode_type.H
integration/integrator.H
integration/utils/Make.package
integration/utils/temperature_integration.H
interfaces/Make.package
interfaces/burn_type.H
interfaces/burner.H
networks/powerlaw/Make.package
networks/powerlaw/actual_network.H
unit_test/test_react/GNUmakefile
unit_test/test_react/Make.package
unit_test/test_react/inputs_powerlaw
unit_test/test_react/main.cpp
unit_test/test_react/probin.powerlaw
unit_test/test_react/react_zones.H
unit_test/test_react/variables.H
commit 46ae1df9137a54fd9c34179ca6b5e356c9158464
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 9 18:56:24 2020 -0400
update to the pynucastro 1.4
networks/ECSN/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/URCA-simple/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/nova/actual_network.F90
networks/subch/actual_network.F90
networks/subch2/actual_network.F90
commit 9c4bc8332175a47f10384f52d719a18bfe3688a6
Author: XinlongSBU <42697364+XinlongSBU@users.noreply.github.com>
Date: Fri Apr 3 12:22:11 2020 -0400
delete print and aion(:) which are used for debug (#298)
networks/ECSN/actual_network.F90
commit 3cc9e6d1488592089a56f4f4d527121c7dfdfc22
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 3 10:22:37 2020 -0400
add init
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/nova/actual_network.F90
networks/sn160/actual_network.F90
networks/subch/actual_network.F90
networks/subch2/actual_network.F90
commit bd3d97fca35fd0d3f3ab276df9ae5218150fff6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 3 10:19:44 2020 -0400
add init
networks/ECSN/actual_network.F90
commit 12baac070e908a97a91fcc56cd4fe2c31c91096b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 3 09:29:55 2020 -0400
update nets to latest starkiller format via pynucastro
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/pynucastro.net
networks/ignition_reaclib/C-test/Make.package
networks/ignition_reaclib/C-test/NETWORK_PROPERTIES
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/pynucastro.net
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/NETWORK_PROPERTIES
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/pynucastro.net
networks/nova/Make.package
networks/nova/NETWORK_PROPERTIES
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/pynucastro.net
networks/sn160/Make.package
networks/sn160/NETWORK_PROPERTIES
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/sn160/pynucastro.net
networks/subch/NETWORK_PROPERTIES
networks/subch/pynucastro.net
networks/subch2/Make.package
networks/subch2/NETWORK_PROPERTIES
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/pynucastro.net
commit f07d0084b592fedddb7a3a54d27aa4371c4cd378
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 3 01:15:25 2020 -0700
CUDA version of powerlaw
networks/powerlaw/Make.package
networks/powerlaw/actual_burner.F90
networks/powerlaw/actual_network.F90
networks/powerlaw/actual_rhs.F90
commit a3ecddab872e35daa667c2c1fabe7329eb8dcf49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 2 14:01:29 2020 -0400
fix typo
networks/ECSN/ecsn_network_generation.py
commit 13c9b0374fb06e97b87b4678463dddc90886403f
Author: XinlongSBU <42697364+XinlongSBU@users.noreply.github.com>
Date: Thu Apr 2 13:56:27 2020 -0400
Updates networks/ECSN (#296)
networks/ECSN/20180319default2
networks/ECSN/Make.package
networks/ECSN/NETWORK_PROPERTIES
networks/ECSN/_parameters
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/ecsn.png
networks/ECSN/ecsn_network_generation.py
networks/ECSN/net_work_zingale.ipynb
networks/ECSN/physical_constants.f90
networks/ECSN/pynucastro.net
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
commit 701006c3db2841df646b8641f300c05090f44cd0
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 2 00:02:54 2020 -0700
Protect against n_cell=1 divide-by-zero
unit_test/test_react/util.f90
commit c935544dc38e34ddee4d54a407621a1661761097
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 1 08:59:31 2020 -0400
update changes
CHANGES.md
commit 3f4981ed051656d64730519a58efc6c8f6cf2392
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 31 13:22:31 2020 -0400
eliminate screenz (#293)
Only 3 networks were using screenz (triple_alpha_plus_cago, ignition_simple, ignition_chamulak).
We swap them over to screen5.
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_simple/actual_rhs.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/screen_module.F90
screening/screen.F90
commit c083cf080e74d4496b2445f376c44608dacfef51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 31 12:47:19 2020 -0400
remove wion -- it is unused (#294)
networks/aprox13/actual_network.F90
networks/aprox19/actual_network.F90
networks/aprox21/actual_network.F90
networks/ignition_chamulak/actual_network.F90
networks/ignition_simple/actual_network.F90
commit 803138c4649b08954c98eb0b6a02ca44aaaf09d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 30 15:44:50 2020 -0400
check for NSCREEN > 0
screening/screen_data.H
screening/screen_data.cpp
commit cc6155d8b690ed9a16fdffbe2eb1bdaea1fb24eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 10:46:29 2020 -0400
fix my min hack
screening/screen.H
commit d774034ab96e5702e755241060362880a21883d3
Merge: 3acf4d34 7ae76f15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 10:26:13 2020 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 3acf4d34dbd2f9de4157d64fc6cff023c8bb0d61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 28 10:26:00 2020 -0400
update changes
CHANGES.md
commit 7ae76f15cd3e36e5cbb1ce8824961e3d08beeda0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 19:39:44 2020 -0400
do screening init off GPU
unit_test/test_screening/screening_util.F90
unit_test/test_screening/unit_test.f90
commit 6718c20b02bc97c37ec968ed96d084f739deb7aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 19:19:00 2020 -0400
hack around a min
screening/screen.H
commit eb8fe42e0e10ba2f54ba9e9d48708958bad9dfc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 16:17:03 2020 -0400
fix output name
unit_test/test_screening/main.cpp
commit 09187840b109ccebc98237b4e82f36d0a02b2322
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 16:09:50 2020 -0400
fix compilation
screening/screen.H
unit_test/test_screening_C/main.cpp
commit 94bd750c600c269f39d80f37db5da3485cc2123e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 16:03:05 2020 -0400
remove cond bits
unit_test/test_screening/main.cpp
unit_test/test_screening/test_screening_F.H
unit_test/test_screening/variables.F90
commit ba8eba094cc6a0ecf0f873bf7420acba3183334c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 15:59:15 2020 -0400
add _C to output name
unit_test/test_aprox_rates_C/main.cpp
commit 9a8c693626225ffd8bf2fd89c97194c8fa7931de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 13:02:05 2020 -0400
a header only implementation
screening/Make.package
screening/screen.H
screening/screening.H
screening/screening.cpp
commit 0d5af3ff2e97e34d7f8bbfda6b3cac5902943a39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 12:14:47 2020 -0400
switch to network properties
networks/subch/Make.package
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
commit c40401334c9281f3ed25e28f94cafb701cb1cfd8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 12:14:27 2020 -0400
fallback to pynucastro.net
networks/update_headers.py
commit f2df1cf5cd2a7af60e19999a318ad19e731f6538
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 10:56:08 2020 -0400
add a debugging target
networks/Make.package
commit d16b4286e6e0bfd912210d3b1a7686e89b1e514b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 27 08:33:02 2020 -0400
fix compilation
EOS/rad_power_law/rad_power_law.F90
commit 3ec6f18bff4e752bbd8b89056bbe526757b26c5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 18:50:09 2020 -0400
update changes
CHANGES.md
commit d8ffa66a03d14593eb0b9f35b9debb7e68708058
Merge: b60c87dc 5b48458e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:52:57 2020 -0700
Merge pull request #290 from starkiller-astro/cxx-screening
C++ screening -- thanks @zingale !
commit 5b48458e13ef7afa783dc8f844da208f25fcf8df
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:52:03 2020 -0700
e -> d in _parameters for F & C screening tests.
unit_test/test_screening/_parameters
unit_test/test_screening_C/_parameters
commit 1ff1da03a5f5a2301da0e6e30a261e41b6776bb0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:50:34 2020 -0700
e -> d in real extern parameter for C test.
unit_test/test_screening_C/probin
commit b60c87dc29f6f81b3e1787ad211ef9d760f75857
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 15:47:35 2020 -0400
add is_input_valid (#291)
We can now query an EOS to see if it supports a given input mode
EOS/breakout/actual_eos.F90
EOS/breakout/actual_eos.H
EOS/gamma_law/actual_eos.H
EOS/gamma_law/gamma_law.F90
EOS/gamma_law_general/actual_eos.F90
EOS/gamma_law_general/actual_eos.H
EOS/helmholtz/actual_eos.F90
EOS/helmholtz/actual_eos.H
EOS/multigamma/actual_eos.F90
EOS/multigamma/actual_eos.H
EOS/polytrope/actual_eos.F90
EOS/polytrope/actual_eos.H
EOS/rad_power_law/actual_eos.H
EOS/rad_power_law/rad_power_law.F90
EOS/stellarcollapse/actual_eos.F90
EOS/ztwd/actual_eos.F90
EOS/ztwd/actual_eos.H
unit_test/test_eos_C/main.cpp
commit 1f232b0d00ae4491e130448964a4d747a49a6a5b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:34:17 2020 -0700
delete build output file
unit_test/test_screening_C/out
commit ed568937d07a954169a4a47ee56cf3c91a69da6a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:33:20 2020 -0700
fix EOS -> screening in readme
unit_test/test_screening_C/README
commit ca955cd5f01f1b00cbfc46175b4f295935026136
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:32:23 2020 -0700
add newline for readability
unit_test/test_screening/variables.F90
commit 46994197d508c3c74b7795e12733d56beb1feb97
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:21:42 2020 -0700
removed trailing whitespace
unit_test/test_screening/test_screening_F.H
commit a06dfe8fb0962cda7f0ebbb873a341611fddfe72
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:20:11 2020 -0700
e -> d in real extern parameter
unit_test/test_screening/probin
commit 27f68483e1615fc538fb7f1ac74285d2df0cde86
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 12:19:10 2020 -0700
fix comment. clarify other comments to specify rate type.
unit_test/test_screening/screening_util.F90
commit 92edae66554bc0da5d8013e3d7548807450a362b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 13:16:26 2020 -0400
hide the automatically generated files
Make.Microphysics
commit 88bd23735766e7facccbbe6eb5ee1aa922efaf79
Merge: 64c41450 01abe059
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 10:04:45 2020 -0700
Merge branch 'cxx-screening' of github.com:starkiller-astro/Microphysics into cxx-screening
commit 64c41450f9f6c3a7a60c51239949755daadb92b0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 26 10:04:34 2020 -0700
remove unnecessary string format for setting the path to the network properties file.
networks/update_headers.py
commit 01abe0599c48e6144682e0f109d7ebba02449682
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 13:04:20 2020 -0400
remove stray .format
networks/update_headers.py
commit abf7e5f9b33a782779872e6571c75e4680bdf393
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 12:33:13 2020 -0400
commit the new interface
screening/screen_data.H
commit c773b9680db04cd2b1d750e79851f8e2a18381a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 12:19:40 2020 -0400
add asserts
unit_test/test_screening_C/main.cpp
commit 12db438d93829a6bf6abad2228ed6c20b766cbe6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 10:51:31 2020 -0400
fix spelling of sulfur
unit_test/test_screening_C/main.cpp
commit 855f567991521bc8f4c4ce3818c9630893d59d11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 10:38:18 2020 -0400
add a << method
screening/screen.H
commit 5ea83a63d9089d778421dc2bf4109c85c94e9fab
Merge: 16b8cc0f ca525a05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 10:12:56 2020 -0400
Merge branch 'development' into cxx-screening
commit ca525a05a27e46d0d5f513bcab9f75e402077e56
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 09:28:13 2020 -0400
remove unused variables
integration/BS/bs_jac.F90
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_type.F90
commit 16b8cc0fe9ae23e39657b9a7e84af2065f0e63b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 09:17:44 2020 -0400
remove unused var
screening/screen.F90
screening/screening.cpp
commit 65c7fdaa46ae76249cc610b1ae6c54a541f764c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 26 09:17:27 2020 -0400
fix some shadowing
unit_test/test_screening_C/main.cpp
unit_test/test_screening_C/out
commit b57a2a7c4e533acc9824713d3f356afdc6be9d31
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 21:33:39 2020 -0400
add missing file
screening/Make.package
screening/screening.H
commit 91fb03a26d75b23a9dadf07cbfad044eebfd137c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 21:33:13 2020 -0400
remove unused vars
screening/screen.F90
commit f514510c627f1b66cfc842fff1ede8c95369979a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 21:31:28 2020 -0400
make pass by ref
screening/screen.H
commit b22cb987d713d52ed73bf905b198700053cdb91a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 21:02:20 2020 -0400
this builds
unit_test/test_screening_C/GNUmakefile
unit_test/test_screening_C/main.cpp
commit 3fc30673df74e46f82ad735e650ad54a946a30d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 19:28:33 2020 -0400
almost compiling...
unit_test/test_screening_C/GNUmakefile
unit_test/test_screening_C/main.cpp
unit_test/test_screening_C/variables.cpp
commit 34f024145cdfccba6f78db68d0edac0dd3c93eaf
Merge: 4af90564 02a6986b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 18:50:18 2020 -0400
Merge branch 'development' into cxx-screening
commit 02a6986befb6ca545ba79d6ddbf30dadd56e5a7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 18:48:10 2020 -0400
log10 -> std::log10
unit_test/test_aprox_rates_C/main.cpp
unit_test/test_conductivity_C/main.cpp
unit_test/test_eos_C/main.cpp
commit 4af905643d6358307e2246293999c501208da55e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 18:45:06 2020 -0400
setup the screening factors
unit_test/test_screening_C/main.cpp
commit c2bfb2b3fdc9dd011267af95ecfe52720be65d0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 18:34:41 2020 -0400
start of C++ screening work
unit_test/test_screening_C/GNUmakefile
unit_test/test_screening_C/Make.package
unit_test/test_screening_C/README
unit_test/test_screening_C/_parameters
unit_test/test_screening_C/inputs
unit_test/test_screening_C/main.cpp
unit_test/test_screening_C/out
unit_test/test_screening_C/probin
unit_test/test_screening_C/test_screen.H
unit_test/test_screening_C/test_screen_F.H
unit_test/test_screening_C/unit_test.f90
unit_test/test_screening_C/variables.H
unit_test/test_screening_C/variables.cpp
commit fe4edb260fc0626e8f7f2f3bb80a33ce47cf6cc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 17:09:08 2020 -0400
also store the derivatives
unit_test/test_screening/screening_util.F90
unit_test/test_screening/variables.F90
commit 2f095788002676e902c08825e7396638cbb4278f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 16:30:57 2020 -0400
F90 screening unit test seems to work
unit_test/test_screening/GNUmakefile
unit_test/test_screening/Make.package
unit_test/test_screening/screening_util.F90
unit_test/test_screening/test_screening.H
unit_test/test_screening/test_screening_F.H
commit c2dbbffd8b23fa319199ee10e8dc38177a47dd10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 15:29:00 2020 -0400
start working on a unit test
unit_test/test_screening/GNUmakefile
unit_test/test_screening/Make.package
unit_test/test_screening/_parameters
unit_test/test_screening/inputs
unit_test/test_screening/main.cpp
unit_test/test_screening/probin
unit_test/test_screening/screening_util.F90
unit_test/test_screening/test_screening.H
unit_test/test_screening/test_screening_F.H
unit_test/test_screening/unit_test.f90
unit_test/test_screening/variables.F90
commit cd1b08f6186d46a92b64a27420990a7f9b4fc7f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 14:29:05 2020 -0400
add missing files
screening/screen_data.H
screening/screen_data.cpp
commit c86050f17393c536256df3593e6f2b36d4a76238
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 14:20:29 2020 -0400
this compiles!!!
screening/Make.package
screening/screen.H
screening/screening.cpp
commit 46c8c820a5c5d9d9d4da2594de27a0d9edc99f3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 13:55:08 2020 -0400
first pass
screening/Make.package
screening/screen.H
commit 433e79afd5f30d0e7c85a90cba779b5b728fc890
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 12:00:01 2020 -0400
automatically find NSCREEN
networks/general_null/network_header.template
networks/general_null/write_network.py
networks/update_headers.py
commit 485eb943ceb98701047b39e10a6df96540fb832f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 10:43:24 2020 -0400
add number of screenings
networks/aprox13/NETWORK_PROPERTIES
networks/aprox19/NETWORK_PROPERTIES
networks/aprox21/NETWORK_PROPERTIES
networks/breakout/NETWORK_PROPERTIES
networks/general_null/NETWORK_PROPERTIES
networks/ignition_chamulak/NETWORK_PROPERTIES
networks/ignition_simple/NETWORK_PROPERTIES
networks/iso7/NETWORK_PROPERTIES
networks/powerlaw/NETWORK_PROPERTIES
networks/rprox/NETWORK_PROPERTIES
networks/triple_alpha_plus_cago/NETWORK_PROPERTIES
networks/xrb_simple/NETWORK_PROPERTIES
commit b616d66eaa3f93faf9c8c1b8f6b4343854e5ebb3
Merge: c9bdd939 e7b5cceb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 09:48:35 2020 -0400
Merge branch 'development' into cxx-screening
commit e7b5cceb3f879e61d894f851ce8976d3abe1d27d
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Wed Mar 25 09:45:29 2020 -0400
Convert aprox_rates to C++ (#288)
This converts the aprox_rates_module to C++ and adds unit tests for both the original Fortran and new C++ implementations.
rates/Make.package
rates/aprox_rates.F90
rates/aprox_rates.H
rates/aprox_rates_data.H
rates/aprox_rates_data.cpp
rates/tfactors.H
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/README
unit_test/test_aprox_rates/_parameters
unit_test/test_aprox_rates/aprox_rates_util.F90
unit_test/test_aprox_rates/input_aprox_rates
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/probin
unit_test/test_aprox_rates/test_aprox_rates.H
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/unit_test.f90
unit_test/test_aprox_rates/variables.F90
unit_test/test_aprox_rates_C/GNUmakefile
unit_test/test_aprox_rates_C/Make.package
unit_test/test_aprox_rates_C/README
unit_test/test_aprox_rates_C/_parameters
unit_test/test_aprox_rates_C/input_aprox_rates
unit_test/test_aprox_rates_C/main.cpp
unit_test/test_aprox_rates_C/probin
unit_test/test_aprox_rates_C/test_aprox_rates.H
unit_test/test_aprox_rates_C/test_aprox_rates_F.H
unit_test/test_aprox_rates_C/unit_test.f90
unit_test/test_aprox_rates_C/variables.H
unit_test/test_aprox_rates_C/variables.cpp
commit c9bdd93930bb57d420eccac9f09853182fc88d30
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 25 09:19:51 2020 -0400
add screening header
screening/screen.H
commit 064f0f5d83a77f81ae458a71f8130c3a822a683b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Mar 24 14:00:19 2020 -0700
Update model analysis notebook to show behavior when helm_table.dat is not in the working directory.
python_library/StarKiller/StarKiller/examples/rotating_star/Analyze-Model.ipynb
commit d3d1fbcce12ef119f47782fbd6bb5dc138c67a52
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Mar 24 13:58:01 2020 -0700
Add AmrexAstroModel.set() to allow manually setting specific model entries.
python_library/StarKiller/StarKiller/models/amrex_astro.py
commit 893fc11d36c01559e8da51b5e89d0b5178428970
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Mar 24 13:57:16 2020 -0700
Add a function for writing an AmrexAstroModel to a model file.
python_library/StarKiller/StarKiller/models/amrex_astro.py
commit 9c29a1eef2b046b754d19f0dd81929ff6abbfd76
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 16:38:49 2020 -0400
M_PI -> M_PI*M_PI
rates/aprox_rates.H
commit de276c592285e4f0fa6c34164d92e63910efc8cf
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 16:34:52 2020 -0400
fix iron 56 rate
rates/aprox_rates.H
commit 315b347579e2c0f229d1f7ada272fe80f57a6e87
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 16:21:32 2020 -0400
initialize dNi the same in the Fortran and C++ tests
unit_test/test_aprox_rates/aprox_rates_util.F90
commit b1d7304a3485cd4bee8b2f6f1fa15156272ca0d1
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 16:16:47 2020 -0400
fix(?) strings in Fortran aprox_rates test
unit_test/test_aprox_rates/variables.F90
commit 34686a6cf2db312fce636d532455de7b47f8e41e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 10:31:07 2020 -0400
Fortran test for aprox_rates
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/aprox_rates_util.F90
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/variables.F90
unit_test/test_aprox_rates/variables.H
unit_test/test_aprox_rates/variables.cpp
commit 579672d90d4cb8dab428e4b063e785fe3d86846a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 09:29:36 2020 -0400
move C++ test to _C directory so can make a Fortran test
unit_test/test_aprox_rates_C/GNUmakefile
unit_test/test_aprox_rates_C/Make.package
unit_test/test_aprox_rates_C/README
unit_test/test_aprox_rates_C/_parameters
unit_test/test_aprox_rates_C/input_aprox_rates
unit_test/test_aprox_rates_C/main.cpp
unit_test/test_aprox_rates_C/probin
unit_test/test_aprox_rates_C/test_aprox_rates.H
unit_test/test_aprox_rates_C/test_aprox_rates_F.H
unit_test/test_aprox_rates_C/unit_test.f90
unit_test/test_aprox_rates_C/variables.H
unit_test/test_aprox_rates_C/variables.cpp
commit 5b78910b09f6727a55c5c9494b305b861da47cdd
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 24 09:25:39 2020 -0400
finished C++ unit test for aprox_rates
rates/aprox_rates.H
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/variables.H
unit_test/test_aprox_rates/variables.cpp
commit aed392bf8f426288cd71b81c89995ce7bf93308f
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 23 18:04:02 2020 -0400
wrote out the unit tests
rates/aprox_rates.H
rates/aprox_rates_data.H
rates/aprox_rates_data.cpp
rates/tfactors.H
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/test_aprox_rates.H
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/variables.H
unit_test/test_aprox_rates/variables.cpp
commit 8a9afe15336c5f88c934ef145a767706b3303db4
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 23 15:02:11 2020 -0400
copied conductivity unit test to test_aprox_rates
unit_test/test_aprox_rates/GNUmakefile
unit_test/test_aprox_rates/Make.package
unit_test/test_aprox_rates/README
unit_test/test_aprox_rates/_parameters
unit_test/test_aprox_rates/input_aprox_rates
unit_test/test_aprox_rates/main.cpp
unit_test/test_aprox_rates/probin
unit_test/test_aprox_rates/test_aprox_rates.H
unit_test/test_aprox_rates/test_aprox_rates_F.H
unit_test/test_aprox_rates/unit_test.f90
unit_test/test_aprox_rates/variables.H
unit_test/test_aprox_rates/variables.cpp
commit ff42b3d0e1c102cbb15f6b0890fdb9991a4d9703
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 23 14:26:25 2020 -0400
C++ aprox_rates compiles
rates/Make.package
rates/aprox_rates_data.H
rates/aprox_rates_data.cpp
commit 6af3faa5346bf93f2c986bfb49924804f8b294b3
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 23 13:54:14 2020 -0400
add semicolons
rates/aprox_rates.H
commit 786cdc5a76e1f2c29075139ec9aef97ed6af5935
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 23 11:29:13 2020 -0400
copypasta from aprox_rates.F90 to aprox_rates.H
rates/aprox_rates.F90
rates/aprox_rates.H
rates/tfactors.H
commit ddacc714bbe460bd1f4ae16a1daafdb8c99fb131
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 23 08:59:11 2020 -0400
started converting the aprox_rates to C++
rates/Make.package
rates/aprox_rates.H
rates/aprox_rates_data.H
rates/aprox_rates_data.cpp
commit bcdd4ab07118ea45beb582235516fe76ed91b49b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 11:10:37 2020 -0700
Fix compile bug
integration/VODE/vode_type.F90
commit cd6d035e4ac7e2285c5cd505cf6923fbe94ba40f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 10:40:50 2020 -0700
Move some data out of the dvode_t
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuvode_parameters.F90
commit 2ac5b16c2be7c6bdf2c861aa5850c086f9b748ec
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 09:37:44 2020 -0700
Move UROUND and SRUR outside the dvode_t
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_type.F90
commit fd069fe71bf3c4a96acf6051fbd3bf53c9b33a94
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 09:29:41 2020 -0700
Undo CUDA choice for Jacobian caching, this was wrong
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
commit fdc0eef27355dcb1d19a37c147add28b321ff805
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 08:51:35 2020 -0700
Fix typo
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
commit 5f8665020f53d63d39275349810bf733a39879d4
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 00:56:53 2020 -0700
Non-linear solver cleanup
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
commit 32c3d6ea2ffb63f78603c6a5a587f604fbc5a56d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Mar 20 00:36:13 2020 -0700
Modify Jacobian parameter handling for dvode_state
Rather than use MF_JAC and its non-intuitive arithmetic properties,
we directly copy the Jacobian into the DVODE state using the same
properties as elsewhere in Microphysics (jacobian == 1 means analytic,
2 means numerical). Also, we directly load the use_jacobian_caching
parameter into JSV.
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
commit f584f77900229b68b7069d42e1475d1bc67145c9
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 19 00:35:32 2020 -0700
Syntax cleanup
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit 5272bb9a08b464adf1b030ca3f93c38785b22564
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 19 00:24:25 2020 -0700
Linpack cleanup
integration/VODE/cuVODE/source/linpack_module.F90
commit c2e238f0a94b2208ca7bfc92a75462808e43d0a6
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 19 00:07:37 2020 -0700
We always have jstart >= 0
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit e23ca4248eadf9ae15f6c85808a2aad4e8bb56aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:46:42 2020 -0700
Don't need condopt
integration/VODE/cuVODE/source/cuvode_type.F90
commit 4376b7c930d8beb85244ac186ed8208cfcfe5c20
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:44:14 2020 -0700
Inline dvindy
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
commit 13206b932045189ad8c0a08b7f11aa430d80c28c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:25:37 2020 -0700
Remove METH
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_type.F90
commit 02caf96cb7faa046aa8ae08a91f1f6a459de4ec0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:18:23 2020 -0700
Print directly instead of using xerrwd
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_output.F90
commit ad131d928070f3f4723d3d833cbdb1e139a2e2b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:13:47 2020 -0700
Skip some unnecessary error checks
integration/VODE/cuVODE/source/cuvode.F90
commit d16fe23561171a0aa2764f8c002c3ceec7925878
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:09:28 2020 -0700
K = 0 always
integration/VODE/cuVODE/source/cuvode_dvindy.F90
commit a97e103bd58ce95870ed672cbd3cd0538b04fa54
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 23:03:45 2020 -0700
Merge Nordsieck functions into dvstep module
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
commit b1daf3874e60e995261b9b74ab3dc7860ca9cd25
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 22:58:43 2020 -0700
Inline dvnorm
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit 6407d3b011db8efc5fa008cdcf2cbc848c36ac31
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 22:49:21 2020 -0700
Remove dacopy
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode_dacopy.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
commit 219190cfd9f8ab08cbeea62328cc43d0736444b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 22:44:34 2020 -0700
Hardcode the constants
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_constants.F90
integration/VODE/cuVODE/source/cuvode_dacopy.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
integration/VODE/cuVODE/source/cuvode_output.F90
integration/VODE/cuVODE/source/cuvode_type.F90
commit abcd9983f098631d62a3a1107cc8d5ea6fdcdea2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 22:19:39 2020 -0700
Remove MITER == 0 case
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
commit 9ab0b2e4f1a6998ffa07f29f23d89a24f3a87a48
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 21:49:29 2020 -0700
Move MF_JAC into dvode_state
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
commit 6937a2048dfe40db753ef6c4fd2d210dc59dae40
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 21:41:47 2020 -0700
Remove iwork from the DVODE interface
The user must now set dvode_state % MXSTEP so we know how many
steps to take.
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
commit 8a75008323d38e64c1ec7df632d4f0267a5d3ced
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 21:20:04 2020 -0700
Move rwork data into the dvode state
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_type.F90
commit 2d64ea9c168ef74b55a33e89c376d1ae74c05510
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 20:25:54 2020 -0700
We only need to pass around pivot
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit b7a5824c617353c535cbc88c1dc5187de1e86121
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 20:01:39 2020 -0700
Inline the dgesl call
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvsol.F90
commit c9bfa42a1411da6e1d5325b6489ee77c14185c8f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 19:41:32 2020 -0700
Narrator: IMXER was not, in fact, relevant
integration/VODE/cuVODE/source/cuvode.F90
commit 45f821452bffea05cb32cc5929653ca85056e861
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 19:32:51 2020 -0700
Remove IOPT from the dvode interface
We now always check iwork to see if the user requested a maximum
number of steps, so they should initialize to zero if they don't
want to do so.
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
commit f07457ac0d47c8b8df089f6e70df17a09a52ff92
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 19:10:12 2020 -0700
We always come in with istate == 1
integration/VODE/cuVODE/source/cuvode.F90
commit 4df7db27742d8f03e9d757558eddb054acb34f26
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 18:52:52 2020 -0700
Remove ITASK
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
commit bd1441ea5a1c04e24f6d55a810ee1fcee15cc021
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 21:37:10 2020 -0400
update changes
CHANGES.md
commit 5e8a0553927763cf90c5a03b60b907a6b599dddd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 21:32:27 2020 -0400
Vode dvstep 3 (#287)
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit 449a37c6f53ee4cea21b27d8d9323656bba5a5c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 21:24:24 2020 -0400
Vode dvstep 2 (#286)
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit c2609f6dea4e49c63a4d1c7364a9895e5adbeeed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 21:16:00 2020 -0400
eliminate some go tos from vode_dvstep_1 (#285)
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit 0c0081a91a17e0728f65d8595c491858da3c5ac4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 20:36:59 2020 -0400
last of the go tos in cuvode.F90 (#283)
integration/VODE/cuVODE/source/cuvode.F90
commit c8009dfcc1ac8df476080eb3a21f22a01138c85c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 20:09:55 2020 -0400
Vode goto 6 (#282)
more go to elimination
integration/VODE/cuVODE/source/cuvode.F90
commit d116b5c19fff3434477eb19bb260b7116688b448
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 09:48:34 2020 -0700
Remove transpose version of dgesl
integration/VODE/cuVODE/source/linpack_module.F90
commit ea266f79b12e40cf57272b29271fedc6d62f6236
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 18 09:04:38 2020 -0700
Remove gotos in linpack_module (#284)
integration/VODE/cuVODE/source/linpack_module.F90
commit da6f2ee413f7c0955be64bb309fd6bc11a4be612
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 10:43:38 2020 -0400
Vode goto 5 (#281)
eliminate more go tos
integration/VODE/cuVODE/source/cuvode.F90
commit 1fa48992e0a4687e77c023059eb7d1d1303aef58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 10:28:19 2020 -0400
more VODE opts (#256)
Pass the dvode_t directly into the conversion routines to save on memory.
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs_simplified_sdc.F90
integration/VODE/vode_type.F90
integration/VODE/vode_type_simplified_sdc.F90
commit c2ffeef6af3ce00cdd0e4f526ae34892c8d742b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 09:12:23 2020 -0400
update changes
CHANGES.md
commit f87c1b3ff0d9ca8a6b511bbe7817bcf5474bac67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 09:03:28 2020 -0400
add in a blanket nspec_evolve for application codes
interfaces/network.F90
commit f0e3ed16e3c1925b61454f78cc82b472882bb07d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 18 00:53:09 2020 -0400
more goto extermination (#280)
integration/VODE/cuVODE/source/cuvode.F90
commit 8147834516c4a1c4c649593bd3e404e16237db2e
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 17 21:12:54 2020 -0700
Remove unused banded linpack routines
integration/VODE/cuVODE/source/linpack_module.F90
commit db905d32340082cc5dcd2b2677975d383989ba0a
Merge: b7a6efaf d3f96d78
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Mar 17 19:20:18 2020 -0700
Merge pull request #279 from starkiller-astro/nspec_evolve
get rid of nspec_evolve
commit b7a6efaf932b6bc668b663c5699945c168b47e97
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 17 10:31:15 2020 -0700
Sync up the standalone VODE test
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
commit 3e0268e617edf3d6a98b89656604d98032ba0128
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 17 10:18:21 2020 -0700
Inline dewset
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dewset.F90
commit 00be551e6cc4f42f9af7af69dd4040a7a7681a8b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 17 10:14:20 2020 -0700
VODE_ITOL is always 4
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dewset.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvsol.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
commit e97abddf12f46f780d9261b514d60a804399f7dc
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 17 10:08:08 2020 -0700
Simplify output code
integration/VODE/cuVODE/source/cuvode_output.F90
commit 0b4bfbb3001276aa2c5bbb542254c8f211705116
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 19:22:06 2020 -0400
add C++ versions of the conductivities (#273)
As part of this change, the stellar conductivity was updated to the constants from the fundamental_constants_module (for both Fortran and C++)
conductivity/constant/Make.package
conductivity/constant/actual_conductivity.H
conductivity/constant_opacity/Make.package
conductivity/constant_opacity/actual_conductivity.H
conductivity/powerlaw/Make.package
conductivity/powerlaw/actual_conductivity.H
conductivity/stellar/Make.package
conductivity/stellar/actual_conductivity.H
conductivity/stellar/stellar_conductivity.F90
interfaces/Make.package
interfaces/conductivity.H
unit_test/test_conductivity_C/GNUmakefile
unit_test/test_conductivity_C/Make.package
unit_test/test_conductivity_C/README
unit_test/test_conductivity_C/_parameters
unit_test/test_conductivity_C/input_conductivity
unit_test/test_conductivity_C/main.cpp
unit_test/test_conductivity_C/probin
unit_test/test_conductivity_C/test_cond.H
unit_test/test_conductivity_C/test_cond_F.H
unit_test/test_conductivity_C/unit_test.f90
unit_test/test_conductivity_C/variables.H
unit_test/test_conductivity_C/variables.cpp
commit 605b8efa996004c6af09d7ed87cf934ea01bfa6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 13 19:01:49 2020 -0400
rid the world of more go tos (#278)
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit 22594394667fed59f3cfd296f4e47f0b115d73aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 12:41:01 2020 -0400
Vode goto 2 (#276)
more go to removal
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
commit d3f96d780e8facd4bc266be2e4b4309e78e62a72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 11:59:18 2020 -0400
more nspec_evolve extermination
interfaces/burn_type.F90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
python_library/StarKiller/StarKiller/integration/sdc.py
python_library/StarKiller/StarKiller/network/network.py
sphinx_docs/source/data_structures.rst
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react_F.H
util/eval_rhs/evaluate_rhs.f90
commit 75cfee00b87636a0410d071dc9056f7b42bc55bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 11:48:37 2020 -0400
more nspec_evolve work
integration/BS/bs_integrator.F90
integration/CVODE/cvode_type.F90
integration/VBDF/vbdf_integrator.F90
integration/VODE/vode_integrator.F90
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_network.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_network.F90
networks/aprox21/actual_rhs.F90
networks/breakout/actual_network.f90
networks/breakout/actual_rhs.f90
networks/general_null/actual_rhs.F90
networks/general_null/network.template
networks/ignition_chamulak/actual_network.F90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_rhs.F90
networks/iso7/actual_network.F90
networks/iso7/actual_rhs.F90
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_network.F90
networks/rprox/actual_rhs.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/triple_alpha_plus_cago/actual_network.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/dydt.F90
networks/xrb_simple/actual_network.f90
networks/xrb_simple/actual_rhs.f90
sphinx_docs/source/networks.rst
commit 246261e66ff254c634da05e599e369f9a6a667b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 11:08:26 2020 -0400
remove nspec_evolve
integration/BS/bs_integrator.F90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_rpar.F90
integration/CVODE/cvode_type.F90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VBDF/vbdf_rpar.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs_simplified_sdc.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type.F90
integration/VODE/vode_type_simplified_sdc.F90
integration/utils/nonaka_plot.f90
integration/utils/numerical_jacobian.F90
integration/utils/temperature_integration.F90
commit 312658c86494ec0066e3a43ad33010ede1edbba7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 12 03:39:54 2020 -0400
Place the Helmholtz globals in a namespace (#271)
Place the Helmholtz global variables in a helmholtz namespace; this helps avoid shadowing.
Co-authored-by: Max Katz <maxpkatz@gmail.com>
EOS/helmholtz/actual_eos.H
EOS/helmholtz/actual_eos_data.H
EOS/helmholtz/actual_eos_data.cpp
commit 4d25f2ef9ab0e87ff1023f62e6725c68f0cd8122
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Mar 12 00:22:59 2020 -0700
Fix compiler warnings
EOS/helmholtz/actual_eos.H
interfaces/eos_F.H
commit 6a83079d0a4b71a17d3962931043192dd664fae0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 11 20:32:31 2020 -0400
VODE optimizations (#255)
Eliminate the storage of the old state in rpar
remove a lot of the burn_to_vode stuff
integration/VODE/vode_integrator.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type.F90
commit 88e8c39a70f194985fbcf6e3bd76de8f00906486
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 11 16:02:06 2020 -0400
remove some unused code paths and go tos (#275)
this gets rid of some of the non-stiff code
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dewset.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvsol.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
commit 1cc10b49ad0787879b5c968e1754ececad08ee5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 11 15:11:14 2020 -0400
get rid of a lot of "go to"s in VODE (#274)
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
commit b3432ea84048f5933889962dc49d0ebf10fb6eee
Merge: c369ff8d 3844b105
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 10:41:33 2020 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit c369ff8da3077f34acdfd3b539f1975fff2053ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 10 10:41:12 2020 -0400
switch eos_name to a parameter so it works on GPUs
EOS/breakout/actual_eos.F90
EOS/gamma_law/gamma_law.F90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
EOS/rad_power_law/rad_power_law.F90
EOS/stellarcollapse/actual_eos.F90
EOS/ztwd/actual_eos.F90
commit 3844b1056c892780d7e34c24540891f1964f4714
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 8 10:44:55 2020 -0700
Remove unused Jacobian options
integration/VODE/cuVODE/source/cuvode_dvjac.F90
commit bdea2f53cc798aea5d49f8dc93a63ca8f6d843c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 4 15:31:41 2020 -0500
make the directory creation smarter to try to avoid a race condition
networks/update_headers.py
commit 80bb87d2e6f6c3ded7c5a794f5044f6fa7a04c06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 1 14:16:33 2020 -0500
update changes
CHANGES.md
commit 7ec6ea8d9c7dd1986331b90a7f52ef210cd91b08
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 08:10:11 2020 -0800
Make C++ EOS functionality opt-in for now
EOS/breakout/Make.package
EOS/gamma_law/Make.package
EOS/gamma_law_general/Make.package
EOS/helmholtz/Make.package
EOS/multigamma/Make.package
EOS/polytrope/Make.package
EOS/rad_power_law/Make.package
EOS/ztwd/Make.package
unit_test/test_eos_C/GNUmakefile
commit 8e8597c1fde2a74dffc8d7333d37a287e6b5413f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 07:46:12 2020 -0800
Convert breakout to C++ (#270)
EOS/breakout/Make.package
EOS/breakout/actual_eos.F90
EOS/breakout/actual_eos.H
EOS/breakout/actual_eos_data.H
EOS/breakout/actual_eos_data.cpp
commit a224400129051e83fd693dc802657ea4455cd0aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 1 07:45:39 2020 -0800
Convert rad_power_law to C++ (#269)
EOS/rad_power_law/Make.package
EOS/rad_power_law/actual_eos.H
EOS/rad_power_law/rad_power_law.F90
commit f12a2db97c9dcc58816ec6eb8241b633279eb714
Merge: 5c672019 e6aa0b4f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 29 15:25:27 2020 -0500
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 5c672019a7beb15e996d1d993928f742cfceb575
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 29 15:25:04 2020 -0500
update changes
CHANGES.md
commit e6aa0b4f2d261136731fe988ff093a76207c513b
Merge: f35c2031 8f24ecc4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Feb 28 18:15:56 2020 -0800
Merge pull request #267 from starkiller-astro/license
License
commit f35c2031ae48f027001b53586eb08f5f44bbd792
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 28 20:51:41 2020 -0500
mark these up for GPU
networks/general_null/Make.package
networks/general_null/actual_burner.F90
networks/general_null/actual_rhs.F90
commit 1692133e570883998d9e312ece9e7a04293e5717
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Feb 27 18:43:49 2020 -0800
Revert "Workaround to link multigamma with network.H in order to compile properly"
This reverts commit c19a466308b16d623bae6c789b6a795422680d8e.
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.H
EOS/multigamma/actual_eos_data.H
commit c19a466308b16d623bae6c789b6a795422680d8e
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Feb 27 09:30:52 2020 -0800
Workaround to link multigamma with network.H in order to compile properly
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.H
EOS/multigamma/actual_eos_data.H
commit 7bf603592cda66bbad855311430633c9c115f7e3
Merge: 5d88eac2 26958c1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 25 08:53:08 2020 -0500
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit 5d88eac21b72d86f65683a276242cbe034b00837
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 25 08:51:57 2020 -0500
update changes
CHANGES.md
commit 26958c1cb5bbfbcc7834eef23c1b57dc83102051
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 25 05:49:58 2020 -0800
Convert multigamma to C++ (#265)
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.H
EOS/multigamma/actual_eos_data.H
EOS/multigamma/actual_eos_data.cpp
EOS/multigamma/eos_composition.H
unit_test/test_eos/eos_util.F90
unit_test/test_eos/input_eos.multigamma
unit_test/test_eos/probin.multigamma
unit_test/test_eos_C/input_eos.multigamma
unit_test/test_eos_C/main.cpp
unit_test/test_eos_C/probin.multigamma
commit f2c9e4414ac695afc9033af22a28d0c5daf9d391
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 25 05:46:02 2020 -0800
Convert ztwd to C++ (#268)
This also does a little bit of cleanup on the Fortran to make it safe for CUDA.
EOS/ztwd/Make.package
EOS/ztwd/actual_eos.F90
EOS/ztwd/actual_eos.H
commit a7faf3adae348fb6a50c7f5435f69a71fb1f60fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 24 20:55:37 2020 -0800
Remove unused test_set parameter
unit_test/test_eos/_parameters
unit_test/test_eos_C/_parameters
commit 8a8c73fe47d6305ebc8fd94a2e2399f830f72ddd
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 24 20:44:09 2020 -0800
Network needs to be initialized before EOS
interfaces/microphysics.F90
commit 8f24ecc4baacbdd465b17597fb4085f9b1481b8b
Merge: b4e02de7 f1c3b03e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 21:33:02 2020 -0500
Merge branch 'development' into license
commit f1c3b03efc8366f3abd46b8c3b412248a450ca38
Merge: c4b88825 68b72b21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 21:32:54 2020 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit c4b8882530a8f2cc27ddedd9e24405cda695a00b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 21:32:39 2020 -0500
remove unused DNSQE
util/DNSQE/Make.package
util/DNSQE/README
util/DNSQE/TODO
util/DNSQE/d1mach.f
util/DNSQE/d1mpyq.f
util/DNSQE/d1updt.f
util/DNSQE/ddoglg.f
util/DNSQE/denorm.f
util/DNSQE/dfdjc1.f
util/DNSQE/dnsq.f
util/DNSQE/dnsqe.f
util/DNSQE/dqform.f
util/DNSQE/dqrfac.f
util/DNSQE/fdump.f
util/DNSQE/i1mach.f
util/DNSQE/j4save.f
util/DNSQE/orig/dnsqe.f
util/DNSQE/test/GNUmakefile
util/DNSQE/test/test.f90
util/DNSQE/xercnt.f
util/DNSQE/xerhlt.f
util/DNSQE/xermsg.f
util/DNSQE/xerprn.f
util/DNSQE/xersve.f
util/DNSQE/xgetua.f
commit 68b72b2168ffafe9c7b9c90cc7b2259a92a6a9bb
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 24 08:57:41 2020 -0800
Convert Helmholtz EOS to C++ (#262)
EOS/helmholtz/Make.package
EOS/helmholtz/actual_eos.H
EOS/helmholtz/actual_eos_data.H
EOS/helmholtz/actual_eos_data.cpp
interfaces/eos_type.H
commit b4e02de79e5cade597b2d8a4a0bf4ff190df0d93
Merge: 291e30a4 b433808e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 10:46:27 2020 -0500
Merge branch 'development' into license
commit b433808ec07df0c942bc15382dce321ca4580b06
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 23 15:31:09 2020 -0800
Convert polytrope to C++ (#264)
EOS/polytrope/Make.package
EOS/polytrope/actual_eos.H
EOS/polytrope/actual_eos_data.H
EOS/polytrope/actual_eos_data.cpp
commit 35f7ab146bac2eee0a2984834cdab91bbe0f77fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 17:42:13 2020 -0500
get gamma_law compiling
skip unsupported tp for gamma_law
EOS/gamma_law/actual_eos.H
unit_test/test_eos_C/main.cpp
commit ddbd42f2764561beb32f825c2d2ccbfa0ca9d548
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 17:37:27 2020 -0500
put some guards for gamma_law
unit_test/test_eos/eos_util.F90
commit 0d233cc43890c01a12eb329015e47e60663edb6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 23 14:28:41 2020 -0800
Convert gamma_law to C++ (#263)
EOS/gamma_law/Make.package
EOS/gamma_law/actual_eos.H
EOS/gamma_law/actual_eos_data.H
EOS/gamma_law/actual_eos_data.cpp
commit 74b8f4d2b9a1c25f40575fa6f0bbc3898cfc0fcd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 17:17:01 2020 -0500
the probin as ignored because we used the wrong name for it
also now add a polytrope inputs/probin
unit_test/test_eos/input_eos
unit_test/test_eos/input_eos.polytrope
unit_test/test_eos/probin.polytrope
commit d16bc9e863055ea7ad20fd9e51b9b0ea925b11fb
Merge: b33b68de 58e3052d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 16:07:36 2020 -0500
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit b33b68dedaddbab1ea25992e5e4ef34ff102ffb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 23 16:07:24 2020 -0500
example of string passing of parameters
interfaces/extern_probin.template
unit_test/test_parameters/_parameters
unit_test/test_parameters/main.cpp
unit_test/test_parameters/probin
commit 58e3052dd057b01c5b7ca69d463be418de05dd1d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 23 10:57:28 2020 -0800
Add const for safety
EOS/eos_composition.H
commit bc1e828ab2189e60e50811e4dd7a226d422d8ba5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 22 18:36:21 2020 -0800
Use std::abs to avoid unintentional casting
unit_test/test_eos_C/main.cpp
commit 98287ff1b5c4f8a21b9785be5ec1cbe0989fdd50
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 22 18:35:16 2020 -0800
Handle the n_cell == 1 case in test_eos
unit_test/test_eos/eos_util.F90
unit_test/test_eos_C/main.cpp
commit 0de37d13d8cf2fcd6a616199a8a1e59f292d42f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 12:04:45 2020 -0500
fix header include
Make.Microphysics
commit c38e9b98d810232219405326028c241dffb4b42b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 22 08:34:51 2020 -0800
Need to define extern variables
interfaces/Make.package
interfaces/eos.H
interfaces/eos_data.H
interfaces/eos_data.cpp
interfaces/eos_type.H
commit d3bf37b4102ec65b342adbc5c828c8e44435873b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 11:24:48 2020 -0500
move constants into Make.Microphysics_extern
Make.Microphysics
Make.Microphysics_extern
commit 7a2e6caad2ab9355b238f59a5efcd80266be38ea
Merge: 5ebd0b08 8d3a4086
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 08:27:32 2020 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 5ebd0b08fbab6951a82f25db64f784533c9c1d83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 22 08:26:22 2020 -0500
rename files as test_eos_C.XXX
unit_test/test_eos_C/main.cpp
commit 8d3a40869e4ab85b8a70a74e4e9c06f12c512e44
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 21 20:26:16 2020 -0800
Real -> amrex::Real
interfaces/eos_type.H
commit b1d2ccfcbcae1fd3c9e41932e210ce45c789dfe3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 21 10:54:52 2020 -0500
update changes
CHANGES.md
commit 659a6caaf9980b8315ff54547a9bad08dd1c09a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 21 10:49:46 2020 -0500
create a C++ EOS interface (#246)
This creates a C++ interface for the gamma_law_general EOS as well as a pure C++ unit test, test_eos_C.
Co-authored-by: Max Katz <maxpkatz@gmail.com>
EOS/Make.package
EOS/eos_composition.H
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/actual_eos.H
constants/Make.package
constants/fundamental_constants.H
interfaces/Make.package
interfaces/eos.H
interfaces/eos_F.H
interfaces/eos_override.H
interfaces/eos_type.F90
interfaces/eos_type.H
interfaces/network.H
networks/general_null/network_header.template
sphinx_docs/source/cxx.rst
sphinx_docs/source/index.rst
unit_test/test_eos_C/GNUmakefile
unit_test/test_eos_C/Make.package
unit_test/test_eos_C/README
unit_test/test_eos_C/_parameters
unit_test/test_eos_C/input_eos
unit_test/test_eos_C/main.cpp
unit_test/test_eos_C/probin
unit_test/test_eos_C/test_eos.H
unit_test/test_eos_C/test_eos_F.H
unit_test/test_eos_C/unit_test.f90
unit_test/test_eos_C/variables.H
unit_test/test_eos_C/variables.cpp
commit bafff355959ce1226beb51e0b2f04a3a5e337e91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 20 11:21:48 2020 -0500
restructure makefiles (#261)
This reorganizes the makefiles to separate out the bits that include all of the various Microphysics modules. This will make it easier for Castro to simply include Make.Microphysics_extern instead of duplicating it all on its own.
Make.CVODE
Make.Microphysics
Make.Microphysics_extern
integration/Make.package
networks/Make.package
networks/general_null/Make.package
commit bac30b98e9f4746eee7f47a2ffdf12a6d3d868d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 20 10:31:26 2020 -0500
add the aux names and 1/aion to the network auto generated stuff (#258)
this adds the aux names to the C++ header, and 1/aion to all of the autogenerated net stuff (including general_null).
Closes #252 #254
interfaces/network.F90
networks/general_null/gammalaw_aux.net
networks/general_null/network.template
networks/general_null/network_header.template
networks/general_null/network_properties.template
networks/general_null/write_network.py
commit 008e6491daa6862b18e855ccef1945c28c5c3bb2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 18 21:18:03 2020 -0500
regenerate via pynucastro
networks/ignition_reaclib/C-burn-simple/_parameters
networks/ignition_reaclib/C-burn-simple/actual_burner.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/C-test/_parameters
networks/ignition_reaclib/C-test/actual_burner.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/physical_constants.f90
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/physical_constants.f90
networks/nova/reaclib_rates.F90
networks/nova/table_rates.F90
networks/sn160/_parameters
networks/sn160/actual_burner.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/sn160/physical_constants.f90
networks/sn160/reaclib_rates.F90
networks/sn160/table_rates.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/physical_constants.f90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/physical_constants.f90
networks/subch2/reaclib_rates.F90
networks/subch2/table_rates.F90
commit 132463e3a5551dd89f74f8ecc5a973033f0ae13f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 18 18:25:26 2020 -0500
fix dependencies
networks/general_null/Make.package
commit 4e6e736a28770d406d0bbeab1e6987ef59a43e73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 17 08:47:38 2020 -0500
remove unused tfactors (#259)
rates/tfactors.F90
commit b8930d5f12638c8c07194730df4af9a70cf95901
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 16 18:44:51 2020 -0500
get general null stuff building again
it doesn't (currently) use network_properties.F90, so we need to
if around that in the makefile
networks/Make.package
networks/general_null/Make.package
commit 0dccd94c03461ded977097444c396f6f48e3f949
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 16 18:16:09 2020 -0500
remove the C++ parameter autogenerated stuff with clean
Make.Microphysics
commit 598408c6644942eafb0bf7c157657a7971537bc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 16 15:09:42 2020 -0500
autogenerate network_properties.{F90,H} (#253)
This adds a rule to networks/Make.package that generates the files network_properties.F90 and network_properties.H at build time. You can set the location to output to by defining NETWORK_HEADERS_DIR. Note: the pynucastro generated networks will need to be updated to output the .net file.
Make.Microphysics
networks/Make.package
networks/aprox13/network_properties.F90
networks/aprox13/network_properties.H
networks/aprox19/network_properties.F90
networks/aprox19/network_properties.H
networks/aprox21/network_properties.F90
networks/aprox21/network_properties.H
networks/breakout/network_properties.F90
networks/breakout/network_properties.H
networks/ignition_chamulak/network_properties.F90
networks/ignition_chamulak/network_properties.H
networks/ignition_simple/network_properties.F90
networks/ignition_simple/network_properties.H
networks/iso7/network_properties.F90
networks/iso7/network_properties.H
networks/powerlaw/network_properties.F90
networks/powerlaw/network_properties.H
networks/rprox/network_properties.F90
networks/rprox/network_properties.H
networks/subch/network_properties.H
networks/triple_alpha_plus_cago/network_properties.F90
networks/triple_alpha_plus_cago/network_properties.H
networks/update_headers.py
networks/xrb_simple/network_properties.F90
networks/xrb_simple/network_properties.H
commit 19008da367d59966ff64aaae09b44135e4a194e8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 15:28:17 2020 -0800
Detabify
networks/aprox13/test-cpp/main.cpp
networks/aprox19/test-cpp/main.cpp
networks/aprox21/test-cpp/main.cpp
networks/ignition_simple/test-cpp/main.cpp
networks/iso7/test-cpp/main.cpp
rates/aprox_rates.F90
commit 668006d21d9eff0020b3fc6e0d70d92b40877e08
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 15 08:53:49 2020 -0800
Update .gitignore
.gitignore
commit 25a276627f7f9f1be3b0162ff03bdfd72be38afc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 15 11:48:48 2020 -0500
C++ parameters (#247)
Gain access to the Microphysics runtime parameters in C++. This includes a new unit test, test_parameters, that tests the access from Fortran and C++.
Make.Microphysics
interfaces/extern_probin.template
unit_test/test_parameters/GNUmakefile
unit_test/test_parameters/Make.package
unit_test/test_parameters/_parameters
unit_test/test_parameters/inputs
unit_test/test_parameters/main.cpp
unit_test/test_parameters/probin
unit_test/test_parameters/test_parameters.F90
unit_test/test_parameters/test_parameters.H
unit_test/test_parameters/test_parameters_F.H
unit_test/test_parameters/unit_test.f90
unit_test/test_react/_parameters
unit_test/test_react/test_network_combinations.py
commit 16119ed19a67d1035be28802f6b27201d1b40c54
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 10:13:03 2020 -0800
Smooth out the radiation pressure at low densities (#235)
added an option to disable radiation pressure below some threshold.
CHANGES.md
EOS/helmholtz/_parameters
EOS/helmholtz/actual_eos.F90
commit 682ab2690a1c68c06c6fb70201dc802ac44a2e93
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Feb 14 05:35:08 2020 -0800
Allow general_null network to be written to custom directory (#249)
networks/general_null/Make.package
commit b0cbc732ca30f3553460f41cf43171cc0541e90b
Merge: 7746ea93 4901f403
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 14:03:00 2020 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 7746ea93424d6be123fc92fdf35ef25409d32994
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 14:02:49 2020 -0500
revert change
networks/breakout/network_properties.H
commit 5a224ce352a157a77006aa5f672875b953e9687d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 14:01:37 2020 -0500
add network_name
networks/breakout/actual_network.f90
networks/breakout/network_properties.H
commit 4901f403486ae72d481e7908a2f09c69473ae5c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 11:45:38 2020 -0500
add network_name
networks/powerlaw/actual_network.f90
commit d193a6103f8a2680ef1afd494f83a5160bd28668
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 11:42:31 2020 -0500
add the powerlaw conductivty
conductivity/powerlaw/Make.package
conductivity/powerlaw/_parameters
conductivity/powerlaw/powerlaw_conductivity.F90
commit 731be424cb899aacfcb8c531a290eea41cd2e615
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Feb 11 11:41:45 2020 -0500
add the constant conductivity and constant opacity modules
conductivity/constant/Make.package
conductivity/constant/_parameters
conductivity/constant/constant_conductivity.F90
conductivity/constant_opacity/Make.package
conductivity/constant_opacity/_parameters
conductivity/constant_opacity/constant_conductive_opacity.F90
commit 20588b71235e5bfef442e4c63acf9e669c2e3d6f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 15:00:37 2020 -0800
Copy over some microphysics from Castro (#248)
This includes the opacity and viscosity directories, as well as two toy equations of state (gamma_law and rad_power_law). A few interfaces are updated, including the EOS, burner, and conductivity.
EOS/gamma_law/Make.package
EOS/gamma_law/_parameters
EOS/gamma_law/gamma_law.F90
EOS/rad_power_law/Make.package
EOS/rad_power_law/_parameters
EOS/rad_power_law/rad_power_law.F90
interfaces/Make.package
interfaces/burner.F90
interfaces/conductivity.F90
interfaces/eos.F90
opacity/Readme
opacity/breakout/Make.package
opacity/breakout/opacity_table_module.F90
opacity/rad_power_law/Make.package
opacity/rad_power_law/_parameters
opacity/rad_power_law/opacity_table_module.F90
viscosity/constant/Make.package
viscosity/constant/_parameters
viscosity/constant/constant_viscosity.f90
commit bb08d212dc054478ab9105ec1a090c7fcfef8bc1
Merge: 587e2bd3 8f7621e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 9 14:21:34 2020 -0500
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit 587e2bd323b5d0f529db6a585667b9120fbacf93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 9 14:21:07 2020 -0500
fix spec names and switch to arrays
networks/aprox13/network_properties.H
networks/aprox19/network_properties.H
networks/aprox21/network_properties.H
networks/breakout/network_properties.H
networks/general_null/network_header.template
networks/general_null/write_network.py
networks/ignition_chamulak/network_properties.H
networks/ignition_simple/network_properties.H
networks/iso7/network_properties.H
networks/powerlaw/network_properties.H
networks/rprox/network_properties.H
networks/triple_alpha_plus_cago/network_properties.H
networks/xrb_simple/network_properties.H
commit 8f7621e0d001b7ee2b016ce142c7348ea122618c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 11:15:54 2020 -0800
double precision -> amrex_real
networks/aprox13/network_properties.F90
networks/aprox19/network_properties.F90
networks/aprox21/network_properties.F90
networks/breakout/network_properties.F90
networks/general_null/network.template
networks/general_null/network_properties.template
networks/ignition_chamulak/network_properties.F90
networks/ignition_simple/network_properties.F90
networks/iso7/network_properties.F90
networks/powerlaw/network_properties.F90
networks/rprox/network_properties.F90
networks/triple_alpha_plus_cago/network_properties.F90
networks/xrb_simple/network_properties.F90
commit 05a8c67bbc0d3c23d0a6dbb824edd35fb04fd7e7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 9 11:07:33 2020 -0800
Remove some stray attributes(managed)
networks/aprox13/actual_network.F90
networks/rprox/actual_network.F90
networks/triple_alpha_plus_cago/actual_network.F90
commit dbe9c12316e8b70d27667d0eafc96d808064933c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Feb 9 11:47:27 2020 -0500
remove stray character
networks/powerlaw/actual_network.f90
commit 744d74576b067be5393d407687a0cd56877c2fb0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 20:44:42 2020 -0500
add AMReX_Array.H header
networks/aprox13/network_properties.H
networks/aprox19/network_properties.H
networks/aprox21/network_properties.H
networks/breakout/network_properties.H
networks/general_null/network_header.template
networks/ignition_chamulak/network_properties.H
networks/ignition_simple/network_properties.H
networks/iso7/network_properties.H
networks/powerlaw/network_properties.H
networks/rprox/network_properties.H
networks/triple_alpha_plus_cago/network_properties.H
networks/xrb_simple/network_properties.H
commit eb93703fc176649f8c4ed4df5c872960994a23c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 20:35:28 2020 -0500
Real -> amrex::Real
networks/aprox13/network_properties.H
networks/aprox19/network_properties.H
networks/aprox21/network_properties.H
networks/breakout/network_properties.H
networks/general_null/network_header.template
networks/ignition_chamulak/network_properties.H
networks/ignition_simple/network_properties.H
networks/iso7/network_properties.H
networks/powerlaw/network_properties.H
networks/rprox/network_properties.H
networks/triple_alpha_plus_cago/network_properties.H
networks/xrb_simple/network_properties.H
commit fd8bfe25bb2d649fa947eced9f141a6046c5bd96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 20:01:11 2020 -0500
update changes
CHANGES.md
commit 8a347c77072e5db7947d3569abc06c766b526ca7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 19:57:29 2020 -0500
add nuclei into to the C++ header (#244)
This renames the actual_network.H file to network_properties.H and updates it to include aion and zion. A .net file is present in each network now that creates the nuclei information for both Fortran and C++. This is done by running the top-level update_headers.py script. That writes actual_network.H and a new module, network_parameters.F90. The actual_network.F90 has been rewritten to use network_parameters.F90.
networks/aprox13/Make.package
networks/aprox13/actual_network.F90
networks/aprox13/actual_network.H
networks/aprox13/aprox13.net
networks/aprox13/network_properties.F90
networks/aprox13/network_properties.H
networks/aprox19/Make.package
networks/aprox19/actual_network.F90
networks/aprox19/actual_network.H
networks/aprox19/aprox19.net
networks/aprox19/network_properties.F90
networks/aprox19/network_properties.H
networks/aprox21/Make.package
networks/aprox21/actual_network.F90
networks/aprox21/actual_network.H
networks/aprox21/aprox21.net
networks/aprox21/network_properties.F90
networks/aprox21/network_properties.H
networks/breakout/Make.package
networks/breakout/actual_network.H
networks/breakout/actual_network.f90
networks/breakout/breakout.net
networks/breakout/network_properties.F90
networks/breakout/network_properties.H
networks/general_null/Make.package
networks/general_null/actual_network.H
networks/general_null/network_header.template
networks/general_null/network_properties.template
networks/general_null/write_network.py
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_network.F90
networks/ignition_chamulak/actual_network.H
networks/ignition_chamulak/ignition_chamulak.net
networks/ignition_chamulak/network_properties.F90
networks/ignition_chamulak/network_properties.H
networks/ignition_reaclib/C-burn-simple/actual_network.H
networks/ignition_reaclib/C-test/actual_network.H
networks/ignition_reaclib/URCA-simple/actual_network.H
networks/ignition_simple/Make.package
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_network.H
networks/ignition_simple/ignition_simple.net
networks/ignition_simple/network_properties.F90
networks/ignition_simple/network_properties.H
networks/iso7/Make.package
networks/iso7/actual_network.F90
networks/iso7/actual_network.H
networks/iso7/iso7.net
networks/iso7/network_properties.F90
networks/iso7/network_properties.H
networks/nova/actual_network.H
networks/powerlaw/Make.package
networks/powerlaw/actual_network.H
networks/powerlaw/actual_network.f90
networks/powerlaw/network_properties.F90
networks/powerlaw/network_properties.H
networks/powerlaw/powerlaw.net
networks/rprox/Make.package
networks/rprox/actual_network.F90
networks/rprox/actual_network.H
networks/rprox/network_properties.F90
networks/rprox/network_properties.H
networks/rprox/rprox.net
networks/sn160/actual_network.H
networks/subch/actual_network.H
networks/subch/network_properties.H
networks/subch2/actual_network.H
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_network.F90
networks/triple_alpha_plus_cago/actual_network.H
networks/triple_alpha_plus_cago/network_properties.F90
networks/triple_alpha_plus_cago/network_properties.H
networks/triple_alpha_plus_cago/triple_alpha_plus_cago.net
networks/update_headers.py
networks/xrb_simple/Make.package
networks/xrb_simple/actual_network.H
networks/xrb_simple/actual_network.f90
networks/xrb_simple/network_properties.F90
networks/xrb_simple/network_properties.H
networks/xrb_simple/xrb_simple.net
commit b4640f8f033ba774f96f86b3449ac2463bfb8346
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 19:51:20 2020 -0500
update changes
CHANGES.md
commit f5927924ee13b9d72cf412735723f74783d14007
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 19:50:38 2020 -0500
move core interfaces to the interfaces/ dir (#240)
this allows other codes to more easily hook into Microphysics
Make.Microphysics
constants/Make.package
constants/constants_cgs.f90
interfaces/Make.package
interfaces/conductivity.F90
interfaces/eos.F90
interfaces/eos_override.F90
interfaces/extern_probin.template
interfaces/microphysics.F90
interfaces/network.F90
unit_test/Make.package
commit a0e404fdf35879fbbfdec006e1aa98cd1804a10c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 19:48:34 2020 -0500
update changes
CHANGES.md
commit 20ee38aee80a602285f3a8b9de84cd24a61dc02d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 8 19:46:21 2020 -0500
remove old build system stuff (#212)
This removes the old *.mak files that are from the FBoxLib build system. We are not using these and not keeping them up to date.
EOS/GPackage.mak
EOS/breakout/GPackage.mak
EOS/gamma_law_general/GPackage.mak
EOS/helmholtz/GPackage.mak
EOS/multigamma/GPackage.mak
EOS/polytrope/GPackage.mak
EOS/stellarcollapse/GPackage.mak
EOS/ztwd/GPackage.mak
GMicrophysics.mak
conductivity/GPackage.mak
conductivity/stellar/GPackage.mak
integration/BS/GPackage.mak
integration/GPackage.mak
integration/VBDF/GPackage.mak
integration/VODE/GPackage.mak
integration/VODE/cuVODE/source/GPackage.mak
integration/utils/GPackage.mak
interfaces/GPackage.mak
networks/ECSN/GPackage.mak
networks/GNetwork.mak
networks/GPackage.mak
networks/aprox13/GPackage.mak
networks/aprox13/test/GPackage.mak
networks/aprox19/GPackage.mak
networks/aprox21/GPackage.mak
networks/breakout/GPackage.mak
networks/general_null/GPackage.mak
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/test/GPackage.mak
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-test/GPackage.mak
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_simple/GPackage.mak
networks/ignition_simple/test/GPackage.mak
networks/iso7/GPackage.mak
networks/nova/GPackage.mak
networks/powerlaw/GPackage.mak
networks/rprox/GPackage.mak
networks/rprox/test/GPackage.mak
networks/sn160/GPackage.mak
networks/subch/GPackage.mak
networks/subch2/GPackage.mak
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/test/GPackage.mak
networks/xrb_simple/GPackage.mak
networks/xrb_simple/test/GPackage.mak
neutrinos/GPackage.mak
rates/GPackage.mak
screening/GPackage.mak
unit_test/GPackage.mak
unit_test/burn_cell/GPackage.mak
unit_test/test_reaclib_rates/GPackage.mak
util/BLAS/GPackage.mak
util/DNSQE/GPackage.mak
util/GPackage.mak
util/LINPACK/GPackage.mak
util/cj_detonation/GPackage.mak
util/eval_rhs/GPackage.mak
commit 30e6cb54584010f24c29b5f132fcd839413bbb51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 12:19:51 2020 -0500
update F90 build system
EOS/GPackage.mak
commit 369624664df738552b0e736046b7a76617755512
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 12:18:10 2020 -0500
fix compilation
networks/general_null/actual_rhs.f90
networks/general_null/network.template
commit eff839a23a0e4416c691184f6904b43e6d745cd0
Merge: 831c8565 a5bb8d24
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Feb 4 14:54:08 2020 -0800
Merge pull request #241 from starkiller-astro/compiler_warnings
clean up some compiler warnings
commit 831c8565fb26fd5ac9945a6caa48f72b541fe863
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 3 15:31:34 2020 -0500
fix plotfile variable name
unit_test/test_eos/variables.F90
commit 9b1bc259ffe5c16f75978584ea191118391aa642
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Feb 1 13:08:17 2020 -0500
update changes
CHANGES.md
commit a5bb8d24982c62fa1e70c43669ff25fb3c3a9f02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 20:00:01 2020 -0500
fix some compilation problems
EOS/helmholtz/actual_eos.F90
commit f8b89ad13bd7d76ee4b33849b8feb3c435b83193
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 19:13:52 2020 -0500
more warnings
EOS/composition.F90
commit e5d5b14c8360a530c4c86efd51b98a152589e1ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 27 19:11:20 2020 -0500
address some compiler warnings
EOS/helmholtz/actual_eos.F90
commit 4774a8bd4c672163048b468e84de344e4a438e4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 26 14:42:29 2020 -0500
add a C++ header with the network size
networks/ECSN/actual_network.H
networks/aprox13/actual_network.H
networks/aprox19/actual_network.H
networks/aprox21/actual_network.H
networks/breakout/actual_network.H
networks/general_null/actual_network.H
networks/ignition_chamulak/actual_network.H
networks/ignition_reaclib/C-burn-simple/actual_network.H
networks/ignition_reaclib/C-test/actual_network.H
networks/ignition_reaclib/URCA-simple/actual_network.H
networks/ignition_simple/actual_network.H
networks/iso7/actual_network.H
networks/nova/actual_network.H
networks/powerlaw/actual_network.H
networks/rprox/actual_network.H
networks/sn160/actual_network.H
networks/subch/actual_network.H
networks/subch2/actual_network.H
networks/triple_alpha_plus_cago/actual_network.H
networks/xrb_simple/actual_network.H
commit 5f8f55045f33af312e6b72eb369951afd23c15fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jan 20 18:32:26 2020 -0800
Add acc routine markings
EOS/helmholtz/actual_eos.F90
commit 207dfc21498da6cc5cf7e04fb6c3a8bae026fa14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jan 11 21:28:37 2020 -0500
get this compiling with latest burn_t
unit_test/burn_cell_C/burn_cell.F90
commit 6fa3b80210c7db4f0878beea34d9f4fc1ae3f6cb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Jan 8 11:43:45 2020 -0800
Add script for calling the integrator on a set of inputs.
python_library/StarKiller/StarKiller/examples/call_integrator.py
commit 9d05a59d327856d0045add4710ad8dab43315248
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Jan 8 08:48:48 2020 -0800
Regenerate from pynucastro to fix compilation.
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
commit 0bf83ebb4d83bafb5e432a744298c98a01eb5d2b
Merge: 8b18b52b 89ab52ac
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Jan 8 07:49:58 2020 -0800
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 89ab52ac3a368e5bec6c4e3460849de967133840
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jan 7 18:29:16 2020 -0800
Regenerate Urca network to re-enable the bugfix from d4f2a543b4e2e429c565b3cb0dab7869d68b3f92 along with latest Microphysics changes.
networks/ignition_reaclib/URCA-simple/_parameters
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
commit 0d7530eb1c0ca9c7b50f34b7ed6d4dcabd095c25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 6 21:34:52 2020 -0500
update some nets to the last pynucastro
networks/nova/_parameters
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/reaclib_rates.F90
networks/nova/table_rates.F90
networks/subch/_parameters
networks/subch/actual_burner.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/physical_constants.f90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
networks/subch2/_parameters
networks/subch2/actual_burner.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/physical_constants.f90
networks/subch2/reaclib_rates.F90
networks/subch2/table_rates.F90
commit a75441a8f85f37bc821bd8ab81c7a3accbd9b7d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 6 14:07:19 2020 -0500
remove
networks/ECSN/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/ECSN/net_work_zingale.ipynb
commit 7a98b705ea9ae7f35489be3e668f755352efb559
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 6 14:06:46 2020 -0500
update with Xinlongs development branch + the new_starkiller_format branch
networks/ECSN/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/ECSN/_parameters
networks/ECSN/actual_burner.F90
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/ecsn.png
networks/ECSN/inputs.burn_cell.VODE
networks/ECSN/physical_constants.f90
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
commit 56e54d9c99004c58a481e3266fdcffe7fd79d3a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jan 5 19:32:07 2020 -0500
remove dupe files, update to latest format
networks/nova/actual_burner.f90
networks/nova/actual_network.F90
networks/nova/actual_network.f90
networks/nova/actual_rhs.F90
networks/nova/actual_rhs.f90
networks/nova/physical_constants.f90
networks/nova/reaclib_rates.F90
networks/nova/reaclib_rates.f90
networks/nova/table_rates.F90
networks/nova/table_rates.f90
commit 4a38768ebe5a53420561e6e2a2c74398d232ce1a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 1 13:45:48 2020 -0500
update changes1
CHANGES.md
commit 930626c34b4f657c785c766ef4ba257af4cf0ec7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 31 20:00:56 2019 -0500
update CHANGES
CHANGES.md
commit 59e53f9b9703a059d7acd45e7a7d7eceb6e691f5
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 19 16:15:21 2019 -0800
Use jac instead of referencing now nonexistent state % sparse_jac in jacobian sparsity module.
integration/utils/jacobian_sparsity.F90
commit d28bcddd44341c73a78e15fdb9fde3e74e972345
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Thu Dec 19 11:12:30 2019 -0500
Convert all floats to _rt (#239)
This converts all values with decimal points in them to be of the form #.#e#_rt
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
conductivity/stellar/stellar_conductivity.F90
integration/BS/stiff_ode.F90
integration/BS/test/test.f90
integration/VBDF/bdf.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE/cuVODE/source/cuvode.F90
networks/aprox13/test-cpp/testburn.f90
networks/aprox19/actual_rhs.F90
networks/aprox19/test-cpp/testburn.f90
networks/aprox21/actual_rhs.F90
networks/aprox21/test-cpp/testburn.f90
networks/ignition_simple/test-cpp/testburn.f90
networks/iso7/actual_rhs.F90
networks/iso7/test-cpp/testburn.f90
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/reaclib_rates.F90
networks/nova/table_rates.F90
networks/rprox/test/testburn.f90
networks/xrb_simple/actual_network.f90
neutrinos/sneut5.F90
rates/aprox_rates.F90
screening/screen.F90
unit_test/test_eos/eos_util.F90
unit_test/test_sdc/react_zones.F90
util/DNSQE/test/test.f90
util/cj_detonation/main.f90
commit e7dfd7049d581744f4f12a1081ff767a5d71982a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 17 14:21:30 2019 -0500
d -> e_rt
networks/nova/reaclib_rates.f90
networks/powerlaw/actual_network.f90
rates/aprox_rates.F90
util/code_checker/code_checker.py
commit 74fb3f50b5673b75565cd32a5409b50c4f20b3fd
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 17 13:52:58 2019 -0500
revert rates file
rates/aprox_rates.F90
commit 1f5f373545283b441f41cb91d11d2db19e3cec59
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 17 13:33:56 2019 -0500
dexp -> exp and dlog10 -> log10
EOS/gamma_law_general/actual_eos.F90
EOS/stellarcollapse/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_simple/actual_rhs.F90
networks/triple_alpha_plus_cago/rates_module.F90
rates/aprox_rates.F90
util/cj_detonation/main.f90
util/code_checker/code_checker.py
commit e66f774e9f5b43731274086919762fbf5dc48711
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 17 13:21:19 2019 -0500
add python script and fix function return types
EOS/ztwd/actual_eos.F90
util/code_checker/code_checker.py
commit 37c6e395cdd332f0b8451d71d89f364a86628da1
Merge: a69b4cb7 d44e8052
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 17 13:06:53 2019 -0500
git couldn't merge the rates properly
commit d44e805232ba50c2b32fe54dfa20754c01b4b5e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 17 13:03:05 2019 -0500
run the dpconvert.py script to address precision issues (#237)
EOS/breakout/actual_eos.F90
EOS/composition.F90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/multigamma/composition.F90
EOS/polytrope/actual_eos.F90
EOS/stellarcollapse/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
EOS/ztwd/actual_eos.F90
conductivity/stellar/stellar_conductivity.F90
integration/BS/bs_integrator.F90
integration/BS/bs_integrator_sdc.F90
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/numerical_jacobian_sdc.f90
integration/BS/stiff_ode.F90
integration/BS/test/f_rhs.f90
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_rpar.F90
integration/CVODE/cvode_type.F90
integration/VBDF/bdf.f90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VBDF/vbdf_rpar.F90
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_dewset.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/source/linpack_module.F90
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuVODE/test/vode_rhs.F90
integration/VODE/cuVODE/test/vode_rpar.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_integrator_true_sdc.F90
integration/VODE/vode_rhs_true_sdc.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type_simplified_sdc.F90
integration/integrator.F90
integration/integrator_sdc.F90
integration/utils/jacobian_sparsity.F90
integration/utils/network_rhs.F90
integration/utils/nonaka_plot.f90
integration/utils/numerical_jacobian_sdc.f90
integration/utils/temperature_integration.F90
networks/ECSN/actual_burner.F90
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/physical_constants.f90
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/aprox13/actual_burner.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox13/test-cpp/testburn.f90
networks/aprox13/test-cpp/testjacobian.f90
networks/aprox13/test/testburn.f90
networks/aprox19/actual_burner.F90
networks/aprox19/actual_network.F90
networks/aprox19/actual_rhs.F90
networks/aprox19/test-cpp/testburn.f90
networks/aprox19/test-cpp/testjacobian.f90
networks/aprox21/actual_burner.F90
networks/aprox21/actual_network.F90
networks/aprox21/actual_rhs.F90
networks/aprox21/test-cpp/testburn.f90
networks/aprox21/test-cpp/testjacobian.f90
networks/breakout/actual_burner.f90
networks/breakout/actual_network.f90
networks/breakout/actual_rhs.f90
networks/general_null/actual_burner.f90
networks/general_null/actual_rhs.f90
networks/ignition_chamulak/actual_burner.F90
networks/ignition_chamulak/actual_network.F90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_chamulak/test/eval.f90
networks/ignition_reaclib/C-burn-simple/actual_burner.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/C-test/actual_burner.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/physical_constants.f90
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_simple/actual_burner.F90
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_rhs.F90
networks/ignition_simple/test-cpp/testburn.f90
networks/ignition_simple/test/testjacobian.f90
networks/iso7/actual_burner.F90
networks/iso7/actual_network.F90
networks/iso7/actual_rhs.F90
networks/iso7/test-cpp/testburn.f90
networks/iso7/test-cpp/testjacobian.f90
networks/nova/actual_burner.f90
networks/nova/actual_network.f90
networks/nova/actual_rhs.f90
networks/nova/physical_constants.f90
networks/nova/reaclib_rates.f90
networks/nova/table_rates.f90
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_rhs.f90
networks/rate_type.f90
networks/rprox/actual_burner.F90
networks/rprox/actual_network.F90
networks/rprox/actual_rhs.F90
networks/rprox/rates_module.F90
networks/rprox/test/eval.f90
networks/rprox/test/testburn.f90
networks/rprox/tfactors.F90
networks/sn160/actual_burner.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/sn160/physical_constants.f90
networks/sn160/reaclib_rates.F90
networks/sn160/table_rates.F90
networks/subch/actual_burner.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/physical_constants.f90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
networks/subch2/actual_burner.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/physical_constants.f90
networks/subch2/reaclib_rates.F90
networks/subch2/table_rates.F90
networks/triple_alpha_plus_cago/actual_burner.F90
networks/triple_alpha_plus_cago/actual_network.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/dydt.F90
networks/triple_alpha_plus_cago/test/testjacobian.f90
networks/xrb_simple/actual_burner.f90
networks/xrb_simple/actual_network.f90
networks/xrb_simple/actual_rhs.f90
neutrinos/sneut5.F90
python_library/starkiller_initialization.f90
rates/aprox_rates.F90
rates/tfactors.F90
screening/screen.F90
unit_test/burn_cell/main.f90
unit_test/burn_cell_C/burn_cell.F90
unit_test/conductivity.F90
unit_test/eos.F90
unit_test/eos_override.F90
unit_test/microphysics.F90
unit_test/test_cvode_react/react_utils.F90
unit_test/test_eos/eos_util.F90
unit_test/test_reaclib_rates/main.f90
unit_test/test_react/variables.F90
unit_test/test_sdc/variables.f90
util/DNSQE/test/test.f90
util/esum_module.F90
util/microphysics_math.F90
util/test/bl_error.f90
util/test/bl_types.f90
commit 9332c4d30b9e5771544e0ba68d14c40edb7ced60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 17 09:18:51 2019 -0500
set the species
unit_test/test_react/probin.reaclib_cburn.BS
commit 779cdd0aa8f6d1dfe913eff5c417a9e56d8b45be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 16 19:28:37 2019 -0500
add network_name
networks/ignition_chamulak/actual_network.F90
networks/ignition_simple/actual_network.F90
commit 997d5dcfba397ec8aa8fce4017c2089692c361f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 16 17:09:55 2019 -0500
update with network name:
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/nova/20180319default2
networks/nova/_parameters
networks/nova/actual_burner.F90
networks/nova/actual_network.F90
networks/nova/actual_rhs.F90
networks/nova/inputs.burn_cell.VODE
networks/nova/reaclib_rate_metadata.dat
networks/nova/reaclib_rates.F90
networks/nova/table_rates.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/subch/actual_network.F90
networks/subch2/actual_network.F90
commit c3fb95d334f119f3675044bdc3897bc666b24ed9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 16 16:15:06 2019 -0500
add alice
.zenodo.json
commit a69b4cb7c9078c0f054bc13ef816c7e13d7137fa
Merge: bcaba170 44a9b4ad
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Dec 16 11:38:47 2019 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 8b18b52bb667adf265ff5660b5e1c9522ff014d9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Dec 14 20:56:21 2019 -0800
Delete trailing whitespaces.
python_library/StarKiller/StarKiller/models/amrex_astro.py
commit 44a9b4ad384f49cec029eef4ce214fe567627ed5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 14 15:56:34 2019 -0500
remove the jac and ydot from burn_t (#220)
This removes jac and ydot from the burn_t to save on memory and copying.
Make.Microphysics
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/stiff_ode.F90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs_simplified_sdc.F90
integration/VODE/vode_type.F90
integration/VODE/vode_type_simplified_sdc.F90
integration/utils/jacobian_sparsity.F90
integration/utils/network_rhs.F90
integration/utils/nonaka_plot.f90
integration/utils/numerical_jacobian.F90
integration/utils/temperature_integration.F90
interfaces/burn_type.F90
networks/ECSN/20180319default2
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_rhs.F90
networks/breakout/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/_parameters
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/C-test/_parameters
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/reaclib_rate_metadata.dat
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/URCA-simple/_parameters
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_simple/actual_rhs.F90
networks/iso7/actual_rhs.F90
networks/nova/GPackage.mak
networks/nova/Make.package
networks/nova/physical_constants.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_rhs.F90
networks/sn160/NETWORK_REQUIRES
networks/sn160/actual_rhs.F90
networks/sn160/table_rates.F90
networks/subch/Make.package
networks/subch/_parameters
networks/subch/actual_burner.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/physical_constants.f90
networks/subch/reaclib_rate_metadata.dat
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
networks/subch2/actual_rhs.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/xrb_simple/actual_rhs.f90
unit_test/test_react/GNUmakefile
commit bd605493c4ab833acc74c6251011d3634576dbe8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Dec 13 13:46:56 2019 -0800
more output diagnostics in burn_cell
added MAESTRO and initial Lagrangian test cases at the inner edge of the Si shell. Want to add the evolved CASTRO data as well at that same physical spot
unit_test/burn_cell_C/GNUmakefile
unit_test/burn_cell_C/burn_cell.F90
unit_test/burn_cell_C/inputs_aprox21_rot1
unit_test/burn_cell_C/inputs_aprox21_rot2
unit_test/burn_cell_C/probin_aprox21_rot1
unit_test/burn_cell_C/probin_aprox21_rot2
commit bcaba1709a3442ee7034eeca30d22788b5179d2f
Merge: 61f0bde1 616b7ff5
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Dec 12 09:47:42 2019 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 616b7ff56cfa0c7bf13448bb7d075e341f21ce83
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 11 14:41:50 2019 -0800
Change initialization safety checking a bit, print EOS, network name after initialization.
python_library/StarKiller/StarKiller/eos/eos.py
python_library/StarKiller/StarKiller/initialization/initialization.py
python_library/StarKiller/StarKiller/network/network.py
unit_test/network.F90
commit e56445773a5385259fc9e98b7756f76305cbb9aa
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 11 14:06:10 2019 -0800
Fix helmholtz initialization for python package. If not found, attempt to symlink it from MICROPHYSICS_HOME.
python_library/StarKiller/StarKiller/eos/eos.py
python_library/StarKiller/StarKiller/initialization/initialization.py
commit 29e289e1928e587367c53274de8eaac6b6cf25a9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 11 11:52:25 2019 -0800
StarKiller package fails gracefully if using the Helmholtz EOS and the table is not found.
python_library/StarKiller/StarKiller/eos/eos.py
python_library/StarKiller/StarKiller/initialization/initialization.py
unit_test/eos.F90
commit 69ed0c6633ad1a30549bc3517767be15847083a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 11 13:52:08 2019 -0500
remove the .so on realclean
python_library/GNUmakefile
commit bacc5dfe490848bb9ba7abad877582a170b65313
Merge: 462d6b54 16888ed4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 11 07:57:50 2019 -0800
Merge pull request #230 from starkiller-astro/python
Thanks!
commit 16888ed4a4aaadb01cb005a1d2f856febadbaa33
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 11 10:26:15 2019 -0500
move into a proper module
python_library/StarKiller/StarKiller/__init__.py
python_library/StarKiller/StarKiller/burner/BurnUtils.py
python_library/StarKiller/StarKiller/burner/__init__.py
python_library/StarKiller/StarKiller/eos/__init__.py
python_library/StarKiller/StarKiller/eos/eos.py
python_library/StarKiller/StarKiller/examples/Burn Cell.ipynb
python_library/StarKiller/StarKiller/examples/Burn-Subch.ipynb
python_library/StarKiller/StarKiller/examples/BurnProfile/Burn-Cell-Aprox21.ipynb
python_library/StarKiller/StarKiller/examples/BurnProfile/probin_aprox21
python_library/StarKiller/StarKiller/examples/ECSN/ECSN-Test.ipynb
python_library/StarKiller/StarKiller/examples/ECSN/ECSN-Test.pdf
python_library/StarKiller/StarKiller/examples/ECSN/eps_nuc_eos_compare.png
python_library/StarKiller/StarKiller/examples/ECSN/eps_nuc_network_compare.png
python_library/StarKiller/StarKiller/examples/ECSN/probin_ecsn
python_library/StarKiller/StarKiller/examples/Jacobian-Test-subch.ipynb
python_library/StarKiller/StarKiller/examples/Jacobian-Test.ipynb
python_library/StarKiller/StarKiller/examples/README.md
python_library/StarKiller/StarKiller/examples/StarKiller Notebook Test.ipynb
python_library/StarKiller/StarKiller/examples/Test-Aprox13.ipynb
python_library/StarKiller/StarKiller/examples/aprox13_sdc.py
python_library/StarKiller/StarKiller/examples/call_eos.py
python_library/StarKiller/StarKiller/examples/probin.ignition
python_library/StarKiller/StarKiller/examples/probin_aprox13
python_library/StarKiller/StarKiller/examples/probin_burn_subch
python_library/StarKiller/StarKiller/examples/rotating_star/.ipynb_checkpoints/Analyze-Model-checkpoint.ipynb
python_library/StarKiller/StarKiller/examples/rotating_star/15m_500_sec.hse.6400
python_library/StarKiller/StarKiller/examples/rotating_star/Analyze-Model.ipynb
python_library/StarKiller/StarKiller/examples/rotating_star/probin_aprox21
python_library/StarKiller/StarKiller/initialization/__init__.py
python_library/StarKiller/StarKiller/initialization/initialization.py
python_library/StarKiller/StarKiller/integration/__init__.py
python_library/StarKiller/StarKiller/integration/integration.py
python_library/StarKiller/StarKiller/integration/numerical_jacobian.py
python_library/StarKiller/StarKiller/integration/sdc.py
python_library/StarKiller/StarKiller/interfaces/__init__.py
python_library/StarKiller/StarKiller/interfaces/burn_type.py
python_library/StarKiller/StarKiller/interfaces/eos_type.py
python_library/StarKiller/StarKiller/models/__init__.py
python_library/StarKiller/StarKiller/models/amrex_astro.py
python_library/StarKiller/StarKiller/network/__init__.py
python_library/StarKiller/StarKiller/network/network.py
commit 61f0bde1ade12f796f9108395198a07a407af021
Merge: 33a62b31 462d6b54
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Dec 11 08:54:55 2019 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 462d6b5444a7a2a51551e63489a4550e5c843ae7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 10 14:05:06 2019 -0800
Add ydot plots. Remake with aprox21.
python_library/StarKiller/examples/rotating_star/Analyze-Model.ipynb
commit 33a62b31352f91de0019d02c39dcc0b9932a8405
Merge: 5dff66e4 45418040
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 10 16:20:51 2019 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 454180409163def3132e6eda2f9cffbc405e295f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 10 13:17:58 2019 -0800
Add analysis notebook for the rotating_star model.
python_library/StarKiller/examples/rotating_star/15m_500_sec.hse.6400
python_library/StarKiller/examples/rotating_star/Analyze-Model.ipynb
python_library/StarKiller/examples/rotating_star/probin_aprox21
commit 5dff66e438c8b9cab50550b48e519db420b9f2bc
Merge: db0b4716 c26b7e8b
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 10 12:20:28 2019 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit c26b7e8b3839761af7804bcc347ee04e1608fbf9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 10 08:03:40 2019 -0500
switch over to the new xn parameter format
unit_test/test_sdc/_parameters
unit_test/test_sdc/probin.aprox13
unit_test/test_sdc/react_zones.F90
unit_test/test_sdc/util.f90
unit_test/test_sdc/xin.aprox13
commit 1887b2897d0094de2353fa441f83697450220995
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 10 07:54:20 2019 -0500
remove xin_file
unit_test/test_react/probin.reaclib_cburn.BS
commit db0b4716e855ea467bdb05ccbb99e4ad03c9a962
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Dec 9 15:54:08 2019 -0500
redo rates
rates/aprox_rates.F90
commit 2cbf12b6ab9bd311ab8e6db89bc5defb065248aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 9 10:01:17 2019 -0500
sync up with the MAESTROeX version
interfaces/sdc_type.F90
commit fc1ca7741863d58cd7a28e48fc7cc561db0c2256
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 9 09:23:06 2019 -0500
update how composition is set
sphinx_docs/source/unit_tests.rst
commit ed80b7ba2acff2698f69a1eeca47dc0d8d4e8b32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 9 08:27:51 2019 -0500
update changes
CHANGES.md
unit_test/test_sdc/probin.aprox13
commit d0705d2933d221dd15c6653411168acfd9623d87
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 9 08:23:16 2019 -0500
get rid of the xin files for test_react (#211)
This does away with the composition input files xin.* in favor of computing the composition on the fly. The advantage of this is that we can easily change the size of the test to investigate scaling. There are now 3 runtime parameters (to be set in the &extern namelist): primary_species_1, primary_species_2, primary_species_3. These primary species will vary from X = 0.2 to X = 0.7 to 0.9 (depending on the number). Only one primary species varies at a time. The non-primary species will be set equally to share whatever fraction of 1 is not accounted for by the primary species mass fractions.
Note: tests will be completely different because we are completely changing the species info.
unit_test/test_react/_parameters
unit_test/test_react/probin.3alpha
unit_test/test_react/probin.3alpha.BS
unit_test/test_react/probin.3alpha.VBDF
unit_test/test_react/probin.aprox13
unit_test/test_react/probin.aprox13.burning_mode_0
unit_test/test_react/probin.aprox13.cvode_compare
unit_test/test_react/probin.aprox19
unit_test/test_react/probin.aprox19.burning_mode_0
unit_test/test_react/probin.aprox21
unit_test/test_react/probin.ignition
unit_test/test_react/probin.ignition.BS
unit_test/test_react/probin.ignition_chamulak
unit_test/test_react/probin.ignition_chamulak.BS
unit_test/test_react/probin.iso7
unit_test/test_react/probin.nova
unit_test/test_react/probin.reaclib_cburn
unit_test/test_react/probin.reaclib_ctest
unit_test/test_react/probin.reaclib_ctest.BS
unit_test/test_react/probin.reaclib_urca
unit_test/test_react/probin.reaclib_urca.BS
unit_test/test_react/probin.reaclib_urca_cfcvode
unit_test/test_react/probin.rprox
unit_test/test_react/probin.sn160
unit_test/test_react/probin.xrb_simple
unit_test/test_react/react_zones.F90
unit_test/test_react/util.f90
unit_test/test_react/xin.3alpha_plus_o
unit_test/test_react/xin.aprox13
unit_test/test_react/xin.aprox13.1
unit_test/test_react/xin.aprox13.128
unit_test/test_react/xin.aprox13.2
unit_test/test_react/xin.aprox13.256
unit_test/test_react/xin.aprox13.32
unit_test/test_react/xin.aprox13.64
unit_test/test_react/xin.aprox19
unit_test/test_react/xin.aprox21
unit_test/test_react/xin.ignition
unit_test/test_react/xin.ignition.128
unit_test/test_react/xin.ignition.32
unit_test/test_react/xin.ignition.64
unit_test/test_react/xin.iso7
unit_test/test_react/xin.nova
unit_test/test_react/xin.reaclib_cburn
unit_test/test_react/xin.reaclib_cburn.128
unit_test/test_react/xin.reaclib_cburn.32
unit_test/test_react/xin.reaclib_cburn.64
unit_test/test_react/xin.reaclib_ctest
unit_test/test_react/xin.reaclib_urca
unit_test/test_react/xin.reaclib_urca.256
unit_test/test_react/xin.reaclib_urca.32
unit_test/test_react/xin.reaclib_urca.64
unit_test/test_react/xin.rprox
unit_test/test_react/xin.sn160.16
unit_test/test_react/xin.xrb_simple
commit c0fe55e8b354c85f77ec4b80523989bf88e50006
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 9 07:51:52 2019 -0500
remove networks that are unmaintained and/or simply would not work (#224)
networks/MESA/Do_One_Zone_Burn.f90
networks/MESA/GPackage.mak
networks/MESA/NETWORK_REQUIRES
networks/MESA/Net-Files/carbon_burning.net
networks/MESA/Net-Files/carbon_burning_extended.net
networks/MESA/Net-Files/test_16_null.net
networks/MESA/Net-Files/test_2.net
networks/MESA/Net-Files/test_3.net
networks/MESA/Net-Files/test_approx19.net
networks/MESA/Net-Files/test_approx8.net
networks/MESA/Net-Files/test_ignition_simple.net
networks/MESA/Net-Files/test_triple_alpha.net
networks/MESA/README
networks/MESA/burn_solout.f90
networks/MESA/burner.f90
networks/MESA/get_mesa_ebin.f90
networks/MESA/net_utils.f90
networks/MESA/network.template.mesa
networks/MESA/scripts/compile-all-mods.sh
networks/MESA/scripts/compile-one-mod.sh
networks/MESA/setup_mesa_net.f90
networks/MESA/shutdown_mesa_net.f90
networks/MESA/write_network.py
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/Make.package
networks/ignition_simple_SDC/NETWORK_REQUIRES
networks/ignition_simple_SDC/actual_burner.f90
networks/ignition_simple_SDC/actual_network.f90
networks/ignition_simple_SDC/actual_rhs.f90
networks/ignition_simple_SDC/burner_aux.f90
networks/kpp/GPackage.mak
networks/kpp/Make.package
networks/kpp/NETWORK_REQUIRES
networks/kpp/_parameters
networks/kpp/actual_burner.f90
networks/kpp/actual_network.f90
networks/kpp/f_rhs.f90
commit 7de73891e48edfda4a42cdea5f46f479c46d1194
Author: XinlongSBU <42697364+XinlongSBU@users.noreply.github.com>
Date: Sat Dec 7 12:50:53 2019 -0500
Add files via upload (#226)
networks/ECSN/net_work_zingale.ipynb
commit c74b7d366d4b4c08632c659d461a39b574b77f1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 5 18:47:26 2019 -0500
revert the nspec_evolve changes
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_type_simplified_sdc.F90
commit 86e4ab611bd01793c7c9be2e18de918eaddf7db8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 5 11:39:08 2019 -0500
some nspec != nspec_evolve work
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_type_simplified_sdc.F90
commit 48b8841be112f09a7e9b6d5bd40a7dd528210f10
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 5 08:09:20 2019 -0800
Bugfixes for VODE's simplified SDC interface when nspec_evolve != nspec (#223)
VODE's simplified SDC interface assumed that nspec_evolve == nspec by accessing nspec species elements of burn_t % ydot and burn_t % jac in the rhs_to_vode and jac_to_vode subroutines.
For simplified SDC, the integrator integrates all the species along with the energy terms, the unevolved species just see the advective sources. So accessing nspec elements from ydot and jac like we were doing yielded incorrect right hand side terms seen by the integrator for the unevolved species.
This is a likely culprit for the NaN in electron fraction observed in MAESTROeX simplified SDC tests with ignition_simple.
The BS integrator did this correctly.
integration/VODE/cuVODE/source/rpar.F90.template
integration/VODE/vode_type_simplified_sdc.F90
commit 66fefcc6d3acc9122aa5663282a2a1fd52da2e2f
Merge: 89b19887 8c0d7aa0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 13:02:56 2019 -0800
Merge pull request #221 from starkiller-astro/bye_bye_vode
remove old VODE, rename VODE90 -> VODE
commit 8c0d7aa06ec5b26298084ddf9f6be79ea2ce3632
Merge: 8d66767e 89b19887
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 13:00:54 2019 -0800
Merge branch 'development' into bye_bye_vode
commit 8d66767eff781c023847c997421f05f071ee37d8
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 12:46:20 2019 -0800
Fix path to cuVODE source in GNetwork.mak.
networks/GNetwork.mak
commit 89b198879a4b55bb7cef8c94ae7cfb4aa6c42f8e
Author: Doreen Fan <dfan@lbl.gov>
Date: Wed Dec 4 12:45:18 2019 -0800
add SDC_EVOLVE_ENERGY and SDC_EVOLVE_ENTHALPY constraints where necessary
integration/BS/bs_integrator_sdc.F90
integration/VODE90/vode_integrator_simplified_sdc.F90
commit fb72970292b8c172d21e6aabd63c6679fc02d4a4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 12:37:00 2019 -0800
Removed plotfile from cuVODE test.
integration/VODE/cuVODE/test/plt_test.cuVODE/Header
integration/VODE/cuVODE/test/plt_test.cuVODE/Level_0/Cell_D_00000
integration/VODE/cuVODE/test/plt_test.cuVODE/Level_0/Cell_H
commit 2c3ae1ba30e33086e2465747f4df3f198d1ccb9a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 12:33:55 2019 -0800
Update name of Doxygen project to VODE.
integration/VODE/cuVODE/docs/doxyfile_vode
commit 3ff3c48e6159d2c51b75750dc97f118811eb9c47
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 11:28:41 2019 -0800
Fix path for VODE90-VODE.
integration/VODE/GPackage.mak
commit 476987df2379a5db8a0deeadaccdc295c58599e6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 4 11:28:25 2019 -0800
Update sources for GPackage to use vode name in files.
integration/VODE/GPackage.mak
commit 24e562a2c157349489dc186a0e4edac1132e23f1
Merge: 95ae16de 7f618852
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 3 15:31:17 2019 -0800
Merge pull request #222 from starkiller-astro/mz-bugfix
nspec -> nspec_evolve
commit 95ae16de66cceabfa440aa32b5402fc016b5d574
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 17:25:58 2019 -0500
eliminate a copy of burn_t to save memory
integration/utils/numerical_jacobian.F90
commit 7f61885261216d69435c281f1af0690d505157fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 17:03:18 2019 -0500
nspec -> nspec_evolve
integration/utils/nonaka_plot.f90
commit 0c421083b8e058bd96845207ecc4c94bd4af708b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 14:34:21 2019 -0500
update changes
CHANGES.md
commit 4eaf4bc8bfe44472fcbb84e56583e94bf984fc0e
Merge: 78bd70d6 f91d5580
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Dec 3 14:14:36 2019 -0500
Merge branch 'development' into bye_bye_vode
commit f91d55800a6eab160bfb845a1c8c67fd0fab66b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 2 09:27:14 2019 -0500
update release
CHANGES.md
commit 62bb9169b64249a5536a5565e825245f74803683
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 30 11:13:17 2019 -0800
Enable the retry mechanism for simplified SDC (#215)
This is in conjunction with #695 for Castro. MAESTROeX will need a minor update since the sdc_t has had a field added.
CHANGES.md
integration/BS/bs_integrator.F90
integration/BS/bs_integrator_sdc.F90
integration/VODE90/vode_integrator_simplified_sdc.F90
integration/VODE90/vode_integrator_true_sdc.F90
integration/integrator_sdc.F90
interfaces/sdc_type.F90
commit 78bd70d6357765a6fb7c4234c047f8443f3d0037
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 13:45:18 2019 -0500
update integrator numbers
integration/integrator.F90
integration/integrator_sdc.F90
commit fcf372adf2c00667ba03ac432d4e0aefefd944f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 13:14:02 2019 -0500
need make overrides
integration/Make.package
networks/Make.package
commit 75df97d76d5d44af42eb373f3cbe3b08da93c303
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 12:56:49 2019 -0500
more VODE90 -> VODE
integration/_parameters
networks/GNetwork.mak
networks/Make.package
sphinx_docs/source/gpu.rst
sphinx_docs/source/networks.rst
sphinx_docs/source/sdc.rst
unit_test/burn_cell/README.md
unit_test/burn_cell_C/GNUmakefile
unit_test/test_conductivity/GNUmakefile
unit_test/test_cvode_react/README.md
unit_test/test_eos/GNUmakefile
unit_test/test_react/GNUmakefile
unit_test/test_react/README.md
unit_test/test_sdc/GNUmakefile
commit c5d9fc7e88992ea9090071475c10527f458b799c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 12:56:34 2019 -0500
these files are in actual_test_files now
util/regression_testing/Microphysics-tests-pgi.ini
util/regression_testing/Microphysics-tests.ini
commit b9110723bcd2e2c8025350749cd6269a009a81ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 11:11:40 2019 -0500
VODE90 -> VODE
integration/BS/stiff_ode.F90
integration/Make.package
integration/VODE/Make.package
commit c05d5523f01c5eb753ba67297b99899216deb413
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 30 11:07:08 2019 -0500
remove old VODE, VODE90 -> VODE
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/_parameters
integration/VODE/cuVODE/Make.cuVODE
integration/VODE/cuVODE/README
integration/VODE/cuVODE/docs/Makefile
integration/VODE/cuVODE/docs/NOTES.md
integration/VODE/cuVODE/docs/doxyfile_vode
integration/VODE/cuVODE/source/GPackage.mak
integration/VODE/cuVODE/source/Make.package
integration/VODE/cuVODE/source/cuvode.F90
integration/VODE/cuVODE/source/cuvode_constants.F90
integration/VODE/cuVODE/source/cuvode_dacopy.F90
integration/VODE/cuVODE/source/cuvode_dewset.F90
integration/VODE/cuVODE/source/cuvode_dvhin.F90
integration/VODE/cuVODE/source/cuvode_dvindy.F90
integration/VODE/cuVODE/source/cuvode_dvjac.F90
integration/VODE/cuVODE/source/cuvode_dvjust.F90
integration/VODE/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE/cuVODE/source/cuvode_dvnorm.F90
integration/VODE/cuVODE/source/cuvode_dvset.F90
integration/VODE/cuVODE/source/cuvode_dvsol.F90
integration/VODE/cuVODE/source/cuvode_dvstep.F90
integration/VODE/cuVODE/source/cuvode_nordsieck.F90
integration/VODE/cuVODE/source/cuvode_output.F90
integration/VODE/cuVODE/source/cuvode_parameters.F90
integration/VODE/cuVODE/source/cuvode_type.F90
integration/VODE/cuVODE/source/linpack_module.F90
integration/VODE/cuVODE/source/rpar.F90
integration/VODE/cuVODE/test/GNUmakefile
integration/VODE/cuVODE/test/Make.package
integration/VODE/cuVODE/test/README.md
integration/VODE/cuVODE/test/cuvode_parameters.F90
integration/VODE/cuVODE/test/extern_probin.template
integration/VODE/cuVODE/test/inputs
integration/VODE/cuVODE/test/main.cpp
integration/VODE/cuVODE/test/plt_test.cuVODE/Header
integration/VODE/cuVODE/test/plt_test.cuVODE/Level_0/Cell_D_00000
integration/VODE/cuVODE/test/plt_test.cuVODE/Level_0/Cell_H
integration/VODE/cuVODE/test/react_zones.F90
integration/VODE/cuVODE/test/test_react.H
integration/VODE/cuVODE/test/test_react_F.H
integration/VODE/cuVODE/test/vode_rhs.F90
integration/VODE/cuVODE/test/vode_rpar.F90
integration/VODE/cuvode_parameters.F90
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_sdc.f90
integration/VODE/vode_integrator_simplified_sdc.F90
integration/VODE/vode_integrator_true_sdc.F90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_rhs_simplified_sdc.F90
integration/VODE/vode_rhs_true_sdc.F90
integration/VODE/vode_rpar.F90
integration/VODE/vode_source/GPackage.mak
integration/VODE/vode_source/Make.package
integration/VODE/vode_source/dacopy.f
integration/VODE/vode_source/dewset.f
integration/VODE/vode_source/docs/doxyfile_vode
integration/VODE/vode_source/dumach.f
integration/VODE/vode_source/dvhin.f
integration/VODE/vode_source/dvindy.f
integration/VODE/vode_source/dvjac.f
integration/VODE/vode_source/dvjust.f
integration/VODE/vode_source/dvnlsd.f
integration/VODE/vode_source/dvnorm.f
integration/VODE/vode_source/dvode.f
integration/VODE/vode_source/dvset.f
integration/VODE/vode_source/dvsol.f
integration/VODE/vode_source/dvsrco.f
integration/VODE/vode_source/dvstep.f
integration/VODE/vode_source/iumach.f
integration/VODE/vode_source/ixsav.f
integration/VODE/vode_source/test/GNUmakefile
integration/VODE/vode_source/test/tvode.f
integration/VODE/vode_source/vode.H
integration/VODE/vode_source/xerrwd.f
integration/VODE/vode_source/xsetf.f
integration/VODE/vode_source/xsetun.f
integration/VODE/vode_type.F90
integration/VODE/vode_type_sdc.f90
integration/VODE/vode_type_simplified_sdc.F90
integration/VODE/vode_type_true_sdc.F90
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/_parameters
integration/VODE90/cuVODE/docs/Makefile
integration/VODE90/vode_integrator.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_rpar.F90
integration/VODE90/vode_type.F90
commit e20f00ee5694e1dba2c21644c5b9db02ceb3a72a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 21 10:56:44 2019 -0500
add comment
integration/utils/temperature_integration.F90
commit b7bd98dc9d071364ae7d23a7b8a62f977c56b9f4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 20 12:26:52 2019 -0800
Add enthalpy evolution mode for simplified SDC (#217)
To support the MAESTROeX style of simplified SDC, this PR adds an enthalpy evolution mode for the BS and VODE90 integrators with simplified SDC enabled.
The enthalpy evolution mode integrates an ODE system with rhoX and rhoh, the species partial densities and enthalpy.
This mode is turned on when SIMPLIFIED_SDC and SDC_EVOLVE_ENTHALPY are defined.
The Castro style energy evolution mode is enabled when SIMPLIFIED_SDC and SDC_EVOLVE_ENERGY are defined.
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type_sdc.F90
integration/VBDF/bdf_rhs.f90
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_integrator.F90
integration/VODE/vode_integrator_sdc.f90
integration/VODE/vode_rhs.F90
integration/VODE90/vode_integrator.F90
integration/VODE90/vode_integrator_simplified_sdc.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_rhs_simplified_sdc.F90
integration/VODE90/vode_rpar.F90
integration/VODE90/vode_type_simplified_sdc.F90
integration/integrator_sdc.F90
integration/utils/network_rhs.F90
integration/utils/nonaka_plot.f90
unit_test/test_sdc/GNUmakefile
commit b32b3f451bdb01a9f9e179592bb2c2de7515cfea
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Nov 19 13:08:01 2019 -0500
switched variables from being save'd at definition to setting them in the body of the subroutine
networks/MESA/Do_One_Zone_Burn.f90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_rhs.F90
commit 4471365df1a758126835ffb96b8c1b81536f2fd2
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Nov 19 13:01:32 2019 -0500
added save parameter to fortran variables initialized at definition
networks/MESA/Do_One_Zone_Burn.f90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_rhs.F90
commit 392dd793d8403db465ef3b993c4439b49aa61f63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 18 17:01:13 2019 -0500
fix compilation
integration/VODE90/vode_integrator_true_sdc.F90
commit 1f49333061c8197611ae4cefdb7b90adef6cba03
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 18 14:07:22 2019 -0500
fix latexism
sphinx_docs/source/basics.rst
commit bf072bd95a3d727fc995c2707ba2828ecc1fb1b5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 18 11:28:14 2019 -0700
Sync up VODE90 with VODE/BS retry strategy (#201)
CHANGES.md
integration/BS/stiff_ode.F90
integration/Make.package
integration/VODE90/Make.package
integration/VODE90/vode_integrator.F90
integration/VODE90/vode_integrator_simplified_sdc.F90
integration/VODE90/vode_integrator_true_sdc.F90
integration/integrator.F90
integration/integrator_sdc.F90
commit 18b8af3c4be2db76d42a1d38f5b24d5c528dfc4d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 18 09:05:07 2019 -0700
Use ode_max_steps consistently (#214)
CHANGES.md
integration/VODE/vode_integrator.f90
integration/VODE/vode_integrator_sdc.f90
integration/VODE90/actual_integrator.F90
integration/VODE90/actual_integrator_simplified_sdc.F90
integration/_parameters
commit f5b5a12185a741b32ea8bacb29bebeb7af25e6db
Merge: 9230ef8a 792ffdc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 17:49:45 2019 -0500
Merge branch 'burn_cell_cbuild' into development
commit 9230ef8a31ff84e6c54238a0a004315dfff64c08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 17:46:26 2019 -0500
store the final time
integration/VODE90/actual_integrator.F90
commit 792ffdc18f921601f6a3b23e0edbbc41ddf3f9b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 17:45:18 2019 -0500
add another inputs
unit_test/burn_cell_C/GNUmakefile
unit_test/burn_cell_C/burn_cell.F90
unit_test/burn_cell_C/inputs_aprox21
unit_test/burn_cell_C/probin_aprox21
commit 2da867be5be035989f2f1c6baae8b636200c645f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 17:26:29 2019 -0500
this works
unit_test/burn_cell_C/burn_cell.F90
unit_test/burn_cell_C/probin_aprox13
commit 9806ef16cecfcaa2dde0d1bab1ebc7c51e64f7c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 16:47:45 2019 -0500
more porting progress
unit_test/burn_cell_C/_parameters
unit_test/burn_cell_C/burn_cell.F90
unit_test/burn_cell_C/inputs_aprox13
unit_test/burn_cell_C/main.cpp
unit_test/burn_cell_C/probin_aprox13
commit 0c0a523df50eac29870867a1d0dd9a362be4c983
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 16:20:57 2019 -0500
start of a C++ single zone burn
unit_test/burn_cell_C/GNUmakefile
unit_test/burn_cell_C/Make.package
unit_test/burn_cell_C/_parameters
unit_test/burn_cell_C/burn_cell.F90
unit_test/burn_cell_C/burn_cell_F.H
unit_test/burn_cell_C/inputs_burn_aprox13
unit_test/burn_cell_C/main.cpp
unit_test/burn_cell_C/matplotlibrc
commit abb557018985b7883eb293f3d4d9e59e34767b26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 17 08:52:44 2019 -0500
move references to the end so they work
sphinx_docs/source/index.rst
sphinx_docs/source/zreferences.rst
commit 1e1336b91ed314c8a9d6ba4a010de14dc0224e44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 16 19:44:36 2019 -0500
add some Jacobian bits
sphinx_docs/source/refs.bib
sphinx_docs/source/sdc.rst
commit c5255f156da715c28619c3b17b14ac12052c128b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 16 19:28:35 2019 -0500
update the sdc docs to be based on VODE90
sphinx_docs/source/sdc.rst
commit 561deef746a36fb738e76487849e939831f709e3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Nov 16 12:18:45 2019 -0500
Mark up simplified SDC integrator for GPUs
integration/integrator_sdc.F90
commit 079a3f1f8ce46213b3e0662aa9c8ad507f1e3468
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Nov 15 11:20:15 2019 -0800
For simplified SDC, apply advection sources at end of integration using integration time (#213)
When calling vode_to_sdc at the end of the simplified SDC integration with VODE and VODE90, we were previously passing time as the time step to update unevolved variables rho and rho*u.
time was the simulation time in Castro at the start of the burner call, not the ODE integration end time. The difference is that the ODE integration end time is just the time advanced by the ODE integrator relative to its starting time of 0. So this is the reaction timestep from Castro that we should use to apply the advection sources to rho and rho*u before returning to Castro.
Note: Castro was not using the result of this last update, so no changes are expected.
integration/VODE/vode_integrator_sdc.f90
integration/VODE90/actual_integrator_simplified_sdc.F90
commit a45dc9e93bdaa4c3edfbfe499aa1ddbaf508b5b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Nov 11 20:45:48 2019 -0500
Account for new no-host version in aprox13
networks/aprox13/actual_rhs.F90
commit ed3775718dba10eb936fab7782d46fc6f3df1f49
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 19:14:53 2019 -0600
Fix the Jacobian contributions from the neutrino cooling (#210)
The neutrino cooling term returns d(S_nu)/dT, d(S_nu)/d(Abar), and d(S_nu)/d(Zbar). Since we're interested in dE/dY_j, we need to use the chain rule to obtain -dE/dY_j = d(Abar)/dY_j * d(S_nu)/d(Abar) + d(Zbar)/dY_j * d(S_nu)/d(Zbar). The latter term is correctly computed by all networks, since an analytic calculation reveals that d(Zbar)/dY_j is (Z_j - Zbar) * Abar. For the former term, it can either be -Abar^2, or (A_j - Abar) * Abar, depending on whether you enforce that sum(X) = 1 prior to taking the derivative.
Out of Frank Timmes' public networks as of this date, the 7 isotope and 34 isotope networks do it the way recommended by this PR, but the 13, 19 and 21 isotope networks do it the other way (the way that Microphysics does it, prior to this PR).
networks/ECSN/actual_rhs.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/iso7/actual_rhs.F90
networks/nova/actual_rhs.f90
networks/sn160/actual_rhs.F90
networks/subch/actual_rhs.F90
networks/subch2/actual_rhs.F90
commit beecc92240328ca4814680cd8ed5d200cb3ab165
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 17:48:51 2019 -0600
Replace the derivatives by abar and zbar in the neutrino term (#209)
These were removed in the beginning of Microphysics (bdef8c8) because at the time,
we had not ported the analytic Jacobian from Frank Timmes' network, and instead were
relying on VODE's numerical Jacobian, and there was no need to evaluate the derivatives
for calculating the RHS. However, we later inserted the analytic Jacobians, including the
contribution from the neutrinos, and then centralized on a neutrino source file, but did
not restore the derivatives by abar and zbar, so the Jacobian was not including all of
the relevant terms.
neutrinos/sneut5.F90
commit 46a1a6a120775cd2ce5acea78e28ee553c8d51e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 10 18:44:19 2019 -0500
actually mu is the total mean molecular weight
EOS/helmholtz/actual_eos.F90
commit 9511882a51b469342ccf1d55eca62c2871558bc7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 10 18:31:29 2019 -0500
define mu
EOS/helmholtz/actual_eos.F90
commit 9c42057e9a6a38f680d8c6f52f602ba6ea27ae7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 10 18:29:55 2019 -0500
update changes
CHANGES.md
commit 0ae03a6e60eac08d3e0a5cb2c199d31dbb37dac4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Nov 10 12:42:06 2019 -0600
Helmholtz refactor (#200)
This PR splits Helmholtz up from one monolithic function into separate functions that add the radiation, ion, electron-positron, and Coulomb correction terms.
It also applies some optimizations to the electron-positron contribution involving the table read, including reusing some arrays to save on flops, and combining some tables to enhance coalesced memory accesses when reading the tabular data.
EOS/helmholtz/actual_eos.F90
commit 16f221c588789f88e8de782f79f5815e566d5bcd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Nov 7 11:30:46 2019 -0800
Fix simplified SDC rpar indexing for irp_t0.
integration/VODE90/vode_rpar.F90
commit 0d3a42a884a96d314b940d113f2158e00054a258
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 6 21:05:05 2019 -0800
Revert changes to iso7 problem
unit_test/test_react/probin.iso7
unit_test/test_react/xin.iso7
commit b86645691992ee231cf8ca1cb1908f4cd85d62e5
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 6 20:44:46 2019 -0800
Apply iso7 screening in place
networks/iso7/actual_rhs.F90
unit_test/test_react/probin.iso7
unit_test/test_react/xin.iso7
commit 0866c7064bc0337840eefcc06c3ceb5128c114f1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 6 22:42:14 2019 -0500
Fix indexing in iso7 screening (#204)
Fix indexing bug in iso7 screening that caused the C12+O16 rate to be screened twice and the O16+O16 rate to not be screened.
networks/iso7/actual_rhs.F90
commit 708bd4861a75551fa863f55060a560e600faa252
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Nov 6 19:31:23 2019 -0800
Remove unused density derivatives in iso7
networks/iso7/actual_rhs.F90
commit a3e3452debff1fef5098f5eee222b1b4542f99ac
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Nov 6 16:21:27 2019 -0500
fixed SIMPLIFIED_SDC CUDA compilation
integration/VODE90/actual_integrator_simplified_sdc.F90
integration/VODE90/vode_rhs_simplified_sdc.F90
commit 10610b03b54513884cd8cd638fe3e9f13ea843d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 6 15:44:34 2019 -0500
a lot of simplified-SDC GPU porting
integration/VODE90/actual_integrator_simplified_sdc.F90
integration/VODE90/vode_rhs_simplified_sdc.F90
integration/VODE90/vode_type_simplified_sdc.F90
commit 89dc291f4ecbdb08b4d69e780182af0d4640a792
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 6 08:07:42 2019 -0500
fix compilation
integration/VBDF/bdf_type.f90
commit 5acbdda444fbb2f8d5c49b6b2c95247b2eb734ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 6 08:04:14 2019 -0500
initialize mu
EOS/helmholtz/actual_eos.F90
commit 6e295c49e4ecbee8d62a0755ec183fb6656dbdfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 5 19:20:02 2019 -0500
fix some equatiosn
sphinx_docs/source/data_structures.rst
sphinx_docs/source/eos.rst
sphinx_docs/source/networks.rst
commit 3625855d60ded2db10893f6adf010d66d0e16e5a
Author: Doreen Fan <dfan@lbl.gov>
Date: Tue Nov 5 12:41:27 2019 -0800
fix compile issue with maestroex double_bubble problem
EOS/multigamma/composition.F90
commit cd29bdba1ef66aec0381c890d21d1e83378ff155
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 4 16:40:00 2019 -0500
update changes
CHANGES.md
commit 3d8bfee78d7c290bb4a81ebfc2d652b4c9f7a99e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 4 16:33:30 2019 -0500
remove X derivs from eos_t (#207)
This removes the X derivatives from the eos_t and instead creates a new type eos_xderivs_t and routine (composition_derivatives(eos_t, eos_xderivs_t)) to fill them only as needed. This cuts down on the memory in the EOS by 3*nspec and boosts GPU performance.
PRs in Castro and MAESTROeX will coordinate.
EOS/Make.package
EOS/composition.F90
EOS/multigamma/actual_eos.F90
EOS/multigamma/composition.F90
integration/BS/bs_type.F90
integration/VODE/vode_type.F90
integration/VODE90/vode_type.F90
interfaces/Make.package
interfaces/eos_type.F90
unit_test/eos.F90
unit_test/microphysics.F90
unit_test/test_eos/GNUmakefile
unit_test/test_eos/eos_util.F90
commit 8ec59ed77d278b1bdcca4c90e7bc96ae4605dfea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 3 18:51:30 2019 -0500
fix mu as well
EOS/gamma_law_general/actual_eos.F90
commit 1968e26daf189687f59cf9001a0b47abe7b8e7c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 3 18:42:14 2019 -0500
remove 2 resets that are actually done in composition()
EOS/gamma_law_general/actual_eos.F90
commit d1471b5dc5d28dc07216e41ea6ff6539c6d93204
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 3 18:37:48 2019 -0500
fix some undefined quantities
EOS/gamma_law_general/actual_eos.F90
commit 585fcfdfcb7e43ff06bdd36f45ff5df9357b51d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 3 07:51:11 2019 -0500
update changes
CHANGES.md
commit 096d3d1b5ca513fe3a23d72c28ff889cee46d85d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 18:29:52 2019 -0400
remove a space
unit_test/test_eos/variables.F90
commit 85728a00d574f8747ef8dfb4bc46458a7a5864ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 18:12:35 2019 -0400
add all of the quantities in the eos_t to the plotfile
unit_test/test_eos/GNUmakefile
unit_test/test_eos/eos_util.F90
unit_test/test_eos/variables.F90
commit 45c814573989a92fe0beee5e5209990a475aa95a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 2 14:21:43 2019 -0400
turn on retry_burn
unit_test/test_react/probin.3alpha
commit 3e6ce0f286bcbb63511ef926c1dca579b47d9351
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 1 07:42:34 2019 -0400
changes for 19.11
CHANGES.md
commit f25dc42e3065ad4f6817ac5dd89b67e3220c43b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 15:45:31 2019 -0400
update changes with rprox
CHANGES.md
commit a34abc888078badcf8e1191c8656372245066dcf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 31 15:42:40 2019 -0400
port to CUDA
networks/rprox/GPackage.mak
networks/rprox/Make.package
networks/rprox/actual_burner.F90
networks/rprox/actual_network.F90
networks/rprox/actual_rhs.F90
networks/rprox/rates_module.F90
networks/rprox/tfactors.F90
commit 67f33c10e4c99dabe9a056fa8fdf465941d8515e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 29 17:21:08 2019 -0400
fix some sizes
integration/VODE90/cuvode_parameters.F90
commit 464dc7ffeec074a65da58fd18512b3d31b6cdf45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 29 15:50:10 2019 -0400
get VODE_NEQS from the cuvode_params module
integration/VODE90/vode_type_simplified_sdc.F90
commit 41cb05f6c871a8976a74d3f5102aeaf2bd1a0d7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 29 15:18:20 2019 -0400
for simplified SDC, the size of the system if SVAR_EVOLVE
integration/VODE90/cuvode_parameters.F90
commit 54a6fe4157f7cb1abe3882ad4734b892d83d5972
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 29 07:35:07 2019 -0700
Remove extra line
EOS/helmholtz/Make.package
commit b47be203e6b64a07f98113f8f2742b55c9d16521
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 27 20:15:56 2019 -0700
Initialize state separately to avoid paying UVM cost while timing
unit_test/test_eos/main.cpp
commit 3a72e49bd4cf5f1c0e4990a5c6848b810ac0396d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 27 19:05:02 2019 -0700
Disable CUDA verbosity by default
Make.Microphysics
commit cde1cbb2a55c1b582fdb043eb07fcf8d18fc46a3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 27 07:48:44 2019 -0700
Exclude plotfile write time from reported runtime
unit_test/test_conductivity/main.cpp
unit_test/test_cvode_react/main.cpp
unit_test/test_eos/main.cpp
unit_test/test_react/main.cpp
unit_test/test_sdc/main.cpp
commit ca688ef84dbcbe9dd4f1201e646f7c8076662118
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 27 08:06:10 2019 -0400
fix markdown formatting
CHANGES.md
commit 1a587899ece1034ae5c4e13173d38436c556ca08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 27 08:04:39 2019 -0400
rename to get markdown
update changes
CHANGES
CHANGES.md
commit 9d347b77ab51f438aff4ba1b2c60c8345829c275
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 16 14:59:27 2019 -0400
switch to using the conductivity in the output file name
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/test_conductivity_F.H
unit_test/test_conductivity/variables.F90
commit e53e62164022c1e03ff1e6d5ec1627fa0530a2cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 16 14:56:30 2019 -0400
fix compilation
conductivity/stellar/stellar_conductivity.F90
commit 05c2e8b4786ce8739f43e83091ddd8de190492c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 16 14:55:58 2019 -0400
add cond_name
conductivity/stellar/stellar_conductivity.F90
commit 41f6f06c4b391853360043cb44faa3e3d8b7da3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 19:21:13 2019 -0700
Hardcode more VODE_NEQS
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvsol.F90
integration/VODE90/cuVODE/source/linpack_module.F90
commit 0b8f758528dae70f8630b474e5ec0a15b4a0b258
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 19:14:50 2019 -0700
Hardcode VODE_NEQS into dgbfa
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/linpack_module.F90
commit 87fb0c9c2a9642b49cf6be18ab2de282b40cbc0b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 18:42:12 2019 -0700
Clean up dgesl interface
integration/VODE90/cuVODE/source/cuvode_dvsol.F90
integration/VODE90/cuVODE/source/linpack_module.F90
commit 7ae74f4ef03d12abd14da20ca76e40903a608ac0
Merge: a7cf562f d4c3a1d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 21:27:01 2019 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit a7cf562f723cd7a4bed2b51f93e5a65c0dcdb862
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 21:26:50 2019 -0400
rpar is 1-based not 0-based
integration/VODE90/vode_rpar.F90
commit d4c3a1d5dccf45cf43351c602bdb1d44af47d66b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 18:01:44 2019 -0700
Move linpack into cuVODE source
integration/VODE90/cuVODE/Make.cuVODE
integration/VODE90/cuVODE/linear_algebra_modules/GPackage.mak
integration/VODE90/cuVODE/linear_algebra_modules/Make.package
integration/VODE90/cuVODE/source/GPackage.mak
integration/VODE90/cuVODE/source/Make.package
integration/VODE90/cuVODE/source/linpack_module.F90
networks/GNetwork.mak
networks/Make.package
commit 856e5a9aa5effb008cb49e1d75694fcfaccd99ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 17:00:11 2019 -0400
remove blas_module to get this compiling again
integration/VODE90/cuVODE/linear_algebra_modules/GPackage.mak
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dacopy.F90
integration/VODE90/cuVODE/source/cuvode_dvindy.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvjust.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
commit 395fa6474b690680d783322e4b9fb4f4864f39b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 12:47:39 2019 -0700
Inline vddot
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit 194fd265f7f621a83202b5e1ab9dc06c3636344c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 12:42:40 2019 -0700
Move idamax into linpack module
integration/VODE90/cuVODE/linear_algebra_modules/Make.package
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit aaca2fce8e49eb249f8d68559e80b6570f2e3efc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 12:37:36 2019 -0700
Simplify idamax
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit 81ff463cf60e5ee9a2705c105cda20dbe7d1b1e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 11:24:51 2019 -0700
Inline dscal
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit c830dadfb1d517f801ebe182a6f4596475cd5530
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 11:22:05 2019 -0700
Inline dscaln
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dvindy.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
commit 46fd542592623ec912933d8b28dea148ac80dd61
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 11:16:03 2019 -0700
Inline ddot
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit 8d54df3be5877d3f06ae2a3b38ba1ca468efdf0d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 11:12:46 2019 -0700
Inline daxpy
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit 0b86581f18ae31ceb867bdb42d811c6773424ac6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 10:55:09 2019 -0700
Inline daxpyn
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/source/cuvode_dvjust.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
commit ec74f4b80994b77adb8a2c3fe6ef7f91410a2f64
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 13 10:39:48 2019 -0700
Remove unused BLAS routines
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
commit 95d5ec38bd2b6983e6695da1585ec9b1ff7cc473
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 13 12:42:05 2019 -0400
VODE90 for simplified SDC (#194)
These changes let us use the VODE90 integrator for the Simplified-SDC
Note: the preprocessor option SDC is now named SIMPLIFIED_SDC
GMicrophysics.mak
Make.Microphysics
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/bs_rpar.F90
integration/BS/stiff_ode.F90
integration/CVODE/cvode_rpar.F90
integration/GPackage.mak
integration/Make.package
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_rpar.F90
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/actual_integrator_simplified_sdc.F90
integration/VODE90/actual_integrator_true_sdc.F90
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dvhin.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
integration/VODE90/cuVODE/source/cuvode_type.F90
integration/VODE90/cuvode_parameters.F90
integration/VODE90/vode_rhs_simplified_sdc.F90
integration/VODE90/vode_rhs_true_sdc.F90
integration/VODE90/vode_rpar.F90
integration/VODE90/vode_type_simplified_sdc.F90
integration/VODE90/vode_type_true_sdc.F90
integration/integrator_sdc.F90
integration/utils/GPackage.mak
integration/utils/Make.package
interfaces/GPackage.mak
interfaces/Make.package
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox19/Make.package
networks/aprox21/Make.package
networks/breakout/Make.package
networks/general_null/Make.package
networks/ignition_chamulak/Make.package
networks/ignition_simple/Make.package
networks/iso7/Make.package
networks/kpp/Make.package
networks/powerlaw/Make.package
networks/rprox/Make.package
networks/triple_alpha_plus_cago/Make.package
networks/xrb_simple/Make.package
unit_test/microphysics.F90
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/react_zones.F90
commit 7de7159bbdfe7bde307a88a780b0dd7d0149e569
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 1 14:59:25 2019 -0400
remove unused variables
integration/VODE90/vode_rhs.F90
commit 6804966172a1189d82c40a829cd22356b83569a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 1 09:38:52 2019 -0400
update release
CHANGES
commit 125c9e5640e7b500e489fb36c6d9403a32c095e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 29 11:10:20 2019 -0400
update changes
CHANGES
commit 234ec378076400ab5434126080b5b5aaa1eb3981
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 19:41:09 2019 -0400
remove unused LAPACK
integration/BS/LAPACK/dgetf2.f
integration/BS/LAPACK/dgetrf.f
integration/BS/LAPACK/dlamch.f
integration/BS/LAPACK/dlaswp.f
integration/BS/LAPACK/ieeeck.f
integration/BS/LAPACK/ilaenv.f
integration/BS/LAPACK/iparmq.f
integration/BS/LAPACK/lsame.f
integration/BS/LAPACK/xerbla.f
commit 968b6432ff55bb9919596cd3ad91baf07089cd04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 15:10:07 2019 -0400
another fix
sphinx_docs/source/networks.rst
commit c49c727d15a062410a602c5242a7fb8b947669f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 14:53:14 2019 -0400
fix an indent
sphinx_docs/source/networks.rst
commit 7a673b5f84006fcff98ca5074152401ee4cdec7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 14:34:46 2019 -0400
fix some more refs
sphinx_docs/source/conf.py
sphinx_docs/source/networks.rst
sphinx_docs/source/tolerances.png
commit 5267c78a333e0c8ded73b0fc2a074279f24ae6bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 13:17:56 2019 -0400
fix some indents
sphinx_docs/source/basics.rst
commit 94b4fdd9536f74fa2433215c78235edb51a41e90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:29:03 2019 -0400
don't store runtime_parameters.rst
.gitignore
commit 376859991e839a30524e29e4308e0a634c9efa83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:26:23 2019 -0400
get rid of the copy
sphinx_docs/Makefile
commit e457feb77abe3f61a71c44ef67d317410047e998
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:25:53 2019 -0400
we serve docs from gh-pages
docs/.nojekyll
docs/_images/doxygen_network.png
docs/_images/react_aprox13_logX.png
docs/_images/subch.png
docs/_images/tolerances.png
docs/_sources/basics.rst.txt
docs/_sources/burn_cell.rst.txt
docs/_sources/data_structures.rst.txt
docs/_sources/eos.rst.txt
docs/_sources/index.rst.txt
docs/_sources/networks.rst.txt
docs/_sources/openacc.rst.txt
docs/_sources/preface.rst.txt
docs/_sources/references.rst.txt
docs/_sources/rp_intro.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/_sources/sdc.rst.txt
docs/_sources/transport.rst.txt
docs/_sources/unit_tests.rst.txt
docs/_static/ajax-loader.gif
docs/_static/basic.css
docs/_static/comment-bright.png
docs/_static/comment-close.png
docs/_static/comment.png
docs/_static/css/badge_only.css
docs/_static/css/theme.css
docs/_static/doctools.js
docs/_static/documentation_options.js
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docs/_static/down.png
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docs/_static/fonts/Inconsolata-Bold.ttf
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docs/_static/fonts/Inconsolata.ttf
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docs/_static/fonts/RobotoSlab-Bold.ttf
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docs/_static/fonts/fontawesome-webfont.eot
docs/_static/fonts/fontawesome-webfont.svg
docs/_static/fonts/fontawesome-webfont.ttf
docs/_static/fonts/fontawesome-webfont.woff
docs/_static/fonts/fontawesome-webfont.woff2
docs/_static/jquery-3.1.0.js
docs/_static/jquery-3.2.1.js
docs/_static/jquery.js
docs/_static/js/modernizr.min.js
docs/_static/js/theme.js
docs/_static/mathjax_conf.js
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docs/_static/pygments.css
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docs/_static/underscore-1.3.1.js
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docs/_static/websupport.js
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/references.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
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commit 13cb2a9cd906c8e90f8e829ead00d6a9951a7328
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:23:16 2019 -0400
use the same style as Castro
sphinx_docs/source/_static/theme_overrides.css
commit fe5356b4e49e478919de170ea03094952e123024
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:21:15 2019 -0400
more fixes
sphinx_docs/rp.py
commit 7b37f127188e7eb25851d47b3862420c51ef3aa6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:17:29 2019 -0400
switch to python 3 + widen table to fix build errors
sphinx_docs/rp.py
commit cfa036858e52085b819efe5884f7e7c545a7dacd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 28 09:14:01 2019 -0400
fix some sphinx formatting
docs/_sources/burn_cell.rst.txt
docs/_sources/index.rst.txt
docs/_sources/networks.rst.txt
docs/_sources/preface.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/_sources/sdc.rst.txt
docs/_static/css/badge_only.css
docs/_static/css/theme.css
docs/_static/documentation_options.js
docs/_static/fonts/Lato/lato-bold.ttf
docs/_static/fonts/Lato/lato-bolditalic.ttf
docs/_static/fonts/Lato/lato-italic.ttf
docs/_static/fonts/Lato/lato-regular.ttf
docs/_static/js/theme.js
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/references.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
integration/_parameters
sphinx_docs/rp.py
commit 17285966f14a7e8f4439c3e8dbe4dd2ca457a0a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 27 21:47:58 2019 -0400
update script to python3 + argparse
networks/general_null/write_network.py
commit b1e02b3743a19b8398d6bef4c66d9bec8a1e37b3
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 27 11:13:08 2019 -0400
Port iso7 for GPUs (#172)
iso7 seems to work well on GPUs now with these changes.
networks/iso7/Make.package
networks/iso7/actual_burner.F90
networks/iso7/actual_network.F90
networks/iso7/actual_rhs.F90
commit 1655f5d49999e51606dff56b7463a4a0d3cedb53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 26 15:08:47 2019 -0400
sync VODE90 up with VODE (#192)
this also now implements the reaction boost
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_type.F90
commit 6ba2936339b3ec3b877b3317ad3a8511acb4679c
Merge: cc900251 8991cde6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 25 13:51:59 2019 -0700
Merge pull request #191 from jmsexton03/development
Add attributes(device) if not compiled with AMREX_USE_GPU_PRAGMA for …
commit 8991cde65eaaad8af1e8a2c6dc472f845a4e4a77
Author: Jean M. Sexton <jmsexton@lbl.gov>
Date: Wed Sep 25 16:43:42 2019 -0400
Add attributes(device) if not compiled with AMREX_USE_GPU_PRAGMA for linear_algebra_modules
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit cc900251be76d8431f6ddff5300d1e06d3354925
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 25 11:30:50 2019 -0400
tweak the thermodynamic conditions so it runs without crashes
unit_test/test_react/probin.iso7
commit 5738d6bc9ff714d71d95257c501c996b51138ece
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 25 08:02:11 2019 -0700
Move !$gpu to right places for cuVODE linear algebra modules. closes #155
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
commit 838ae2930647d1402fa45c3c4019e9039519d293
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 25 07:58:32 2019 -0700
Move !$gpu to the right places for subch network.
networks/subch/actual_burner.F90
networks/subch/actual_rhs.F90
networks/subch/reaclib_rates.F90
commit 0d268b62b0491dba8eead61421ead70e4836fc97
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 24 16:22:41 2019 -0700
If compiling with AMREX_USE_CUDA but not the GPU Pragmas, then manually add attributes(device) to VODE90 subroutines.
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dacopy.F90
integration/VODE90/cuVODE/source/cuvode_dewset.F90
integration/VODE90/cuVODE/source/cuvode_dvhin.F90
integration/VODE90/cuVODE/source/cuvode_dvindy.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvjust.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvnorm.F90
integration/VODE90/cuVODE/source/cuvode_dvset.F90
integration/VODE90/cuVODE/source/cuvode_dvsol.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
integration/VODE90/cuVODE/source/cuvode_nordsieck.F90
commit d8a2c4f1a8f527533ed091555faec5919ce2f3ea
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 24 16:22:01 2019 -0700
Update name of rpar template module.
integration/VODE90/cuVODE/source/rpar.F90
commit 0036b6ccfa0555998104964136bfaf8c065ab5ed
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 19 16:05:45 2019 -0700
Update Nonaka plot feature (#190)
This updates the support for making Nonaka plots for all the integrators.
Along the way, this PR rearranges the modules in integration/ for clarity.
Some utility modules useful for all integrators but not directly called by user code has been moved to integration/utils.
This also fixes some misuse of the rpar functionality when multiple integrators are built.
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/bs_integrator.F90
integration/BS/bs_integrator_sdc.F90
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_rpar.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/CVODE/Make.package
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_rpar.F90
integration/CVODE/cvode_type.F90
integration/GPackage.mak
integration/Make.package
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VBDF/vbdf_rpar.F90
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_integrator.f90
integration/VODE/vode_integrator_sdc.f90
integration/VODE/vode_rhs.F90
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_rpar.F90
integration/VODE/vode_type.F90
integration/VODE/vode_type_sdc.f90
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/actual_integrator.F90
integration/VODE90/actual_integrator_sdc.f90
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_type.F90
integration/VODE90/cuVODE/test/Make.package
integration/VODE90/cuVODE/test/README.md
integration/VODE90/cuVODE/test/vode_rhs.F90
integration/VODE90/cuVODE/test/vode_rpar.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_rhs_sdc.f90
integration/VODE90/vode_rpar.F90
integration/VODE90/vode_type.F90
integration/VODE90/vode_type_sdc.f90
integration/utils/GPackage.mak
integration/utils/Make.package
integration/utils/jacobian_sparsity.F90
integration/utils/network_rhs.F90
integration/utils/nonaka_plot.f90
integration/utils/numerical_jacobian.F90
integration/utils/numerical_jacobian_sdc.f90
integration/utils/temperature_integration.F90
networks/GNetwork.mak
commit ba79abb10a2705032014ac2f77f30c19b986b620
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Aug 30 14:55:23 2019 -0700
Move call to nonaka_rhs to before the conversion from Ydot to Xdot since we do that inside the nonaka_rhs subroutine now.
integration/VODE/vode_rhs.F90
commit 5b36d39e700b856dacc5ae61fdeb5fe23916d073
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Aug 30 14:41:29 2019 -0700
Add nonaka plot interface to VODE.
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_rhs.F90
integration/VODE/vode_type.F90
commit 7e97058bb7ba1d17667f4f2ba93e704cedae7fe9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Aug 30 14:39:30 2019 -0700
Initialize Nonaka plot module.
integration/integrator.F90
commit 0c4c5651ccc38a5079a1d33d8bbad2679ab3cb85
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Aug 30 14:38:37 2019 -0700
Add a module for making Nonaka (TM) plots, enabled when compiling with USE_NONAKA_PLOT=TRUE.
integration/GPackage.mak
integration/Make.package
integration/_parameters
integration/nonaka_plot.f90
commit fbd07bcb270955dc82f592fb09f888fe2936975f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 10:00:00 2019 -0400
update changes
CHANGES
commit 279c1ea497f7106b0d82e934c217693a92787d21
Merge: 4520e856 dcb60ede
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 1 09:59:46 2019 -0400
Merge branch 'development'
commit dcb60edeb4423c39f33e0013eb5aedf1449811c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 31 19:52:29 2019 -0400
update changes
CHANGES
commit 291e30a406c7b785ea372e4f3a14257a2806d0bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 20 14:51:00 2019 -0400
add some license information
integration/BS/LAPACK/LICENSE.txt
integration/VODE/vode_source/license.txt
license.txt
util/BLAS/license.txt
util/DNSQE/GPackage.mak
util/DNSQE/Make.package
util/DNSQE/README
util/DNSQE/TODO
util/DNSQE/d1mach.f
util/DNSQE/d1mpyq.f
util/DNSQE/d1updt.f
util/DNSQE/ddoglg.f
util/DNSQE/denorm.f
util/DNSQE/dfdjc1.f
util/DNSQE/dnsq.f
util/DNSQE/dnsqe.f
util/DNSQE/dqform.f
util/DNSQE/dqrfac.f
util/DNSQE/fdump.f
util/DNSQE/i1mach.f
util/DNSQE/j4save.f
util/DNSQE/orig/dnsqe.f
util/DNSQE/test/GNUmakefile
util/DNSQE/test/test.f90
util/DNSQE/xercnt.f
util/DNSQE/xerhlt.f
util/DNSQE/xermsg.f
util/DNSQE/xerprn.f
util/DNSQE/xersve.f
util/DNSQE/xgetua.f
util/LINPACK/license.txt
commit 177684fb271b11abee06e5949c6c118a4d245bfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 15 18:52:35 2019 -0400
remove unused variables
integration/BS/bs_integrator.F90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
commit e82dafc44cdae2f4f7ef50a35e7e2a7cb9bef84b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 15 18:19:28 2019 -0400
remove unused vars
integration/jacobian_sparsity.F90
networks/aprox13/actual_rhs.F90
commit 4520e856d8eb7a2b76756857e500ba073d0f897f
Merge: f5b9c9b4 4295c850
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 3 10:37:26 2019 -0400
Merge branch 'development'
commit 4295c85048ba1e24f1c41fd4978fc04d73e5f618
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Sat Jun 1 20:50:52 2019 -0400
Added the subch2 network which combines aprox13 and the subch networks. 0b9d5bd (#184)
This is a mix of an alpha chain and the subch nets
networks/subch2/20180319default2
networks/subch2/GPackage.mak
networks/subch2/Make.package
networks/subch2/NETWORK_REQUIRES
networks/subch2/_parameters
networks/subch2/actual_burner.F90
networks/subch2/actual_network.F90
networks/subch2/actual_rhs.F90
networks/subch2/inputs.burn_cell.VODE
networks/subch2/physical_constants.f90
networks/subch2/reaclib_rate_metadata.dat
networks/subch2/reaclib_rates.F90
networks/subch2/subch2.py
networks/subch2/table_rates.F90
networks/subch2/xin.pynucastro.128
networks/subch2/xin.pynucastro.16
networks/subch2/xin.pynucastro.256
networks/subch2/xin.pynucastro.32
networks/subch2/xin.pynucastro.64
commit 085981348b29169a58d186391e69dd892fb34bf1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 30 10:43:15 2019 -0700
Add uniform rho, T inputs.
unit_test/test_cvode_react/inputs_aprox13_uniform
unit_test/test_cvode_react/probin.aprox13.uniform
commit 1914c63789eb0ca951e25e304cc7936ded06d5bc
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed May 29 08:43:18 2019 -0400
updated GPackage.mak to include F90 instead of f90 in ignition_chamulak and triple_alpha_plus_cago
networks/ignition_chamulak/GPackage.mak
networks/triple_alpha_plus_cago/GPackage.mak
commit bb4464e997f56629320123b7c27e0645d2d2a448
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 15:18:22 2019 -0400
marked ignition_chamulak routines for offloading to the gpu
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_burner.F90
networks/ignition_chamulak/actual_network.F90
networks/ignition_chamulak/actual_network.f90
networks/ignition_chamulak/actual_rhs.F90
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
commit 7745ac6d5cec1515be10c8f33c182213b400b879
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 12:04:57 2019 -0400
more .f90 -> .F90
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_burner.F90
networks/triple_alpha_plus_cago/actual_rhs.F90
networks/triple_alpha_plus_cago/dydt.F90
networks/triple_alpha_plus_cago/rates_module.F90
networks/triple_alpha_plus_cago/screen_module.F90
commit 5915d710cf4659e81c1e886d1936f1467660ebb7
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 09:45:27 2019 -0400
actual_network.f90 -> actual_network.F90
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_network.F90
python_library/StarKiller/examples/Burn Cell.ipynb
python_library/StarKiller/examples/Burn-Subch.ipynb
python_library/StarKiller/examples/BurnProfile/Burn-Cell-Aprox21.ipynb
python_library/StarKiller/examples/BurnProfile/probin_aprox21
python_library/StarKiller/examples/StarKiller Notebook Test.ipynb
python_library/StarKiller/examples/Test-Aprox13.ipynb
commit 3556ca2862d53a10146776a4467cb929a37e9f35
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 09:38:48 2019 -0400
marked aion, zion and ebin in triple_alpha_plus_cago as managed memory so this network works on the GPU
networks/triple_alpha_plus_cago/actual_network.f90
commit 76950944767c87a1124b4b0e1b65bae735f254b2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 9 11:52:35 2019 -0700
Return size of AmrexAstroModel.
python_library/StarKiller/models/amrex_astro.py
commit 44fa14c0a723000637d704ef4942c16909068c96
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue May 7 21:57:37 2019 -0400
Markup aprox21 RHS for GPU.
networks/aprox21/actual_rhs.F90
commit 0ae597a3111e5e6a784c1098e7e891939acd7711
Merge: 636046ab 520021df
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 20:21:31 2019 -0700
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 636046abd5fa13d3ba58b5b657c732928b100757
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 20:20:35 2019 -0700
Fix code formatting.
sphinx_docs/source/gpu.rst
commit 00d326e147d50dbc55194ab01afef57c077a7568
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 20:09:48 2019 -0700
OpenACC page -> GPU page.
sphinx_docs/source/index.rst
commit 65d73c357177404aed46d934343d1e5437bfd327
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 20:05:32 2019 -0700
Update GPU section of docs with description of current strategy, status of integration, and pointers for compiling and running tests.
sphinx_docs/source/gpu.rst
sphinx_docs/source/openacc.rst
commit 520021df3a56b372c8ad9b33acafc9e473540d7a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 14:45:15 2019 -0400
Add instructions for running the GPU aprox13 test.
unit_test/test_react/README.md
commit 88d8dfaf428448814931f09ed82cb5c80cde47af
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 14:41:08 2019 -0400
Add sample git hashes for testing to the CVODE readme.
unit_test/test_cvode_react/README.md
commit 4904cc35d729e52d313444c195853dae60520e8d
Merge: 769b6478 9c4a91af
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 14:33:06 2019 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 769b6478470edf10c2cd8ff7238b06bb44c2f6eb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 6 14:32:58 2019 -0400
Add AMREX_USE_CUDA=TRUE and USE_GPU_PRAGMA=TRUE to Readme.
integration/VODE90/cuVODE/test/README.md
commit 9c4a91afa3c16f1dbf171279ad31031f7d4546db
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 18:38:19 2019 -0400
Add compile modes and interfaces to readme.
unit_test/test_cvode_react/README.md
commit b426bdffd5fcde59e91f85e95989962fbafd199e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 18:33:32 2019 -0400
Fix rpath line for compiling with CVODE either with CUDA (pgi) or without (gnu)
Make.Microphysics
commit 417834f2896458442bd90480185ee855c09f7e97
Merge: 59783d36 6e1f34a1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 15:26:32 2019 -0700
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 59783d36bc2d1c3d8c1cd304b8eacc20bb667c25
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 15:26:28 2019 -0700
Use scale_jac_entry in test_numerical_jacobian in case the Jacobian is sparse.
integration/numerical_jacobian.F90
commit 6e1f34a101b32bb28721d8ba360b756cd49ac612
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 17:50:20 2019 -0400
Add xin files for aprox13 with bigger grids as duplicates of the size-16 grid.
unit_test/test_cvode_react/xin.aprox13.128
unit_test/test_cvode_react/xin.aprox13.256
unit_test/test_cvode_react/xin.aprox13.32
unit_test/test_cvode_react/xin.aprox13.64
commit f420b37a8a0008973dcae1ef6446fc0f0b4d331a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 17:48:13 2019 -0400
Expand instructions for compiling and running.
unit_test/test_cvode_react/README.md
commit 1db46f63925bd012e2480e6092a3227e94872e00
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 17:47:47 2019 -0400
Use 1e-12 absolute tolerance for species the same as test_react.
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_serial.cpp
commit f5a632c238bd54117b4b365e77d2747088ce06d1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 2 17:28:25 2019 -0400
Add Summit build line to readme.
unit_test/test_cvode_react/README.md
commit f5b9c9b4591ed30d0036bd063d0bab5e9285a5ed
Merge: 780812b8 06bfa2c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 08:51:45 2019 -0400
Merge branch 'development'
commit 06bfa2c0a7ce48a9f47bf334b9e551596e09107f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 1 08:51:30 2019 -0400
update changes
CHANGES
commit be0af567fe7875a109db159c7f14ef95c3e1844c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 30 22:07:43 2019 -0400
add note
util/DNSQE/TODO
commit 79d87353c3262e7bacdd32e530e37c6c85b88797
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 30 21:58:40 2019 -0400
add Make.package
util/DNSQE/Make.package
commit a57d1611f7e7173cdb2b00b5b25352ce464d30dc
Merge: 1de421e5 88a4a5aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 30 21:46:32 2019 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 1de421e52f9618c9edc758cf3d887f12a07161e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 30 21:46:14 2019 -0400
add an rpar that gets passed through all the interfaces
util/DNSQE/README
util/DNSQE/dfdjc1.f
util/DNSQE/dnsq.f
util/DNSQE/dnsqe.f
util/DNSQE/test/test.f90
commit 88a4a5aaaaa6dc0e4e89974d852bdfefdb8ea5c1
Merge: c44a468c 2191ad9d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 29 19:04:15 2019 -0700
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 2191ad9d0236cf4ae2e1efeffa2bfd67588a0815
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 29 19:47:02 2019 -0400
update changes
CHANGES
commit a6f227ff62a9b19e21f4452fe6ac69c705bbe11b
Merge: 5fa2c911 e16e4dcd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 29 16:43:21 2019 -0700
Merge pull request #180 from starkiller-astro/numerical_jac
Numerical jac fixes
commit c44a468c7cd3b011c3f6ceccd13ece8ffa511c15
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:39:35 2019 -0700
Add Jacobian test notebooks.
(cherry picked from commit f10af7f4e6f66ca5b0e94e733a069af0b0a54c40)
python_library/StarKiller/examples/Jacobian-Test-subch.ipynb
python_library/StarKiller/examples/Jacobian-Test.ipynb
commit 5fa2c911b76d21e85ab652936a08351402f1e1f9
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Apr 29 16:05:18 2019 -0400
add integrator file to dowrap.sh
python_library/dowrap.sh
commit 0d7a06d18f9a30a5c1bd0a981fe141ee34c77d41
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 29 11:55:24 2019 -0700
Example burn using the new StarKiller python interfaces.
python_library/StarKiller/examples/BurnProfile/Burn-Cell-Aprox21.ipynb
python_library/StarKiller/examples/BurnProfile/probin_aprox21
commit e16e4dcd4c87e7814481635221f8cae21c7d9948
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 20:11:50 2019 -0400
fix compilation
integration/numerical_jacobian.F90
commit 533e909053415e537899a2636062feb8bbb0d720
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 09:26:41 2019 -0400
compare Jacobians in terms of X
integration/numerical_jacobian.F90
commit 8fd8eb8c5989c08e624e69159a0bdff43b5112fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 09:16:15 2019 -0400
remove the runtime parameters -- it's auto generated
some doc updates
sphinx_docs/source/mathsymbols.tex
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/sdc.rst
commit a2999e3c5d5ef2cacf9228f6e2b5b58d2c0b1ac6
Merge: f10af7f4 71beec50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 09:14:56 2019 -0400
Merge branch 'development' into numerical_jac
commit 71beec502e849e9a7c831a327f693f5c83be5a1e
Merge: ecbfec43 a9b1b7e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 27 09:14:44 2019 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit f10af7f4e6f66ca5b0e94e733a069af0b0a54c40
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:39:35 2019 -0700
Add Jacobian test notebooks.
python_library/StarKiller/examples/Jacobian-Test-subch.ipynb
python_library/StarKiller/examples/Jacobian-Test.ipynb
commit 9ce3c080a41c4bfd50bd3c2ae2cbf75d983ff0f2
Merge: 7629e2e1 a9b1b7e9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:39:17 2019 -0700
Merge remote-tracking branch 'origin/development' into numerical_jac
commit a9b1b7e991f515eb50ee91b7d9a10acd97252e8f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:36:22 2019 -0700
Wrap the numerical jacobian module.
python_library/dowrap.sh
commit 8b9fd8003149756de416bc812fa6eb049bf86240
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:33:57 2019 -0700
Add interface to the numerical jacobian module.
python_library/StarKiller/integration/__init__.py
python_library/StarKiller/integration/numerical_jacobian.py
commit 860b3a1af271bbb0b4a53a16e01f5d4c497417ab
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:33:19 2019 -0700
Add an interface to the integrators.
python_library/StarKiller/integration/__init__.py
python_library/StarKiller/integration/integration.py
commit 106cd38fa61de6681fadf2fdf57e252e913e797a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 26 18:29:23 2019 -0700
Add aion and aion_inv to network class.
python_library/StarKiller/network/network.py
commit 7629e2e1250f182f0db5dc81c72a7c519bf9132a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 26 12:44:50 2019 -0400
fix some more Jacobian issues
we were modifying the input state's RHS -- now we don't anymore
we were not scaling the forward difference unperturbed state by aion
we were improperly scaling the centered diff minus state
integration/numerical_jacobian.F90
commit daec387990be677b9c123cbe78c747e28bb79bed
Merge: 6eb345ef c3c3e954
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 21:58:28 2019 -0400
Merge branch 'development' into numerical_jac
commit 6eb345efb0b04b5f1a8ff09448ecb8cc6d0c2aef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 21:33:40 2019 -0400
fix the scaling of the numerical Jacobian
integration/numerical_jacobian.F90
commit 780812b8ec0b2227cef50d37c967dfc43c63aa0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 20:07:59 2019 -0400
add the travis badge
README.md
commit c3c3e954adfd164829d4262357b1371b74b56872
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 20:07:59 2019 -0400
add the travis badge
README.md
commit a012e1dc65c94ff411285a29e853621f8a640947
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 20:00:18 2019 -0400
add a note about what form we expect the Jacobian in
sphinx_docs/source/networks.rst
commit 78313a2ea1db3579421bbaed061a2d4c25b54cc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 15:57:29 2019 -0400
some work on robustifying the numerical Jac
integration/numerical_jacobian.F90
commit 1d0681f09735a69e5a44e7c2bb44b7f48d74dca5
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Apr 22 08:54:44 2019 -0400
Fix reversed definition of dcopyn from #178
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dacopy.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
commit 312a226aa42d2153543d4fb0089acf58b1757507
Merge: ffc7bd74 ff364de0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Apr 20 20:08:10 2019 -0700
Merge pull request #178 from starkiller-astro/rm_dcopyn
Remove dcopyn, explicitly write out array copies
commit ff364de0bced1b063da40669c78910a6473b2c1d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Apr 20 19:48:51 2019 -0700
Remove dcopyn, explicitly write out array copies
This works around a PGI 19.1+ bug compiling blas_module.F90 for CUDA.
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dacopy.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
commit ffc7bd746d2d17320713864e845a3fc3dffd8721
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Apr 20 00:17:50 2019 -0700
Do not print species names when constructing an AmrexAstroModel object.
python_library/StarKiller/models/amrex_astro.py
commit 18e3feb0af6ecd2e6a27be607bb2dffa5084365e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Apr 20 00:11:11 2019 -0700
Add an AMReX-Astro model reader.
python_library/StarKiller/models/__init__.py
python_library/StarKiller/models/amrex_astro.py
python_library/StarKiller/network/network.py
python_library/StarKiller/setup.py
commit 58c6ce4f273981a3867d7fccef0a08176874a493
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 10 10:58:33 2019 -0700
print out evaluated EOS e to test thermodynamic consistency of integration.
unit_test/burn_cell/main.f90
commit 1ef6d58001eabb1ad8cae10c1e872f87367fbe66
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 10 10:23:40 2019 -0700
Added inputs for Case 1 test from Josian (T peak with O-burning)
unit_test/burn_cell/inputs_ECSN_burn_Case-1
commit 2a2626ab1a26717315e7efe5ae7918c7b1ed0d55
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 10 10:22:53 2019 -0700
Print Hnuc for every burn substep. Print total generated energy and average Hnuc at the end.
unit_test/burn_cell/main.f90
commit 9155ccc670f5fe215bb12142a66abda37d4b8873
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 19:21:59 2019 -0700
remove commented prints
networks/ECSN/actual_rhs.F90
commit a5ad1186bddd321946c462e45e40aa137bed61d9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 19:21:29 2019 -0700
remove prints
networks/ECSN/actual_network.F90
commit 70c66ed412822a6b595cbfa41cade7fcb2b64d26
Merge: 2b66a8d2 4f16a454
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Apr 9 21:39:22 2019 -0700
Merge pull request #176 from starkiller-astro/screen-cude
Fix screening for CUDA. Blanket private statements break the GPU pragma script.
commit 2b66a8d24585e9297375295b24f722e9ea063f72
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Apr 10 00:38:24 2019 -0400
Update CHANGES
CHANGES
commit f218f8c23e57ac9856cecb39f56cd292fede74cb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 18:38:05 2019 -0700
Update capitalization for API change.
python_library/StarKiller/examples/aprox13_sdc.py
commit 0e310d1c663d1e63d5762e0882bb2d6e31defefd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 18:37:04 2019 -0700
Add pdf and png files for latest ECSN test results.
python_library/StarKiller/examples/ECSN/ECSN-Test.pdf
python_library/StarKiller/examples/ECSN/eps_nuc_eos_compare.png
python_library/StarKiller/examples/ECSN/eps_nuc_network_compare.png
commit 14983f19f0ef6467d88a3ca3490fafd5c85b5071
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 18:35:55 2019 -0700
updated python API for calling the EOS in the RHS.
python_library/StarKiller/network/network.py
commit 1d9443817736c204960ae9ccc85d2cc44d5abaf0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 18:35:18 2019 -0700
reverted introduction of esum into network as a test, for now...
python_library/StarKiller/examples/ECSN/ECSN-Test.ipynb
commit 10165fb0964106643e578aed58da1505ebeb40ff
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Apr 9 18:17:23 2019 -0700
Update comparison to MESA in ECSN test.
python_library/StarKiller/examples/ECSN/ECSN-Test.ipynb
commit 4f16a454fd73c128807aa8166b72940682caec2c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 9 21:18:07 2019 -0400
blanket privates don't work with our gpu script
screening/screen.F90
commit 1766af6a5358dc38070141fbdfbb8f503289f553
Author: Alice Harpole <harpolea@users.noreply.github.com>
Date: Tue Apr 9 08:57:10 2019 -0400
fix dfdy(ihe4,ini56) (#175)
networks/aprox21/actual_rhs.F90
commit 37bef3e3ebe47a693ec53151a86e8aff65c54d9f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 8 23:42:16 2019 -0700
compilation fixes
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
commit d4f2a543b4e2e429c565b3cb0dab7869d68b3f92
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 8 23:27:59 2019 -0700
Update Urca network with tabular rate fixes.
networks/ignition_reaclib/URCA-simple/_parameters
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
commit f4fd974a01e8bf3b515c580ba97e444c266f2e08
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Apr 4 02:17:51 2019 -0700
Update ECSN test
python_library/StarKiller/examples/Burn-Test-ECSN.ipynb
python_library/StarKiller/examples/ECSN/ECSN-Test.ipynb
python_library/StarKiller/examples/ECSN/probin_ecsn
commit 5ebdd85196f34e3910c6bf04eeaf60d7f1e26799
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Apr 4 02:16:11 2019 -0700
Use non static Eos Type class. Call Eos with eos_state input in Network.
python_library/StarKiller/examples/call_eos.py
python_library/StarKiller/interfaces/eos_type.py
python_library/StarKiller/network/network.py
commit f196a5368f84770817cf00946461b369e19d19ab
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Apr 4 02:02:04 2019 -0700
Make BurnType a non-static class.
python_library/StarKiller/interfaces/burn_type.py
commit 9beed57adfb6ef3e44dba4ee89e016629c5614ad
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Apr 4 00:34:05 2019 -0700
Use nonstatic class for Eos and Network, as Network needs
initialization from the python library.
python_library/StarKiller/eos/eos.py
python_library/StarKiller/examples/call_eos.py
python_library/StarKiller/network/network.py
commit 6d1f3afa428d8555a2463ea97017e3a59cf1efa1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 17:56:29 2019 -0700
Set mu_e and y_e if abar and zbar are specified.
python_library/StarKiller/examples/call_eos.py
commit 13fdda5b9a0689260698458fc9f75f2bb3fde287
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 17:31:11 2019 -0700
Add readme to examples explaining which ones work.
python_library/StarKiller/examples/README.md
commit b03aeed6934f4820110abefd57c7fff89b4586c6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 17:26:48 2019 -0700
Update this example for the StarKiller package.
python_library/StarKiller/examples/Burn-Subch.ipynb
commit 5bc802aeab19feed0da2dbece160a5a36d1b91e2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 17:26:25 2019 -0700
Update for new StarKiller packaging.
python_library/StarKiller/burner/BurnUtils.py
commit bba78b6cd7576a0bd9c9f19bea56af310b1d32aa
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 17:00:29 2019 -0700
Update Readme to describe f90wrap dependency.
python_library/README.md
python_library/StarKiller/README.md
commit fc1a419dd652ec3bbfb5908c97dd1eefbccdffa3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:55:20 2019 -0700
Moved examples/README.md to the root StarKiller directory.
python_library/StarKiller/examples/README.md
commit 5cd2d659fcb2d38ffef3db3fd04e0c583d859df3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:54:55 2019 -0700
Update readme text
python_library/StarKiller/README.md
commit 76f563b1dc4e255d5c270b93f9c931d68e86545b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:50:03 2019 -0700
Add examples to package_data.
python_library/StarKiller/setup.py
commit 1e2511d98bccbd322032831b2aa30db60eadf996
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:45:02 2019 -0700
Add the StarKiller python package
python_library/StarKiller/burner/BurnUtils.py
python_library/StarKiller/burner/__init__.py
python_library/StarKiller/eos/__init__.py
python_library/StarKiller/eos/eos.py
python_library/StarKiller/examples/Burn Cell.ipynb
python_library/StarKiller/examples/Burn-Subch.ipynb
python_library/StarKiller/examples/Burn-Test-ECSN.ipynb
python_library/StarKiller/examples/README.md
python_library/StarKiller/examples/StarKiller Notebook Test.ipynb
python_library/StarKiller/examples/Test-Aprox13.ipynb
python_library/StarKiller/examples/aprox13_sdc.py
python_library/StarKiller/examples/call_eos.py
python_library/StarKiller/examples/probin.ignition
python_library/StarKiller/examples/probin_aprox13
python_library/StarKiller/examples/probin_burn_subch
python_library/StarKiller/examples/probin_ecsn
python_library/StarKiller/initialization/__init__.py
python_library/StarKiller/initialization/initialization.py
python_library/StarKiller/integration/__init__.py
python_library/StarKiller/integration/sdc.py
python_library/StarKiller/interfaces/__init__.py
python_library/StarKiller/interfaces/burn_type.py
python_library/StarKiller/interfaces/eos_type.py
python_library/StarKiller/network/__init__.py
python_library/StarKiller/network/network.py
python_library/StarKiller/setup.py
commit a203587d6dfe6e3b398b38a47fa7a1f9b1b6a153
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:42:05 2019 -0700
Add Readme file explaining how to use the python interface.
python_library/README.md
commit 0adc4fb69d4d79e0f3aab1dbf7d1e11e247895c8
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:36:57 2019 -0700
Add an optional input to the eos subroutine to disable calling the composition routine if desired.
unit_test/eos.F90
commit 00c3156ce4935f374c5576bde47aa6b222214b09
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Apr 3 16:35:25 2019 -0700
Use the python 3 version, f2py3, in dof2py.sh
python_library/dof2py.sh
commit d9b3c2c965251dc509f337d4424fa1d3a2d3338a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 1 20:35:28 2019 -0400
remove the blanket private -- gpus can't deal with this on IBM
EOS/helmholtz/actual_eos.F90
commit 02ba614ccf3478f0b532bdca2609b05950d02a6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 1 15:40:11 2019 -0400
this should not have been readded
networks/ECSN_weak/20f-20ne_betadecay.dat
networks/ECSN_weak/20f-20o_electroncapture.dat
networks/ECSN_weak/20ne-20f_electroncapture.dat
networks/ECSN_weak/20o-20f_betadecay.dat
networks/ECSN_weak/GPackage.mak
networks/ECSN_weak/Make.package
networks/ECSN_weak/NETWORK_REQUIRES
networks/ECSN_weak/_parameters
networks/ECSN_weak/actual_burner.F90
networks/ECSN_weak/actual_network.F90
networks/ECSN_weak/actual_rhs.F90
networks/ECSN_weak/ecsn.png
networks/ECSN_weak/inputs.burn_cell.VODE
networks/ECSN_weak/net_work_zingale.ipynb
networks/ECSN_weak/physical_constants.f90
networks/ECSN_weak/reaclib_rate_metadata.dat
networks/ECSN_weak/reaclib_rates.F90
networks/ECSN_weak/table_rates.F90
networks/ECSN_weak/xin.pynucastro.128
networks/ECSN_weak/xin.pynucastro.16
networks/ECSN_weak/xin.pynucastro.256
networks/ECSN_weak/xin.pynucastro.32
networks/ECSN_weak/xin.pynucastro.64
commit 2731cab5593a8cadae1d520e92419bf4f263cb42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 1 15:37:17 2019 -0400
add DOI badge
README.md
commit 78c608a4b7552be32190859153f0a0dab549ccd7
Merge: eb2ada4e 4c44a8eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 1 13:12:34 2019 -0400
Merge branch 'development'
commit ecbfec4306ceabefb3db247c6ffd025aad72ce7b
Merge: 25d0977d 4c44a8eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 31 16:08:14 2019 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit 4c44a8eb96fc86f165aff67ac433c3dc6becdde9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 27 13:42:18 2019 -0400
add Adam
.zenodo.json
commit b25ee328704cd80fcf395d1a97e4cd2354ddb4ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 26 15:03:36 2019 -0400
add abby
.zenodo.json
commit 6b9e99fa66de19df9d52b240ab080782c9eabb2f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Mar 25 13:33:23 2019 -0700
Move define with USE_CLEANED_CORRECTOR to networks/Make.package for codes
Make.Microphysics
networks/Make.package
commit a4bde32ef0ce6366dae2aadf08eaf59fdee99db8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Mar 25 10:17:46 2019 -0400
add Chris
.zenodo.json
commit 347666995ff84fad7f3ab3c05d3c0c5c7682efa0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 25 03:40:56 2019 -0400
go away
integration/BS/_parameters
commit 218104dac011c53e7117ebf4f4dd6a21b91ba280
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Mar 24 21:59:50 2019 -0700
Move VODE/VODE90 parameters up
integration/VODE/_parameters
integration/VODE90/_parameters
integration/_parameters
commit 25d0977d2b7af6172124a030c4c8518a91d24213
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Mar 24 12:34:49 2019 -0400
add Xinlong
.zenodo.json
commit 0d59a1226420df85536683c87948987357b78db0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 23 16:11:20 2019 -0400
add Frank
.zenodo.json
commit 23fe45126eb78c7b5f0a4bce6e5a534917c1662f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 23 15:24:13 2019 -0400
add Carl
.zenodo.json
commit 3774ed7b8b4a50ff9a5c27a2901b42a9534fd3a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Mar 23 13:15:04 2019 -0400
start of a .zenodo.json
.zenodo.json
commit 5081d91b4eec28140f1036defd1e2d871f66ae52
Merge: d19c043b 5b405509
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 15:31:27 2019 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit d19c043bd020b69044dd013c82267998319a5567
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 22 15:31:16 2019 -0400
add xinlong to mailmap
.mailmap
commit 5b405509687654ce89f8495acf1b42f8b4b10d0b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Mar 20 12:20:54 2019 -0700
When building against VODE90, if USE_CLEANED_CORRECTOR=TRUE then the corrector iterations will call clean_state.
Make.Microphysics
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
commit e71e715b4bbc8f2b2a0b167800b85a4e5ced4de2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Mar 20 08:48:36 2019 -0400
Create iso7 unit test burn
unit_test/test_react/inputs_iso7
unit_test/test_react/probin.iso7
unit_test/test_react/xin.iso7
commit 19217bc367cbd5bb80d733dda78b28508cdae1ad
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Mar 15 17:29:21 2019 -0700
Add probin for aprox13
unit_test/burn_cell_python/probin_aprox13
commit 9f87176dac3b3e205d4bd6012bc23a7f8a9f9032
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Mar 15 17:27:51 2019 -0700
Added test notebook for aprox13 rhs.
unit_test/burn_cell_python/Test-Aprox13.ipynb
commit e94c5a3e968d5035a606cf242193f0bd387c05d0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Mar 15 12:47:46 2019 -0700
Revert "space"
This reverts commit 9fa1f2752b80ac03b8957ea6d548fb8cc7c6e6b5.
README.md
commit 9fa1f2752b80ac03b8957ea6d548fb8cc7c6e6b5
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Mar 15 12:46:13 2019 -0700
space
README.md
commit 66111af543eef48efcaf981ec1c166cfad3ec3ee
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 23:20:44 2019 -0700
Update dumdt in sneut5 to match Itoh paper, eq. 3.3
neutrinos/sneut5.F90
commit 1c18ec9ec7bfef33dd5fa17d2c528bf8cdb2357c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 20:17:09 2019 -0700
update readme for python interface to burner.
unit_test/burn_cell_python/README.md
commit c280cd9c9cc4ce47245714aa385bcc789b23b797
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 20:03:43 2019 -0700
Add Burn notebook example for subch network.
unit_test/burn_cell_python/Burn-Subch.ipynb
commit d563ea9f77c5824ceb94cfb5dcc23ab84a0de0d7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 20:00:50 2019 -0700
Add ECSN burn test to run inputs from Josiah.
unit_test/burn_cell_python/Burn-Test-ECSN.ipynb
unit_test/burn_cell_python/probin_ecsn
commit 1f6f3830b62d7e090891d1c75fe6274206c14ff4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 19:52:14 2019 -0700
Fix bugs in ECSN network by removing dq,vs,mu,gamma energies. Make thermal neutrinos optional.
networks/ECSN/_parameters
networks/ECSN/actual_rhs.F90
networks/ECSN/table_rates.F90
commit de57d1a6c4a915dc5cb78a1b9ff1d953186574dc
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 19:25:43 2019 -0700
Add helper functions to get rhs components for temp and enuc
unit_test/burn_cell_python/BurnUtils.py
commit e6fecfdd49b74fc68ad16411beaf258a9d06013f
Merge: 1ac16745 989c1777
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 17:10:37 2019 -0700
Merge pull request #173 from sailoridy/master
add ECSN network from Xinlong
commit 989c177752309756031b72201c948a96eb2d450c
Merge: 12ed33af 93e1b965
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:53:29 2019 -0400
Merge branch 'master' of https://github.com/sailoridy/Microphysics
commit 12ed33af982f917d03abcee834563d89c8a6cfcb
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:53:10 2019 -0400
ECSN
networks/ECSN/20f-20ne_betadecay.dat
networks/ECSN/20f-20o_electroncapture.dat
networks/ECSN/20ne-20f_electroncapture.dat
networks/ECSN/20o-20f_betadecay.dat
networks/ECSN/GPackage.mak
networks/ECSN/Make.package
networks/ECSN/NETWORK_REQUIRES
networks/ECSN/_parameters
networks/ECSN/actual_burner.F90
networks/ECSN/actual_network.F90
networks/ECSN/actual_rhs.F90
networks/ECSN/ecsn.py
networks/ECSN/network_plot.py
networks/ECSN/physical_constants.f90
networks/ECSN/reaclib_rate_metadata.dat
networks/ECSN/reaclib_rates.F90
networks/ECSN/table_rates.F90
networks/ECSN/xin.pynucastro.128
networks/ECSN/xin.pynucastro.16
networks/ECSN/xin.pynucastro.256
networks/ECSN/xin.pynucastro.32
networks/ECSN/xin.pynucastro.64
unit_test/burn_cell/20f-20ne_betadecay.dat
unit_test/burn_cell/20f-20o_electroncapture.dat
unit_test/burn_cell/20ne-20f_electroncapture.dat
unit_test/burn_cell/20o-20f_betadecay.dat
unit_test/burn_cell/reaclib_rate_metadata.dat
commit 93e1b96545a193bcb63236fe5a64f2cba6725095
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:24:53 2019 -0400
Delete 20f-20o_electroncapture.dat
unit_test/burn_cell/20f-20o_electroncapture.dat
commit 3f55c8f85e54f8825791a7e140687817808ba596
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:24:37 2019 -0400
Delete 20ne-20f_electroncapture.dat
unit_test/burn_cell/20ne-20f_electroncapture.dat
commit 7487aea59298421fa3e75ba622497f3bd6a61f2e
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:24:21 2019 -0400
Delete 20o-20f_betadecay.dat
unit_test/burn_cell/20o-20f_betadecay.dat
commit 93b79743fe7129069faf1f8edcb10a35c4db08a3
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:24:03 2019 -0400
Delete reaclib_rate_metadata.dat
unit_test/burn_cell/reaclib_rate_metadata.dat
commit 39d5e134d216ea717a2d5da29cfe2087a8d380a0
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:23:46 2019 -0400
Delete 20f-20ne_betadecay.dat
unit_test/burn_cell/20f-20ne_betadecay.dat
commit 7d5c806a05adf9d2f6e844406b482727e1f9212b
Merge: f7d14a9b fbc4c0fb
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:17:43 2019 -0400
Merge branch 'master' of https://github.com/sailoridy/Microphysics
commit f7d14a9bab619d6e246f94b9fceeb863b0db7aef
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:17:31 2019 -0400
ECSN
unit_test/burn_cell/main.f90
commit fbc4c0fbabf9806e6beb250e26350bd19857bea2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 14 14:06:49 2019 -0700
Revert changes to burn cell GNUmakefile
Debug compilation flag is NDEBUG for the Fortran build system.
network_test has been deleted.
unit_test/burn_cell/GNUmakefile
commit c9009613a1727b2db30982fe5213955b474a9c84
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:04:07 2019 -0400
ECSN
unit_test/burn_cell/.main.f90.swp
unit_test/burn_cell/inputs_ECSN_test
unit_test/burn_cell/react_ECSN_output/react_ECSN_000000
unit_test/burn_cell/react_ECSN_output/react_ECSN_000001
unit_test/burn_cell/react_ECSN_output/react_ECSN_000002
unit_test/burn_cell/react_ECSN_output/react_ECSN_000003
unit_test/burn_cell/react_ECSN_output/react_ECSN_000004
unit_test/burn_cell/react_ECSN_output/react_ECSN_000005
unit_test/burn_cell/test_ECSN_output/test_ECSN_000000
unit_test/burn_cell/test_ECSN_output/test_ECSN_000001
unit_test/burn_cell/test_ECSN_output/test_ECSN_000002
unit_test/burn_cell/test_ECSN_output/test_ECSN_000003
unit_test/burn_cell/test_ECSN_output/test_ECSN_000004
unit_test/burn_cell/test_ECSN_output/test_ECSN_000005
unit_test/burn_cell/test_ECSN_output/test_ECSN_000006
unit_test/burn_cell/test_ECSN_output/test_ECSN_000007
unit_test/burn_cell/test_ECSN_output/test_ECSN_000008
commit 59c2e7bc8208ff4ba482137706232996a71b203f
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 17:01:06 2019 -0400
ECSN
networks/ECSN_weak/ecsn.png
networks/ECSN_weak/net_work_zingale.ipynb
networks/network_test/20ne-20f_electroncapture.dat
networks/network_test/GPackage.mak
networks/network_test/Make.package
networks/network_test/NETWORK_REQUIRES
networks/network_test/_parameters
networks/network_test/actual_burner.F90
networks/network_test/actual_network.F90
networks/network_test/actual_rhs.F90
networks/network_test/ecsn.png
networks/network_test/inputs.burn_cell.VODE
networks/network_test/net_work_zingale.ipynb
networks/network_test/physical_constants.f90
networks/network_test/reaclib_rate_metadata.dat
networks/network_test/reaclib_rates.F90
networks/network_test/table_rates.F90
networks/network_test/xin.pynucastro.128
networks/network_test/xin.pynucastro.16
networks/network_test/xin.pynucastro.256
networks/network_test/xin.pynucastro.32
networks/network_test/xin.pynucastro.64
commit 81442759dddce36799befa84675427295cd1b713
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 16:00:06 2019 -0400
Delete main.f90
unit_test/burn_cell/main.f90
commit ba44b7b595eb41961cd87ac904cc86c8634683ce
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 14 15:58:52 2019 -0400
Delete net_work_zingale-checkpoint.ipynb
networks/network_test/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
commit 1ac16745962e66c6178f85365e3f88ba954031ac
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Mar 13 17:20:55 2019 -0400
use CUDA_VERSION=70 for Groot
unit_test/test_cvode_react/make_aprox13_cusolver.sh
commit d5696241c20fccbdf6d8b4f6449dcf9ef4aecd79
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Mar 13 15:55:37 2019 -0400
Add build script for this test on Groot
unit_test/test_cvode_react/make_aprox13_cusolver.sh
commit 489e64babd9eb3254ab43f11ddad290fac76a6a3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Mar 13 15:54:39 2019 -0400
use input temp, dens ranges from test_react
unit_test/test_cvode_react/probin.aprox13
commit 62e0e156d7b17690d0d32776456a36a4d0622699
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 03:53:27 2019 -0400
aprox13 optimization: avoid local rate arrays
networks/aprox13/actual_rhs.F90
commit b617ac6b58664a44539496e83624f97132690e5c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Mar 12 02:46:54 2019 -0400
Remove scfac arrays -- these are not ever used
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_rhs.F90
networks/iso7/actual_rhs.f90
commit 7acdf011c6a14e754f7f072e68aaee1dd6510936
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Mar 11 23:01:32 2019 -0400
ECSN
networks/ECSN_weak/actual_rhs.F90
networks/network_test/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/network_test/20ne-20f_electroncapture.dat
networks/network_test/GPackage.mak
networks/network_test/Make.package
networks/network_test/NETWORK_REQUIRES
networks/network_test/_parameters
networks/network_test/actual_burner.F90
networks/network_test/actual_network.F90
networks/network_test/actual_rhs.F90
networks/network_test/ecsn.png
networks/network_test/inputs.burn_cell.VODE
networks/network_test/net_work_zingale.ipynb
networks/network_test/physical_constants.f90
networks/network_test/reaclib_rate_metadata.dat
networks/network_test/reaclib_rates.F90
networks/network_test/table_rates.F90
networks/network_test/xin.pynucastro.128
networks/network_test/xin.pynucastro.16
networks/network_test/xin.pynucastro.256
networks/network_test/xin.pynucastro.32
networks/network_test/xin.pynucastro.64
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/inputs_ECSN_test
unit_test/burn_cell/main.f90
unit_test/burn_cell/test_ECSN_output/test_ECSN_000000
unit_test/burn_cell/test_ECSN_output/test_ECSN_000001
unit_test/burn_cell/test_ECSN_output/test_ECSN_000002
unit_test/burn_cell/test_ECSN_output/test_ECSN_000003
unit_test/burn_cell/test_ECSN_output/test_ECSN_000004
unit_test/burn_cell/test_ECSN_output/test_ECSN_000005
unit_test/burn_cell/test_ECSN_output/test_ECSN_000006
unit_test/burn_cell/test_ECSN_output/test_ECSN_000007
unit_test/burn_cell/test_ECSN_output/test_ECSN_000008
commit 43b77105074d902eb9c1649c4eb23a878c99e9c7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Mar 11 07:53:44 2019 -0400
Define CUDA
Make.Microphysics
commit a67a3b468a874bfe4fc57be4bd0faa6942bcd14c
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Mar 7 13:14:04 2019 -0500
ECSN
networks/ECSN_weak/actual_network.F90
networks/ECSN_weak/actual_rhs.F90
networks/network_test/.actual_rhs.F90.swp
networks/network_test/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/network_test/20ne-20f_electroncapture.dat
networks/network_test/GPackage.mak
networks/network_test/Make.package
networks/network_test/NETWORK_REQUIRES
networks/network_test/_parameters
networks/network_test/actual_burner.F90
networks/network_test/actual_network.F90
networks/network_test/actual_rhs.F90
networks/network_test/ecsn.png
networks/network_test/inputs.burn_cell.VODE
networks/network_test/net_work_zingale.ipynb
networks/network_test/physical_constants.f90
networks/network_test/reaclib_rate_metadata.dat
networks/network_test/reaclib_rates.F90
networks/network_test/table_rates.F90
networks/network_test/xin.pynucastro.128
networks/network_test/xin.pynucastro.16
networks/network_test/xin.pynucastro.256
networks/network_test/xin.pynucastro.32
networks/network_test/xin.pynucastro.64
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/inputs_ECSN_burn
unit_test/burn_cell/inputs_ECSN_test
unit_test/burn_cell/react_ECSN_output/react_ECSN_000000
unit_test/burn_cell/react_ECSN_output/react_ECSN_000001
unit_test/burn_cell/react_ECSN_output/react_ECSN_000002
unit_test/burn_cell/react_ECSN_output/react_ECSN_000003
unit_test/burn_cell/react_ECSN_output/react_ECSN_000004
unit_test/burn_cell/react_ECSN_output/react_ECSN_000005
unit_test/burn_cell/test_ECSN_output/test_ECSN_000000
unit_test/burn_cell/test_ECSN_output/test_ECSN_000001
commit 1a93931299c82f9a547f0db88aecb04c351f54e7
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Mar 4 08:57:15 2019 -0500
add test_networks
networks/network_test/.actual_rhs.F90.swp
networks/network_test/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/network_test/20ne-20f_electroncapture.dat
networks/network_test/GPackage.mak
networks/network_test/Make.package
networks/network_test/NETWORK_REQUIRES
networks/network_test/_parameters
networks/network_test/actual_burner.F90
networks/network_test/actual_network.F90
networks/network_test/actual_rhs.F90
networks/network_test/ecsn.png
networks/network_test/inputs.burn_cell.VODE
networks/network_test/net_work_zingale.ipynb
networks/network_test/physical_constants.f90
networks/network_test/reaclib_rate_metadata.dat
networks/network_test/reaclib_rates.F90
networks/network_test/table_rates.F90
networks/network_test/xin.pynucastro.128
networks/network_test/xin.pynucastro.16
networks/network_test/xin.pynucastro.256
networks/network_test/xin.pynucastro.32
networks/network_test/xin.pynucastro.64
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/inputs_ECSN_test
unit_test/burn_cell/test_ECSN_output/test_ECSN_000000
unit_test/burn_cell/test_ECSN_output/test_ECSN_000001
unit_test/burn_cell/test_ECSN_output/test_ECSN_000002
unit_test/burn_cell/test_ECSN_output/test_ECSN_000003
unit_test/burn_cell/test_ECSN_output/test_ECSN_000004
unit_test/burn_cell/test_ECSN_output/test_ECSN_000005
commit eb2ada4e4a5989a7706baa33c423dc2ce2b6a04d
Merge: 921d63b6 3a0365bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 1 08:45:43 2019 -0500
Merge branch 'development'
commit 992b0d600abb4da2fa192269a061876de58bd88f
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Feb 28 13:08:57 2019 -0500
ECSN
unit_test/burn_cell/react_ECSN_output/react_ECSN_000000
unit_test/burn_cell/react_ECSN_output/react_ECSN_000001
unit_test/burn_cell/react_ECSN_output/react_ECSN_000002
unit_test/burn_cell/react_ECSN_output/react_ECSN_000003
unit_test/burn_cell/react_ECSN_output/react_ECSN_000004
unit_test/burn_cell/react_ECSN_output/react_ECSN_000005
unit_test/burn_cell/react_ECSN_output/react_ECSN_000006
unit_test/burn_cell/react_ECSN_output/react_ECSN_000007
unit_test/burn_cell/react_ECSN_output/react_ECSN_000008
unit_test/burn_cell/react_ECSN_output/react_ECSN_000009
unit_test/burn_cell/react_ECSN_output/react_ECSN_000010
unit_test/burn_cell/react_ECSN_output/react_ECSN_000011
unit_test/burn_cell/react_ECSN_output/react_ECSN_000012
unit_test/burn_cell/react_ECSN_output/react_ECSN_000013
unit_test/burn_cell/react_ECSN_output/react_ECSN_000014
unit_test/burn_cell/react_ECSN_output/react_ECSN_000015
unit_test/burn_cell/react_ECSN_output/react_ECSN_000016
unit_test/burn_cell/react_ECSN_output/react_ECSN_000017
unit_test/burn_cell/react_ECSN_output/react_ECSN_000018
unit_test/burn_cell/react_ECSN_output/react_ECSN_000019
unit_test/burn_cell/react_ECSN_output/react_ECSN_000020
unit_test/burn_cell/react_ECSN_output/react_ECSN_000021
unit_test/burn_cell/react_ECSN_output/react_ECSN_000022
unit_test/burn_cell/react_ECSN_output/react_ECSN_000023
unit_test/burn_cell/react_ECSN_output/react_ECSN_000024
unit_test/burn_cell/react_ECSN_output/react_ECSN_000025
unit_test/burn_cell/react_ECSN_output/react_ECSN_000026
unit_test/burn_cell/react_ECSN_output/react_ECSN_000027
unit_test/burn_cell/react_ECSN_output/react_ECSN_000028
unit_test/burn_cell/react_ECSN_output/react_ECSN_000029
unit_test/burn_cell/react_ECSN_output/react_ECSN_000030
unit_test/burn_cell/react_ECSN_output/react_ECSN_000031
unit_test/burn_cell/react_ECSN_output/react_ECSN_000032
unit_test/burn_cell/react_ECSN_output/react_ECSN_000033
unit_test/burn_cell/react_ECSN_output/react_ECSN_000034
unit_test/burn_cell/react_ECSN_output/react_ECSN_000035
unit_test/burn_cell/react_ECSN_output/react_ECSN_000036
unit_test/burn_cell/react_ECSN_output/react_ECSN_000037
unit_test/burn_cell/react_ECSN_output/react_ECSN_000038
unit_test/burn_cell/react_ECSN_output/react_ECSN_000039
unit_test/burn_cell/react_ECSN_output/react_ECSN_000040
unit_test/burn_cell/react_ECSN_output/react_ECSN_000041
unit_test/burn_cell/react_ECSN_output/react_ECSN_000042
unit_test/burn_cell/react_ECSN_output/react_ECSN_000043
unit_test/burn_cell/react_ECSN_output/react_ECSN_000044
unit_test/burn_cell/react_ECSN_output/react_ECSN_000045
unit_test/burn_cell/react_ECSN_output/react_ECSN_000046
unit_test/burn_cell/react_ECSN_output/react_ECSN_000047
unit_test/burn_cell/react_ECSN_output/react_ECSN_000048
unit_test/burn_cell/react_ECSN_output/react_ECSN_000049
unit_test/burn_cell/react_ECSN_output/react_ECSN_000050
unit_test/burn_cell/react_ECSN_output/react_ECSN_000051
unit_test/burn_cell/react_ECSN_output/react_ECSN_000052
unit_test/burn_cell/react_ECSN_output/react_ECSN_000053
unit_test/burn_cell/react_ECSN_output/react_ECSN_000054
unit_test/burn_cell/react_ECSN_output/react_ECSN_000055
unit_test/burn_cell/react_ECSN_output/react_ECSN_000056
unit_test/burn_cell/react_ECSN_output/react_ECSN_000057
unit_test/burn_cell/react_ECSN_output/react_ECSN_000058
unit_test/burn_cell/react_ECSN_output/react_ECSN_000059
unit_test/burn_cell/react_ECSN_output/react_ECSN_000060
unit_test/burn_cell/react_ECSN_output/react_ECSN_000061
unit_test/burn_cell/react_ECSN_output/react_ECSN_000062
unit_test/burn_cell/react_ECSN_output/react_ECSN_000063
unit_test/burn_cell/react_ECSN_output/react_ECSN_000064
unit_test/burn_cell/react_ECSN_output/react_ECSN_000065
unit_test/burn_cell/react_ECSN_output/react_ECSN_000066
unit_test/burn_cell/react_ECSN_output/react_ECSN_000067
unit_test/burn_cell/react_ECSN_output/react_ECSN_000068
unit_test/burn_cell/react_ECSN_output/react_ECSN_000069
unit_test/burn_cell/react_ECSN_output/react_ECSN_000070
unit_test/burn_cell/react_ECSN_output/react_ECSN_000071
unit_test/burn_cell/react_ECSN_output/react_ECSN_000072
unit_test/burn_cell/react_ECSN_output/react_ECSN_000073
unit_test/burn_cell/react_ECSN_output/react_ECSN_000074
unit_test/burn_cell/react_ECSN_output/react_ECSN_000075
unit_test/burn_cell/react_ECSN_output/react_ECSN_000076
unit_test/burn_cell/react_ECSN_output/react_ECSN_000077
unit_test/burn_cell/react_ECSN_output/react_ECSN_000078
unit_test/burn_cell/react_ECSN_output/react_ECSN_000079
unit_test/burn_cell/react_ECSN_output/react_ECSN_000080
unit_test/burn_cell/react_ECSN_output/react_ECSN_000081
unit_test/burn_cell/react_ECSN_output/react_ECSN_000082
unit_test/burn_cell/react_ECSN_output/react_ECSN_000083
unit_test/burn_cell/react_ECSN_output/react_ECSN_000084
unit_test/burn_cell/react_ECSN_output/react_ECSN_000085
unit_test/burn_cell/react_ECSN_output/react_ECSN_000086
unit_test/burn_cell/react_ECSN_output/react_ECSN_000087
unit_test/burn_cell/react_ECSN_output/react_ECSN_000088
unit_test/burn_cell/react_ECSN_output/react_ECSN_000089
unit_test/burn_cell/react_ECSN_output/react_ECSN_000090
unit_test/burn_cell/react_ECSN_output/react_ECSN_000091
unit_test/burn_cell/react_ECSN_output/react_ECSN_000092
unit_test/burn_cell/react_ECSN_output/react_ECSN_000093
unit_test/burn_cell/react_ECSN_output/react_ECSN_000094
unit_test/burn_cell/react_ECSN_output/react_ECSN_000095
unit_test/burn_cell/react_ECSN_output/react_ECSN_000096
unit_test/burn_cell/react_ECSN_output/react_ECSN_000097
unit_test/burn_cell/react_ECSN_output/react_ECSN_000098
unit_test/burn_cell/react_ECSN_output/react_ECSN_000099
unit_test/burn_cell/react_ECSN_output/react_ECSN_000100
commit 828f21a6e49fc16235f7aab11d28b1d7f63aa42e
Merge: aedc3aaa b223e931
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Feb 28 13:08:27 2019 -0500
Merge branch 'master' of https://github.com/sailoridy/Microphysics
commit aedc3aaa0c01f5d0e4cf74b9048aa128bc8f2526
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Feb 28 13:07:51 2019 -0500
ECSN
unit_test/burn_cell/20f-20ne_betadecay.dat
unit_test/burn_cell/20f-20o_electroncapture.dat
unit_test/burn_cell/20ne-20f_electroncapture.dat
unit_test/burn_cell/20o-20f_betadecay.dat
unit_test/burn_cell/inputs_ECSN_burn
unit_test/burn_cell/main.f90
unit_test/burn_cell/reaclib_rate_metadata.dat
unit_test/burn_cell/react_ECSN_output/react_ECSN_000000
unit_test/burn_cell/react_ECSN_output/react_ECSN_000001
unit_test/burn_cell/react_ECSN_output/react_ECSN_000002
unit_test/burn_cell/react_ECSN_output/react_ECSN_000003
unit_test/burn_cell/react_ECSN_output/react_ECSN_000004
unit_test/burn_cell/react_ECSN_output/react_ECSN_000005
unit_test/burn_cell/react_ECSN_output/react_ECSN_000006
unit_test/burn_cell/react_ECSN_output/react_ECSN_000007
unit_test/burn_cell/react_ECSN_output/react_ECSN_000008
unit_test/burn_cell/react_ECSN_output/react_ECSN_000009
unit_test/burn_cell/react_ECSN_output/react_ECSN_000010
unit_test/burn_cell/react_ECSN_output/react_ECSN_000011
unit_test/burn_cell/react_ECSN_output/react_ECSN_000012
unit_test/burn_cell/react_ECSN_output/react_ECSN_000013
unit_test/burn_cell/react_ECSN_output/react_ECSN_000014
unit_test/burn_cell/react_ECSN_output/react_ECSN_000015
unit_test/burn_cell/react_ECSN_output/react_ECSN_000016
unit_test/burn_cell/react_ECSN_output/react_ECSN_000017
unit_test/burn_cell/react_ECSN_output/react_ECSN_000018
unit_test/burn_cell/react_ECSN_output/react_ECSN_000019
unit_test/burn_cell/react_ECSN_output/react_ECSN_000020
unit_test/burn_cell/react_ECSN_output/react_ECSN_000021
unit_test/burn_cell/react_ECSN_output/react_ECSN_000022
unit_test/burn_cell/react_ECSN_output/react_ECSN_000023
unit_test/burn_cell/react_ECSN_output/react_ECSN_000024
unit_test/burn_cell/react_ECSN_output/react_ECSN_000025
unit_test/burn_cell/react_ECSN_output/react_ECSN_000026
unit_test/burn_cell/react_ECSN_output/react_ECSN_000027
unit_test/burn_cell/react_ECSN_output/react_ECSN_000028
unit_test/burn_cell/react_ECSN_output/react_ECSN_000029
unit_test/burn_cell/react_ECSN_output/react_ECSN_000030
unit_test/burn_cell/react_ECSN_output/react_ECSN_000031
unit_test/burn_cell/react_ECSN_output/react_ECSN_000032
unit_test/burn_cell/react_ECSN_output/react_ECSN_000033
unit_test/burn_cell/react_ECSN_output/react_ECSN_000034
unit_test/burn_cell/react_ECSN_output/react_ECSN_000035
unit_test/burn_cell/react_ECSN_output/react_ECSN_000036
unit_test/burn_cell/react_ECSN_output/react_ECSN_000037
unit_test/burn_cell/react_ECSN_output/react_ECSN_000038
unit_test/burn_cell/react_ECSN_output/react_ECSN_000039
unit_test/burn_cell/react_ECSN_output/react_ECSN_000040
unit_test/burn_cell/react_ECSN_output/react_ECSN_000041
unit_test/burn_cell/react_ECSN_output/react_ECSN_000042
unit_test/burn_cell/react_ECSN_output/react_ECSN_000043
unit_test/burn_cell/react_ECSN_output/react_ECSN_000044
unit_test/burn_cell/react_ECSN_output/react_ECSN_000045
unit_test/burn_cell/react_ECSN_output/react_ECSN_000046
unit_test/burn_cell/react_ECSN_output/react_ECSN_000047
unit_test/burn_cell/react_ECSN_output/react_ECSN_000048
unit_test/burn_cell/react_ECSN_output/react_ECSN_000049
unit_test/burn_cell/react_ECSN_output/react_ECSN_000050
unit_test/burn_cell/react_ECSN_output/react_ECSN_000051
unit_test/burn_cell/react_ECSN_output/react_ECSN_000052
unit_test/burn_cell/react_ECSN_output/react_ECSN_000053
unit_test/burn_cell/react_ECSN_output/react_ECSN_000054
unit_test/burn_cell/react_ECSN_output/react_ECSN_000055
unit_test/burn_cell/react_ECSN_output/react_ECSN_000056
unit_test/burn_cell/react_ECSN_output/react_ECSN_000057
unit_test/burn_cell/react_ECSN_output/react_ECSN_000058
unit_test/burn_cell/react_ECSN_output/react_ECSN_000059
unit_test/burn_cell/react_ECSN_output/react_ECSN_000060
unit_test/burn_cell/react_ECSN_output/react_ECSN_000061
unit_test/burn_cell/react_ECSN_output/react_ECSN_000062
unit_test/burn_cell/react_ECSN_output/react_ECSN_000063
unit_test/burn_cell/react_ECSN_output/react_ECSN_000064
unit_test/burn_cell/react_ECSN_output/react_ECSN_000065
unit_test/burn_cell/react_ECSN_output/react_ECSN_000066
unit_test/burn_cell/react_ECSN_output/react_ECSN_000067
unit_test/burn_cell/react_ECSN_output/react_ECSN_000068
unit_test/burn_cell/react_ECSN_output/react_ECSN_000069
unit_test/burn_cell/react_ECSN_output/react_ECSN_000070
unit_test/burn_cell/react_ECSN_output/react_ECSN_000071
unit_test/burn_cell/react_ECSN_output/react_ECSN_000072
unit_test/burn_cell/react_ECSN_output/react_ECSN_000073
unit_test/burn_cell/react_ECSN_output/react_ECSN_000074
unit_test/burn_cell/react_ECSN_output/react_ECSN_000075
unit_test/burn_cell/react_ECSN_output/react_ECSN_000076
unit_test/burn_cell/react_ECSN_output/react_ECSN_000077
unit_test/burn_cell/react_ECSN_output/react_ECSN_000078
unit_test/burn_cell/react_ECSN_output/react_ECSN_000079
unit_test/burn_cell/react_ECSN_output/react_ECSN_000080
unit_test/burn_cell/react_ECSN_output/react_ECSN_000081
unit_test/burn_cell/react_ECSN_output/react_ECSN_000082
unit_test/burn_cell/react_ECSN_output/react_ECSN_000083
unit_test/burn_cell/react_ECSN_output/react_ECSN_000084
unit_test/burn_cell/react_ECSN_output/react_ECSN_000085
unit_test/burn_cell/react_ECSN_output/react_ECSN_000086
unit_test/burn_cell/react_ECSN_output/react_ECSN_000087
unit_test/burn_cell/react_ECSN_output/react_ECSN_000088
unit_test/burn_cell/react_ECSN_output/react_ECSN_000089
unit_test/burn_cell/react_ECSN_output/react_ECSN_000090
unit_test/burn_cell/react_ECSN_output/react_ECSN_000091
unit_test/burn_cell/react_ECSN_output/react_ECSN_000092
unit_test/burn_cell/react_ECSN_output/react_ECSN_000093
unit_test/burn_cell/react_ECSN_output/react_ECSN_000094
unit_test/burn_cell/react_ECSN_output/react_ECSN_000095
unit_test/burn_cell/react_ECSN_output/react_ECSN_000096
unit_test/burn_cell/react_ECSN_output/react_ECSN_000097
unit_test/burn_cell/react_ECSN_output/react_ECSN_000098
unit_test/burn_cell/react_ECSN_output/react_ECSN_000099
unit_test/burn_cell/react_ECSN_output/react_ECSN_000100
commit 3a0365bf3460d22ebad6ad586f079a1606c9c9ee
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:11:29 2019 -0500
acc routine for copy_burn_t
interfaces/burn_type.F90
commit a29cd01c20bb21c39f1a297949b1ef36094564aa
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:11:21 2019 -0500
acc routine information for ignition_simple
networks/ignition_simple/actual_rhs.F90
commit 582bfc1fbdef355ece6fc891e697c1e55318615a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:11:08 2019 -0500
Create acc version of self_heat
integration/temperature_integration.F90
commit f4ac10c187e0350a89a30a1bb6edf09583d36150
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:10:50 2019 -0500
acc routine information for screening
screening/screen.F90
commit 02b93b277c200983773358b17049c20e6a6933d9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 12:02:03 2019 -0500
Add acc routine information for EOS
interfaces/eos_type.F90
unit_test/eos.F90
unit_test/eos_override.F90
commit b223e9311993cc8548ad6f0f6d2d775dcb61ff97
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 11:01:39 2019 -0500
Delete net_work_zingale-checkpoint.ipynb
networks/ECSN_weak/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
commit 54fdd12e8960cf9e0a1b34566adebffc857f35df
Merge: dcd3b760 3f3b1d4f
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 11:00:00 2019 -0500
ECSN
commit dcd3b760494f74d3c694e6038bdc2efd99e5aaa7
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 10:57:32 2019 -0500
ECSN
networks/ECSN_weak/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/ECSN_weak/reaclib_rates.F90
unit_test/burn_cell/main.f90
commit 3f3b1d4faf5471d0e580ec2763b8081c548b10d4
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 10:33:12 2019 -0500
Delete main.f90
unit_test/burn_cell/main.f90
commit 2765dcaf097f517d46814e9a2e765053a200fb9b
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 10:32:22 2019 -0500
Delete inputs.burn_cell.VODE
networks/ECSN_weak/inputs.burn_cell.VODE
commit 90f4d364476eee64b56061b050b06ecf2e2d3760
Merge: a48dc734 2e4c9c0d
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 10:27:41 2019 -0500
Merge branch 'master' of https://github.com/sailoridy/Microphysics
commit a48dc7348ed51bd8d5d7fd742c230ab1fa9e2b8d
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Mon Feb 25 10:27:16 2019 -0500
burn_cell_ECSN
networks/ECSN_weak/reaclib_rates.F90
unit_test/burn_cell/.main.f90.swp
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/inputs_ECSN_burn
unit_test/burn_cell/main.f90
unit_test/burn_cell/reaclib_rate_metadata.dat
commit 5348885fcc85c1cae29144963d5e5d2e6a82e753
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 03:27:08 2019 -0500
Create symlink to URCA-simple rate metadata file
Make.Microphysics
commit 059b76ed01b91fa5f7e4b37ae1ce4eb4cbe56e9b
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Feb 25 03:10:42 2019 -0500
Fix VODE90 compilation
integration/VODE90/actual_integrator.F90
commit 5b293a9d0d9966b5c25155ac6e874097a61deb3f
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Feb 23 07:12:36 2019 -0800
Store self_heat as a module parameter (#169)
integration/BS/bs_integrator.F90
integration/CVODE/cvode_type.F90
integration/VBDF/vbdf_integrator.F90
integration/VODE/vode_integrator.f90
integration/VODE90/actual_integrator.F90
integration/integrator.F90
integration/temperature_integration.F90
commit d3c7e0ca90a18e45c44fb4e9ebc7e96dbd4f67e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Feb 17 19:04:33 2019 -0800
Restore acc routine seq
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
commit 921d63b678cfd822ac9e871a783dca9933afba08
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Feb 14 14:45:06 2019 -0500
updata ECSN networks (#167)
* add ECSN
* updata ECSN_weak netwoks
* Delete net_work_zingale-checkpoint.ipynb
networks/ECSN_weak/20f-20ne_betadecay.dat
networks/ECSN_weak/20f-20o_electroncapture.dat
networks/ECSN_weak/20ne-20f_electroncapture.dat
networks/ECSN_weak/20o-20f_betadecay.dat
networks/ECSN_weak/GPackage.mak
networks/ECSN_weak/Make.package
networks/ECSN_weak/NETWORK_REQUIRES
networks/ECSN_weak/_parameters
networks/ECSN_weak/actual_burner.F90
networks/ECSN_weak/actual_network.F90
networks/ECSN_weak/actual_rhs.F90
networks/ECSN_weak/ecsn.png
networks/ECSN_weak/inputs.burn_cell.VODE
networks/ECSN_weak/net_work_zingale.ipynb
networks/ECSN_weak/physical_constants.f90
networks/ECSN_weak/reaclib_rate_metadata.dat
networks/ECSN_weak/reaclib_rates.F90
networks/ECSN_weak/table_rates.F90
networks/ECSN_weak/xin.pynucastro.128
networks/ECSN_weak/xin.pynucastro.16
networks/ECSN_weak/xin.pynucastro.256
networks/ECSN_weak/xin.pynucastro.32
networks/ECSN_weak/xin.pynucastro.64
commit 2e4c9c0d3cc30aeea6edb4bd3c1bd2a410eaf253
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Feb 14 14:43:17 2019 -0500
Delete net_work_zingale-checkpoint.ipynb
networks/ECSN_weak/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
commit 32001e0e9094f49a4022490d236af906b3f4976e
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Thu Feb 14 14:31:45 2019 -0500
updata ECSN_weak netwoks
networks/ECSN_weak/20f-20ne_betadecay.dat
networks/ECSN_weak/20f-20o_electroncapture.dat
networks/ECSN_weak/20ne-20f_electroncapture.dat
networks/ECSN_weak/20o-20f_betadecay.dat
networks/ECSN_weak/actual_network.F90
networks/ECSN_weak/actual_rhs.F90
networks/ECSN_weak/ecsn.png
networks/ECSN_weak/net_work_zingale.ipynb
networks/ECSN_weak/reaclib_rate_metadata.dat
networks/ECSN_weak/table_rates.F90
commit 1483bb9be9721224ae951f63d6ef23158413ea18
Author: Xinlong Li <xinlong.li@stonybrook.edu>
Date: Wed Feb 6 01:40:42 2019 -0500
add ECSN
networks/ECSN_weak/.ipynb_checkpoints/net_work_zingale-checkpoint.ipynb
networks/ECSN_weak/20f-20o.dat
networks/ECSN_weak/20ne-20f.dat
networks/ECSN_weak/GPackage.mak
networks/ECSN_weak/Make.package
networks/ECSN_weak/NETWORK_REQUIRES
networks/ECSN_weak/_parameters
networks/ECSN_weak/actual_burner.F90
networks/ECSN_weak/actual_network.F90
networks/ECSN_weak/actual_rhs.F90
networks/ECSN_weak/ecsn.png
networks/ECSN_weak/inputs.burn_cell.VODE
networks/ECSN_weak/net_work_zingale.ipynb
networks/ECSN_weak/physical_constants.f90
networks/ECSN_weak/reaclib_rate_metadata.dat
networks/ECSN_weak/reaclib_rates.F90
networks/ECSN_weak/table_rates.F90
networks/ECSN_weak/xin.pynucastro.128
networks/ECSN_weak/xin.pynucastro.16
networks/ECSN_weak/xin.pynucastro.256
networks/ECSN_weak/xin.pynucastro.32
networks/ECSN_weak/xin.pynucastro.64
commit 719edc0ca3d050947697f54211c4e4c79b93ebe9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Feb 1 09:27:03 2019 -0500
update changes
CHANGES
commit da53ec663bcbaafbc19e602d1834d3124cf6a89c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jan 31 13:29:46 2019 -0500
ECSN composition
networks/general_null/ECSN.net
commit a37a226f701fbf19788a745b7e7aed755ff77072
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 11:52:46 2019 -0500
make this GPUable
EOS/multigamma/actual_eos.F90
commit 59f62c24aa5611b32e7435176ba842cf49db666f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 2 09:48:18 2019 -0500
update changes
CHANGES
commit e0cda1172837fd7c44a7661ca1e7943c60df8f6f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 20 19:56:48 2018 -0800
For Urca network, invert the sign of the tabulated chemical potential for the beta decay to get its contribution to energy generation right.
networks/ignition_reaclib/URCA-simple/table_rates.F90
commit 2e671df4d25675eb8104aa4f77376653822065ca
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 20 18:31:13 2018 -0800
Allow multiple burns with python driver. Fix plot legend.
unit_test/burn_cell_python/BurnUtils.py
commit 382459e298e21ad8b2ecf4c5ad21b32ce10a8d04
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 20 18:30:41 2018 -0800
Add Fermi heating term to Urca network.
networks/ignition_reaclib/URCA-simple/_parameters
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
commit e3d2d1d3645820cf1190509496c65b8b8e7c52ff
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 19:23:21 2018 -0800
testing -- Preface
sphinx_docs/source/preface.rst
commit c0e5e28c10af2265c29692767048e2e9cfa46d95
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 19:19:04 2018 -0800
Add jupyter and ipywidgets to requirements.
requirements.txt
commit 8ef98593320246c721f273e80f265894fc59ef4c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 18:46:11 2018 -0800
Use python 3.7 again. Fix requirements.
.travis.yml
requirements.txt
commit 2cc602eec58647478c9d901898863eddd50dc31d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 18:41:45 2018 -0800
Use Python 3.5 for building docs.
.travis.yml
commit 18da27c91d3d2f6acd4cdc92956c751682701524
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 18:17:13 2018 -0800
Use 1 space after periods.
README.md
commit a2942c03c31e6c6edbed3962ea1cb0e65c5a3b74
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 17:40:11 2018 -0800
Add Travis CI deployment from development branch.
.travis.yml
deploy_docs.sh
id_rsa_travis.enc
requirements.txt
commit 4d03d101c7df961fefba873e19260270fbb04e2a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Dec 19 17:21:53 2018 -0800
Wrap rhs module with f90wrap. Add methods to BurnUtils for evaluating rhs and jacobian.
python_library/dowrap.sh
unit_test/burn_cell_python/BurnUtils.py
commit cdc6f6c6427178bb831837ec3d6d31f653fea984
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 10 17:15:50 2018 -0800
Remove redundant lines.
GMicrophysics.mak
commit 50bdc55c20ec7771af5656dc950e68c05c855f97
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 10 17:08:38 2018 -0800
Fix conductivity compilation bug when building with FBoxLib.
GMicrophysics.mak
commit da3850067abf957847fe52ae657587cfb7b2d547
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 10 14:13:56 2018 -0800
Add USE_READ_RATE_DATA variable for copying rate metadata file.
networks/sn160/NETWORK_REQUIRES
commit 1f9d7992ba6b99878193041ca0596ac3c710c689
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 10 14:13:18 2018 -0800
Do not specify use_cse since it defaults to False.
networks/ignition_reaclib/URCA-simple/urca.py
commit 080fbed2523c36b0c261eebd24511b6fbc2756d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:34:09 2018 -0500
add the .nojekyll
docs/.nojekyll
commit 5ca9c52a5ef62fe07384485fce802f3bf69fca1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:29:27 2018 -0500
update docs version
docs/_static/documentation_options.js
docs/basics.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/references.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/transport.html
docs/unit_tests.html
sphinx_docs/source/conf.py
commit 7b8a712d1bd3a3c6ad1b150ce9fbb1d6beb8d44a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:25:56 2018 -0500
update docs
docs/_sources/burn_cell.rst.txt
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/index.html
docs/networks.html
docs/openacc.html
docs/preface.html
docs/references.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
commit a1729e2dc316b87167283fd97c42e795d217d9c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 3 10:25:05 2018 -0500
update changes
CHANGES
commit bfb58eec9390d1bfc1257994c9d7e1ee43a96cdb
Merge: 5c6caed2 8529022a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 1 16:40:12 2018 -0500
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 5c6caed2bb35175885bc5d4522b25caf187305be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 1 16:39:43 2018 -0500
update docs
docs/.nojekyll
docs/_sources/burn_cell.rst.txt
docs/_sources/unit_tests.rst.txt
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/index.html
docs/networks.html
docs/openacc.html
docs/preface.html
docs/references.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
commit 41acd2922cd4d39813dbe19611250f282f2505e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 1 16:38:44 2018 -0500
update some of the unit test info
sphinx_docs/source/unit_tests.rst
commit 8529022a7c69fcc0d010debd80c16440e60fe7b3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Nov 29 16:01:00 2018 -0500
Replace computed GO TO in VODE90 with select case to workaround PGI compiler error.
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dvjust.F90
integration/VODE90/cuVODE/source/cuvode_dvset.F90
commit 8f1f75e369a96fd5fa1d970995c756d15b3adfee
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Nov 29 15:58:25 2018 -0500
Add inputs, probin, xin for sn160 network for test_cvode_react.
unit_test/test_cvode_react/inputs_sn160
unit_test/test_cvode_react/probin.sn160
unit_test/test_cvode_react/xin.sn160.16
commit a12d083e84f87ff4fd8ac0f7cb042b1916b12b09
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 28 14:37:13 2018 -0800
If USE_READ_RATE_DATA=TRUE, link in reaclib rate data file.
Make.Microphysics
commit 3fa353a8d1ced41df3cc541dcfddd8c6589023c8
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 28 14:24:40 2018 -0800
Add inputs, probin, xin files for sn160 that run with VODE.
networks/sn160/xin.pynucastro.128
networks/sn160/xin.pynucastro.16
networks/sn160/xin.pynucastro.256
networks/sn160/xin.pynucastro.32
networks/sn160/xin.pynucastro.64
unit_test/test_react/inputs_sn160
unit_test/test_react/probin.sn160
unit_test/test_react/xin.sn160.16
commit b0a92f8a90f29c76223dbeaead7f581aa3a1090d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 28 13:16:31 2018 -0800
Switch from iMultiFab.norm1 to iMultiFab.sum per AMReX
unit_test/test_react/main.cpp
commit a0aea9e2adbb0f1e2946e933d7f31916ddfe1cae
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Nov 20 01:08:53 2018 -0500
Make default compiler options more useful.
unit_test/test_cvode_react/GNUmakefile
commit d932ebea7df812cf915f49e4bff3d366c1c95dff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:50:32 2018 -0500
add doxy_files
.gitignore
commit 33cc4432172f712c85a1465cc56ffda7fe28756c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:49:59 2018 -0500
add doxygen file
sphinx_docs/Doxyfile
commit eeaa2cf6614f66cd6fb2cd8d4a337caf7d22b7fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:49:32 2018 -0500
add new stuff
docs/_static/fonts/Inconsolata.ttf
docs/_static/fonts/Lato/lato-bold.eot
docs/_static/fonts/Lato/lato-bold.ttf
docs/_static/fonts/Lato/lato-bold.woff
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docs/_static/fonts/fontawesome-webfont.woff2
commit 6882070dac040f510b3f58dc411b8946b5d37229
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 12 13:49:00 2018 -0500
fix math (newcommands) in sphinx docs, start of Doxygen
docs/_sources/runtime_parameters.rst.txt
docs/_static/css/badge_only.css
docs/_static/css/theme.css
docs/_static/fonts/fontawesome-webfont.eot
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docs/_static/fonts/fontawesome-webfont.ttf
docs/_static/fonts/fontawesome-webfont.woff
docs/_static/js/theme.js
docs/basics.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/references.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
sphinx_docs/Makefile
sphinx_docs/converting_docs.txt
sphinx_docs/create_newcommands.py
sphinx_docs/source/_static/mathjax_conf.js
sphinx_docs/source/_templates/layout.html
sphinx_docs/source/conf.py
sphinx_docs/source/mathsymbols.tex
sphinx_docs/source/runtime_parameters.rst
commit 2b867aa6550ef5005de8c30b45e80be79eb61267
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 7 18:58:43 2018 -0800
Add the f2py f2cmap for the new f90 f2c map.
python_library/.f2py_f2cmap
commit 4a03ee7dfb16b317ab8c49a0a2f228bfbc6fef7f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 7 18:53:46 2018 -0800
Fix type mappings for f90wrap so no custom fork is needed.
python_library/.f2py_f2cmap
python_library/.f90wrap_kind_map
commit c379123ce14454d1bcad48db049f18071fdf34dc
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 7 18:52:52 2018 -0800
Compile in conductivity and neutrinos.
python_library/GNUmakefile
commit 76b16951269d6d95f57bc48038743e6c02bfc737
Merge: d27d694d 6eab5828
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 7 16:58:28 2018 -0800
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 6eab5828c6f55835c84b57a411ef9470fc3c5d77
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 7 16:24:39 2018 -0800
Add conductivity to eos_type (#164)
Add conductivity to eos_type when compiling with USE_EXTRA_THERMO=TRUE.
Pass only the eos_t in and out of the conductivity routine.
Add conductivity unit test.
CHANGES
GMicrophysics.mak
Make.Microphysics
conductivity/stellar/stellar_conductivity.F90
interfaces/eos_type.F90
python_library/GNUmakefile
unit_test/microphysics.F90
unit_test/test_conductivity/GNUmakefile
unit_test/test_conductivity/Make.package
unit_test/test_conductivity/_parameters
unit_test/test_conductivity/conductivity_util.F90
unit_test/test_conductivity/input_conductivity
unit_test/test_conductivity/main.cpp
unit_test/test_conductivity/probin
unit_test/test_conductivity/test_conductivity.H
unit_test/test_conductivity/test_conductivity_F.H
unit_test/test_conductivity/unit_test.f90
unit_test/test_conductivity/variables.F90
commit 4bd0c67581ca2867da280d5759804281400c508d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 1 10:15:07 2018 -0400
update changes
CHANGES
commit 380c1d074060497bcb11e6916d2e989eaacbb1a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 1 10:14:21 2018 -0400
remove old docs
Docs_old/.gitignore
Docs_old/EOS/eos.tex
Docs_old/GNUmakefile
Docs_old/MicrophysicsUsersGuide.tex
Docs_old/README.md
Docs_old/basics/basics.tex
Docs_old/burn_cell/burn_cell.tex
Docs_old/burn_cell/react_aprox13_logX.png
Docs_old/data_structures/data_structures.tex
Docs_old/maestrosymbols.tex
Docs_old/networks/doxygen_network.png
Docs_old/networks/networks.tex
Docs_old/networks/tolerances.png
Docs_old/openacc/openacc.tex
Docs_old/pandoc.sh
Docs_old/preface/preface.tex
Docs_old/refs.bib
Docs_old/runtime_parameters/rp.py
Docs_old/runtime_parameters/rp_intro.tex
Docs_old/runtime_parameters/runtime_parameters.tex
Docs_old/sdc/sdc.tex
Docs_old/tests/ode_scaling.ipynb
Docs_old/textsymbols.tex
Docs_old/transport/transport.tex
Docs_old/unit_tests/unit_tests.tex
commit 55d61a24bf55e09fe919148792892f0e8bdd78ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 1 10:13:57 2018 -0400
add more doc stuff
docs/_images/doxygen_network.png
docs/_images/react_aprox13_logX.png
docs/_images/subch.png
docs/_images/tolerances.png
docs/_sources/burn_cell.rst.txt
docs/_sources/references.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/burn_cell.html
docs/objects.inv
docs/references.html
docs/runtime_parameters.html
docs/searchindex.js
commit 049d5107f9b72e66f80df18e2229897790f4848e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 1 10:13:28 2018 -0400
update
sphinx_docs/source/runtime_parameters.rst
commit d27d694ddced1178d81295a7d9490302316523c7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 31 23:24:42 2018 -0700
Update sn160 to store Reaclib metadata in external file.
networks/sn160/actual_network.F90
networks/sn160/reaclib_rate_metadata.dat
networks/sn160/reaclib_rates.F90
commit c61f639ced5be0ebac44dbfcbf3195510897e5b5
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 31 23:05:38 2018 -0700
Read Reaclib parameterization metadata from file instead of embedding in executable.
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/reaclib_rate_metadata.dat
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/xin.urca.128
networks/ignition_reaclib/URCA-simple/xin.urca.16
networks/ignition_reaclib/URCA-simple/xin.urca.256
networks/ignition_reaclib/URCA-simple/xin.urca.32
networks/ignition_reaclib/URCA-simple/xin.urca.64
commit b2491ecefb3b7e166c37f2e5974fcfdab3aa6a57
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 31 22:15:10 2018 -0700
Add xin files for sn160.
networks/sn160/xin.sn160.128
networks/sn160/xin.sn160.16
networks/sn160/xin.sn160.256
networks/sn160/xin.sn160.32
networks/sn160/xin.sn160.64
commit 480b6862daf60fcc4a5973ff57a3b2c997da9b3a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 30 21:55:43 2018 -0400
Optimizations for CVODE driver and improved testing defaults.
We can now save the Jacobian for the corrector iterations in a single
step but recalculate the Jacobian when taking a new step. This is
generally what the other CVODE linear solvers do, except they might
also save the Jacobian for multiple steps, per Carol Woodward.
Now we print out the integrator statistics after the run.
Also, maximum tile sizes are set to 1024**3 so we react a grid of size
n_cells together up until n_cells = 1024. This makes comparisons with
VODE90 easier.
Fix bug where the inputs were undefined for n_cell = 1.
Add ParmParse parameter allowing us to print the number of RHS calls
for each cell.
Use large tile sizes to effectively turn off tiling.
Print integrator statistics and add option for saving the Jacobian for some number of steps.
Get the number of steps to save the Jacobian from the inputs.
Save the Jacobian for each step's corrector iterations, but recalculate Jacobian on a step change.
Add getter function for number of steps to save Jac to header.
Add num_steps_save_jacobian to CVODE/_parameters file
integration/CVODE/_parameters
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/probin.aprox13
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react_F.H
unit_test/test_react/main.cpp
unit_test/test_react/react_zones.F90
unit_test/test_react/test_react_F.H
commit 9a1bf5ccf5efa01c4d32d7dcc09f7710eebd8e44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 29 10:46:37 2018 -0400
fix density
networks/ECSN/network_plot.py
commit 94f2a69613886e77dd9ed8e5aa86f758fb701069
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 27 23:50:05 2018 -0700
Add a basic python version of burn_cell that does plotting.
unit_test/burn_cell_python/Burn Cell.ipynb
unit_test/burn_cell_python/BurnUtils.py
unit_test/burn_cell_python/README.md
unit_test/burn_cell_python/probin_burn_subch
commit d08e4e8b73ce13580d3e3e84cff4663e64cea100
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 27 23:49:05 2018 -0700
Do not re-initialize StarKiller Microphysics python module if already initialized.
python_library/starkiller_initialization.f90
commit 243c393dade0e2df5b989a14cea391f18c1f1c7a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 27 23:48:29 2018 -0700
Add function for getting short species names.
unit_test/network.F90
commit 212c6d369b1633b717e885892cf1bec8d9c3defc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 21:51:36 2018 -0400
add a note
sphinx_docs/notes.txt
commit bc4af6182e8f10ad61fb53f27d6b46a8bc582407
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 18:58:09 2018 -0400
more cleaning
Docs_old/networks/networks.tex
docs/_sources/burn_cell.rst.txt
docs/_sources/index.rst.txt
docs/_sources/networks.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/_sources/unit_tests.rst.txt
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
integration/BS/_parameters
sphinx_docs/source/burn_cell.rst
sphinx_docs/source/index.rst
sphinx_docs/source/networks.rst
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/unit_tests.rst
commit 058c64620b699250c6f38a5940a28abed587d39a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 12:36:13 2018 -0400
get rid of a lot of errors
docs/_sources/basics.rst.txt
docs/_sources/burn_cell.rst.txt
docs/_sources/eos.rst.txt
docs/_sources/index.rst.txt
docs/_sources/networks.rst.txt
docs/_sources/sdc.rst.txt
docs/_static/basic.css
docs/_static/doctools.js
docs/_static/jquery.js
docs/_static/searchtools.js
docs/_static/websupport.js
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
commit 9a4303623f28d34ba9c3c654e81ce8c58c82aa88
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 12:36:04 2018 -0400
more work
sphinx_docs/source/eos.rst
sphinx_docs/source/index.rst
sphinx_docs/source/networks.rst
sphinx_docs/source/references.rst
sphinx_docs/source/refs.bib
sphinx_docs/source/sdc.rst
commit 5423b41f15a91b05abcd212a2021c8281ba6c2f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 12:26:01 2018 -0400
automagically run the rp.py script when we build
sphinx_docs/Makefile
commit b674c16653a6765d1cf83e72078fd10f0f00eac5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 12:25:41 2018 -0400
add references
fix figures
sphinx_docs/source/basics.rst
sphinx_docs/source/burn_cell.rst
sphinx_docs/source/conf.py
sphinx_docs/source/doxygen_network.png
sphinx_docs/source/eos.rst
sphinx_docs/source/networks.rst
sphinx_docs/source/react_aprox13_logX.png
sphinx_docs/source/refs.bib
sphinx_docs/source/subch.png
sphinx_docs/source/tolerances.png
commit 5676a954911a2714b5c26e41c6432bcc64c01519
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 27 12:15:34 2018 -0400
add a network plot
networks/subch/network_plot.py
commit 0656f9862802f83ae565a00cabe394938e4a131c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 22:15:32 2018 -0700
Wrap conductivity with f2py
Make.Microphysics
conductivity/GPackage.mak
conductivity/Make.package
conductivity/stellar/GPackage.mak
conductivity/stellar/Make.package
conductivity/stellar/stellar_conductivity.F90
python_library/dowrap.sh
commit 21bcacfd9606dc0869a5a70d612831bc5f014730
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 21:58:28 2018 -0700
Wrap screen and sneut5 in f2py as well.
python_library/dowrap.sh
commit 8670638780291c12662072377790b771c701ac17
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 18:17:38 2018 -0700
Wrap extern with f2py.
python_library/dowrap.sh
commit 1cef25e36f3b6026255cc8eace0dd4408bcabd3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 20:59:23 2018 -0400
more doc clean-up
docs/_sources/eos.rst.txt
docs/eos.html
docs/searchindex.js
sphinx_docs/source/eos.rst
commit 8494628a2a52895059ac481aa4e5cdfd9dd47451
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 20:39:41 2018 -0400
more static
docs/_static/jquery-3.1.0.js
docs/_static/theme_overrides.css
commit 1d70a284e63437dc1de4375b3c25b46f15e25429
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 20:39:09 2018 -0400
make the tables sphinx-ified
Docs_old/runtime_parameters/rp.py
docs/_sources/runtime_parameters.rst.txt
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
commit 2c0eb3623059e757cf665ebaf32106ef920e8ce6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 20:38:48 2018 -0400
hack around a rtd theme table wrapping bug
sphinx_docs/source/_static/theme_overrides.css
sphinx_docs/source/conf.py
commit 3c0607f709eabb2a8bb51614d092e4f2c443524b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 20:33:47 2018 -0400
this parses the _parameter files and makes a ReST file with tables
sphinx_docs/notes.txt
sphinx_docs/rp.py
sphinx_docs/source/runtime_parameters.rst
commit 64b85a48ef09b63502966c71a91a4b077b42fec1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 19:09:16 2018 -0400
some notes on tables
sphinx_docs/notes.txt
commit 51823a4a449723fc91a032985963a2f469929326
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 18:55:43 2018 -0400
some docs updates
docs/_sources/basics.rst.txt
docs/_sources/data_structures.rst.txt
docs/_sources/rp_intro.rst.txt
docs/_static/basic.css
docs/_static/doctools.js
docs/_static/jquery.js
docs/_static/searchtools.js
docs/_static/websupport.js
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/searchindex.js
docs/unit_tests.html
sphinx_docs/source/basics.rst
sphinx_docs/source/data_structures.rst
sphinx_docs/source/rp_intro.rst
commit 4a23e8e8b100ad8b76339292e9014ba790568c3e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 17:52:29 2018 -0400
Added Urca probin file for test_react for comparisons with CVODE.
unit_test/test_react/probin.reaclib_urca_cfcvode
commit 564370ea958eb44e3e3930d1554e2469e4e0046f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 17:50:36 2018 -0400
Update probin file for Urca for CVODE.
unit_test/test_cvode_react/probin.reaclib_urca
commit 03ad503f7c19dbe2aacbde2a0aa5142337cf75f1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 17:49:11 2018 -0400
Add use_jacobian_caching extern parameter for VODE90 to turn on/off
caching regardless of CPU or GPU compilation.
integration/VODE90/_parameters
integration/VODE90/actual_integrator.F90
integration/VODE90/cuvode_parameters.F90
commit 6d21c83a7c99831f7c5327a236aefaf82bc7a49b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 26 17:33:42 2018 -0400
Add patch from Weiqun for updated amrex::Gpu::Device.
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/test_react.H
commit 141eaa8f1c365ae547b6eb22f63fde1d2ce8f316
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 22:14:42 2018 -0400
Add inputs and probin for urca network
unit_test/test_cvode_react/inputs_reaclib_urca
unit_test/test_cvode_react/probin.reaclib_urca
commit 489eb732f59f3c1a4372ce7754d9c1644767908e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 15:10:58 2018 -0400
add .nojekyll
docs/.nojekyll
commit b9cddc0b3ab3bf8a2de6ca4ecf329084a06b8899
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 15:10:35 2018 -0400
sphinx source
docs/_sources/basics.rst.txt
docs/_sources/burn_cell.rst.txt
docs/_sources/data_structures.rst.txt
docs/_sources/eos.rst.txt
docs/_sources/index.rst.txt
docs/_sources/networks.rst.txt
docs/_sources/openacc.rst.txt
docs/_sources/preface.rst.txt
docs/_sources/rp_intro.rst.txt
docs/_sources/runtime_parameters.rst.txt
docs/_sources/sdc.rst.txt
docs/_sources/transport.rst.txt
docs/_sources/unit_tests.rst.txt
docs/_static/ajax-loader.gif
docs/_static/basic.css
docs/_static/comment-bright.png
docs/_static/comment-close.png
docs/_static/comment.png
docs/_static/css/badge_only.css
docs/_static/css/theme.css
docs/_static/doctools.js
docs/_static/documentation_options.js
docs/_static/down-pressed.png
docs/_static/down.png
docs/_static/file.png
docs/_static/fonts/Inconsolata-Bold.ttf
docs/_static/fonts/Inconsolata-Regular.ttf
docs/_static/fonts/Lato-Bold.ttf
docs/_static/fonts/Lato-Regular.ttf
docs/_static/fonts/RobotoSlab-Bold.ttf
docs/_static/fonts/RobotoSlab-Regular.ttf
docs/_static/fonts/fontawesome-webfont.eot
docs/_static/fonts/fontawesome-webfont.svg
docs/_static/fonts/fontawesome-webfont.ttf
docs/_static/fonts/fontawesome-webfont.woff
docs/_static/jquery-3.2.1.js
docs/_static/jquery.js
docs/_static/js/modernizr.min.js
docs/_static/js/theme.js
docs/_static/mathjax_conf.js
docs/_static/minus.png
docs/_static/plus.png
docs/_static/pygments.css
docs/_static/searchtools.js
docs/_static/underscore-1.3.1.js
docs/_static/underscore.js
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docs/_static/up.png
docs/_static/websupport.js
docs/basics.html
docs/burn_cell.html
docs/data_structures.html
docs/eos.html
docs/genindex.html
docs/index.html
docs/networks.html
docs/objects.inv
docs/openacc.html
docs/preface.html
docs/rp_intro.html
docs/runtime_parameters.html
docs/sdc.html
docs/search.html
docs/searchindex.js
docs/transport.html
docs/unit_tests.html
sphinx_docs/source/basics.rst
sphinx_docs/source/burn_cell.rst
sphinx_docs/source/data_structures.rst
sphinx_docs/source/eos.rst
sphinx_docs/source/networks.rst
sphinx_docs/source/openacc.rst
sphinx_docs/source/preface.rst
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/sdc.rst
sphinx_docs/source/transport.rst
sphinx_docs/source/unit_tests.rst
commit c07f56cbed558ba50366a5f5efd029a60710edce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 14:56:44 2018 -0400
add build/
.gitignore
commit ac683ad23bd035117be1cb1920a4b431a9d28afa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 14:56:00 2018 -0400
rename in prep for Sphinx docs
Docs/networks/subch.pdf
Docs_old/.gitignore
Docs_old/EOS/eos.tex
Docs_old/GNUmakefile
Docs_old/MicrophysicsUsersGuide.tex
Docs_old/README.md
Docs_old/basics/basics.tex
Docs_old/burn_cell/burn_cell.tex
Docs_old/burn_cell/react_aprox13_logX.png
Docs_old/data_structures/data_structures.tex
Docs_old/maestrosymbols.tex
Docs_old/networks/doxygen_network.png
Docs_old/networks/networks.tex
Docs_old/networks/tolerances.png
Docs_old/openacc/openacc.tex
Docs_old/pandoc.sh
Docs_old/preface/preface.tex
Docs_old/refs.bib
Docs_old/runtime_parameters/rp.py
Docs_old/runtime_parameters/rp_intro.tex
Docs_old/runtime_parameters/runtime_parameters.tex
Docs_old/sdc/sdc.tex
Docs_old/tests/ode_scaling.ipynb
Docs_old/textsymbols.tex
Docs_old/transport/transport.tex
Docs_old/unit_tests/unit_tests.tex
sphinx_docs/Makefile
sphinx_docs/converting_docs.txt
sphinx_docs/create_newcommands.py
sphinx_docs/mathsymbols.tex
sphinx_docs/pandoc.sh
sphinx_docs/source/_static/mathjax_conf.js
sphinx_docs/source/_templates/layout.html
sphinx_docs/source/basics.rst
sphinx_docs/source/burn_cell.rst
sphinx_docs/source/conf.py
sphinx_docs/source/data_structures.rst
sphinx_docs/source/eos.rst
sphinx_docs/source/index.rst
sphinx_docs/source/networks.rst
sphinx_docs/source/openacc.rst
sphinx_docs/source/preface.rst
sphinx_docs/source/rp_intro.rst
sphinx_docs/source/runtime_parameters.rst
sphinx_docs/source/sdc.rst
sphinx_docs/source/transport.rst
sphinx_docs/source/unit_tests.rst
sphinx_docs/textsymbols.tex
commit 4a3a559960bf98189cedb6bca49d2ba8afa0cd2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 14:48:29 2018 -0400
unneeded
docs_new/source/_temp.rst
commit 3e22db16cfa9a8699eda2d7c149be30c1504e0a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 14:48:12 2018 -0400
needed files
docs_new/source/_static/mathjax_conf.js
docs_new/source/_temp.rst
docs_new/source/_templates/layout.html
commit f6c7877ff42f3fac653d2bdd54a2929a22f3a973
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 14:47:29 2018 -0400
instructions on converting latex to sphinx with math macros
docs_new/converting_docs.txt
docs_new/create_newcommands.py
docs_new/mathsymbols.tex
docs_new/pandoc.sh
docs_new/source/basics.rst
docs_new/source/conf.py
docs_new/source/data_structures.rst
docs_new/source/eos.rst
docs_new/source/maestrosymbols.rst
docs_new/source/maestrosymbols.tex
docs_new/source/networks.rst
docs_new/source/openacc.rst
docs_new/source/preface.rst
docs_new/source/rp_intro.rst
docs_new/source/runtime_parameters.rst
docs_new/source/sdc.rst
docs_new/source/transport.rst
docs_new/source/unit_tests.rst
docs_new/textsymbols.tex
commit 3add9a8fae1ba0f7aad9a04fce628c9ca5411a37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 26 11:49:42 2018 -0400
more work on getting newcommands working
docs_new/source/conf.py
docs_new/source/maestrosymbols.tex
commit 102283c7b4eecca8fb9211a62b8e7e4607ccb06a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 19:13:29 2018 -0400
add a plot
networks/ECSN/network_plot.py
commit 5a20b3eed492214f7224a316e8ae9e0df5955358
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 19:00:07 2018 -0400
enable reverse rates
networks/ECSN/ecsn.py
commit da52422bec0a1dfc3eca5248258c6213b5059ff8
Merge: 94214961 a1cf4b6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 18:31:32 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 942149611dbb4043a5a4b87e3d890bfdee43224e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 25 18:31:09 2018 -0400
start of an ECSN network
needs electron captures
networks/ECSN/ecsn.py
commit a1cf4b6cfec626fa7b3e8272e017ac4b5daf5049
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Oct 25 14:21:42 2018 -0400
Added solar radius to constants
unit_test/constants_cgs.f90
commit 205ec965b71b2004b989056dafc06ea1fe01b26e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 24 22:33:51 2018 -0700
Add function to return species name given its index.
unit_test/network.F90
commit 823f2d20068087413332f2ec906fe691e769fb0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 13:02:44 2018 -0400
add an aprox21
networks/general_null/aprox21.net
commit 85984c07c38bbf8b785687c72295d1ef339afc96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 12:32:13 2018 -0400
update changes
CHANGES
commit fd438e5ea43f399d74a8a4f8b7bca239bb2488be
Merge: e6e1e331 21e0dbbe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 12:31:34 2018 -0400
Merge branch 'master' into development
commit e6e1e331b2950efdd6428dcd66d7cbb418ecb24b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 12:30:55 2018 -0400
fix some symbols
Docs/maestrosymbols.tex
commit 497cf00640f5b1a9a80922f3dfc4c475beee98e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 23 12:24:20 2018 -0400
first pass at sphinx docs for microphysics
docs_new/Makefile
docs_new/source/basics.rst
docs_new/source/burn_cell.rst
docs_new/source/conf.py
docs_new/source/data_structures.rst
docs_new/source/eos.rst
docs_new/source/index.rst
docs_new/source/maestrosymbols.rst
docs_new/source/networks.rst
docs_new/source/openacc.rst
docs_new/source/preface.rst
docs_new/source/rp_intro.rst
docs_new/source/runtime_parameters.rst
docs_new/source/sdc.rst
docs_new/source/transport.rst
docs_new/source/unit_tests.rst
commit 2809e9e12d72c5d624b675faca96f555896f6828
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Oct 22 22:06:42 2018 -0700
ifdef out parallel broadcasting the helm table for compiling with f2py.
EOS/helmholtz/actual_eos.F90
commit c3af584b0e06a4d1f5836e85aef7d756717b52d1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Oct 22 21:52:09 2018 -0700
Add python library interface for StarKiller Microphysics.
Make.Microphysics
python_library/.f2py_f2cmap
python_library/.f90wrap_kind_map
python_library/GNUmakefile
python_library/Make.package
python_library/StarKiller Notebook Test.ipynb
python_library/_parameters
python_library/dof2py.sh
python_library/dowrap.sh
python_library/probin.ignition
python_library/starkiller_initialization.f90
unit_test/extern_probin.template
commit 478b58c8cf9a65e880fc15c5cc4d2e386e7b07c2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Oct 22 15:16:16 2018 -0700
Allow for taking logs of input rho, T, or p between 0 and 1.
EOS/stellarcollapse/eos_aux_data.f90
commit 500f31120e7cce59853411cf9428a6c6e7f9a128
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Oct 22 15:05:54 2018 -0700
Fix bug in stellarcollapse EOS and improve input sanitation (#162)
* In stellarcollapse EOS, only take log10 of inputs if they are defined.
* CRITICAL -- fix energy shift bug in stellar collapse EOS.
EOS/stellarcollapse/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
interfaces/eos_type.F90
commit faaf4cd1f2948637ac21d9999b387477d2aef056
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 20 01:35:49 2018 -0700
Add -ffree-line-length-none to F90FLAGS and FFLAGS for burn_cell.
unit_test/burn_cell/GNUmakefile
commit 4c0f7d9aaee21e92a942efd66f08e7bc0f448711
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 21:25:54 2018 -0700
Add sn160 network from XNet.
networks/sn160/20180319default2
networks/sn160/GPackage.mak
networks/sn160/Make.package
networks/sn160/NETWORK_REQUIRES
networks/sn160/actual_burner.F90
networks/sn160/actual_network.F90
networks/sn160/actual_rhs.F90
networks/sn160/inputs.burn_cell.VODE
networks/sn160/physical_constants.f90
networks/sn160/reaclib_rates.F90
networks/sn160/sn160.py
networks/sn160/table_rates.F90
commit b0ca36b17fbd55716aecbad44c8469a95459af3e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 19:32:39 2018 -0700
Urca - Fix bug in CSR metadata where we were not counting diagonal zeros.
networks/ignition_reaclib/URCA-simple/actual_network.F90
commit c6cbc88cc2bbe13ed81e32db72365ca85dbc8ab1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 19:06:05 2018 -0700
Add sparse jacobian metadata for Urca simple network.
networks/ignition_reaclib/URCA-simple/actual_network.F90
commit 11d9743ea64bfc303245e21439116ec4b79859d6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 18:04:31 2018 -0700
pynucastro -- Updated C-test network.
networks/ignition_reaclib/C-test/GPackage.mak
networks/ignition_reaclib/C-test/Make.package
networks/ignition_reaclib/C-test/NETWORK_REQUIRES
networks/ignition_reaclib/C-test/actual_burner.F90
networks/ignition_reaclib/C-test/actual_network.F90
networks/ignition_reaclib/C-test/actual_rhs.F90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/C-test/c.py
networks/ignition_reaclib/C-test/inputs.burn_cell.VODE
networks/ignition_reaclib/C-test/physical_constants.f90
networks/ignition_reaclib/C-test/reaclib_rates.F90
networks/ignition_reaclib/C-test/table_rates.F90
networks/ignition_reaclib/C-test/table_rates.f90
networks/ignition_reaclib/C-test/test/GNUmakefile
networks/ignition_reaclib/C-test/test/GPackage.mak
networks/ignition_reaclib/C-test/test/testjacobian.f90
commit 716b95bc68411c733ae88b8c513ea9ff9fef2961
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 18:03:03 2018 -0700
pynucastro -- Updated C-burn-simple network
networks/ignition_reaclib/C-burn-simple/NETWORK_REQUIRES
networks/ignition_reaclib/C-burn-simple/actual_burner.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/c.py
networks/ignition_reaclib/C-burn-simple/inputs.burn_cell.VODE
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
commit 11e5452d501df649a6c6f8d9fd1414644be4f04b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 18:01:00 2018 -0700
pynucastro updates. Fix bug when screening is turned off.
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
commit c207ff17479ce5a52ea7eee27670cf18c0fb4b8b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 16:13:11 2018 -0700
Updated Urca net for pynucastro improvements to screening and tables.
I have confirmed that test_react gives exactly the same answers as
before this update on both CPU and GPU. (PLOTFILES_AGREE from
fcompare)
networks/ignition_reaclib/URCA-simple/README.md
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/inputs.burn_cell.VODE
networks/ignition_reaclib/URCA-simple/na23--ne23-toki
networks/ignition_reaclib/URCA-simple/ne23--na23-toki
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_reaclib/URCA-simple/test/GNUmakefile
networks/ignition_reaclib/URCA-simple/test/GPackage.mak
networks/ignition_reaclib/URCA-simple/test/testjacobian.f90
networks/ignition_reaclib/URCA-simple/urca.py
commit 9bb6bdc7a936b3fae49d806c49319a52d7e5040c
Merge: 3ee9c2ba 6edd7679
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 14:56:24 2018 -0700
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 3ee9c2baf6508ed4f9ec79581b307c6a8375c431
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 16 14:56:18 2018 -0700
Link electron capture and beta decay tables in for the Urca network
Make.Microphysics
commit 6edd7679f35d06cd4141695f615456f8ee539827
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 13 22:21:56 2018 -0400
Add jacobian sparsity module to GPackage.mak
integration/GPackage.mak
interfaces/burn_type.F90
commit 09fe2aff3606d9666116414a7261e55b7e1c11e2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 13 21:55:17 2018 -0400
Add parameter for setting jacobian storage for CVODE.
integration/CVODE/_parameters
commit 2e3f9031d9c25564c3d035b72cc7be2262545506
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Oct 13 21:54:50 2018 -0400
Move Jacobian sparsity subroutines into jacobian sparsity module.
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_type.F90
integration/Make.package
integration/jacobian_sparsity.F90
integration/numerical_jacobian.F90
integration/temperature_integration.F90
interfaces/burn_type.F90
networks/aprox13/actual_rhs.F90
networks/ignition_simple/actual_rhs.F90
commit 3a9aee16c59b616ee2e41a00f155b537dac2fd4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 13 09:45:42 2018 -0400
longer integration time
unit_test/test_react/probin.nova
commit 3d4ec3d085394a77252f6a889c348fc0e1c0f0c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 13 09:44:18 2018 -0400
this nova inputs works
unit_test/test_react/probin.nova
commit 0b99f22b61db1244940e0aa01cfc09fb122e6109
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 13 09:41:55 2018 -0400
updated via pynucastro
networks/nova/actual_burner.f90
networks/nova/actual_network.f90
networks/nova/actual_rhs.f90
networks/nova/reaclib_rates.f90
commit cc1c6efe5a22faeb304d0a2e13f3098c086dfb2d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 12 20:50:55 2018 -0400
More classy user data. Add option for cuSolver CVODE driver to store J.
Add integrator statistics for CVODE serial and SPGMR drivers.
Use classy user data for CVODE SPGMR and serial drivers.
Use 0.1 second tmax for ignition like for test_react.
Cleanup CVODE driver. Add number of Jac evaluations output.
Use scaling in ignition probin.
Update SPGMR driver for classy user data.
Update serial CVODE driver for classy user data.
Support classy user data and number of J evaluations in header.
Tell CVODE cuSolver driver whether to store J or not.
unit_test/test_cvode_react/inputs_ignition
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/probin.aprox13
unit_test/test_cvode_react/probin.ignition
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_serial.cpp
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react.H
unit_test/test_cvode_react/test_react_F.H
commit c07496d1e2d9064d64a4b0a136525cfa9d4aa97b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 12 20:47:48 2018 -0400
Add test probin files for comparing CVODE and VODE90
unit_test/test_cvode_react/probin.aprox13
unit_test/test_react/probin.aprox13.cvode_compare
commit afe58dd847d038fa4a91bf4f8cfa18615ebd6fa0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 12 20:36:48 2018 -0400
Print out the RHS, Jacobian statistics for CVODE driver.
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/test_react.H
commit fde7dafb00f93b30f7cf6dac7237b94312d3e0b7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 12 20:06:14 2018 -0400
Make user data classy and CUDA memadvise it to the device.
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/test_react.H
commit b7bcf6131f78675925dc617194233ea6e2c3a39b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 12 19:39:21 2018 -0400
Fix tmax in aprox13 inputs for CVODE driver.
unit_test/test_cvode_react/inputs_aprox13
commit ea984780aaae72a03070e563cbac958a4ef43fff
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Oct 12 15:41:02 2018 -0400
Improve CUDA error checking.
unit_test/test_cvode_react/react_cuda_cusolver.cpp
commit f14d4c92dd50e8ec86d78528c9e3d516597301a7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 22:03:05 2018 -0400
Remove unused variable.
integration/VODE90/vode_type.F90
commit 7a42b381927ebefbd3b8e568f8f48bc19c04aa6c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 20:05:25 2018 -0400
Implement sparse/dense Jacobian interface for aprox13. Cleanup rhs and jacobian to avoid creating temporary arrays for rates.
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
commit d25e32d4bfdbf9dc0dcd4685c624edad968e6a73
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 19:56:15 2018 -0400
Print the reaction timestep.
unit_test/test_cvode_react/main.cpp
commit ee684624f36906de2654b7ed83255bec26bc10cb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 19:55:42 2018 -0400
Add USE_SPARSE_STOP_ON_OOB to GNUmakefile.
unit_test/test_cvode_react/GNUmakefile
commit 7328993bce5c160c14bda929420f96a1bf05063a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 17:15:14 2018 -0400
If USE_SPARSE_STOP_ON_OOB=TRUE then out-of-bounds sparse Jacobian set or scale operations will stop the program.
Make.Microphysics
commit 8ae7c8187fe7574d7968daa0aaae7e4969b02310
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 17:14:19 2018 -0400
Fix intent bug in burn type Jacobian interface. Add option for stopping on out-of-bound Jacobian accesses for sparse Jacobian.
interfaces/burn_type.F90
commit b0bcbdebe18a793ac0a21bb2985a25056f2fab7d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Oct 11 02:23:00 2018 -0400
Added set/get interface for Jacobian in burn type that supports sparse
or dense Jacobians via the compile flag
USE_REACT_SPARSE_JACOBIAN. Updated ignition_simple to use this
interface. More networks to come. CVODE drivers no longer need to
evaluate the dense Jacobian.
Make.Microphysics
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_type.F90
integration/numerical_jacobian.F90
integration/temperature_integration.F90
interfaces/burn_type.F90
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_rhs.F90
unit_test/test_cvode_react/GNUmakefile
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react.H
unit_test/test_cvode_react/test_react_F.H
commit 75fea12ac0a1164790b4b661f072c51c9b03d7e3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Oct 9 20:58:40 2018 -0400
Squashed -- test_cvode_react now works for the CUDA CVODE driver with
both the matrix-free solver in CVODE and my cuSolver sparse QR
factorization solver for CVODE. So far only ignition_simple is set up
for the latter.
Add CUDA cuSolver linear solver driver for CUDA CVODE integration.
Use COMPILE_CUDA_PATH for consistency in the makefile.
Use NETWORK_CSR_JAC_NNZ
Fix abundance normalization logic, clarify comment.
Fix energy scaling for VODE90 integrator.
Fix CSR Jacobian indexing in ignition_simple.
Add some status checking and printing to main.
Synchronize device following kernel launches for CVODE CUDA driver.
Synchronize device following kernel launches for cuSolver CUDA CVODE driver. Add status checking. Free cudaMallocManaged memory.
Add helper functions for setting CSR jacobian structure parameters.
Cleanup test_react.H header.
Add helper functions to header.
Set zone indices in test_react/react_zones.
Make.Microphysics
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_type.F90
integration/VODE90/actual_integrator.F90
networks/ignition_simple/actual_network.F90
unit_test/test_cvode_react/GNUmakefile
unit_test/test_cvode_react/Make.package
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_cuda_cusolver.cpp
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react.H
unit_test/test_cvode_react/test_react_F.H
unit_test/test_react/react_zones.F90
commit f7158ebf11214b7fcbb77296eeb4ebbcca423524
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 9 09:05:39 2018 -0400
add integrator_scaling.F90
integration/GPackage.mak
commit a49be99acd498f6572e05614e4da5d7e0a316509
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Oct 7 21:10:43 2018 -0400
Fix bug in CVODE scaling, enable scaling for VODE90, add missing module file.
Add density, energy, temperature scaling for VODE90 integrator. Confirmed identical behavior for scalings of 1.
Fix bug in scaling for CVODE where I was resetting the energy in update_thermodynamics.
Add missing integrator_scaling module.
Put back integrator scaling because I added it.
integration/CVODE/cvode_type.F90
integration/Make.package
integration/VODE90/vode_type.F90
integration/integrator_scaling.F90
commit eecb75583f8c7ddd1c8f47a4236ea5613df986cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 8 10:08:43 2018 -0400
take out integrator_scaling.F90 -- it does not exist
integration/Make.package
commit 62fabf33ee39d6777157bf2a9cd560ebb2c06e49
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Oct 7 20:43:45 2018 -0400
Add CVODE test driver and enable rho, e, T scaling for CVODE.
Add CVODE integrator directory.
Add CVODE options to the Microphysics build system.
Add CVODE driver test for Microphysics networks.
Put density, temperature, energy scaling back in for CVODE integrator.
Make.Microphysics
integration/CVODE/Make.package
integration/CVODE/actual_integrator.F90
integration/CVODE/cvode_rhs.F90
integration/CVODE/cvode_type.F90
integration/CVODE/rpar.F90
integration/Make.package
integration/_parameters
integration/integrator.F90
unit_test/test_cvode_react/GNUmakefile
unit_test/test_cvode_react/Make.package
unit_test/test_cvode_react/README.md
unit_test/test_cvode_react/_parameters
unit_test/test_cvode_react/inputs_aprox13
unit_test/test_cvode_react/inputs_ignition
unit_test/test_cvode_react/main.cpp
unit_test/test_cvode_react/probin.aprox13
unit_test/test_cvode_react/probin.ignition
unit_test/test_cvode_react/react_cuda.cpp
unit_test/test_cvode_react/react_serial.cpp
unit_test/test_cvode_react/react_utils.F90
unit_test/test_cvode_react/test_react.H
unit_test/test_cvode_react/test_react_F.H
unit_test/test_cvode_react/unit_test.f90
unit_test/test_cvode_react/util.f90
unit_test/test_cvode_react/variables.F90
unit_test/test_cvode_react/xin.aprox13
unit_test/test_cvode_react/xin.ignition
commit 5c92b132ae35ab42189f2869777a6782c962787e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 4 10:21:31 2018 -0400
move USE_CUDA block
Make.Microphysics
commit abb3c1a34813beb7539c2c15c93836b88f27014b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 16:07:44 2018 -0400
remove old commented out F90 build stuff
Make.Microphysics
commit a58ad3b5ba0f1555c8fc4ef6e55e401788af35c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 15:55:44 2018 -0400
remove space
Make.Microphysics
commit 21e0dbbe8cb6a66b1b9d03fd8f3b5e38522b2c11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 15:55:44 2018 -0400
remove space
Make.Microphysics
commit 8bdbe4578af3254d5063ae82859b1fc9bf720c89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 15:48:13 2018 -0400
add USE_GPU_PRAGMA
Make.Microphysics
commit 29177c8053832f67cafd2d52014e0a90b8ce4c49
Merge: 7e5f9182 dc4db807
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 14:04:17 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 7e5f918204f2255608c5c797cdb5e5f85fda1315
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 2 14:04:01 2018 -0400
nova inputs -- this crashes because of screening bug
unit_test/test_react/inputs_nova
unit_test/test_react/probin.nova
unit_test/test_react/xin.nova
commit dc4db807f62866f3f59f0e34128f7b9bcdc63271
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Oct 2 13:16:19 2018 -0400
Update defines
EOS/gamma_law_general/actual_eos.F90
commit e33020a2c8e63e7499243d16495ba2e970b3f824
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 1 12:52:29 2018 -0400
update changes
CHANGES
commit 8fd850f2a5281723104a569d4306b538fbd8fda3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 1 08:42:58 2018 -0400
get rid of OMP reduction clause since we now use an iMultiFab
unit_test/test_react/main.cpp
commit 3801bf7e4aa9fb04e336b1948b5176a9390952bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 30 19:43:01 2018 -0400
add a mailmap
.mailmap
commit 0d65d1d572aff7b56104d94f6a5abc7fa87e43ce
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Sep 28 16:37:26 2018 -0400
Implement #RHS call reduction for USE_CUDA=TRUE.
unit_test/test_react/main.cpp
unit_test/test_react/react_zones.F90
unit_test/test_react/test_react_F.H
commit 38600897e3934a738b8c4fec648ecd33d05674e1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Sep 28 16:36:42 2018 -0400
USE_CUDA->AMREX_USE_CUDA to fix compilation.
unit_test/test_react/variables.F90
commit 76ab5dc003bb25ba65709c61200c0a5c713ba8dd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 27 21:50:12 2018 -0400
actually set the species jacobian elements for aprox19
networks/aprox19/actual_rhs.F90
commit db3d7584a776ac1d595182d18dfbfea246d62937
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 27 18:17:02 2018 -0400
Get test_eos running on GPU. Got aprox19 RHS compiling with CUDA.
Make.Microphysics
networks/aprox19/actual_rhs.F90
unit_test/test_eos/GNUmakefile
unit_test/test_eos/Make.package
unit_test/test_eos/eos_util.F90
unit_test/test_eos/main.cpp
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/variables.F90
commit da3e22e1209a6650abd372a6313a933abf5f1360
Author: Sydney Andrews <sandshrews@electra.iacs.stonybrook.edu>
Date: Thu Sep 27 11:22:19 2018 -0400
Adding input files for subch and xrb problems (#157)
unit_test/burn_cell/inputs_burn_subch.VODE
unit_test/burn_cell/inputs_burn_xrb.VODE
commit 4dc236cdc3374ed061315ed64251ddc5a33aab58
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 23:03:11 2018 -0400
Fix compilation issue.
integration/VODE90/cuVODE/source/GPackage.mak
integration/VODE90/cuVODE/source/Make.package
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_dvindy.F90
integration/VODE90/cuVODE/source/cuvode_output.F90
commit 0a690a36cb73f6e766e215d010917f8942a61e4e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 19:20:31 2018 -0700
Added a standalone test problem using cuVODE.
integration/VODE90/cuVODE/Make.cuVODE
integration/VODE90/cuVODE/test/GNUmakefile
integration/VODE90/cuVODE/test/GPackage.mak
integration/VODE90/cuVODE/test/Make.package
integration/VODE90/cuVODE/test/README.md
integration/VODE90/cuVODE/test/cuvode_parameters.F90
integration/VODE90/cuVODE/test/extern_probin.template
integration/VODE90/cuVODE/test/inputs
integration/VODE90/cuVODE/test/main.cpp
integration/VODE90/cuVODE/test/react_zones.F90
integration/VODE90/cuVODE/test/rpar.F90
integration/VODE90/cuVODE/test/test_react.H
integration/VODE90/cuVODE/test/test_react_F.H
integration/VODE90/cuVODE/test/tvode.f90
integration/VODE90/cuVODE/test/tvode_rhs.f90
integration/VODE90/cuVODE/test/vode_rhs.F90
commit 7c24fea07eb9c7e569480587de05d84c3e2c1aab
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 19:17:53 2018 -0700
Moved notes to docs.
integration/VODE90/cuVODE/docs/NOTES.md
commit 1dda19cbb199bcbcbb3cf8c4d92a2e868f318fa7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 19:17:29 2018 -0700
Added template rpar to cuVODE/source
integration/VODE90/cuVODE/source/rpar.F90
commit 1d0569b3b49c12db2eda3f01705abbc0a95f5865
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 19:15:21 2018 -0700
Revert "Changed name of rpar module to cuvode_rpar_module."
This reverts commit 94a3088da6a715501be1c1be587e1e0cb2c5d89a.
integration/VODE90/actual_integrator.F90
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_type.F90
integration/VODE90/cuVODE/source/rpar.F90
integration/VODE90/rpar.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_type.F90
commit 94a3088da6a715501be1c1be587e1e0cb2c5d89a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 19:14:53 2018 -0700
Changed name of rpar module to cuvode_rpar_module.
integration/VODE90/actual_integrator.F90
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_type.F90
integration/VODE90/cuVODE/source/rpar.F90
integration/VODE90/rpar.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_type.F90
commit caa36d6157aa6194d4900025a838fca81f6c5ad4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 26 17:32:47 2018 -0700
Collected CUDA-VODE specific code into cuVODE directory for portability.
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/actual_integrator.F90
integration/VODE90/cuVODE/NOTES.md
integration/VODE90/cuVODE/README
integration/VODE90/cuVODE/docs/Makefile
integration/VODE90/cuVODE/docs/doxyfile_vode
integration/VODE90/cuVODE/linear_algebra_modules/GPackage.mak
integration/VODE90/cuVODE/linear_algebra_modules/Make.package
integration/VODE90/cuVODE/linear_algebra_modules/blas_module.F90
integration/VODE90/cuVODE/linear_algebra_modules/linpack_module.F90
integration/VODE90/cuVODE/source/GPackage.mak
integration/VODE90/cuVODE/source/Make.package
integration/VODE90/cuVODE/source/cuvode.F90
integration/VODE90/cuVODE/source/cuvode_constants.F90
integration/VODE90/cuVODE/source/cuvode_dacopy.F90
integration/VODE90/cuVODE/source/cuvode_dewset.F90
integration/VODE90/cuVODE/source/cuvode_dvhin.F90
integration/VODE90/cuVODE/source/cuvode_dvindy.F90
integration/VODE90/cuVODE/source/cuvode_dvjac.F90
integration/VODE90/cuVODE/source/cuvode_dvjust.F90
integration/VODE90/cuVODE/source/cuvode_dvnlsd.F90
integration/VODE90/cuVODE/source/cuvode_dvnorm.F90
integration/VODE90/cuVODE/source/cuvode_dvset.F90
integration/VODE90/cuVODE/source/cuvode_dvsol.F90
integration/VODE90/cuVODE/source/cuvode_dvstep.F90
integration/VODE90/cuVODE/source/cuvode_nordsieck.F90
integration/VODE90/cuVODE/source/cuvode_output.f90
integration/VODE90/cuVODE/source/cuvode_parameters.F90
integration/VODE90/cuVODE/source/cuvode_type.F90
integration/VODE90/cuVODE/test/GNUmakefile
integration/VODE90/cuVODE/test/GPackage.mak
integration/VODE90/cuVODE/test/tvode.f90
integration/VODE90/cuVODE/test/tvode_rhs.f90
integration/VODE90/cuvode_parameters.F90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_type.F90
networks/GNetwork.mak
networks/Make.package
commit 62da279825b747c12b0daa3458638c39b870a68e
Author: Sydney Andrews <sandshrews@electra.iacs.stonybrook.edu>
Date: Wed Sep 26 15:38:58 2018 -0400
Adding skynet utilities to burn or compare to star-killer (#156)
util/skynet/README.md
util/skynet/burn.py
util/skynet/compare.py
commit 624b1e9f3d8728d42b5ff195d9c408d489c56e22
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Sep 26 14:13:03 2018 -0400
ifdef CUDA -> ifdef AMREX_USE_CUDA
EOS/breakout/actual_eos.F90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
integration/VODE90/actual_integrator.F90
integration/VODE90/vode_parameters.F90
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_source/dvode_dvindy.F90
integration/VODE90/vode_source/dvode_type.F90
integration/numerical_jacobian.F90
interfaces/eos_type.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_network.F90
networks/aprox21/actual_network.F90
networks/general_null/network.template
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_simple/actual_network.F90
networks/subch/actual_network.F90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
rates/aprox_rates.F90
screening/screen.F90
unit_test/dummy.probin.template
unit_test/network.F90
commit 9b9a2e12945bed691de9d5b80df0458bfb11440d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 19:23:07 2018 -0400
fix the fix
networks/subch/Make.package
commit 6f1170f483e677f4fc73702d21c02ae8d1555e66
Merge: 95e3eab0 6d9c27ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 19:09:24 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 95e3eab0d5822758e0ea19b03305a36ac47b3bf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 23 19:09:15 2018 -0400
update files
networks/subch/Make.package
commit 6d9c27ff6b35c59970e94a3aa40e67b6890338f5
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 21 10:31:38 2018 -0400
Remove some acc routines
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
interfaces/eos_type.F90
networks/aprox13/actual_burner.F90
networks/aprox13/actual_rhs.F90
networks/breakout/actual_rhs.f90
networks/general_null/actual_rhs.f90
networks/ignition_simple/actual_burner.F90
networks/ignition_simple/actual_rhs.F90
networks/iso7/actual_rhs.f90
networks/rprox/actual_rhs.f90
networks/xrb_simple/actual_rhs.f90
neutrinos/sneut5.F90
rates/aprox_rates.F90
rates/tfactors.F90
screening/screen.F90
unit_test/eos.F90
unit_test/eos_override.F90
util/BLAS/daxpy.f
util/BLAS/dgemm.f
util/BLAS/dscal.f
util/BLAS/idamax.f
util/LINPACK/dgefa.f
util/LINPACK/dgesl.f
util/LINPACK/vddot.f
util/esum.py
util/esum_module.F90
util/linear_algebra_modules/blas_module.F90
util/linear_algebra_modules/linpack_module.F90
commit a93f98e4fb213d524e53f906e2a451df60763b1e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 18 19:36:46 2018 +0000
Make functions return results.
neutrinos/sneut5.F90
commit 5e6775bd88d6be6276db724f80a308e861d60020
Merge: c3b37415 455528d4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 18 05:45:50 2018 +0000
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit c3b37415f3c01c0a891ff9bd04fec940e8a36ab2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 18 05:40:01 2018 +0000
Moved subroutine and function imports inside subroutines for GPU script.
integration/VODE90/actual_integrator.F90
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_source/dvode_dvjac.F90
integration/VODE90/vode_source/dvode_dvnlsd.F90
integration/VODE90/vode_source/dvode_dvstep.F90
integration/integrator.F90
interfaces/eos_type.F90
unit_test/test_react/Make.package
unit_test/test_react/variables.F90
util/linear_algebra_modules/linpack_module.F90
commit 455528d46818e025693486c3f4b87767cd11446c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 17 20:41:34 2018 -0400
bugfix to the bugfix that fixed a previously introduced bug
networks/Make.package
commit 258bf27bcfd9089d2030d614fc955c1ef51f8146
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 17 17:08:00 2018 -0600
change eos_input_is_constant to true (#154)
* change eos_input_is_constant to true
CHANGES
EOS/helmholtz/_parameters
commit c5ab86d153a9d282e6e2294326d93116acac15d7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 17 19:19:36 2018 +0000
Bugfix for previously introduced bug.
Fix a bug I just introduced for the build system.
networks/Make.package
commit 2844b3c67036468c1c450ddb9af44a7775fda9a0
Merge: 90189c69 c0cf748e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 17 14:22:44 2018 -0400
WIP Getting c++ test_react to run on GPUs.
commit 90189c69bf792048e5577580b53796c57af898af
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 17 14:11:52 2018 -0400
Deprecated AMREX_DEVICE in favor of !$gpu.
EOS/breakout/actual_eos.F90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/polytrope/actual_eos.F90
integration/VODE90/actual_integrator.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_source/dvode_dacopy.F90
integration/VODE90/vode_source/dvode_dewset.F90
integration/VODE90/vode_source/dvode_dvhin.F90
integration/VODE90/vode_source/dvode_dvindy.F90
integration/VODE90/vode_source/dvode_dvjac.F90
integration/VODE90/vode_source/dvode_dvjust.F90
integration/VODE90/vode_source/dvode_dvnlsd.F90
integration/VODE90/vode_source/dvode_dvnorm.F90
integration/VODE90/vode_source/dvode_dvset.F90
integration/VODE90/vode_source/dvode_dvsol.F90
integration/VODE90/vode_source/dvode_dvstep.F90
integration/VODE90/vode_source/dvode_nordsieck.F90
integration/VODE90/vode_type.F90
integration/integrator.F90
integration/numerical_jacobian.F90
integration/temperature_integration.F90
interfaces/burn_type.F90
interfaces/eos_type.F90
networks/GNetwork.mak
networks/Make.package
networks/aprox13/actual_burner.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_burner.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_burner.F90
networks/aprox21/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/actual_burner.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_simple/actual_burner.F90
networks/ignition_simple/actual_rhs.F90
networks/subch/actual_burner.F90
networks/subch/actual_rhs.F90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
neutrinos/sneut5.F90
rates/aprox_rates.F90
rates/tfactors.F90
screening/screen.F90
unit_test/test_react/main.cpp
unit_test/test_react/react_zones.F90
unit_test/test_react/test_react_F.H
util/linear_algebra_modules/blas_module.F90
util/linear_algebra_modules/linpack_module.F90
commit c0cf748ef084c4f792d1e4361ac01f6e0d37f3a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 11 11:11:08 2018 -0400
don't have actual_burner_init() call actual_network_init()
networks/ignition_reaclib/C-test/actual_burner.f90
networks/nova/actual_burner.f90
networks/subch/actual_burner.F90
commit 9bad354ce566e8c86400185f0378aff1d11f9068
Author: Sydney Andrews <sandshrews@electra.iacs.stonybrook.edu>
Date: Tue Sep 11 10:20:08 2018 -0400
adding subch input file
unit_test/burn_cell/inputs_burn_subch.VODE
commit 479414e8cd1287a5b1d4fb2feedc562f8946727d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 9 20:31:41 2018 -0400
sync up with Castro
interfaces/eos_type.F90
commit 7ea83e5422fe425651f4f0231d8e9f1a8c85e6bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 9 20:06:40 2018 -0400
VODE90 doesn't need BLAS or linpack
networks/Make.package
commit 84a52c56ca73d7c44bdfaae17a977e7b6f65d6c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 9 15:56:08 2018 -0400
if USE_CUDA=TRUE, then use VODE90
unit_test/test_react/GNUmakefile
commit c6125598ddb5e6a7974c00151f61f9f4c3dd0244
Merge: cc24413f 1d0fa9e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 9 15:15:41 2018 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit cc24413fd91c9cc26cd14f757ab1908eb1f83e39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 9 15:15:29 2018 -0400
remove AMREX_ARLIM_ARG
unit_test/test_react/main.cpp
commit 1d0fa9e30efa7862973458ccf6eacc5c09eb8c3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 7 21:00:22 2018 -0400
swap out bl_types
networks/nova/actual_burner.f90
networks/nova/actual_network.f90
networks/nova/actual_rhs.f90
commit 69a18dd066f4b7277324316c36cc5c050f8af514
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 7 15:40:44 2018 -0400
now with actual rates ;)
networks/nova/actual_network.f90
networks/nova/actual_rhs.f90
networks/nova/network_plot.py
networks/nova/nova.py
networks/nova/reaclib_rates.f90
commit 0c96400dd0c57ce18bbe0926096b41b1e80bc2bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 7 14:42:58 2018 -0400
remove comment
networks/nova/nova.py
commit 2d9b2f21f01e59249e28255edb4b686e7548aa3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 7 14:26:19 2018 -0400
add a pynucastro generated nova network for hotcno
networks/nova/GPackage.mak
networks/nova/Make.package
networks/nova/NETWORK_REQUIRES
networks/nova/actual_burner.f90
networks/nova/actual_network.f90
networks/nova/actual_rhs.f90
networks/nova/nova.py
networks/nova/physical_constants.f90
networks/nova/reaclib_rates.f90
networks/nova/table_rates.f90
commit 3079e40787f7076a33ead329fd8c0b9610329023
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 7 09:54:51 2018 -0400
add the non-stiff integrator parameter as an option
integration/VODE/vode_integrator.f90
commit 0471e2ee305bf514351d83c53f36da784f6c5866
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 6 20:47:38 2018 -0400
burning_mode = 0 requires integrate_temperature = F
closes #137
unit_test/test_react/probin.aprox19.burning_mode_0
commit 7a11a004818f7e63ce1eadeda0438ea270314447
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 6 20:03:02 2018 -0400
update changes
CHANGES
commit 78beecbbc4c911fe77cf0e1fcecd54b639e76ec8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 6 18:01:47 2018 -0600
Screen fix (#150)
* fix the intermediate screen blend, following MESA
* set h12_max to agree with MESA and kepler
remove unused variables
screening/screen.F90
commit 2eaee4132779987664b93a0fe2bb79d7dd726540
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 6 13:39:19 2018 -0400
fix compilation
networks/general_null/actual_burner.f90
commit 9d42ce2e9d7932257c542216c92c50ed96cb7046
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 6 13:31:13 2018 -0400
.f90 -> .F90
networks/general_null/GPackage.mak
commit a0352d73b76a03f01fb3b21b9431ba9a4c525b5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 6 13:22:48 2018 -0400
fix FBoxLib compilation
networks/general_null/GPackage.mak
commit d213ff756a232c635ffb5a4a86f8e4d13b7def9d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 3 12:40:45 2018 -0400
update changes
CHANGES
commit 12f57a5a9dfd8bc1b3bcd9559aef6d15ae5cecdf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 28 12:09:40 2018 -0400
bl_types -> amrex_type_module
networks/ignition_reaclib/URCA-simple/actual_burner.F90
commit 37f6260c885b4368efc7db991ad5aa564d82c2d1
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 10:56:53 2018 -0400
Add option for disabling esum loop unrolling
util/esum.py
commit bcb98986ced32efb84b378b66f385c14fee898cf
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 05:55:22 2018 -0400
Add option to do the sum in 128-bit arithmetic
util/esum.py
commit b313e58fbe829b4efe24c1db25b92a92ac594f01
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 05:45:44 2018 -0400
Mark esum as pure
util/esum.py
util/esum_module.F90
commit b58084c92c1733a779bf1c48e002dfb34ac34655
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 05:42:55 2018 -0400
Add Kahan summation
util/esum.py
util/esum_module.F90
commit cb3bdab34dbe249e87c214cce4e20fb44981cd83
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 04:48:16 2018 -0400
Add debugging option to have esum be the sum intrinsic
util/esum.py
commit ccdc279b2cb197d32f3ff3f247dc35d401e24609
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 03:38:19 2018 -0400
Update comment on compiler optimizations
util/esum.py
util/esum_module.F90
commit f206fbfeedb7666cac412d50d6d36046b7791927
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 03:04:00 2018 -0400
Fix typo
util/esum.py
util/esum_module.F90
commit 0d9c362d65e041621af1e863e2a8adf4b0f90e97
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 02:33:16 2018 -0400
Clean up esum comments
util/esum.py
util/esum_module.F90
commit 79dd3a437d08d78969aae9b28701ca58c857c0ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 20 02:05:57 2018 -0400
Now we run esum.py from the util directory
util/esum.py
util/esum_module.F90
commit e2d1d6d16794477a6fdec11b3604f538a48b3019
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 19 15:28:14 2018 -0400
Revert change to aprox13 probin
unit_test/test_react/probin.aprox13
commit ababcd813384a1d0d3c160893872c00b110c9e26
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 19 15:12:26 2018 -0400
Optimize esum by working in groups of 3 or 4
unit_test/test_react/probin.aprox13
util/esum.py
util/esum_module.F90
commit 3ffbc0a8933da23f4e004c92dccc1a25fa2b30f7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 19 01:37:25 2018 -0400
Make the network names uniform length parameters
networks/MESA/network.template.mesa
networks/aprox13/actual_network.F90
networks/aprox19/actual_network.F90
networks/aprox21/actual_network.F90
networks/ignition_simple_SDC/actual_network.f90
networks/iso7/actual_network.f90
networks/triple_alpha_plus_cago/actual_network.f90
networks/xrb_simple/actual_network.f90
commit 4ac89dc064b0c2a56df0e33fd4cad6e2d1dd624f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 17 01:13:06 2018 -0400
Add an extra explicit statement to avoid compiler optimizations
util/esum.py
util/esum_module.F90
commit 0166e599ae3619ad7b7bd4dddc1388bc2711b1fb
Merge: dffc609b e5078b3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 14 13:17:07 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit e5078b3da5c1d779a7c800c25ebd3352b43a5d98
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 18:28:38 2018 -0400
Fix accidentally edited file
util/microphysics_math.F90
commit 5f7a3a0d78d34ea2e3d87f70c44678cc3aee8022
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 18:26:41 2018 -0400
Hardcode the esum generation, up to 30 for now
util/esum.py
util/esum_module.F90
util/microphysics_math.F90
commit d6dccc0992ae5eb2c378b6f0a2665577f519cd3c
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 17:06:35 2018 -0400
Make the composition derivatives array smaller
networks/iso7/actual_rhs.f90
commit dba37cfd2f789813cbdc08b1629d4ae5a571fe5e
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 16:46:57 2018 -0400
Comment out some unused density derivatives
networks/iso7/actual_rhs.f90
commit 6c4a5e50796f0fa9c98859a46e50bbc44ee8fec7
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 05:07:47 2018 -0700
Mark some variables as volatile to avoid compiler optimizations (#144)
util/esum.py
util/esum_module.F90
commit 3e4da50f897989a305ab6a6309ec656a5508a4fe
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 03:49:01 2018 -0400
Update CHANGES
CHANGES
commit 5d451cc5c0b3be973c5ec1dec6d0670b7c6ff44d
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 03:47:29 2018 -0400
Make ttol and dtol available on the device
EOS/helmholtz/actual_eos.F90
commit 5cafa4286a32e80456cc07aecc4538b87e8da029
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 13 03:29:51 2018 -0400
Enable Newton solver tolerance as a runtiem parameter
EOS/helmholtz/_parameters
EOS/helmholtz/actual_eos.F90
commit ed7046685f9e95bc8f99ca464cba3a8e4d74f087
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 12 23:44:00 2018 -0400
Initialize some density dependences to zero
networks/aprox13/actual_rhs.F90
commit c59dde3585f58e5fad269d9f758c32dc7d2a053e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 12 23:38:03 2018 -0400
Initialize Si/Ni density dependence to zero
networks/iso7/actual_rhs.f90
commit 1278345515760aa8a3b8723fc85a214828b00a84
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 12 04:07:13 2018 -0400
Add tabulation for iso7
networks/iso7/actual_rhs.f90
commit 749f9c9e84dbb4c24e793e0f0d84ef38037fe1cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 8 12:30:44 2018 -0400
initialize rpar(:) to ZERO
if we are not extrapolating T during the burn, then the specific heat
derivatives were undefined, which causes floating point exceptions
if we try to print the state in burn_cell
integration/VODE/vode_integrator.f90
commit 7ad7e7b5a0d74105d9c44cd05d73f5808c0f564c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 8 11:48:16 2018 -0400
update the time so it is reflected in the output files
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/main.f90
commit dffc609be1b98d5825fc327d7709acc6e56fff16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 1 08:40:04 2018 -0400
update CHANGES
CHANGES
commit 0203d68fa2e838133a528197aa399e693193f55c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 25 11:35:41 2018 -0400
get burn_cell compiling again
networks/subch/GPackage.mak
unit_test/GPackage.mak
commit 4f14aee660ef8a8f34abad5fb938a0503b7c371d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 24 16:01:23 2018 -0400
this doesn't work -- remove
util/FAT/LICENSE
util/FAT/Make.package
util/FAT/README.md
util/FAT/kind_module.f90
util/FAT/minpack_module.f90
util/FAT/numbers_module.f90
commit 30504d8328a81dd913eaece2b69cbe546c777095
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 18 18:39:29 2018 -0400
pass rpar through the jacobian version too
util/FAT/minpack_module.f90
commit 31bf41a9f5fabc6f5a26088ba14eac195a11c773
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 17 21:18:51 2018 -0400
add an rpar passthrough for the hybrid Powell method
util/FAT/minpack_module.f90
commit b68774e3f50f961c57148ec26d5753abd6418079
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 17 13:13:31 2018 -0400
a Powell hybrid nonlinear system solver from the Fortran Astrodynamics Toolkit
util/FAT/LICENSE
util/FAT/Make.package
util/FAT/README.md
util/FAT/kind_module.f90
util/FAT/minpack_module.f90
util/FAT/numbers_module.f90
commit 9976fbd2fa3ced6d22e6a7a561a39f178394678c
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 12 01:38:41 2018 -0400
Move suppression of burning to the end of the integration
integration/BS/bs_integrator.F90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/VBDF/bdf_rhs.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE/vode_integrator.f90
integration/VODE/vode_rhs.f90
integration/VODE90/actual_integrator.F90
integration/VODE90/vode_rhs.F90
commit a18d9bc61f596e5a3a4e6f8d7e5705e34b4f39d3
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 10 22:40:36 2018 -0400
Check in start of convert helm table script
EOS/helmholtz/convert_helm_table.py
commit a306d3a7e75feb782fece9dc389308808dd0e0f0
Merge: 5a6421d3 39e3ce8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 18:52:56 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 5a6421d38632bf442897f5f74333f389c2427827
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 10 18:52:48 2018 -0400
fix arrows
Docs/networks/networks.tex
commit 39e3ce8e774996a981b644c56264867a24efda49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 9 09:54:34 2018 -0400
update for the C++ build system
util/regression_testing/Microphysics-tests-pgi.ini
commit 6a1baed9f51eab980869d79ce6c793fd85b0d183
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 9 09:09:53 2018 -0400
update for C++ build
util/regression_testing/Microphysics-tests.ini
commit b7a859c0b350a58d3a6195fac6d3cb1130a2efd0
Merge: a43907cb 37a3bfca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 8 19:19:10 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit a43907cbcb32c87be35983c202ff815a343b5811
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 8 19:18:57 2018 -0400
update changes
CHANGES
commit 37a3bfcaab14d840e0aaec9bedd9fea4c60a2fa6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 8 15:35:30 2018 -0400
port to C++ buildsystem (#135)
move the unit test infrastructure to the C++ AMReX buildsystem.
The core functionality of these tests is unchanged. This will make it easier to do the GPU ports.
.gitignore
Make.Microphysics
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
interfaces/Make.package
interfaces/burn_type.F90
networks/Make.package
unit_test/Make.package
unit_test/eos.F90
unit_test/eos_override.F90
unit_test/extern_probin.template
unit_test/microphysics.F90
unit_test/network.F90
unit_test/test_eos/GNUmakefile
unit_test/test_eos/GPackage.mak
unit_test/test_eos/Make.package
unit_test/test_eos/eos_util.f90
unit_test/test_eos/gr0_3d.small
unit_test/test_eos/input_eos
unit_test/test_eos/main.cpp
unit_test/test_eos/main.f90
unit_test/test_eos/probin
unit_test/test_eos/test_eos.H
unit_test/test_eos/test_eos_F.H
unit_test/test_eos/unit_test.f90
unit_test/test_eos/variables.f90
unit_test/test_react/GNUmakefile
unit_test/test_react/GPackage.mak
unit_test/test_react/Make.package
unit_test/test_react/gr0_3d.1
unit_test/test_react/gr0_3d.128
unit_test/test_react/gr0_3d.2
unit_test/test_react/gr0_3d.256
unit_test/test_react/gr0_3d.large
unit_test/test_react/gr0_3d.medium
unit_test/test_react/gr0_3d.small
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_3alpha.VBDF
unit_test/test_react/inputs_aprox13
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_aprox19.burning_mode_0
unit_test/test_react/inputs_aprox21
unit_test/test_react/inputs_ignition
unit_test/test_react/inputs_ignition.BS
unit_test/test_react/inputs_ignition_chamulak
unit_test/test_react/inputs_ignition_chamulak.BS
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_cburn.BS
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_ctest.BS
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/inputs_reaclib_urca.BS
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_xrb_simple
unit_test/test_react/main.F90
unit_test/test_react/main.cpp
unit_test/test_react/old/inputs_3alpha.BS.ACC
unit_test/test_react/old/inputs_aprox13.1
unit_test/test_react/old/inputs_aprox13.128
unit_test/test_react/old/inputs_aprox13.2
unit_test/test_react/old/inputs_aprox13.256
unit_test/test_react/old/inputs_aprox13.32
unit_test/test_react/old/inputs_aprox13.64
unit_test/test_react/old/inputs_aprox13.BS.ACC
unit_test/test_react/old/inputs_aprox13.VBDF
unit_test/test_react/old/inputs_aprox13_tinystep
unit_test/test_react/old/inputs_aprox19.BS
unit_test/test_react/old/inputs_ignition.128
unit_test/test_react/old/inputs_ignition.32
unit_test/test_react/old/inputs_ignition.64
unit_test/test_react/old/inputs_reaclib_cburn.128
unit_test/test_react/old/inputs_reaclib_cburn.32
unit_test/test_react/old/inputs_reaclib_cburn.64
unit_test/test_react/old/inputs_reaclib_urca.32
unit_test/test_react/old/inputs_reaclib_urca.64
unit_test/test_react/probin.3alpha
unit_test/test_react/probin.3alpha.BS
unit_test/test_react/probin.3alpha.VBDF
unit_test/test_react/probin.aprox13
unit_test/test_react/probin.aprox13.burning_mode_0
unit_test/test_react/probin.aprox19
unit_test/test_react/probin.aprox19.burning_mode_0
unit_test/test_react/probin.aprox21
unit_test/test_react/probin.ignition
unit_test/test_react/probin.ignition.BS
unit_test/test_react/probin.ignition_chamulak
unit_test/test_react/probin.ignition_chamulak.BS
unit_test/test_react/probin.reaclib_cburn
unit_test/test_react/probin.reaclib_cburn.BS
unit_test/test_react/probin.reaclib_ctest
unit_test/test_react/probin.reaclib_ctest.BS
unit_test/test_react/probin.reaclib_urca
unit_test/test_react/probin.reaclib_urca.BS
unit_test/test_react/probin.rprox
unit_test/test_react/probin.xrb_simple
unit_test/test_react/react_zones.F90
unit_test/test_react/react_zones_module.F90
unit_test/test_react/test_react.H
unit_test/test_react/test_react_F.H
unit_test/test_react/unit_test.f90
unit_test/test_react/util.f90
unit_test/test_react/variables.f90
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/GPackage.mak
unit_test/test_sdc/Make.package
unit_test/test_sdc/_parameters
unit_test/test_sdc/gr0_3d.small
unit_test/test_sdc/inputs_aprox13
unit_test/test_sdc/main.cpp
unit_test/test_sdc/main.f90
unit_test/test_sdc/probin.aprox13
unit_test/test_sdc/react_zones.F90
unit_test/test_sdc/test_react.H
unit_test/test_sdc/test_react_F.H
unit_test/test_sdc/unit_test.f90
unit_test/test_sdc/util.f90
unit_test/test_sdc/variables.f90
unit_test/write_job_info.f90
commit c477d24a85eb3aeb178cdd2f36ff288d41e8fe51
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Jul 7 17:20:51 2018 -0400
Remove eos dependence, fix compile issues.
unit_test/test_reaclib_rates/GNUmakefile
unit_test/test_reaclib_rates/main.f90
commit b5bd0586e31b46d04d5c176b94c4ea1fe3e14e9b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Jul 7 16:49:53 2018 -0400
Added test program for evaluating reaclib rates in the reaclib networks.
unit_test/test_reaclib_rates/GNUmakefile
unit_test/test_reaclib_rates/GPackage.mak
unit_test/test_reaclib_rates/_parameters
unit_test/test_reaclib_rates/inputs_urca
unit_test/test_reaclib_rates/main.f90
unit_test/test_reaclib_rates/matplotlibrc
commit 9153532879a99ab525062b9d00a0059826051108
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 5 15:45:41 2018 -0400
no longer need xin
unit_test/test_eos/_parameters
commit abcee83992bc15f1abc1c1c581aba03079e181ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 5 15:44:35 2018 -0400
xin_file has no meaning
unit_test/test_eos/input_eos
commit 3034b8c6aee3ccbc3ad37e3bfd6218b3485ae600
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jul 3 20:54:04 2018 -0400
Urca: Make some indices public in table rates module.
networks/ignition_reaclib/URCA-simple/table_rates.F90
commit bcbe198206b71ce8a04e0fc5708495111eac2bc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 2 09:46:23 2018 -0400
update changes
CHANGES
commit 6bd3d789284cc96e964bf056f679fc53bb264efb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 26 03:03:06 2018 -0700
Mark up Helmholtz with !$gpu
EOS/helmholtz/actual_eos.F90
commit 4b06c0337accccb72f776789355810322a81e868
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 25 23:24:57 2018 -0700
Add !$gpu
EOS/gamma_law_general/actual_eos.F90
commit 023729c5114d8fe145a662dfda7ada0d25bfed46
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 25 00:30:28 2018 -0700
Add !$gpu
networks/aprox13/actual_burner.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/actual_burner.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/actual_burner.F90
networks/aprox21/actual_rhs.F90
networks/ignition_simple/actual_burner.F90
networks/ignition_simple/actual_rhs.F90
commit 7f9cacbb21abf0a0606f86a4ac8ee71c789e047a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 25 00:24:11 2018 -0700
vector -> array
integration/BS/stiff_ode.F90
commit df1fa863b1554198d9424e801472c19e89536801
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 25 00:02:51 2018 -0700
Update esum
util/GPackage.mak
util/Make.package
util/esum.py
util/esum_module.F90
util/microphysics_math.F90
util/test/test_esum.f90
commit b1e70b25ce1807e0f46690c254c0b030464f5ced
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jun 21 06:12:41 2018 -0700
vector -> array
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_source/dvode_dewset.F90
integration/VODE90/vode_source/dvode_dvhin.F90
integration/VODE90/vode_source/dvode_dvindy.F90
integration/VODE90/vode_source/dvode_dvjac.F90
integration/VODE90/vode_source/dvode_dvnlsd.F90
integration/VODE90/vode_source/dvode_dvnorm.F90
integration/VODE90/vode_source/dvode_dvset.F90
integration/VODE90/vode_source/dvode_dvsol.F90
integration/VODE90/vode_source/dvode_dvstep.F90
integration/VODE90/vode_source/dvode_type.F90
networks/aprox13/actual_rhs.F90
util/linear_algebra_modules/blas_module.F90
util/linear_algebra_modules/linpack_module.F90
commit 0c9c779de6a6eb3a26abbf5c2d45ff42b46fada6
Merge: 78bc3983 32e7beba
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 20 17:58:18 2018 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 78bc3983b7c3006fabe933faf921885bd4e4258e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 20 16:32:19 2018 -0400
Update name of grid file the inputs uses to match convention.
unit_test/test_react/inputs_aprox13.32
commit 32e7beba1cb88c5dc708b708e13df067ab7abbe4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 20 12:36:49 2018 -0400
update changes
CHANGES
commit 076f276b9d09de283d3d7545a027cfa05c8e54c5
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Jun 20 02:17:46 2018 -0400
Fix CUDA compilation of numerical jacobian. Adds copy subroutine for burn type on the device.
integration/numerical_jacobian.F90
interfaces/burn_type.F90
commit 6f4c6a8af6fb30c7bc3152deffb7bc281b48c0cd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 23:13:08 2018 -0400
Use CUDA-enabled probin template.
unit_test/dummy.probin.template
commit 9fc45dc278db388149ceaaeb4fa652b6a490458d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 22:20:53 2018 -0400
Add CUDA version of VODE90 to the integration options (#133)
* Update main integration driver for CUDA.
* Update numerical jacobian for CUDA.
* update build files for integration.
* Markup temperature integration for CUDA.
* Added VODE90 from cudadevice, cleaned up with AMREX_DEVICE and using amrex_real.
* Use AMREX_DEVICE.
* Module updates for actual_integrator_sdc.f90
* Module updates for vode_rhs_sdc.f90
* Module updates for vode_type_sdc.f90
integration/GPackage.mak
integration/Make.package
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/actual_integrator.F90
integration/VODE90/actual_integrator.f90
integration/VODE90/actual_integrator_sdc.f90
integration/VODE90/rpar.F90
integration/VODE90/vode_parameters.F90
integration/VODE90/vode_rhs.F90
integration/VODE90/vode_rhs_sdc.f90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_source/NOTES.md
integration/VODE90/vode_source/docs/Makefile
integration/VODE90/vode_source/docs/doxyfile_vode
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_source/dvode_constants.F90
integration/VODE90/vode_source/dvode_dacopy.F90
integration/VODE90/vode_source/dvode_dewset.F90
integration/VODE90/vode_source/dvode_dvhin.F90
integration/VODE90/vode_source/dvode_dvindy.F90
integration/VODE90/vode_source/dvode_dvjac.F90
integration/VODE90/vode_source/dvode_dvjust.F90
integration/VODE90/vode_source/dvode_dvnlsd.F90
integration/VODE90/vode_source/dvode_dvnorm.F90
integration/VODE90/vode_source/dvode_dvset.F90
integration/VODE90/vode_source/dvode_dvsol.F90
integration/VODE90/vode_source/dvode_dvstep.F90
integration/VODE90/vode_source/dvode_nordsieck.F90
integration/VODE90/vode_source/dvode_output.f90
integration/VODE90/vode_source/dvode_type.F90
integration/VODE90/vode_source/test/GNUmakefile
integration/VODE90/vode_source/test/tvode.f90
integration/VODE90/vode_source/test/tvode_rhs.f90
integration/VODE90/vode_type.F90
integration/VODE90/vode_type_sdc.f90
integration/integrator.F90
integration/numerical_jacobian.F90
integration/temperature_integration.F90
commit c7d43d0bd6cdc2e3fc43ebf9feb19c481e53d176
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 19:49:20 2018 -0400
Markup several networks for CUDA (#132)
* Marked up aprox13 for CUDA.
* Markup aprox19 for CUDA.
* Move ifdef cuda attributes managed to a more sensible spot.
* Marked up aprox21 for CUDA.
* Marked up ignition_simple for CUDA.
* Marked up C-burn-simple for CUDA.
* Add CUDA markup to URCA-simple network.
* Marked up subch network for CUDA.
* Update name of xin file the aprox13 test is looking for.
* Take out the 16 for comparisons.
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_burner.F90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.F90
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox19/actual_burner.F90
networks/aprox19/actual_network.F90
networks/aprox19/actual_rhs.F90
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/aprox21/actual_burner.F90
networks/aprox21/actual_network.F90
networks/aprox21/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/actual_burner.F90
networks/ignition_reaclib/C-burn-simple/actual_network.F90
networks/ignition_reaclib/C-burn-simple/actual_rhs.F90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.F90
networks/ignition_reaclib/C-burn-simple/table_rates.F90
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/actual_burner.F90
networks/ignition_reaclib/URCA-simple/actual_network.F90
networks/ignition_reaclib/URCA-simple/actual_rhs.F90
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.F90
networks/ignition_reaclib/URCA-simple/table_rates.F90
networks/ignition_reaclib/URCA-simple/urca.py
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/actual_burner.F90
networks/ignition_simple/actual_network.F90
networks/ignition_simple/actual_rhs.F90
networks/subch/actual_burner.F90
networks/subch/actual_network.F90
networks/subch/actual_rhs.F90
networks/subch/reaclib_rates.F90
networks/subch/table_rates.F90
commit 01d3870dd8330bc006c9de6b3c46bc0f53f858b7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 17:32:51 2018 -0400
Revert "update inputs for 16**3 aprox13 problem."
This reverts commit 38588d5a0672a05206c706f6409bda5fbd74c19a.
unit_test/test_react/inputs_aprox13
commit 4b2daece0a1380c3a368a6ea6adf3be1eb33f3d0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 14:31:12 2018 -0400
Use the CUDA-enabled reactions test driver. (#130)
* Mark eos as AMREX_DEVICE. Add eos_finalize call.
* Call finalize routines.
* Make aion_inv a CUDA managed variable. Add network_finalize.
* f90->F90 in the build for network.F90
* Drop in test react driver from cudadevice.
* Update GPackage.mak.
* Add managed probin flag to build system.
* Update main, react_zones_module for FBoxLib.
* Put the bl_space import back in.
* Add module imports for microphysics_finalize.
* Use small_temp and small_dens from probin instead of mintemp, mindens when initializing microphysics.
* Put n_rhs stats back in for CPU.
* ifdef out call to screening_finalize for networks that do not require it.
GMicrophysics.mak
networks/GNetwork.mak
unit_test/GPackage.mak
unit_test/eos.F90
unit_test/microphysics.F90
unit_test/network.F90
unit_test/test_react/GPackage.mak
unit_test/test_react/main.F90
unit_test/test_react/react_zones_module.F90
commit 11d400628707cbb90c7ee5600ea5abfcb4c625e6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 13:08:51 2018 -0400
Move blas and linpack module files into linear_algebra_modules. Only build them for VODE90.
networks/GNetwork.mak
util/BLAS/GPackage.mak
util/BLAS/Make.package
util/LINPACK/GPackage.mak
util/LINPACK/Make.package
util/linear_algebra_modules/GPackage.mak
util/linear_algebra_modules/Make.package
util/linear_algebra_modules/blas_module.F90
util/linear_algebra_modules/linpack_module.F90
commit daa186c85859b8bb17c72a9d0bca14fc07eba901
Merge: bc486a1c 65865724
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 19 12:36:06 2018 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 6586572440bf5f94b80bd94290cee7e8ee52f261
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 19 11:50:38 2018 -0400
fix file name
EOS/breakout/Make.package
commit 7daf820d44ffdbda7745ca2b4f8be7f39a9a556e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 19:14:24 2018 -0400
Marked up aprox rates for CUDA. (#129)
rates/GPackage.mak
rates/Make.package
rates/aprox_rates.F90
rates/tfactors.F90
commit bc486a1cba4ef0f74fb010df92923b94fdf9ab24
Merge: d935d210 0ea881a6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 18:42:19 2018 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 0ea881a6edf178d2161bf7193a2cada89391c7d6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 18:12:24 2018 -0400
Add utility modules and specialized esums (#128)
* Add specialized esums from cudadevice branch to microphysics math.
* dp_t => amrex_real in microphysics math specialized esums.
* Added BLAS module with CUDA markup.
* Added linpack module marked up for CUDA.
* Use specialized esums in aprox13 rhs.
* Use specialized esums in iso7.
* Use specialized esums in aprox19.
* Use specialized esums in aprox21.
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
util/BLAS/GPackage.mak
util/BLAS/Make.package
util/BLAS/blas_module.F90
util/LINPACK/GPackage.mak
util/LINPACK/Make.package
util/LINPACK/linpack_module.F90
util/microphysics_math.F90
commit b98e82d2f8516aaac74ea41356a76c686f1713c2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 16:43:33 2018 -0400
Markup EOS routines for CUDA (#127)
* Update interfaces for CUDA. Allocate and initialize eos quantities in eos.F90
* Markup neutrino routine for CUDA.
* Update screening module for CUDA.
* minor cleanups.
* Minor revisions to ifdef amrex_error.
* Update multigamma EOS for CUDA.
* Update polytrope EOS for CUDA.
* Add CUDA markup to subroutines in eos.F90
EOS/breakout/actual_eos.F90
EOS/gamma_law_general/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
unit_test/eos.F90
commit e52566499e0a29e2832026c8722c8290a2315ae0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 15:44:40 2018 -0400
Update screening module for CUDA (#126)
* Update interfaces for CUDA. Allocate and initialize eos quantities in eos.F90
* Markup neutrino routine for CUDA.
* Update screening module for CUDA.
screening/GPackage.mak
screening/Make.package
screening/screen.F90
commit 783906afdd229b64cf1d2e4585d0b4865f79c498
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 15:23:40 2018 -0400
Update neutrinos module for CUDA (#125)
* Update interfaces for CUDA. Allocate and initialize eos quantities in eos.F90
* Markup neutrino routine for CUDA.
* LAUNCH->DEVICE
neutrinos/GPackage.mak
neutrinos/Make.package
neutrinos/sneut5.F90
commit 8094ce60d9f505deb0e84128e9dde233a9e5f45e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 14:52:56 2018 -0400
Update interfaces for CUDA. Allocate and initialize eos quantities in eos.F90 (#124)
interfaces/burn_type.F90
interfaces/eos_type.F90
unit_test/eos.F90
commit d935d2105346e9c297a50a24de77467ef3b2f411
Merge: 38588d5a ded6c108
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Jun 18 14:13:12 2018 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit ded6c1082ab9db05187e043287c73d7987345f06
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:21:56 2018 -0700
f90 -> F90
integration/GPackage.mak
integration/Make.package
integration/temperature_integration.F90
commit 8d412a10e564c0496c0f885024918e380f3e5976
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:18:07 2018 -0700
vector -> array
integration/VODE90/vode_source/dvode.F90
interfaces/burn_type.F90
commit e0fb0aec32eb16670b9d00fb9e81322f27b4b37b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:18:00 2018 -0700
Capital F
GMicrophysics.mak
commit 449ccaed9ef75f99c45fe2bc66e8dfb186dcdb0e
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 23:09:29 2018 -0700
probin.f90 -> probin.F90
GMicrophysics.mak
commit 3df01617f7575f6eb98833379014097bd6765744
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 22:49:41 2018 -0700
Define AMREX_DEVICE for CUDA
GMicrophysics.mak
commit 38588d5a0672a05206c706f6409bda5fbd74c19a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Jun 17 02:05:06 2018 -0400
update inputs for 16**3 aprox13 problem.
unit_test/test_react/inputs_aprox13
commit 080b309053498967c07ce89886f3802cc15b2426
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 22:59:26 2018 -0700
New unit test inputs files
unit_test/burn_cell/inputs_burn_urca
unit_test/test_react/gr0_3d.1
unit_test/test_react/gr0_3d.128
unit_test/test_react/gr0_3d.2
unit_test/test_react/gr0_3d.256
unit_test/test_react/inputs_aprox13.1
unit_test/test_react/inputs_aprox13.128
unit_test/test_react/inputs_aprox13.2
unit_test/test_react/inputs_aprox13.256
unit_test/test_react/inputs_aprox13.32
unit_test/test_react/inputs_aprox13.64
unit_test/test_react/inputs_aprox13_tinystep
unit_test/test_react/inputs_ignition.128
unit_test/test_react/inputs_ignition.32
unit_test/test_react/inputs_ignition.64
unit_test/test_react/inputs_reaclib_cburn.128
unit_test/test_react/inputs_reaclib_cburn.32
unit_test/test_react/inputs_reaclib_cburn.64
unit_test/test_react/inputs_reaclib_urca.32
unit_test/test_react/inputs_reaclib_urca.64
unit_test/test_react/xin.aprox13.1
unit_test/test_react/xin.aprox13.128
unit_test/test_react/xin.aprox13.2
unit_test/test_react/xin.aprox13.256
unit_test/test_react/xin.aprox13.32
unit_test/test_react/xin.aprox13.64
unit_test/test_react/xin.ignition.128
unit_test/test_react/xin.ignition.32
unit_test/test_react/xin.ignition.64
unit_test/test_react/xin.reaclib_cburn.128
unit_test/test_react/xin.reaclib_cburn.32
unit_test/test_react/xin.reaclib_cburn.64
unit_test/test_react/xin.reaclib_urca.256
unit_test/test_react/xin.reaclib_urca.32
unit_test/test_react/xin.reaclib_urca.64
commit 756806feaa8787ca8154a019112d65c8c5ce6654
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 22:53:44 2018 -0700
dp_t -> rt
integration/BS/test/test.f90
commit 1f218f4ff4e8a2752e067873b9ac70a8410e71dc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 22:52:55 2018 -0700
Helmholtz cleanup
EOS/helmholtz/actual_eos.F90
commit 53d4289efd699c3a71354529e7ff1940a9bc3344
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 16 22:26:58 2018 -0700
vector -> vektor
neutrinos/sneut5.f90
commit 8c7547e2ba790694e78df9453681259228dcff83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 14 21:07:55 2018 -0400
odule -> module
networks/ignition_simple_SDC/actual_network.f90
commit d3f47c35d0177e3a90120ee5986231917536801c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 13 10:19:55 2018 -0400
BOXLIB_HOME -> FBOXLIB_HOME
unit_test/test_sdc/GNUmakefile
commit 3523ac0ee2bc077d8b2c4ac1ba6799fdda021800
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 14:18:55 2018 -0400
dp_t -> rt
networks/rprox/actual_burner.f90
networks/rprox/actual_rhs.f90
commit 4b6c72cbb7a2e2ad98f26cb35c00f71099789e26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 10:27:02 2018 -0400
for some reason, the setting of T9 was deleted -- restore
networks/rprox/actual_burner.f90
commit d6e180d5785c8d9425c70165e15b6038ffec3804
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 10:08:23 2018 -0400
success was being overwritten and undefined
integration/BS/bs_integrator.F90
commit 022beb248efe500cdf12bb55dcfe12ae63ae79ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 18:23:28 2018 -0400
ignore AMREX_DEVICE
GMicrophysics.mak
commit e82452b891c4bc629b979b5927ad923dced6ed70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:54:32 2018 -0400
update for FBoxLib
util/regression_testing/Microphysics-tests.ini
commit f500aa3fd148b5bf4563258ef4bfee17c95383bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:52:06 2018 -0400
update SDC dp_t
integration/VODE/vode_type_sdc.f90
commit 605664719d532a36bd6d8d6d164048b58ef1ed94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:50:18 2018 -0400
dp_t -> rt
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/rates_module.f90
commit 122f4996571094cb3ca5a0cf980d2dd2ca4488de
Merge: 69659eab cd096f72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:39:09 2018 -0400
Merge branch 'development' of ssh://github.com/starkiller-astro/microphysics into development
commit 69659eabe2c844cdeabcc81e60bb2da65fb4e468
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:38:56 2018 -0400
update the probin template
unit_test/dummy.probin.template
commit cd096f72909515407f60306c65667a49569eedc7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:32:35 2018 -0400
dpdT (the derivative) was mistakenly changed to rt
util/cj_detonation/cj_det.f90
commit 1772c35ed44b273ab0484782abb1254ec05805a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:24:00 2018 -0400
more rt fixes
networks/xrb_simple/actual_rhs.f90
commit c0dda7c6f254e631c476115a8eb39fe1a3520ac7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:20:10 2018 -0400
more rt fixes
integration/VODE/vode_rhs_sdc.f90
networks/ignition_chamulak/actual_network.f90
networks/xrb_simple/actual_network.f90
commit 82d0383aff18c6a9b0001db05a4ed25c5f638313
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 17:15:05 2018 -0400
fix some rt's
integration/VODE90/vode_type.f90
commit 2e1d67c0d31d55fce3a4a4fe52bae56b6f2dfeb8
Merge: 2405a6f0 c0e7bb25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 15:24:45 2018 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit 2405a6f01ca3331602a02a1e21ad65b41b304144
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 15:24:32 2018 -0400
bl_error -> amrex_error
EOS/polytrope/actual_eos.F90
integration/VODE/vode_integrator_sdc.f90
integration/VODE90/actual_integrator.f90
integration/integrator_sdc.F90
networks/MESA/burn_solout.f90
networks/MESA/setup_mesa_net.f90
networks/ignition_reaclib/C-test/test/testjacobian.f90
networks/ignition_reaclib/URCA-simple/test/testjacobian.f90
networks/ignition_simple/test/eval.f90
networks/ignition_simple/test/testjacobian.f90
networks/ignition_simple_SDC/actual_burner.f90
networks/kpp/actual_burner.f90
unit_test/burn_cell/main.f90
unit_test/test_eos/main.f90
unit_test/test_react/main.f90
unit_test/test_sdc/main.f90
util/cj_detonation/cj_det.f90
commit c0e7bb25498c134a190aa9eb3ca0dfe8a5941dbc
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 11 14:48:42 2018 -0400
Update to use FBoxLib
GMicrophysics.mak
integration/VODE90/vode_source/test/GNUmakefile
interfaces/eos_type.F90
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/README.md
unit_test/dummy.probin.template
unit_test/eos.F90
unit_test/network.f90
unit_test/test_eos/GNUmakefile
unit_test/test_react/GNUmakefile
unit_test/write_job_info.f90
util/cj_detonation/GNUmakefile
commit 07498ff2581bdf37d809c5152982f821917370dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 11 14:40:51 2018 -0400
fix compilation
EOS/multigamma/actual_eos.F90
commit 2e61d9a8501cbef6527832ace76a1dd6c2d845fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 23:40:53 2018 -0400
Add a success parameter to the burn_type
integration/BS/bs_integrator.F90
integration/VODE/vode_integrator.f90
integration/integration_data.f90
integration/integrator.F90
interfaces/burn_type.F90
commit c8847607278988cbf0126ee185bff097ccad1d5a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 23:40:17 2018 -0400
Do not retry if retry_burn is false
integration/integrator.F90
commit 13ceba689d47df34ac912e2f43a890a1162f13fc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 23:33:40 2018 -0400
Add an option to not abort on failure
integration/_parameters
integration/integrator.F90
commit f74c1e9e1e8fbc9ffbb8d0ebc724d811a38c927b
Merge: cfff24b3 980b9e1a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 22:16:37 2018 -0400
Merge branch 'burn_retry_fix' into development
commit 980b9e1a7a2f9ee3cdfe7c4b0d8a41c241d49487
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 10 22:13:55 2018 -0400
Fix logic error in retrying a burn
The loop wasn't actually advancing to the next integrator
integration/integrator.F90
commit cfff24b3bfc5a421753a9ff35e8a1b788356732d
Merge: 222c5afa e23a50b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 15:06:51 2018 -0400
Merge branch 'master' into development
commit e23a50b003acc4398b4a095beb81ab09d9d562ff
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 15:05:12 2018 -0400
Revert "Merge pull request #111 from starkiller-astro/f_baselib"
This reverts commit 160de1d3e4e02432bbdfcaba5a7e160f614f8442, reversing
changes made to 9866ec0eee50a7051a020c8e631a690ec0fb58f8.
EOS/breakout/actual_eos.f90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
EOS/stellarcollapse/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
EOS/ztwd/actual_eos.F90
conductivity/stellar/stellar_conductivity.f90
integration/BS/bs_integrator.F90
integration/BS/bs_integrator_sdc.F90
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/numerical_jacobian_sdc.f90
integration/BS/stiff_ode.F90
integration/VBDF/bdf.f90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE/_parameters
integration/VODE/vode_integrator.f90
integration/VODE/vode_integrator_sdc.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_type.f90
integration/VODE/vode_type_sdc.f90
integration/VODE90/actual_integrator.f90
integration/VODE90/actual_integrator_sdc.f90
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_rhs_sdc.f90
integration/VODE90/vode_type.f90
integration/VODE90/vode_type_sdc.f90
integration/integration_data.f90
integration/integrator.F90
integration/integrator_sdc.F90
integration/numerical_jacobian.f90
integration/temperature_integration.f90
interfaces/burn_type.F90
interfaces/eos_type.F90
interfaces/sdc_type.F90
networks/MESA/Do_One_Zone_Burn.f90
networks/MESA/burn_solout.f90
networks/MESA/burner.f90
networks/MESA/get_mesa_ebin.f90
networks/MESA/net_utils.f90
networks/MESA/network.template.mesa
networks/MESA/setup_mesa_net.f90
networks/aprox13/actual_burner.f90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.f90
networks/aprox13/test/testburn.f90
networks/aprox19/actual_burner.f90
networks/aprox19/actual_network.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_burner.f90
networks/aprox21/actual_network.f90
networks/aprox21/actual_rhs.f90
networks/breakout/actual_network.f90
networks/general_null/actual_burner.f90
networks/general_null/actual_network.f90.test
networks/general_null/actual_rhs.f90
networks/general_null/network.template
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-test/actual_burner.f90
networks/ignition_reaclib/C-test/actual_network.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_rhs.f90
networks/ignition_simple/test/eval.f90
networks/ignition_simple/test/testburn.f90
networks/ignition_simple/test/testjacobian.f90
networks/ignition_simple_SDC/actual_burner.f90
networks/ignition_simple_SDC/actual_network.f90
networks/ignition_simple_SDC/actual_rhs.f90
networks/ignition_simple_SDC/burner_aux.f90
networks/iso7/actual_burner.f90
networks/iso7/actual_network.f90
networks/iso7/actual_rhs.f90
networks/kpp/actual_burner.f90
networks/kpp/actual_network.f90
networks/kpp/f_rhs.f90
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_burner.f90
networks/rprox/actual_network.f90
networks/rprox/actual_rhs.f90
networks/rprox/rates_module.f90
networks/rprox/reaclib/make_rates_module.py
networks/rprox/test/eval.f90
networks/rprox/test/testburn.f90
networks/subch/actual_burner.f90
networks/subch/actual_network.f90
networks/subch/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_network.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
networks/triple_alpha_plus_cago/test/eval.f90
networks/triple_alpha_plus_cago/test/testburn.f90
networks/triple_alpha_plus_cago/test/testjacobian.f90
networks/xrb_simple/actual_burner.f90
networks/xrb_simple/actual_network.f90
networks/xrb_simple/actual_rhs.f90
networks/xrb_simple/test/testburn.f90
neutrinos/sneut5.f90
screening/screen.f90
unit_test/burn_cell/main.f90
unit_test/conductivity.F90
unit_test/constants_cgs.f90
unit_test/dummy.probin.template
unit_test/eos.F90
unit_test/network.f90
unit_test/test_eos/main.f90
unit_test/test_eos/variables.f90
unit_test/test_react/main.f90
unit_test/test_react/util.f90
unit_test/test_react/variables.f90
unit_test/test_sdc/main.f90
unit_test/test_sdc/util.f90
unit_test/test_sdc/variables.f90
unit_test/write_job_info.f90
util/cj_detonation/cj_det.f90
util/cj_detonation/main.f90
util/esum.py
util/eval_rhs/evaluate_rhs.f90
util/microphysics_math.F90
util/test/test_esum.f90
commit 222c5afa4cff64c870f447ae2cecfe0fceed3159
Merge: 2d571abe 84ebe1b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 11:49:53 2018 -0700
Merge pull request #116 from starkiller-astro/f_baselib
Migrate away from F_BaseLib
commit 160de1d3e4e02432bbdfcaba5a7e160f614f8442
Merge: 9866ec0e 84ebe1b0
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 4 10:07:26 2018 -0700
Merge pull request #111 from starkiller-astro/f_baselib
Migrate away from F_Baselib
commit 84ebe1b0cacd252603855584daec4e704c1f42f9
Merge: 2690b22c 2d571abe
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 20:38:35 2018 -0700
Merge branch 'development' of https://github.com/starkiller-astro/Microphysics into development
commit 2690b22c5a1a6e716e7e873b6250686e0847c470
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 20:36:42 2018 -0700
Migrate to not needing F_BaseLib.
EOS/breakout/actual_eos.f90
EOS/gamma_law_general/actual_eos.F90
EOS/multigamma/actual_eos.F90
EOS/polytrope/actual_eos.F90
EOS/stellarcollapse/actual_eos.F90
EOS/stellarcollapse/eos_aux_data.f90
EOS/ztwd/actual_eos.F90
conductivity/stellar/stellar_conductivity.f90
integration/BS/bs_integrator_sdc.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_type_sdc.F90
integration/BS/numerical_jacobian_sdc.f90
integration/VBDF/bdf.f90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE/vode_integrator_sdc.f90
integration/VODE90/actual_integrator.f90
integration/VODE90/actual_integrator_sdc.f90
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_rhs_sdc.f90
integration/VODE90/vode_type.f90
integration/VODE90/vode_type_sdc.f90
integration/integrator.F90
integration/integrator_sdc.F90
interfaces/burn_type.F90
interfaces/eos_type.F90
interfaces/sdc_type.F90
networks/MESA/Do_One_Zone_Burn.f90
networks/MESA/burn_solout.f90
networks/MESA/burner.f90
networks/MESA/get_mesa_ebin.f90
networks/MESA/net_utils.f90
networks/MESA/network.template.mesa
networks/MESA/setup_mesa_net.f90
networks/aprox13/actual_burner.f90
networks/aprox13/actual_network.F90
networks/aprox13/actual_rhs.f90
networks/aprox13/test/testburn.f90
networks/aprox19/actual_burner.f90
networks/aprox19/actual_network.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_burner.f90
networks/aprox21/actual_network.f90
networks/aprox21/actual_rhs.f90
networks/breakout/actual_network.f90
networks/general_null/actual_burner.f90
networks/general_null/actual_network.f90.test
networks/general_null/actual_rhs.f90
networks/general_null/network.template
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-test/actual_burner.f90
networks/ignition_reaclib/C-test/actual_network.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_rhs.f90
networks/ignition_simple/test/eval.f90
networks/ignition_simple/test/testburn.f90
networks/ignition_simple/test/testjacobian.f90
networks/ignition_simple_SDC/actual_burner.f90
networks/ignition_simple_SDC/actual_network.f90
networks/ignition_simple_SDC/actual_rhs.f90
networks/ignition_simple_SDC/burner_aux.f90
networks/iso7/actual_burner.f90
networks/iso7/actual_network.f90
networks/iso7/actual_rhs.f90
networks/kpp/actual_burner.f90
networks/kpp/actual_network.f90
networks/kpp/f_rhs.f90
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_burner.f90
networks/rprox/actual_network.f90
networks/rprox/actual_rhs.f90
networks/rprox/rates_module.f90
networks/rprox/reaclib/make_rates_module.py
networks/rprox/test/eval.f90
networks/rprox/test/testburn.f90
networks/subch/actual_burner.f90
networks/subch/actual_network.f90
networks/subch/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_network.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
networks/triple_alpha_plus_cago/test/eval.f90
networks/triple_alpha_plus_cago/test/testburn.f90
networks/triple_alpha_plus_cago/test/testjacobian.f90
networks/xrb_simple/actual_burner.f90
networks/xrb_simple/actual_network.f90
networks/xrb_simple/actual_rhs.f90
networks/xrb_simple/test/testburn.f90
neutrinos/sneut5.f90
screening/screen.f90
unit_test/burn_cell/main.f90
unit_test/conductivity.F90
unit_test/constants_cgs.f90
unit_test/dummy.probin.template
unit_test/eos.F90
unit_test/network.f90
unit_test/test_eos/main.f90
unit_test/test_eos/variables.f90
unit_test/test_react/main.f90
unit_test/test_react/util.f90
unit_test/test_react/variables.f90
unit_test/test_sdc/main.f90
unit_test/test_sdc/util.f90
unit_test/test_sdc/variables.f90
unit_test/write_job_info.f90
util/cj_detonation/cj_det.f90
util/cj_detonation/main.f90
util/esum.py
util/eval_rhs/evaluate_rhs.f90
util/microphysics_math.F90
util/test/test_esum.f90
commit 7faf6c856be77eb6f0f62575cb08ed18b547d28e
Author: Ann Almgren <asalmgren@lbl.gov>
Date: Sat Jun 2 18:40:34 2018 -0700
Move towards not needing F_BaseLib.
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
integration/BS/bs_integrator.F90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/BS/bs_type.F90
integration/BS/stiff_ode.F90
integration/VODE/vode_integrator.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_type.f90
integration/VODE/vode_type_sdc.f90
integration/integration_data.f90
integration/integrator.F90
integration/numerical_jacobian.f90
integration/temperature_integration.f90
util/microphysics_math.F90
commit 2d571abe8bb3d3896f18d451e0a242ccf62f588f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jun 2 14:53:16 2018 -0400
Make number of VODE steps a probin parameter
integration/VODE/_parameters
integration/VODE/vode_integrator.f90
commit 9866ec0eee50a7051a020c8e631a690ec0fb58f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed May 16 20:12:42 2018 -0400
sync up with the Castro version -- this is more PEP-8 compliant
networks/general_null/write_network.py
commit adb8a53a2cc5c5b8def463c17842e53274f6c523
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed May 16 16:24:55 2018 -0700
change string.replace to line.replace so it's compatible with python 3 (#107)
networks/general_null/write_network.py
commit b3ca34cb476999ed7ecc85c3530803da332344d8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 15 16:00:44 2018 -0400
Mark up gamma law for CUDA
EOS/gamma_law_general/actual_eos.F90
commit 8d16ff353f4753bab3ca23cd84eb3cdb271555b1
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 15 15:17:00 2018 -0400
Port general_null for CUDA
networks/general_null/Make.package
networks/general_null/network.template
commit e0112bc4516bd59d8e353bbb8ea60d702c341db3
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Wed May 2 15:57:05 2018 -0400
Add Tolerance Testing to Microphysics Users Guide (#105)
* Changed GNUmakefile from aprox13 to subch
* Add subch network to users guide. Included a citation of Shen and Bildsten 2009.
* Added Tolerance testing to the user's guide
Docs/networks/networks.tex
Docs/networks/tolerances.png
commit 1cdd2920bcf71a0d7f9e950c22d32c262be127d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 1 12:57:44 2018 -0400
update CHANGES
CHANGES
commit b46fb1c3ffb0d70a7eb60baeeacab6c71a02b9a7
Merge: 60070f5b f17c5464
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 30 19:00:16 2018 -0400
Merge branch 'master' into development
commit 60070f5b5d9e3a5d63b7688e09b2f0f58c2997d2
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Mon Apr 30 18:59:23 2018 -0400
Added subch to Users Docs (#103)
* Changed GNUmakefile from aprox13 to subch
* remove some relic table stuff
* Add subch network to users guide. Included a citation of Shen and Bildsten 2009.
Docs/networks/networks.tex
Docs/networks/subch.pdf
Docs/refs.bib
networks/aprox13/actual_rhs.f90
unit_test/burn_cell/GNUmakefile
commit 57f38e9218c3cf807e987c97ef8404e057b7118b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 13 15:58:53 2018 -0400
update runtime parameters
Docs/runtime_parameters/runtime_parameters.tex
commit 9c62803475babcc5e12d485d16255a451af93a41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 13 15:36:25 2018 -0400
some fixes
Docs/EOS/eos.tex
Docs/MicrophysicsUsersGuide.tex
Docs/basics/basics.tex
Docs/data_structures/data_structures.tex
Docs/maestrosymbols.tex
Docs/networks/networks.tex
commit a464e66d64626af1df2a13fc05e63c798255d7ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 12 22:11:02 2018 -0400
illustrate the Jacobian matrix -- quite complicated latex
Docs/MicrophysicsUsersGuide.tex
Docs/networks/networks.tex
commit 9bae442cd3b1566c012ff3b2d738f657999080af
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Apr 12 08:41:53 2018 -0700
Fix the calculation of the numerical Jacobian terms wrt X (#100)
* Fix the calculation of the numerical Jacobian terms wrt X
These were missing a factor of A, so the Jacobian was actually using
d(Y-dot) / dX.
integration/numerical_jacobian.f90
commit 448e53ea992d6e6b866b450b2963a44b87aaabd2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 12 00:25:02 2018 -0400
Fix comment
integration/BS/bs_rhs.F90
commit f17c5464507fe83ec36e76fe7f1b034369ba2755
Merge: 23fa9b17 ce462ad0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 9 19:34:16 2018 -0400
Merge branch 'master' of ssh://github.com/starkiller-astro/Microphysics
commit 23fa9b17ea8c47dc142241b5af551bce557e0765
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 9 19:34:02 2018 -0400
remove some relic table stuff
networks/aprox13/actual_rhs.f90
commit 0d29b679860b20ce9e68bad5ede8bc55299d359e
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Mon Apr 9 18:28:55 2018 -0400
Implement new 12C(A,G)16O Reaction Rate From Deboer + 2017 (#56)
* new routine for deboer 2017 c12ag rate, initialize variables
* change call to c12ag to a logical check to determine which rate to use, default is the old cf88 * 1.7
CHANGES
networks/_parameters
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
rates/aprox_rates.f90
commit fe7006f5949238424260a33adb4fa7a5bc4e1753
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 9 14:26:02 2018 -0400
Do not define extra thermo components of eos_t ifndef EXTRA_THERMO (#88)
* Do not define extra thermo components of eos_t if EXTRA_THERMO is undefined.
EOS/helmholtz/actual_eos.F90
GMicrophysics.mak
interfaces/GPackage.mak
interfaces/eos_type.F90
commit c484f6dc148302b5f52c3fab8c4d14f70f3a1fb4
Merge: bf6da127 532698d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 9 14:15:51 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit bf6da127f944ce3a66a105dee4d6d0331966a0b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 9 14:15:37 2018 -0400
remove a bunch of unused variables
integration/BS/bs_integrator.F90
integration/BS/bs_type.F90
integration/BS/stiff_ode.F90
integration/VODE/vode_integrator.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
integration/integrator.F90
interfaces/eos_type.f90
unit_test/write_job_info.f90
commit 532698d70cb1459e54d0a1ea75bde17e222ebb13
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Apr 9 13:24:21 2018 -0400
Switch to use only from amrex constants to avoid name conflict per https://github.com/AMReX-Codes/amrex/issues/244\#issuecomment-379823787
EOS/helmholtz/actual_eos.F90
commit 1f5a391b78e6ed8bda55c111643057ed38ac1a64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 8 21:59:27 2018 -0400
update README
util/cj_detonation/README.md
commit 0cd265c46c6e2d95e3607d964ddab74323708c1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 21:58:07 2018 -0400
add CJ note
CHANGES
commit 49daae3f6322d4383f4b6bb912e46c79bfaf2916
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 21:57:14 2018 -0400
this works now
util/cj_detonation/cj_plot.py
util/cj_detonation/main.f90
commit d3857d28b0f3f49b6f3beb3a04e096314a74c3d6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 19:49:54 2018 -0400
this almost works -- I think we are still doing something wrong in finding the CJ speed
util/cj_detonation/cj_det.f90
util/cj_detonation/cj_plot.py
util/cj_detonation/main.f90
commit 7246bf704bc9752e4baab248c9e22ff2c08b8dfe
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Apr 6 18:53:06 2018 -0400
Move ener_gener_rate into actual_rhs (#98)
networks/subch/actual_network.f90
networks/subch/actual_rhs.f90
commit 47ac35804cb33283ebb1d06c30c9d26ad521ad6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 16:50:40 2018 -0400
this gets the Hugoniot curves for the shock and detonation
util/cj_detonation/cj_det.f90
util/cj_detonation/main.f90
commit 7ec1201925a10e8d862cb9fd05cdaa69efe9fd0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 15:54:00 2018 -0400
more progress
util/cj_detonation/cj_det.f90
util/cj_detonation/inputs
util/cj_detonation/main.f90
commit 864d6b0e0ab182825faff741cd412b46d8024150
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 12:53:48 2018 -0400
make it
util/cj_detonation/GPackage.mak
commit 8df2c62a7c13b5db5b2b1330900b1fbfe173e081
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 12:51:11 2018 -0400
add some of the guts of the det root find
util/cj_detonation/cj_det.f90
util/cj_detonation/main.f90
commit 4515998fe16b78fcd842a0b9a67f90377c751547
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 11:36:20 2018 -0400
outline
util/cj_detonation/_parameters
util/cj_detonation/main.f90
commit 622975d38aacd255997c540b6c250164aea22136
Merge: 97dcad4f 626bdc57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 11:13:34 2018 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit 97dcad4f37f9e572d9c910a7058bd04558d9bc21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Apr 6 11:12:05 2018 -0400
start of the CJ det
util/cj_detonation/GNUmakefile
util/cj_detonation/GPackage.mak
util/cj_detonation/README.md
util/cj_detonation/main.f90
commit 626bdc570b5c10c150055f3fe3c84da0d20a4ebd
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Apr 6 08:05:51 2018 -0700
Modify burn retry strategy to stick with current integrator as long as possible (#96)
* Modify burn retry strategy to stick with current integrator as long as possible
Instead of swapping integrators at a fixed tolerance, we will instead hold the integrator
constant and first attempt loosening the tolerance when a burn fails. This allows for a
more consistent evolution when a burn fails, at the expense of a looser tolerance.
Closes #95
integration/integrator.F90
commit 3b76a76d661e68c7638acd2ac24799599a4df6bc
Merge: ce462ad0 708065d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 4 18:10:44 2018 -0400
Merge pull request #94 from abigailbishop/development
Updated subch network to include the C14(a,g)O18 reaction.
commit 708065d5dee521bc939bb542a2ef34c34bc07b89
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Wed Apr 4 16:43:48 2018 -0400
Updated subch to include the C14(a,g)O18 reaction.
networks/subch/20180319default2
networks/subch/actual_network.f90
networks/subch/actual_rhs.f90
networks/subch/inputs.burn_cell.VODE
networks/subch/reaclib_rates.f90
networks/subch/subch.py
commit ce462ad02d75c7e09c8a72dbf0d845fe072c5808
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 2 12:12:25 2018 -0400
update changes
CHANGES
commit 11a46077e38d88bfdb0ec641d0128c9e5a0cb91b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 1 12:51:22 2018 -0400
update changes
CHANGES
commit 3be68f5f0c67bf47eb6ff19dd359b6f64e1416ff
Merge: e633d35f 71c69867
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 29 22:35:51 2018 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit e633d35f9d302e9fb8b19c560098ed9658c576e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 29 22:35:26 2018 -0400
remove integrate_molar_fractions
unit_test/test_react/test_network_combinations.py
commit 71c69867b6d85c5d7b1db467f686746f856a65d8
Merge: f1245d8c 1a70814e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 29 21:58:35 2018 -0400
Merge branch 'development' of github.com:StarKiller-astro/Microphysics into development
commit f1245d8cb3c9dcf8d2401af67ac2b3e9dfa51da6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 29 21:57:31 2018 -0400
update params
Docs/runtime_parameters/runtime_parameters.tex
commit 1a70814e19ef5ab455d0be4fbd77f10a87e78b2a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Mar 6 02:35:05 2018 -0500
Added a plotting script to compare variables from txt files in two different runs. Can be different networks.
unit_test/burn_cell/burn_cell_compare_ordinate.py
commit 8d0afccd7c90830445c46d5d3f19be32fbfc1747
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 28 20:15:01 2018 -0500
update the README
networks/subch/README.md
commit 27b290bdfa503494a726b3966f93f8f7a33405e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 28 17:05:37 2018 -0500
this is a subCh net generated by pynucastro
networks/subch/GPackage.mak
networks/subch/Make.package
networks/subch/NETWORK_REQUIRES
networks/subch/README.md
networks/subch/actual_burner.f90
networks/subch/actual_network.f90
networks/subch/actual_rhs.f90
networks/subch/physical_constants.f90
networks/subch/reaclib_rates.f90
networks/subch/subch.py
networks/subch/table_rates.f90
commit 08cf0f4b94fc5f0ace239d3f8723b1b04fc26e9e
Merge: 42ac1fdd e30548d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 21 16:10:24 2018 -0500
Merge pull request #86 from abigailbishop/development
Changed graph file naming convention to match the name of the script.
commit e30548d84274628f02b7ef201966ea3d03aeafde
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Wed Feb 21 16:01:01 2018 -0500
Changed graph file naming convention to match the name of the script.
Changed from ..._2networks.png to ..._2tests.png
unit_test/burn_cell/burn_cell_compare_2tests.py
commit 42ac1fdd4fbcddffbf2fa225a45838bdd24542fd
Merge: 8854ebfe be64b94a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 21 15:57:50 2018 -0500
Merge pull request #85 from abigailbishop/development
Burn_cell relative/absolute error plotter and two test grapher.
commit be64b94a885c904f2cf48e9d9ee7e59eb420fef3
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Wed Feb 21 15:45:50 2018 -0500
Created scripts to plot relative and absolute errors of mass fraction, moller fraction, temperature, and energy generation rate. Will also plot the graphs generated by burn_cell.py for two runs on the same figure.
the README.txt explains how to do this.
unit_test/burn_cell/README.txt
unit_test/burn_cell/burn_cell_compare_2tests.py
unit_test/burn_cell/burn_cell_compare_abs.py
unit_test/burn_cell/burn_cell_compare_rel.py
unit_test/burn_cell/burn_cell_testing.py
commit 8854ebfe95898aa1d978c946fccedb296e19913d
Merge: bdbf600d 90f8a672
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 5 18:40:33 2018 -0500
Merge pull request #83 from abigailbishop/development
Created 4 plotting codes for analysis of burn_cell unit tests.
commit 90f8a6720aae236986c10cf090fb91f9ebca5b7b
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Mon Feb 5 15:56:41 2018 -0500
The xn, y, T, and edot graphs now save with names including the test prefix so they aren't over written everytime burn_cell.py or burn_cell_testing.py is run
unit_test/burn_cell/burn_cell_testing.py
commit d898d21f6502f33565c491394bcf23a9ab1dfbc2
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Mon Feb 5 15:11:07 2018 -0500
burn_cell_testing.py can run in place of burn_cell.py. This creates files
that allow the following codes to run:
burn_cell_compare_rel.py will make relative comparisons between burn_cell runs
burn_cell_compare_abs.py will make absolute comparisons between burn_cell runs
burn_cell_compare_2tests.py will show xn, Y, T, and edot graphs of two tests
unit_test/burn_cell/burn_cell_compare_2tests.py
unit_test/burn_cell/burn_cell_compare_abs.py
unit_test/burn_cell/burn_cell_compare_rel.py
unit_test/burn_cell/burn_cell_testing.py
commit bdbf600d8d113fb953f4479fb37241883dc41e82
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Jan 18 00:43:33 2018 -0500
Switch from /) to ] notation for Fortran arrays.
networks/ignition_reaclib/URCA-simple/reaclib_rates.f90
commit 463c75f6f2ae4afa40c14f90b0a30705defe73ce
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Dec 20 15:13:15 2017 -0500
Add CUDA attributes for aprox13
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_network.F90
commit a91a4582ac938a8d2c70502e29c8a8fff0774574
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Dec 17 23:30:18 2017 -0500
Print more data when retrying a burn
integration/integrator.F90
commit 2aebdeb62aa5b87ad347eca7b4e7566b6db0fd90
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Dec 8 09:32:15 2017 -0500
fix some OpenMP stuff
unit_test/test_sdc/main.f90
commit 760071e2c952bccdd933059f4c67cfb8f380382e
Merge: 8b7c4336 5b32b082
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Dec 2 14:48:49 2017 -0500
Merge branch 'master' into development
commit 8b7c4336374bea99c1c399bba5c711981cabcc0a
Merge: f483bce6 1c0075bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 30 22:09:44 2017 -0500
Merge pull request #76 from starkiller-astro/contrib
add development and contribution notes
commit f483bce6634e5aa57ddbf9fc9ffc5e34dadb82b1
Merge: e237f830 09e8fd13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 30 22:09:23 2017 -0500
Merge pull request #80 from abigailbishop/development
Updated burn_cell docs to reflect the removal of the init file and the generation of the output directory
commit 09e8fd131141c16cb02c1d0f7aee1f9e803d937a
Merge: 38f0f21e a14bf157
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Thu Nov 30 15:56:45 2017 -0500
Merge branch 'development' of https://github.com/abigailbishop/Microphysics into development
commit 38f0f21e6cc2b62bb07437446ce7d7a8c2849bc3
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Thu Nov 30 15:52:44 2017 -0500
Updated the burn_cell documentations to reflect the merger of the inputs and init files as well as the generation of the output directory.
Docs/burn_cell/burn_cell.tex
commit e237f8305f4ea63dd57d5eead6f18ed7e7290da7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Nov 21 16:42:23 2017 -0500
Update OpenACC versions of mintemp, maxtemp, etc.
EOS/helmholtz/actual_eos.F90
commit 4917406cabf2627cafe0af7368fbca02c1ea0df7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Nov 13 15:44:35 2017 -0500
Fix rpar indexing -- array was too large by one
integration/BS/rpar.F90
integration/VODE/rpar.F90
integration/VODE90/rpar.F90
integration/rpar.F90
commit df6f3f075251f4c9694e1ea60dba5fad89242fcd
Merge: d9c64cc9 ab549a8d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Nov 8 15:24:41 2017 -0500
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit ab549a8d8ab1d07f9df889e1b52f966fe2ba11a8
Merge: 6d3bd0ea a14bf157
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 6 10:48:40 2017 -0500
Merge pull request #79 from abigailbishop/development
Set burn_cell.py to look into 'runprefix_output'
commit a14bf157d19c908ab5adf69965bea865309980c1
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Mon Nov 6 10:41:19 2017 -0500
Update burn_cell.py
unit_test/burn_cell/burn_cell.py
commit e3b79fa24e16c8865e4a15054a213e1ad78c4dee
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Mon Nov 6 10:20:12 2017 -0500
Set burn_cell.py to look into 'runprefix_output' for the files required for plotting.
unit_test/burn_cell/burn_cell.py
commit d9c64cc952e0c6b36bc9ae5f21e2f9ad214c5244
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Nov 4 23:07:09 2017 -0400
Added BS version of inputs_burn_urca.
unit_test/burn_cell/inputs_burn_urca
unit_test/burn_cell/inputs_burn_urca.BS
commit 6d3bd0ea3f0c1b966d6c532e1b1cf1ad9e72b79c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Nov 4 22:16:15 2017 -0400
Sanitize mass fraction inputs so each must be in the interval `[0,1]`. Does not check if `sum(X)==1`.
unit_test/burn_cell/main.f90
commit d09da667e83f01b0e5219b12e7ced0cf83ae2c8b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Nov 4 22:02:01 2017 -0400
burn_cell stores its output in a directory named by appending "output" to `run_prefix` in the probin.
unit_test/burn_cell/main.f90
commit 8e7e7e9108879bfc97a9421d74591e2469777cf9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Nov 4 21:33:17 2017 -0400
burn_cell now takes the initial zone conditions from the cellparams namelist in the inputs file.
unit_test/burn_cell/init_aprox13
unit_test/burn_cell/init_aprox19_bad
unit_test/burn_cell/init_cburn
unit_test/burn_cell/init_ctest
unit_test/burn_cell/init_urca
unit_test/burn_cell/inputs_burn_aprox13
unit_test/burn_cell/inputs_burn_aprox19_bad
unit_test/burn_cell/inputs_burn_urca.VODE
unit_test/burn_cell/inputs_cburn.VODE
unit_test/burn_cell/inputs_ctest.BS
unit_test/burn_cell/main.f90
commit 1c0075bfd6f4f4865fd3f21257b11fcfe017c602
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 3 09:31:00 2017 -0400
add development and contribution notes
README.md
commit 7c51872bfc1bcb43b040e37568cc7aac8bf2c1e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 2 16:26:47 2017 -0400
VODE is the default now
unit_test/burn_cell/GNUmakefile
commit 5b32b0824cb2086444b883d786cc7b782fc7f2a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 1 14:42:40 2017 -0400
update CHANGES
CHANGES
commit a7db0384a229b129bc60487552b06499aa1da23a
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 30 23:19:05 2017 -0400
Make actual_eos_finalize public
EOS/helmholtz/actual_eos.F90
commit 19d56b4bf72139c050c249fb88ef2771bc2b8089
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 30 23:00:59 2017 -0400
Mark up helmholtz with CUDA device functions
EOS/helmholtz/actual_eos.F90
commit e52efee47785facdc4b0e56fca4560a71357f856
Merge: 4295b768 05130972
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 29 19:56:12 2017 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 4295b768f3fd77cba85e237a9a8a8080d23590e6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Oct 29 19:56:00 2017 -0400
Update Helmholtz for CUDA
EOS/helmholtz/actual_eos.F90
commit 05130972130ad35b80873961228013b4b5668cad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 28 21:39:37 2017 -0400
VODE is now default
unit_test/test_react/GNUmakefile
commit 9918f222d4df55c0132330668040209773dc2f3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 28 21:19:07 2017 -0400
fix num
util/esum.py
commit 05809aacf685ccda7f41dd7b5d76117fc688c8da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 28 21:08:45 2017 -0400
fix function end and args
util/esum.py
commit 166bd045cdebc13ee5109eb54ae269dc936d1083
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 28 21:04:06 2017 -0400
this script removes a general esum in favor of N-specific versions
util/esum.py
commit 5eb5d4e67dea5379ab2a81a8d8dd1e21a40d6faf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 27 13:10:45 2017 -0400
update changes
CHANGES
commit 471ed7b962b6f13080deaaeedb5d99e66c5511cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 27 12:05:40 2017 -0400
store the updated time on output
integration/VODE/vode_integrator.f90
commit 3d48c19ec330cd27eca09cb22b6338d613ffb332
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 27 11:59:58 2017 -0400
remove debug and fix comment
integration/VODE/vode_integrator.f90
commit c671b7f54208d32c54a428f1f5bb6c2e8bc959df
Merge: 82699da8 dcf15c46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 27 10:15:33 2017 -0400
Merge pull request #72 from abigailbishop/development
Added burn_cell to the GNUmakefile and MicrophysicsUsersGuide.tex
commit dcf15c4664410b99f01673c1d2da9ee38840176f
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Fri Oct 27 10:08:14 2017 -0400
Added burn_cell to the GNUmakefile and MicrophysicsUsersGuide.tex
Docs/GNUmakefile
Docs/MicrophysicsUsersGuide.tex
commit 82699da86091af99b12dd2be64e53083ae7aaecb
Merge: 09b997b4 5099c434
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 27 06:55:05 2017 -0400
Merge pull request #71 from abigailbishop/development
Development
commit 5099c434e9541a8bee4bfac4633ac432d9f5e9d3
Merge: 73c0f196 09b997b4
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Fri Oct 27 01:30:56 2017 -0400
Merge branch 'development' of https://github.com/abigailbishop/Microphysics into development
commit 73c0f196b7b9d93dfa3f4e737cb6c8e348522d23
Author: Abigail Bishop <ms.abigailbishop@gmail.com>
Date: Thu Oct 26 12:52:42 2017 -0400
Added a section to the user's manual addressing the burn_cell unit test.
Docs/burn_cell/burn_cell.tex
Docs/burn_cell/react_aprox13_logX.png
commit 09b997b4e6de921ba8e73e0d1d15eb2d4afb0b37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 23 17:29:37 2017 -0400
move the internal EOS functions to pure functions (#68)
EOS/helmholtz/actual_eos.F90
commit 386008ce76dd5e8fcd28151f28ee3a2fbd42864e
Merge: 3c6aa72c 1d3bd739
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Oct 22 15:40:07 2017 -0400
Merge branch 'boost' into development.
closes #64
commit 1d3bd73970e50f14223ea6ce9e9f71ba073dd49e
Merge: 15f05dba 3c6aa72c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Oct 22 15:39:14 2017 -0400
Merged branch boost into development.
Fixed merge conflict in VODE90/vode_rhs.f90.
closes #64
commit 3c6aa72c375034a5c161e732563fc28c091230da
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Oct 22 14:25:51 2017 -0400
Move renormalize_abundances call into clean_state.
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_type.f90
commit 15f05dbad8eb43a704bd8a36be08c38ae59556d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 22 14:11:56 2017 -0400
add the boost to the other integrators
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/VBDF/bdf_rhs.f90
integration/VODE/vode_rhs.f90
integration/VODE90/vode_rhs.f90
commit ef35eb65b045ed81c6ee3df6c792d9378fe3ecea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 22 11:12:28 2017 -0400
a notebook to explore boosting
Docs/tests/ode_scaling.ipynb
commit e9fcf9d2e7a16da6ea699765bf60910d842d0bf8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 21:02:32 2017 -0400
don't define the system blas library here, just check if we need to compile our blas
networks/GNetwork.mak
commit 55245684cbc29b84beef94386707a6ed03ef0761
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 18:40:28 2017 -0400
add an override to use a system blas. If USE_SYSTEM_BLAS=TRUE, then we do not
compile in blas
networks/Make.package
commit 7458992830aa30c920fbb772f353ca74da9a2937
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 17:43:33 2017 -0400
add sdc to runtime prefix
unit_test/test_sdc/inputs_aprox13
commit d160e49534d0071248d2e11f28d87ba9d14ead09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 21 17:33:57 2017 -0400
remove esum() for sums of 1 or 2 terms (#65)
* don't do esum on 2 quantities
* remove all esum() on 1 or 2 elements
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
commit 95252072e63b896d7a9a075012440804666b7c6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 22:29:07 2017 -0400
a test of 3 numbers
util/test/test_esum.f90
commit b8841dc455ab455fd9041deeb9d25f7159eaddac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 22:18:05 2017 -0400
rename
util/test/GNUmakefile
util/test/test_esum.f90
commit c7a18415fd0adb83f75beea5e2effc068aa862dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 22:15:25 2017 -0400
this works
util/test/GNUmakefile
util/test/test_enum.f90
commit ef7768757d951ccecee561de557d613af7aa53be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 20 22:12:20 2017 -0400
start of a tester
util/test/GNUmakefile
util/test/bl_error.f90
util/test/bl_types.f90
util/test/test_enum.f90
commit 7d1218d239a7da7d07f6d11e8a41614d004d0520
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 19 15:44:52 2017 -0400
fix compilation
integration/VODE/vode_rhs.f90
commit 0ae04e27e263b74730bc1b8c19aab7232562f149
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 19 15:38:36 2017 -0400
add the ability to boost the reaction rate
integration/VODE/vode_rhs.f90
integration/_parameters
commit 12fff9f231ef9a000528d9da42f97c5eda08588f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 16:23:43 2017 -0400
fix OMP
unit_test/test_sdc/main.f90
commit 36e87980fa89157af910125daa4f8650fb17aa6b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 18 13:00:23 2017 -0400
Fix indexing into rpar for VODE SDC. (#63)
integration/VODE/rpar.F90
commit 438315f92206df4222fd555e9c0d5ba6a7ef12c4
Merge: b3cf5417 d3c22c2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 12:38:26 2017 -0400
Merge branch 'master' into development
commit d3c22c2ad2182b9963df1eefefb7eb7a70f419f5
Merge: 6dab20dd b58cdde4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 18 12:36:11 2017 -0400
Merge pull request #57 from starkiller-astro/sdc_fix
Sdc fix
commit b58cdde4b113c854dcf810e7a344fa782fc59cbc
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 18 12:14:38 2017 -0400
Fixed typo so n_jac is set in sdc_to_bs.
integration/BS/bs_type_sdc.F90
commit bc3512fcfc20b8c8c4649c74da07e5535f23ed70
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 18 12:10:26 2017 -0400
Set atol, rtol in integration status derived type.
integration/integrator_sdc.F90
commit ab6e53c48d7cdb27a028dfec8c56a14458ad585a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 18 12:08:14 2017 -0400
We do not need actual_integrator_init since we throw an error.
integration/integrator_sdc.F90
commit b3cf54176db23545c0aa53bbe7d124d774ac09e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 18:52:57 2017 -0400
implement EXTRA_THERMO for composition derivs (#59)
* .f90 -> .F90, + implement EXTRA_THERMO for composition derivs
* don't compute any compositional derivs unless EXTRA_THERMO is set
* comment on EXTRA_THERMO
CHANGES
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/GPackage.mak
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.F90
EOS/polytrope/GPackage.mak
EOS/polytrope/Make.package
EOS/polytrope/actual_eos.F90
EOS/stellarcollapse/GPackage.mak
EOS/stellarcollapse/Make.package
EOS/stellarcollapse/actual_eos.F90
EOS/ztwd/GPackage.mak
EOS/ztwd/Make.package
EOS/ztwd/actual_eos.F90
commit a76b18317d35b5cb0a05e02e9674cdead052cca2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 15:21:30 2017 -0400
change prefix
unit_test/test_react/inputs_aprox19.burning_mode_0
commit 97a0f8eafe5f2ab93d8cd4071b2faf9a78686f30
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 16 15:18:50 2017 -0400
add a test of burning_mode = 0
unit_test/test_react/inputs_aprox19.burning_mode_0
commit 8df99f4801bc3cc03096a9e4109efd0c7e4373f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 14 06:40:36 2017 -0400
fix the SDC BS integrator -- this always gets hooked in now with the
retry mechanism
fixes #216
integration/BS/numerical_jacobian_sdc.f90
integration/BS/stiff_ode.F90
integration/integrator_sdc.F90
commit e019535a9150a3037edad0e19bf51a3c4066b5f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 9 20:42:44 2017 -0400
some compilation fixes
integration/BS/bs_type_sdc.F90
commit 6dab20ddac88166c1d4b45dd7566be1ff4c31ac1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 2 12:59:26 2017 -0400
update changes
CHANGES
commit 82f66f0f21539df943667aa229ee2bba6d718c1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 26 12:53:15 2017 -0400
fix broadcast -- fddt instead of fdd
EOS/helmholtz/actual_eos.F90
commit f6ef78aba8b6921df597811959bfb04a941d04d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 25 15:27:41 2017 -0400
only IO proc needs to close
EOS/helmholtz/actual_eos.F90
commit bb46bdd8efe39f3be2524bbd63402a24b7dca68f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Sep 25 08:52:28 2017 -0700
Read in Helm table with ioproc and broadcast (#53)
the helm_table.dat is now read only by the I/O processor and broadcast to other procs.
EOS/helmholtz/actual_eos.F90
commit 9cf2c3131432cfd0231dd5276bc6e5b1a53a3cd3
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date: Mon Sep 25 11:10:21 2017 -0400
aprox13 versions
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/init_aprox13
unit_test/burn_cell/inputs_burn_aprox13
commit 35b4f4d0e2af56251dd63c39741f5a0c3b4a307a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Sep 25 09:36:39 2017 -0400
update runtime parameters
Docs/runtime_parameters/runtime_parameters.tex
commit 39928f78e658711a96b568ff69c88af11f48aff9
Author: Mu-Hung Chang <mu-hung.chang@stonybrook.edu>
Date: Mon Sep 18 20:27:27 2017 -0400
Add "actual_eos_finalize" subroutine in eos.f90 (#51)
EOS/breakout/actual_eos.f90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.f90
EOS/polytrope/actual_eos.f90
EOS/stellarcollapse/actual_eos.f90
EOS/ztwd/actual_eos.f90
commit a61fa06d692bf6f55b7ad73b056209d99a04979d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 18 14:46:01 2017 -0400
Moved rhs, jac, and rate evaluation into actual_rhs_module for consistency with other networks.
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/actual_burner.f90
networks/ignition_simple_SDC/actual_network.f90
networks/ignition_simple_SDC/actual_rhs.f90
networks/ignition_simple_SDC/f_rhs.f90
networks/ignition_simple_SDC/f_rhs_instantaneous.f90
commit a34aedc95a6916fc35e49003ee86a7ac9d34dbff
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Sep 17 11:26:46 2017 -0700
Do not rely on the numerical Jacobian for aprox19/aprox21 (#49)
* Do not rely on the numerical Jacobian for aprox19/aprox21
The change was made at some point to use the numerical Jacobian for
these networks, because we learned that the hardwired Jacobian has
some missing terms. However, the numerical Jacobian in practice seems
to have big problems -- it can cause VODE to complete the integration
with crazy states that have X >> 1, but VODE thinks it is converged.
We also see NaN's in the Jacobian when we examine it. So we are going
to revert to the analytical Jacobian default -- this seems to work better.
* Update CHANGES for aprox Jacobian changes
CHANGES
networks/aprox19/_parameters
networks/aprox21/_parameters
commit 221d7e5eb4e47538b961dc20fe8bca212d243fb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Sep 17 09:57:06 2017 -0400
add a troublesome burn
unit_test/burn_cell/init_aprox19_bad
unit_test/burn_cell/inputs_burn_aprox19_bad
commit 6ca58bfcead08f628699521bea7bfff56319d8b1
Merge: aa9c0ce1 c6a0e47c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 16 10:55:54 2017 -0700
Merge pull request #47 from starkiller-astro/integration_cleanup
Clean up the consistency checking in the integration state
commit c6a0e47c39549a2ca7b25dd82f67c7f40ac40bce
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Sep 16 12:49:03 2017 -0400
Make the maximum temperature for reactions an input parameter
CHANGES
integration/BS/bs_type.F90
integration/VODE/vode_type.f90
integration/_parameters
commit 06ac3ed469a17332e6d60595c9dcad351035cc6a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Sep 16 12:45:31 2017 -0400
Sync up VODE clean_state with BS
integration/BS/_parameters
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
integration/_parameters
commit aa9c0ce1ba86383ba2ba3e8f5df561c2c5c747c7
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Sep 15 01:57:41 2017 -0400
Exit BS integration if dt gets too small
integration/BS/stiff_ode.F90
commit d98ac7843db80894f78a955f62ca6c3ea282209b
Merge: 62a68248 41671ec4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 12 21:14:06 2017 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 62a6824864999ded6bbb7cfa73ded8d80b931535
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 12 21:14:03 2017 -0400
Add inputs file for urca network.
unit_test/burn_cell/inputs_burn_urca.VODE
commit 41671ec46e96cae424d93695f112fd254a45b90e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Sep 12 21:03:25 2017 -0400
add a README based on Don's slack instructions
unit_test/burn_cell/README.md
commit b21d34d31aae63fcf27b17bd240268dc8c5a77b7
Merge: fac36385 7866023c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 9 09:55:23 2017 -0700
Merge pull request #43 from starkiller-astro/bs_failure_update
Do not crash if non-convergence occurs in a BS step
commit 7866023c4c666ce3531f0c2b568d2aa11b1c9b61
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Sep 9 00:24:01 2017 -0400
Do not crash if non-convergence occurs in a BS step
With the scheme we now have for switching integrators on a failure,
we simply want to abort the integration when this occurs, not crash.
integration/BS/stiff_ode.F90
commit fac363854579e6de07599e9a8baaeb4702a8d4ad
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 7 16:44:07 2017 -0400
Fixed compilation.
unit_test/burn_cell/GNUmakefile
commit 502a05141f86984932d30376be5f05fc48cb65d9
Merge: 13bf2bf5 25bd5b68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 2 21:03:28 2017 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 13bf2bf5c728bfe962e649e9e7b4872c372a2e94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Sep 2 21:03:11 2017 -0400
fix compilation failure -- bl_error_module needs to be included
integration/VODE/vode_integrator.f90
commit 25bd5b68bdad4074901912fbdf643fd3568a1c34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Sep 1 10:12:09 2017 -0400
update changes
CHANGES
commit 7d4b11f9c33aeba9ab9f301df72850e314851bc2
Merge: 16ef070f 665d4714
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 31 20:10:45 2017 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 16ef070fbcc2f5536a7bc6d8c4247e635116b693
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 31 20:10:37 2017 -0400
update changes
CHANGES
commit 665d4714782725f9bda97fa97af26be738fc4048
Merge: 9d3ddb13 240fa0cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 31 20:05:52 2017 -0400
Merge pull request #40 from carlnotsagan/development
Replace Mazurek (1973) Ni56ec rates and energy losses with those computed by LMP (2000)
commit 240fa0cde111354536b42a60cb9aa5db4b78829e
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Wed Aug 30 20:08:57 2017 -0400
a commented out line for use in tests during PR review
rates/aprox_rates.f90
commit 9d3ddb13b8abf8953756ef6dc036ed569d27664b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Aug 25 02:22:57 2017 -0400
Indicate VODE failure if final state is nonsense
integration/VODE/vode_integrator.f90
commit f5ef439516c51b749ed7337710ed1294cf3689a4
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 01:08:29 2017 -0400
use d instead of e
rates/aprox_rates.f90
commit 3d52c45f37ce3ea80ee3377343be0f58c8161beb
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 01:05:16 2017 -0400
change call to mazurek in all routines that use it (aprox21 and aprox19 networks) with call to new langanke routine
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
commit b11b3318766656d8b36f788f8f430f5da3d26563
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 01:01:02 2017 -0400
change s dot conversion. mazurek rates for S__nu are given in emu/particle/s or 0.511 MeV / particle / sec so 8.18683e-7 converts 0.511 MeV to erg, but in LMP, the S_nu is given in MeV / particle /sec so we just need MeV to erg, 1.60218e-6
rates/aprox_rates.f90
commit 90c5c2dff83b3bfe3be4d93f7e32b1b108e7ee1b
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 00:58:17 2017 -0400
update arrays, and ranges for new T-logrhoYe grid
rates/aprox_rates.f90
commit 18ea4cfa31861c8012121a5cb23e8f287841df11
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 00:53:54 2017 -0400
update mazurek routine name to langanke and update header comment
rates/aprox_rates.f90
commit 3421b05e56ecefc15ca6ae123a43b30476edc80c
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 00:50:42 2017 -0400
cubic interp parameters for temp now go from k=2,12
rates/aprox_rates.f90
commit 5b392cd91eeddea1eef0ea5d28d851608c1b13c6
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 00:46:40 2017 -0400
update leps- and lnu rates according to their Langanke et al. 2000 (LMP) values for Ni56 electron capture. Compare with $MESA_DIR/data/rates_data/weakreactions.tables and https://groups.nscl.msu.edu/charge_exchange/weakrate_tables/lmprates.dat
rates/aprox_rates.f90
commit 21c64ba93d457ffd241f67b781fb00fe881cc66e
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 00:32:24 2017 -0400
update t9 array
rates/aprox_rates.f90
commit b261056c586c97d1b1edc8909148c9da0afc2940
Author: Carl E. Fields <fieldsc9@msu.edu>
Date: Fri Aug 25 00:22:09 2017 -0400
update sizes of array to prepare for new rates
rates/aprox_rates.f90
commit d3787b147d5e55f977297308fb7c9ecbb2b478f0
Merge: 38c75854 d8426eb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 14 21:02:51 2017 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 38c7585499611ee15bc7ff335c64a4bcca204dea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 14 21:02:39 2017 -0400
add note about retry
CHANGES
commit d8426eb990203c3c400ff71d859d896658e288dd
Merge: 247ac1dc 0041b71a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 14 18:38:43 2017 -0400
Merge pull request #39 from starkiller-astro/multi-integrator
Move retry functionality up to main integrator
commit 0041b71af25f7462d3fc33cf47081b88e2e8e8f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 13 03:52:03 2017 -0400
Reverse VODE/BS compilation order
integration/Make.package
commit ba5094d56520de041c0c9718196f0c5c03f351bf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Aug 13 02:09:17 2017 -0400
Update the INTEGRATOR definitions for SDC
integration/integrator_sdc.F90
commit 86abbd7ddb6946e2144d94a4ab7885757a2d0e03
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 12 23:44:02 2017 -0400
Treat VODE and BS as special
integration/GPackage.mak
integration/Make.package
integration/VBDF/vbdf_integrator.F90
integration/integrator.F90
networks/GNetwork.mak
commit febe4a07c8c4d2a60c40417503c9ec22df25dace
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 12 12:21:16 2017 -0400
Revert "Hook VBDF back in, fail at VODE90"
This reverts commit 4a7ab3f51b0c7009e88ddda59a7326db4bb10296.
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/BS/stiff_ode.F90
integration/GPackage.mak
integration/Make.package
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/actual_integrator.f90
integration/VODE90/actual_integrator_sdc.f90
integration/VODE90/vode90_source/GPackage.mak
integration/VODE90/vode90_source/Make.package
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_rhs_sdc.f90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_source/README
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_source/dvode_output.f90
integration/VODE90/vode_source/dvode_type.f90
integration/VODE90/vode_source/test/GNUmakefile
integration/VODE90/vode_source/test/GPackage.mak
integration/VODE90/vode_source/test/tvode.f90
integration/VODE90/vode_source/test/tvode_rhs.f90
integration/VODE90/vode_type.f90
integration/VODE90/vode_type_sdc.f90
integration/integrator.F90
integration/integrator_sdc.F90
networks/GNetwork.mak
commit 762b5a657fbb01f25394ade95eae122bc886bc55
Merge: 55a98621 247ac1dc
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 12 11:54:58 2017 -0400
Merge branch 'development' into multi-integrator
commit 247ac1dc380748eb289d880e7cb850d7e340cc52
Merge: 6d8f1128 3a8b401f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 11 20:46:09 2017 -0400
Merge branch 'development' of ssh://github.com/StarKiller-astro/Microphysics into development
commit 6d8f112843d522a650500fff72b3484d49cf5ba2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 11 20:44:52 2017 -0400
update the sdc_type to be in sync with Castro
interfaces/sdc_type.F90
commit 55a986214ae337021d36e91f51a9d46e7c84c6f8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 11 02:50:09 2017 -0400
Fix the SDC interfaces
integration/BS/bs_integrator_sdc.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs_sdc.F90
integration/VODE/vode_integrator_sdc.f90
commit 4a7ab3f51b0c7009e88ddda59a7326db4bb10296
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 11 02:40:07 2017 -0400
Hook VBDF back in, fail at VODE90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/BS/stiff_ode.F90
integration/GPackage.mak
integration/Make.package
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_integrator.F90
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/vode90_integrator.f90
integration/VODE90/vode90_integrator_sdc.f90
integration/VODE90/vode90_rhs.f90
integration/VODE90/vode90_rhs_sdc.f90
integration/VODE90/vode90_source/GPackage.mak
integration/VODE90/vode90_source/Make.package
integration/VODE90/vode90_source/README
integration/VODE90/vode90_source/dvode90.F90
integration/VODE90/vode90_source/dvode90_output.f90
integration/VODE90/vode90_source/dvode90_type.f90
integration/VODE90/vode90_source/test/GNUmakefile
integration/VODE90/vode90_source/test/GPackage.mak
integration/VODE90/vode90_source/test/tvode.f90
integration/VODE90/vode90_source/test/tvode_rhs.f90
integration/VODE90/vode90_type.f90
integration/VODE90/vode90_type_sdc.f90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/integrator.F90
integration/integrator_sdc.F90
networks/GNetwork.mak
commit 63b45ef3647ce7250821a2251f941d62713ded03
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 11 01:30:44 2017 -0400
Retry with another integrator before loosening tolerances
integration/BS/bs_integrator.F90
integration/VODE/vode_integrator.f90
integration/integration_data.f90
integration/integrator.F90
commit 4baef5ea009a9454f3ba19c086536a88bdd53593
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Aug 8 04:02:34 2017 -0400
Build both VODE and BS integrators
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/bs_integrator.F90
integration/BS/bs_integrator_sdc.F90
integration/Make.package
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/vbdf_integrator.F90
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_integrator.f90
integration/VODE/vode_integrator_sdc.f90
integration/integrator.F90
integration/integrator_sdc.F90
commit 3a8b401fe6195eb2d478b5eb7baea430707e1261
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Aug 7 23:20:30 2017 -0400
Call integrator_init wrapper
unit_test/test_sdc/main.f90
commit 9d8202640d9805dd942ccb08cff0699b9cf00c38
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 5 15:40:24 2017 -0400
Make use_tables be network-independent
networks/_parameters
networks/aprox13/_parameters
commit a6825694c031823fe0fee685f531f927f88e5dfe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 1 09:09:17 2017 -0400
update headings
CHANGES
commit 9ff4a33c090ce153b5f16c43262e3818f5207579
Merge: 236502a4 657eae3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 27 20:38:13 2017 -0400
Merge branch 'development' into new_helm_table
commit 657eae3b60e3a592166150d89bc31f414daa2720
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 20:03:20 2017 -0400
can't use rt, must use dp_t for full compatibility with Maestro
conductivity/stellar/stellar_conductivity.f90
unit_test/conductivity.F90
commit 2f7cb52e34cbd25b2851f80ed7f1b7f0fa6ed5e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 15:29:05 2017 -0400
some documentation
CHANGES
Docs/MicrophysicsUsersGuide.tex
Docs/transport/transport.tex
commit 98eedd0a3850952a6be6c165564c5439050dda15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 14:59:28 2017 -0400
add the stellar conductivity from Frank
conductivity/stellar/GPackage.mak
conductivity/stellar/Make.package
conductivity/stellar/README.md
conductivity/stellar/stellar_conductivity.f90
commit fb8d2dc0187c0312788167930807a4c7f9dbe715
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 13:39:58 2017 -0400
for unit tests of conductivity
unit_test/conductivity.F90
commit 236502a4474d962164a7669830d91d95e8fa0299
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 09:49:26 2017 -0400
add to changelog
CHANGES
commit 21458e11efae73c86d01017267d41420f6fa84f6
Merge: 1e9fab55 6af76779
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 25 09:47:54 2017 -0400
Merge branch 'development' into new_helm_table
commit 1e9fab5563de739f44521e62591520af0c248680
Author: Maria Barrios Sazo <maria.barriossazo@stonybrook.edu>
Date: Mon Jul 24 15:50:38 2017 -0700
updating helm_table and limmits of the table
EOS/helmholtz/actual_eos.F90
EOS/helmholtz/helm_table.dat
commit 6af7677990aa618302b8751b6e60067538face0f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 19 12:37:11 2017 -0400
update AMReX
Docs/MicrophysicsUsersGuide.tex
Docs/basics/basics.tex
Docs/networks/networks.tex
Docs/runtime_parameters/rp_intro.tex
Docs/unit_tests/unit_tests.tex
commit 64d5add0859cbc002a0ef43fc8803d5fee40277f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 18 14:31:04 2017 -0400
simple test driver
this gives results that agree with the output in the code comments
util/DNSQE/GPackage.mak
util/DNSQE/test/GNUmakefile
util/DNSQE/test/test.f90
commit fae4afa243fc48e270f72f9f5dbcf583b0c2251c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 18 13:18:42 2017 -0400
add a cleanup TODO
util/DNSQE/TODO
commit c1003393c58e68e1adc5a2cad8858f473ae0c52d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 18 13:07:30 2017 -0400
add more old-school Fortran 66 with gotos abound!
this is a nonlinear system solver. Will use for SDC
util/DNSQE/d1mach.f
util/DNSQE/d1mpyq.f
util/DNSQE/d1updt.f
util/DNSQE/ddoglg.f
util/DNSQE/denorm.f
util/DNSQE/dfdjc1.f
util/DNSQE/dnsq.f
util/DNSQE/dnsqe.f
util/DNSQE/dqform.f
util/DNSQE/dqrfac.f
util/DNSQE/fdump.f
util/DNSQE/i1mach.f
util/DNSQE/j4save.f
util/DNSQE/orig/dnsqe.f
util/DNSQE/xercnt.f
util/DNSQE/xerhlt.f
util/DNSQE/xermsg.f
util/DNSQE/xerprn.f
util/DNSQE/xersve.f
util/DNSQE/xgetua.f
commit afbd29ee51e7906d2a99169ca0d2c9698d6a8dd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 18 11:48:26 2017 -0400
add 'only' clause to use
integration/VODE/vode_type_sdc.f90
commit 7ce413cb8024a7b2ea5bd321cfcaa03bca482d80
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 14 17:15:12 2017 -0400
pass the sdc_iteration into the rpar for use in diags
integration/VODE/actual_integrator_sdc.f90
integration/VODE/rpar.F90
commit d8d99ae122b63a207bacd4c27ff0ca37a42b65d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 11 17:09:32 2017 -0400
store the indices for debugging
integration/VODE/actual_integrator_sdc.f90
integration/VODE/rpar.F90
commit f201b8a6917ad75abfa49cb9e05622ce08dcaa05
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jul 10 23:34:52 2017 -0400
Fix some module scoping in VODE90
integration/VODE90/actual_integrator.f90
integration/VODE90/vode_type.f90
commit ffbb58eda4adb78b4dca6c20ba005a591e9c5d04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 10 23:17:17 2017 -0400
pass the zone index info into rpar (note: it is cast into a float here)
integration/VODE/actual_integrator.f90
integration/VODE/rpar.F90
integration/VODE/vode_rhs.f90
commit 5a1f3c3c826f7f02dc7b818e333f831b8858c3ab
Merge: 6f724cc7 919fcc29
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 9 10:52:57 2017 -0400
Merge branch 'development' of ssh://github.com/starkiller-astro/Microphysics into development
commit 919fcc2921bec0c990d3aaaa260eca6b34ebe8a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 6 09:15:46 2017 -0400
fix compilation with SDC
integration/VODE/vode_type_sdc.f90
commit 2dfe5f95be9516655e5e2778e46c030e92c51b67
Merge: 7f165c16 3d2fcbe1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 5 14:41:48 2017 -0400
Merge branch 'development' of ssh://github.com/starkiller-astro/Microphysics into development
commit 3d2fcbe19ff7d20946634b65628f2c9a3fdb6218
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 12:59:22 2017 -0400
add aprox21 fix
CHANGES
commit efb0e52e0cda64203dc5aedb32202e9b9ae578b8
Merge: 5185e85a 1d1ab783
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 12:58:10 2017 -0400
Merge pull request #34 from starkiller-astro/aprox21
fix from Aron Michel (HITS) that fills in missing reactions.
commit 6f724cc722022fff5708e4ef87edc82ef966d36e
Merge: e87977c4 117abb93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 3 12:35:06 2017 -0400
Merge branch 'master' into development
commit e87977c452837866b81e403ae31274fc70061f84
Merge: 6d511d97 5185e85a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 14 22:12:50 2017 -0400
Merge branch 'development' of ssh://github.com/starkiller-astro/Microphysics into development
commit 7f165c16c334fe6540561a6665702bd6ee2c2874
Merge: 117abb93 5185e85a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 14 17:46:06 2017 -0400
Merge branch 'development' of ssh://github.com/starkiller-astro/Microphysics into development
commit 5185e85afedb67b0fa1fe1e4498badafe3b16995
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jun 14 01:25:29 2017 -0400
BoxLib -> AMReX
unit_test/test_eos/GNUmakefile
commit caf4baf96976e9243661ae6fdc706d2a9cf30bf5
Author: Adam M. Jacobs <ajacobs@pa.msu.edu>
Date: Thu Jun 8 13:06:15 2017 -0400
Set VBDF inputs to limits that it can handle
unit_test/test_react/inputs_aprox13.VBDF
commit 1d1ab783ae0e9686b1dfb861f3cadb1af6fe46cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 7 20:44:48 2017 -0400
fix from Aron Michel (HITS) that fills in missing reactions.
In particular, the additional terms for 56Fe and 56Cr are now
added.
networks/aprox21/actual_rhs.f90
commit a975119868f3523e64177cf5c84fc6f4ebd39a66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 7 11:14:39 2017 -0400
remove a comment that caused cpp to fail (and it was a wrong comment
anyway :)
integration/VBDF/actual_integrator.F90
commit e819d388d243c8847926224da2054e47bde9e6a9
Author: Alan Calder <acalder@icsubmit01.sdcc.bnl.gov>
Date: Tue Jun 6 15:05:47 2017 -0400
Ran VODE90 and VODE for the networks aprox13, aprox19, triple_alpha_plus_cago, ignition_chamulak.
Updated unit_test/test_react/README.md with these results.
unit_test/test_react/README.md
commit 43959e1998d5781040b2706ffeb9ec247125e6f5
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Jun 6 11:38:36 2017 -0400
(Re?)add vode_source includes to the build system for VODE90
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
commit a7bb7faf565e2f22203b5c0378561834a7716b5b
Author: Adam M. Jacobs <ajacobs@pa.msu.edu>
Date: Tue Jun 6 10:11:52 2017 -0400
Increase maximum size of line in xin test_react input files
unit_test/test_react/util.f90
commit 6d511d97504b7187b65013cfbe066e97f942c8e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 5 17:23:05 2017 -0400
fix compilation
integration/VODE/vode_type_sdc.f90
commit 117abb933bf2d273c9b41b2b9cd3d9650386324b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 1 12:46:11 2017 -0400
update for 17.06
CHANGES
commit 79c141af108bfa58c5d7f7a0f136398f9c657a6a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue May 30 18:59:23 2017 -0400
First pass at marking up VODE90 with OpenACC directives.
integration/VODE90/actual_integrator.f90
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_source/dvode.F90
integration/VODE90/vode_type.f90
commit 74aca5e1b51e1ca73269fd0395fd9786357fcdf8
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue May 30 00:38:01 2017 -0400
Updated C-test network with latest pyreaclib modifications.
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/C-test/c.py
networks/ignition_reaclib/C-test/reaclib_rates.f90
commit e6324aa0ec092ed486d77524bebc7cfb5c5adadc
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 29 23:15:37 2017 -0400
Updated test_react makefile to use amrex.
unit_test/test_react/GNUmakefile
commit 9941a15c9f68e6103d458aeb0f0d8615de25aae7
Merge: 9b112314 41fb7b0c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 29 23:13:46 2017 -0400
Merge branch 'development' of github.com:starkiller-astro/Microphysics into development
commit 9b112314d0aafd5ae7640577998570e5982d23f4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 29 23:09:46 2017 -0400
Modified F90 vode test to reset vode state upon every call to DVODE.
This mirrors the behavior of actual_integrator which resets VODE on
every call.
integration/VODE90/vode_source/test/tvode.f90
commit 46faa9bd316e1f9b0ae6a081e28215fd302fb47c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 29 23:08:58 2017 -0400
Updated Makefile for F90 vode test to amrex.
integration/VODE90/vode_source/test/GNUmakefile
commit d9331d16f509ab74d8e2d45b8d11e40dfb9edd76
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 29 23:08:12 2017 -0400
Fixed a segfault due to improper interface RPAR, IPAR declarations.
integration/VODE90/vode_source/dvode.f90
commit 41fb7b0c0bf970857caf99b04638a3c3779624ff
Merge: ea605a78 82d2caf0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon May 29 17:05:28 2017 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit ea605a781c17518b359a1de52dcf5df0a1ba34be
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon May 29 17:05:25 2017 -0400
Fix compilation issues
integration/BS/actual_integrator.F90
integration/BS/bs_type.F90
commit 9e9abb06287f66c57bd7199b78724d3c8aa79f17
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 29 16:57:45 2017 -0400
Fixed a segfault due to improper pointer declaration in vode_rhs.
integration/VODE90/actual_integrator.f90
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_source/dvode.f90
commit 82d2caf024d9627963fdac60032910076be85c18
Merge: 54d469e8 20afe2b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 13:42:04 2017 -0400
Merge branch 'development' of ssh://github.com/starkiller-astro/Microphysics into development
commit 54d469e8cf935fd75141d5b19c2e4595b64e32e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon May 29 13:40:46 2017 -0400
compilation fixes
integration/VODE/actual_integrator.f90
integration/VODE/vode_type.f90
integration/numerical_jacobian.f90
commit 20afe2b631c35c459dd28710e40931107bf6d232
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 28 00:41:52 2017 -0400
Fix some EOS includes
integration/VODE/actual_integrator.f90
integration/VODE/vode_type.f90
integration/numerical_jacobian.f90
commit 097249ed31da900cc94849415ada0889261df930
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 25 13:21:44 2017 -0400
unit tests need AMReX
Docs/maestrosymbols.tex
Docs/preface/preface.tex
GMicrophysics.mak
unit_test/write_job_info.f90
commit b37299add8cf105698aa2efa2b67076fd66fb3d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu May 25 12:35:47 2017 -0400
update to reflect aim for generality
README.md
commit de6adbb02849f327e7d98944cdd481a463bf0281
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri May 19 11:50:42 2017 -0400
Final bugfixing - tvode test program yields identical results as for the F77 VODE.
integration/VODE90/actual_integrator.f90
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/test/tvode.f90
integration/VODE90/vode_source/test/tvode_rhs.f90
commit b8036bc7238f553fca851f202ce1d2cae6899931
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri May 19 09:05:30 2017 -0400
Moved test RHS into module. Added some printing to dvode module for debugging. Save progress, stuff not working yet.
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_type.f90
integration/VODE90/vode_source/test/GNUmakefile
integration/VODE90/vode_source/test/GPackage.mak
integration/VODE90/vode_source/test/tvode.f90
integration/VODE90/vode_source/test/tvode_rhs.f90
commit 9b21863be1d9de721f773dff51991aba395b889d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 18 02:03:39 2017 -0400
Removed commented line with erroneous argument passing.
integration/VODE90/vode_source/dvode.f90
commit 18912af1965cdb5981a0daad2220acac19b67a4b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 18 02:01:15 2017 -0400
Added a print_state subroutine for dvode type for debugging.
integration/VODE90/vode_source/dvode_type.f90
commit d663fb559205afdc89db5278870ebc659f173bd6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 18 02:00:44 2017 -0400
Initialize LMAX in subroutine DVODE so the size of array arguments is known before passing.
integration/VODE90/vode_source/dvode.f90
commit d3a09609197ce68232b65dfe7293477046bf0262
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed May 17 18:52:13 2017 -0400
Removed diagnostic write statements.
integration/VODE90/vode_source/dvode.f90
commit b14d1ff4cadceb358234acac12e0cb4eeaf9be23
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed May 17 18:51:17 2017 -0400
Fixed two SIGFPE due to improperly initialized parameters.
integration/VODE90/vode_source/dvode.f90
commit 79e2ad6fd932c661b7418664799fec720d535c34
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed May 17 05:34:49 2017 -0400
Added dimension of IPAR to rpar for the revised VODE.
integration/VODE90/rpar.F90
commit 8bc7bbb9703f8a990f753e8bae5f85cebbc31d1a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed May 17 05:34:31 2017 -0400
Updated vode module referencing in actual_integrator.
integration/VODE90/actual_integrator.f90
commit bac1c7a1664d59f4a19dd39da6910e3be2fd73ee
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed May 17 05:33:50 2017 -0400
Added test and setup makefiles to build the revised VODE.
integration/VODE90/Make.package
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_output.f90
integration/VODE90/vode_source/test/GNUmakefile
integration/VODE90/vode_source/test/GPackage.mak
integration/VODE90/vode_source/test/tvode.f90
commit 6676a1601d43f533c07d0f47924af4f3cf91e68a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue May 16 05:35:09 2017 -0400
Revised array passing so array sections instead of scalars are passed.
integration/VODE90/vode_source/dvode.f90
commit 89337f0de340da731436637b8a19c7b3a0505031
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 15 23:45:17 2017 -0400
Added some bl types imports. Commented out some rpar dependencies.
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_output.f90
integration/VODE90/vode_source/dvode_type.f90
commit c233692172e1634028129a1dd42c82f66c65dd33
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 15 19:07:17 2017 -0400
Reformatted VODE Readme.
integration/VODE90/vode_source/README
commit f320be64ac22582c20504259c07f144fdd06c2cf
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 15 19:07:01 2017 -0400
Updated makefiles.
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
commit 800af8156e82db3e75b15c18e1d8a437f58ab8d9
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 15 19:06:17 2017 -0400
Replaced common block variables with derived type dvode_state variables.
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_output.f90
integration/VODE90/vode_source/dvode_type.f90
commit a0ec1b3eb7b5e23c3286fe2eb05991a1686054fc
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun May 14 01:24:16 2017 -0400
Cleaned up derived type dvode_t and its use. Still more todo.
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_type.f90
commit 6ce656d4ed0f83c04ac4c118cadc55e6cb5ece8a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun May 14 01:21:29 2017 -0400
Finished moving vode routines into module files.
Still need to finish replacing references to common variables with
references to dvode_state derived type.
integration/VODE90/vode_source/dacopy.f
integration/VODE90/vode_source/dewset.f
integration/VODE90/vode_source/dumach.f
integration/VODE90/vode_source/dvhin.f
integration/VODE90/vode_source/dvindy.f
integration/VODE90/vode_source/dvjac.f
integration/VODE90/vode_source/dvjust.f
integration/VODE90/vode_source/dvnlsd.f
integration/VODE90/vode_source/dvnorm.f
integration/VODE90/vode_source/dvode.f
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_output.f90
integration/VODE90/vode_source/dvode_type.f90
integration/VODE90/vode_source/dvset.f
integration/VODE90/vode_source/dvsol.f
integration/VODE90/vode_source/dvsrco.f
integration/VODE90/vode_source/dvstep.f
integration/VODE90/vode_source/iumach.f
integration/VODE90/vode_source/ixsav.f
integration/VODE90/vode_source/test/tvode.f
integration/VODE90/vode_source/vode.H
integration/VODE90/vode_source/xerrwd.f
integration/VODE90/vode_source/xsetf.f
integration/VODE90/vode_source/xsetun.f
commit 6dfe20b4260523d56cff1adf7d115f0f799d54e4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 13 20:19:10 2017 -0400
Added doxygen input file and Makefile to build VODE documentation.
integration/VODE/vode_source/docs/Makefile
integration/VODE/vode_source/docs/doxyfile_vode
commit 3c8ee8aaefb440e605e44cee0149030666ee64b1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 13 03:59:35 2017 -0400
Just stick that huge comment from dvode in a Readme.
integration/VODE90/vode_source/README
commit 18949906de56d96990802ef6b33e09f79cd3c145
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 13 03:59:15 2017 -0400
First pass at module-ifying the dvode subroutine and common blocks.
integration/VODE90/vode_source/dvode.f90
integration/VODE90/vode_source/dvode_type.f90
commit 896cbec3ad8fc4136a0687a0e4a8cca4c4a9802c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 13 03:58:45 2017 -0400
Removed deck...
integration/VODE90/vode_source/dvnlsd.f
commit 7abb46bc0c32d1bc0105a9468c5e650d89202786
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 13 01:21:28 2017 -0400
Added Fortran-90 VODE directory for conversion.
integration/VODE90/GPackage.mak
integration/VODE90/Make.package
integration/VODE90/actual_integrator.f90
integration/VODE90/actual_integrator_sdc.f90
integration/VODE90/rpar.F90
integration/VODE90/vode_rhs.f90
integration/VODE90/vode_rhs_sdc.f90
integration/VODE90/vode_source/GPackage.mak
integration/VODE90/vode_source/Make.package
integration/VODE90/vode_source/dacopy.f
integration/VODE90/vode_source/dewset.f
integration/VODE90/vode_source/dumach.f
integration/VODE90/vode_source/dvhin.f
integration/VODE90/vode_source/dvindy.f
integration/VODE90/vode_source/dvjac.f
integration/VODE90/vode_source/dvjust.f
integration/VODE90/vode_source/dvnlsd.f
integration/VODE90/vode_source/dvnorm.f
integration/VODE90/vode_source/dvode.f
integration/VODE90/vode_source/dvset.f
integration/VODE90/vode_source/dvsol.f
integration/VODE90/vode_source/dvsrco.f
integration/VODE90/vode_source/dvstep.f
integration/VODE90/vode_source/iumach.f
integration/VODE90/vode_source/ixsav.f
integration/VODE90/vode_source/test/GNUmakefile
integration/VODE90/vode_source/test/tvode.f
integration/VODE90/vode_source/vode.H
integration/VODE90/vode_source/xerrwd.f
integration/VODE90/vode_source/xsetf.f
integration/VODE90/vode_source/xsetun.f
integration/VODE90/vode_type.f90
integration/VODE90/vode_type_sdc.f90
commit 69c8eec8fb6325a75d4b0437b0e68d2c33bc8a0a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat May 13 01:17:30 2017 -0400
Updated makefile for VODE test program so it uses BLAS and LINPACK in util.
integration/VODE/vode_source/test/GNUmakefile
commit 50c9cc7bcf17ee8c74ec3ae28a8526781e16e77e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 3 10:23:34 2017 -0400
styling
CHANGES
commit 88ba21f470b2121802e7c01829f77d6abab8553e
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 23 17:26:12 2017 -0400
Remove latex.
unit_test/burn_cell/burn_cell_nl.py
commit 5aec6b953ded82c9ac2e91da205047651202349f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 23 17:01:24 2017 -0400
Created inputs for the C-burn-simple network
unit_test/burn_cell/init_cburn
unit_test/burn_cell/inputs_cburn.VODE
commit 6a0a62baf3b347bd4a76c2d2c7c81efd66485b29
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Mar 23 16:48:10 2017 -0400
Updated simple C burn network for pyreaclib changes
networks/ignition_reaclib/C-burn-simple/NETWORK_REQUIRES
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/c.py
networks/ignition_reaclib/C-burn-simple/reaclib_rates.f90
commit 8555f4d512fae97a0bbf1cd04ade0e37c254b9b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Mar 1 08:57:46 2017 -0500
use VODE by default
unit_test/test_sdc/GNUmakefile
commit 273ec35b103ed49f30fca51e8dbd45d06b4d59cc
Merge: e0fb6471 9c08513b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 22 09:04:58 2017 -0500
Merge pull request #32 from jaharris87/development
Explicitly declare eos_name as public variable
commit 9c08513baaf4296c355544b0f236403dc6747a5f
Author: Austin Harris <jaharris87@users.noreply.github.com>
Date: Tue Feb 21 18:26:20 2017 -0800
Explicitly declare eos_name as public variable
EOS/breakout/actual_eos.f90
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/actual_eos.F90
EOS/multigamma/actual_eos.f90
EOS/polytrope/actual_eos.f90
EOS/stellarcollapse/actual_eos.f90
EOS/ztwd/actual_eos.f90
commit e0fb64711aec4fe63208d2efb7cdbafbfb452b49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 3 10:12:31 2017 -0500
update for merge
CHANGES
commit 2043246e810d521eba7c8d40fcb8055ed63569d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jan 2 13:44:30 2017 -0500
BS has a stubbornly hard time with aprox19 -- this works (but is damn slow...)
unit_test/test_react/inputs_aprox19.BS
commit 196ff089d1c4395279591926202eadac145e859e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 19:38:08 2016 -0500
add updates
CHANGES
commit 048e6f902bd128b0367788b48ec6f3a4249042aa
Merge: 0ed9e816 d8d8a93d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 17:24:23 2016 -0500
Merge pull request #29 from BoxLib-Codes/nomolar
remove support for integrating molar fractions
commit d8d8a93d00385295e89dc5d3d7cb52bd9f9d8e5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 14:23:33 2016 -0500
restore original default for BS use_timestep_estimator = F
integration/BS/_parameters
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_3alpha.BS.ACC
unit_test/test_react/inputs_reaclib_ctest.BS
commit 4c67f57c7524e9570814146eb59638ef70053b94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 14:02:49 2016 -0500
add a comment
integration/VODE/vode_type_sdc.f90
commit 8985fda1cc7677bea693be4236d5febf6ed34261
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 12:22:42 2016 -0500
sync up names
integration/BS/bs_jac.F90
integration/BS/bs_type.F90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
integration/numerical_jacobian.f90
commit 6b0e1b4177c8f35d54322029b52d6e88ab55e374
Merge: 936a09c0 0ed9e816
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 28 12:10:55 2016 -0500
Merge branch 'development' into nomolar
commit 0ed9e816b2fee9238a0131cd0aeca63602cc86f0
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 15 13:02:14 2016 -0500
Undo debugging comments and needless acc create.
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
commit 636fe074710dfa47f6321475680fe46dc951b509
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Dec 15 12:56:20 2016 -0500
Updated URCA network acc markups and module uses.
networks/ignition_reaclib/URCA-simple/actual_burner.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/table_rates.f90
commit f2632757c27225e0412ceaaed2ba3067debd1fa7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 13 14:44:48 2016 -0500
Use common subexpression elimination for C-burn-simple and aion_inv
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/c.py
commit 3f47106776e3e0bd4a4cda0feb780cc69aa65e02
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 13 14:42:22 2016 -0500
Use common subexpression elimination in c-test RHS and aion_inv.
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/C-test/c.py
commit de0bc28656ac5f4c86262436a947aefe8f3dd141
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 13 14:41:31 2016 -0500
Make urca.py executable.
networks/ignition_reaclib/URCA-simple/urca.py
commit ef631e72bdbed9bcee6db807216a682d35e50554
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 13 14:36:36 2016 -0500
Use common subexpression elimination in urca RHS.
networks/ignition_reaclib/URCA-simple/urca.py
commit ea8feffc79faceeb1903d36dc70462fc8cfb9bc1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 13 14:35:38 2016 -0500
Replaced aion divides with aion_inv multiply in urca net.
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
commit c61663bac7cc976bffa65d162786b2cc97a53919
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Dec 13 14:32:16 2016 -0500
Use common subexpression elimination in urca net RHS
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
commit 646a2d63cf9dfc92cc84aa7e7cf5ed9b0065f4f7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 12 15:13:45 2016 -0500
Revised data init for c-burn-simple network so PGI can compile it.
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.f90
commit 50572979128835859f10f077a41d14fef838a106
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 12 15:09:34 2016 -0500
Revised data init for c-test network so PGI can compile it.
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/C-test/reaclib_rates.f90
commit 36b6257aa3ab9ce58023a4375e5bd834aa8af7d6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Dec 12 15:04:52 2016 -0500
Revised data init for urca network so PGI can compile it.
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.f90
commit 674ed9a59896520cee3c82cfb29761a8adf1b4bb
Merge: c66e8ace ccc4cdc6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Dec 7 08:58:15 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit ccc4cdc6d8f12b7ea5641cca5adaf433b8d22e02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Dec 1 09:29:08 2016 -0500
update changes
CHANGES
commit c66e8ace35e3934450059299c0ab073b314884ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 09:14:27 2016 -0500
changes from the past month
CHANGES
commit 2f29e6dd17d3ebd519244dd433c67b8af1d7332b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 30 09:04:13 2016 -0500
fix compilation
networks/xrb_simple/actual_rhs.f90
commit be323d40d9a863b676be3840b9fbbd270aefd888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 29 21:35:28 2016 -0500
table stuff and runtime parameters should have the save attribute.
Compilers were probably doing this anyway, but this is more correct
by the standard.
Also we should revisit making the physical constants Fortran parameters.
There were GPU issues previously, so leaving these unchanged at the moment.
EOS/helmholtz/actual_eos.F90
commit a120f4fdb873bb33a59d8857f7f4702e9179e4f7
Merge: 037b1ce6 0bd53d5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 29 15:10:32 2016 -0500
Merge pull request #25 from BoxLib-Codes/aioninv
add an aion_inv to network_module and use this to replace divides
commit 0bd53d5bbb5150cf2eb9ebae66188f5f17252c32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 15:30:56 2016 -0500
define an aion_inv at the top-level network module and remove divides
EOS/gamma_law_general/actual_eos.F90
integration/BS/bs_jac.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_type.f90
integration/VODE/vode_type_sdc.f90
integration/integration_data.f90
integration/integrator.f90
integration/integrator_sdc.f90
integration/numerical_jacobian.f90
interfaces/eos_type.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_simple/actual_rhs.f90
networks/ignition_simple_SDC/f_rhs_instantaneous.f90
networks/iso7/actual_rhs.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/xrb_simple/actual_rhs.f90
commit ec67c7d3dcc39e3d9eca5f556d9e1f1bfc863626
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 28 14:49:05 2016 -0500
add aion_inv
unit_test/network.f90
commit 037b1ce6f8f1ad9926cc3a87abce7f951f6ea7a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 22 10:10:19 2016 -0500
clarify indices
integration/VODE/rpar.F90
commit 476ec0b1ece95e7c65f101e38566dfa7012fc311
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 20:59:02 2016 -0500
fix indexing wrt irp_ydot_a
integration/VODE/vode_type_sdc.f90
commit def01b0798b86a36a8f0942abd0fbdaf1b66922c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 20:34:07 2016 -0500
update for SDC
integration/VODE/Make.package
commit 76eac69dc9ab352f27a06ee2958292365cd66bcd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 20:28:38 2016 -0500
fix compilation
integration/BS/actual_integrator_sdc.F90
commit 069c0c50dfe6cc14eb84e668dd5283c3591229a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 19:36:44 2016 -0500
this actually compiles now
integration/VODE/actual_integrator_sdc.f90
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_type_sdc.f90
commit c4554fa76b15ce292b0a01e87af894c77b67fe8b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 18:50:43 2016 -0500
move the BS-specific numerical_jacobian_sdc into its integration
directory
integration/BS/numerical_jacobian_sdc.f90
integration/numerical_jacobian_sdc.f90
commit c4ccc703469eeea4666de894779c0625802d17f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 18:35:23 2016 -0500
some compilation work
integration/VODE/GPackage.mak
integration/VODE/actual_integrator_sdc.f90
integration/VODE/rpar.F90
integration/VODE/vode_type_sdc.f90
commit c275cc4cebf1d0084c9272efe8b34c7c9021df08
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 15:44:25 2016 -0500
first cut at all the VODE SDC stuff. No way will this actually
compile though...
integration/VODE/vode_rhs_sdc.f90
integration/VODE/vode_type_sdc.f90
commit b7a232e26a10af9d3559a13973f240c7bd38711c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 14:52:51 2016 -0500
finish first pass at this
integration/VODE/vode_type_sdc.f90
commit a8a162153dcb8f28341c3998fccb7ae6c2f96c75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 14:00:50 2016 -0500
save current state -- almost complete
integration/VODE/vode_type_sdc.f90
commit e9f4976d3d511c0fd4478bebd2db57a32ea51f82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 13:11:28 2016 -0500
add a preventative call to fill_unevolved_variables
integration/BS/bs_type_sdc.F90
commit 282559ec1f658f5a638e245f9094fb36a57ddd34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 12:31:24 2016 -0500
a lot of progress...
integration/VODE/rpar.F90
integration/VODE/vode_type_sdc.f90
commit 00c071dac80aba60c8982769faab6a3ed8428b5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 21 12:04:43 2016 -0500
add note about fragility of the indexing
integration/BS/rpar.F90
commit f8503c487e8f555e8c923a71bb7ca5f35fa1f872
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 22:14:36 2016 -0500
fix some indexing
integration/VODE/rpar.F90
commit 3b8f3da7a96effa9d857ef51bcdea6ca75a080ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 22:07:13 2016 -0500
also need T_from_eden
integration/VODE/rpar.F90
commit 9c1437b89f07bd40a4ea0c0b410b0f5bf46550f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 21:44:31 2016 -0500
need the advective terms too
integration/VODE/rpar.F90
commit c1ded479e4b041f3fedab5b169428cdd0b1369df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 19:07:18 2016 -0500
SDC vs. non-SDC rpar
integration/VODE/rpar.F90
commit 0e79e90353cd2c3f4ec55286d3f913cdfa5772e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 18:44:20 2016 -0500
a little more on VODE
Docs/networks/networks.tex
commit 8b6671ae008828e2382fdc0f99f5d565114779d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 18:17:52 2016 -0500
first cut at the SDC flow
integration/VODE/actual_integrator_sdc.f90
commit a76a6bc77ff1a85754ae98d07873e1332570dd0b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 18:13:40 2016 -0500
store the offset time for SDC too
integration/BS/actual_integrator_sdc.F90
integration/BS/rpar.F90
commit daa513f9592db9454478c2069ec45ee67687d4ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 18:00:45 2016 -0500
remove unnecessary local code for atol / rtol (closes #23)
integration/BS/actual_integrator_sdc.F90
commit 51302c5e88efde6de31de58539829f2667a732b4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Nov 20 17:47:52 2016 -0500
more work on VODE SDC
integration/VODE/actual_integrator_sdc.f90
integration/VODE/vode_type.f90
integration/VODE/vode_type_sdc.f90
commit 94424dbbcde0b9e77f302f4037cb0482ad748797
Merge: d1c6e647 148a9d5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 19 11:58:45 2016 -0500
Merge branch 'development' into vode-sdc
commit 936a09c05702f8de8b9e8f2f812ee9e9cd488d02
Merge: a8cef279 148a9d5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 19 11:04:03 2016 -0500
Merge branch 'development' into nomolar
commit 148a9d5f530df13f48039b4c35c7f2807720ec5b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 18 14:15:15 2016 -0500
typo
Docs/sdc/sdc.tex
commit b3816eb7e950dac35ece177b92a565248dd46175
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 18 14:01:20 2016 -0500
update the SDC
Docs/sdc/sdc.tex
commit e627df582f73811c1eb729fb40d3f8914f8fabcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 18 10:10:45 2016 -0500
make signs consistent with code
Docs/sdc/sdc.tex
commit 5caaa6feca7ce09a69d30e1374e276f3fbd6dc11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 17 14:39:24 2016 -0500
some SDC doc
Docs/networks/networks.tex
Docs/sdc/sdc.tex
commit 181d55ab8dbfc274b8287ff6223529a900d823ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 17 14:03:37 2016 -0500
fix the comment -- we don't actually do a normalization
integration/BS/actual_integrator_sdc.F90
commit d1c6e6470390200987cee73cb8a3e58594c60335
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 16 21:12:42 2016 -0500
start of work on SDC VODE
integration/VODE/rpar.F90
commit a8cef279b18f202062c83b072edbb5272c40ffc7
Merge: 7c669e11 98c2cad7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 15 14:00:24 2016 -0500
Merge branch 'development' into nomolar
commit 98c2cad7781e57f4eaafa6aa905eabf6fb89efc4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 15 14:00:06 2016 -0500
add rprox
unit_test/test_react/test_network_combinations.py
commit 32a63135a41291af057072ffbfe2c477be55b1ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 18:00:56 2016 -0500
some cleaning
Docs/networks/networks.tex
commit 7c669e1171e841d096061ffbb05a1493603192a9
Merge: f606f53e 9516d433
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 17:50:02 2016 -0500
Merge branch 'development' into nomolar
commit 9516d43360738a36ede8e73adc671897b6c512fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 14 15:32:18 2016 -0500
sdc_t doesn't have self_heat anymore
integration/BS/bs_type_sdc.F90
commit a855c9e5c366362a1f3df0ed83ac34cf1e1096f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 20:43:16 2016 -0500
update rprox
unit_test/test_react/param_testing/rprox-BS-test-results.txt
unit_test/test_react/param_testing/rprox-VBDF-test-results.txt
commit 93cba47bc740011b4808bfc9f9913a8b5a6fe25a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 20:05:45 2016 -0500
rprox testing
unit_test/test_react/param_testing/rprox-VODE-test-results.txt
commit f606f53e0d3f0c2e5db295cabe477c5d2dda1396
Merge: 3500cc39 f3ce1d3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 18:24:50 2016 -0500
Merge branch 'development' into nomolar
commit f3ce1d3bd9b761c69b93b19e9bb1ce7d82f4d571
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 14:42:11 2016 -0500
fix some typos
unit_test/test_react/test_network_combinations.py
commit 86c4a8b6a03d1e09db4c54c3dc6232b2e1dc0470
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 14:32:23 2016 -0500
OMP on by default
unit_test/test_react/GNUmakefile
commit ad6fb586d7dd633a89a0378b83b851b1b8a2024c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 14:32:03 2016 -0500
more options
unit_test/test_react/test_network_combinations.py
commit 9213c43a0732d39eb35c9469a52fdfa400d2aa19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 14:20:46 2016 -0500
new results
unit_test/test_react/param_testing/aprox19-BS-test-results.txt
unit_test/test_react/param_testing/aprox19-VODE-test-results.txt
commit 2b851f3d55c0862e3e0ff6fa17a3702d55d8c56a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 13:14:58 2016 -0500
results for aprox13
unit_test/test_react/param_testing/aprox13-BS-test-results.txt
unit_test/test_react/param_testing/aprox13-VBDF-test-results.txt
unit_test/test_react/param_testing/aprox13-VODE-test-results.txt
commit b9a5dbb67bd2d79ffb8ef0f90cd4245ca8088e6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 12:56:47 2016 -0500
add RHS stats to the summary
unit_test/test_react/test_network_combinations.py
commit ca3cbbc6c1660c44abf530ead1bcf237d87a8b4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 11:56:37 2016 -0500
now with pretty output
unit_test/test_react/test_network_combinations.py
commit 359ca6872cbba71a988574e23cb4973589ee09ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 10:43:25 2016 -0500
add a return code
unit_test/test_react/main.f90
commit 10413865e023c945822740b43dc29d894d9f0c01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 10:27:23 2016 -0500
more progress on the test everything script
unit_test/test_react/test_network_combinations.py
commit 3500cc397874b745ba71231ea16a737f391d1727
Merge: ba84bea5 2d5c49b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 09:14:52 2016 -0500
Merge branch 'development' into nomolar
commit 2d5c49b736f55f7b52548eb4d74bbf40f7911b41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 9 09:14:34 2016 -0500
keep this on development for now
unit_test/test_react/test_network_combinations.py
commit ba84bea535cbbdae61b9d4c11b425064b26d8a5f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 21:28:09 2016 -0500
a little more progress
unit_test/test_react/test_network_combinations.py
commit c77ee9404cbd72ffb124ad5e882628944f783275
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 20:49:48 2016 -0500
start of a script to test out different combinations of parametrs
unit_test/test_react/test_network_combinations.py
commit 368e64decf573652e4397f644ee3f5b39ff7a97c
Merge: 713821e0 8907cac2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 15:25:42 2016 -0500
Merge branch 'development' into nomolar
commit 8907cac2b17196d5d1818227e145109ba248034e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 14:28:41 2016 -0500
add new test
CHANGES
commit 0792cd06a7a332b8af2340c5bd0172fa92051ab7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 13:44:51 2016 -0500
this runs to completion
unit_test/test_sdc/inputs_aprox13
unit_test/test_sdc/main.f90
commit dffd93fbdc049ea0023fbe56e2369af26a063364
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 13:30:22 2016 -0500
we were calculating the internal energy from the total energy density incorrectly
integration/BS/bs_type_sdc.F90
commit 713821e07bc61022dbbef41b35cbd5a298790353
Merge: 3e54062f 3f76b93c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 12:58:36 2016 -0500
Merge branch 'development' into nomolar
commit 3f76b93cceaf7bfb2beb5450b7f86ac778093e71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 11:05:16 2016 -0500
set a small dens that is smaller than what we call this with
unit_test/test_react/inputs_aprox13
commit 094ca6b35404476b31c272abe80c028dcf629914
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 8 10:48:19 2016 -0500
output time in bs dump
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
commit caf6c64fd1fab20e848254749bfd9ec298b9c5fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 7 22:06:52 2016 -0500
we need to call actual_integrator_init() explicitly for SDC otherwise things
are unhappy
unit_test/test_sdc/main.f90
commit 1b4ffeb2ef9a9adcca7f46f1a085fd43b356eb06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 7 21:50:34 2016 -0500
set T_from_eden
unit_test/test_sdc/inputs_aprox13
unit_test/test_sdc/main.f90
commit c3965d2b4790e6301b433aadceebe846c4ca0796
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Nov 7 20:45:24 2016 -0500
start hooking in SDC -- compiles (but don't dare try OpenACC!)
unit_test/test_sdc/main.f90
commit 3d1b9d33d33017d566bb3ff525effe1f07d9a5cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 22:07:46 2016 -0400
some SDC build stuff
integration/GPackage.mak
networks/aprox13/GPackage.mak
commit 3289c11b7445e3951c953d07f0fded12c4480406
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 22:07:18 2016 -0400
fix SDC
unit_test/microphysics.F90
commit e8dd7cf2fbfd454fbfd96946ea900fbd25ff60ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 22:05:32 2016 -0400
f90 -> F90 to allow preprocessing for SDC
unit_test/GPackage.mak
unit_test/microphysics.F90
commit d0d90edaa4aca9373aff2de3a8c1efb30866a3f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 21:47:09 2016 -0400
add the SDC defines
GMicrophysics.mak
commit 1f6b8222832988c8c71a58908408ee5305260663
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 21:41:44 2016 -0400
more SDC cleaning
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/main.f90
commit 1223bdbb85df8d47424ba3eac10a89d7ae1a74b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 21:25:11 2016 -0400
serve a copy here for unit testing
interfaces/GPackage.mak
interfaces/sdc_type.F90
commit 747067f7abdba6f85808313396ea803875c451b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 21:15:24 2016 -0400
use parallel_wtime() instead of the omp versiont
unit_test/test_react/main.f90
commit 81d37ce371f64becc18b7ab475bba472bb604ccc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 21:03:16 2016 -0400
start of an SDC unit test -- at the moment it is a direct copy of test_react
unit_test/test_sdc/GNUmakefile
unit_test/test_sdc/GPackage.mak
unit_test/test_sdc/_parameters
unit_test/test_sdc/gr0_3d.small
unit_test/test_sdc/inputs_aprox13
unit_test/test_sdc/main.f90
unit_test/test_sdc/util.f90
unit_test/test_sdc/variables.f90
unit_test/test_sdc/xin.aprox13
commit cb209f1bae068ad0de0e12b79b8ce3fca8ffafed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Nov 5 20:54:29 2016 -0400
add SDC hooks
integration/BS/GPackage.mak
commit ecfcd6485fa3e06e9df156066e9b92ba19e1c4db
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Nov 5 10:59:54 2016 -0400
Add a timer
unit_test/test_react/main.f90
commit 621aa9deff88dd0aa840b749533961c837b99ef8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Nov 5 10:51:32 2016 -0400
Fill in the species before the burn loop
unit_test/test_react/main.f90
commit d4940464c2cf2341ba9226aa9b541bfa75cfc762
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 4 22:00:29 2016 -0400
a little more on the system
Docs/MicrophysicsUsersGuide.tex
Docs/maestrosymbols.tex
Docs/sdc/sdc.tex
commit f3cf106cfdc6d4ab43f3f2d7e90a083fb625af1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 4 14:48:59 2016 -0400
start of SDC doc
Docs/GNUmakefile
Docs/MicrophysicsUsersGuide.tex
Docs/sdc/sdc.tex
commit 7f6dc94f6b554bd23737eefc74372703d6aefc82
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 4 14:39:43 2016 -0400
a litle cleanup, get small_x_safe from params
integration/BS/bs_type_sdc.F90
commit 3e54062fb80bd0ff7eb335f6f959b2a1649e1fa5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 4 13:11:00 2016 -0400
fix some runtime parameter docs
Docs/runtime_parameters/runtime_parameters.tex
integration/BS/_parameters
commit ead06ae3de8a34df7efec175da61e43ad0fa5c8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 21:48:09 2016 -0400
don't need to explicitly set use_timestep_estimator
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_3alpha.BS.ACC
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_reaclib_ctest.BS
commit a6154c984c9a34a836f7f38d3c574e230aa8ffca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 21:43:30 2016 -0400
use the timestep estimator by default
integration/BS/_parameters
commit 8d5ee5c863e43a9802918a7726721409f91c4bc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 20:15:24 2016 -0400
remove the integrate_molar_fraction stuff
integration/BS/actual_integrator.F90
integration/BS/bs_jac.F90
integration/BS/bs_rhs.F90
integration/BS/bs_type.F90
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf_rhs.f90
integration/VBDF/bdf_type.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
integration/_parameters
integration/numerical_jacobian.f90
unit_test/test_react/inputs_3alpha.VBDF
commit c136823fbecb1fc79d55cd4fb0c120e6260ef30a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 15:29:56 2016 -0400
add a dump_bs_state routine for debugging
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/stiff_ode.F90
commit 378d41bd0d146cef3e6c2fac13ab011b3b6f62b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 3 15:02:36 2016 -0400
define self_heat for SDC and initialize it to false
integration/BS/actual_integrator_sdc.F90
integration/BS/bs_type_sdc.F90
commit 6733a7b2b5637971135ebaf3310b5f17274e737b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 2 21:08:42 2016 -0400
fix invalid members
integration/BS/bs_jac_sdc.F90
integration/BS/bs_type_sdc.F90
commit 84f71b58869da936aca19faec38d0223db676fc4
Merge: f2d0441e 209c975c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Nov 1 09:52:35 2016 -0400
Merge branch 'development'
commit 209c975cc9f819645159a04c7b0e808aeda41aa9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Oct 30 02:06:09 2016 -0400
Only print out message on I/O proc
networks/aprox13/actual_rhs.f90
commit 2b8137128c78560362a811aff78863ae45a75e72
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 28 10:10:15 2016 -0400
add another net
unit_test/test_react/README.md
commit 4eb14bac0072406dd3a5e5decef5ab1dd9d3bbf3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Oct 27 22:54:20 2016 -0400
Check in aprox13 variant
unit_test/test_react/inputs_aprox13.BS.ACC
commit d9403f04123e1ab2437686523b32d16223d3024a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 27 22:13:07 2016 -0400
updates
unit_test/test_react/README.md
commit e5bf0694593b1fdf6d81d3faeef127c458cdfa68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 27 21:48:27 2016 -0400
update table
unit_test/test_react/README.md
commit b6805ca5b074709f9e85d7880640aa30cccda92f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 27 21:33:18 2016 -0400
add the start of a table
unit_test/test_react/README.md
commit 67a00fd6f5f186f46b90b837287579612fd2b406
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 27 18:30:08 2016 -0400
move these from BoxLib
util/regression_testing/Microphysics-tests-pgi.ini
util/regression_testing/Microphysics-tests.ini
commit 30414e5ce95bc7cb654bf3a59c9f0b26b65ab750
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 13:16:15 2016 -0400
reset inputs.aprox13 -- committed options that should not have been there
unit_test/test_react/inputs_aprox13
commit 7c8af1fa15bf44d484748f13e4fb0a86cd24f116
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 12:54:24 2016 -0400
reset iters to 10 -- previous commit was accidental
integration/VBDF/bdf.f90
commit 5cc987689454373e0300fae0924402e57748691c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 12:53:29 2016 -0400
fix merge issues that I missed previously
unit_test/test_react/GNUmakefile
unit_test/test_react/inputs_3alpha.BS.ACC
unit_test/test_react/main.f90
commit e30cf500508b050204afc94462c8f313b125bd99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 19 10:17:10 2016 -0400
fix merge funkiness
unit_test/test_react/main.f90
commit 67f90e9389e765cf2c8a0bce5ae58e429f164179
Merge: 53c8065a b3619952
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 18 21:18:03 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 53c8065aabb510598cb096bd869c4d746a56648a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 18 21:16:44 2016 -0400
GPUs don't like type-bound procedures or string arrays. So don't
try putting pf on the GPU, instead just assign integer keys to the
components and copy those in.
stay classy GPUs...
unit_test/test_react/main.f90
commit b361995288dcf6d1a5b65bba76581adc48563a4d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Oct 16 19:38:48 2016 -0400
Fix the Rosenbrock RHS step counter
integration/BS/stiff_ode.F90
commit f76930a72291723fcf52b1c86288812748a90740
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Oct 16 18:53:11 2016 -0400
Add medium and large size grids
unit_test/test_react/gr0_3d.large
unit_test/test_react/gr0_3d.medium
commit e933f1ef14f6126841eedccd747ac79a4fea8e0a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Oct 16 17:02:02 2016 -0400
Add a do_acc runtime parameter
unit_test/test_react/_parameters
unit_test/test_react/main.f90
commit c8f3e1a3dc7f0f2e20956ca3b13e2b310ae25a1d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Oct 16 16:57:05 2016 -0400
Only copy the current FAB's worth of data
unit_test/test_react/main.f90
commit 6d822072997428d68e2fad8db2fa915a1cce4a8b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Oct 16 16:15:25 2016 -0400
Construct input state in a separate non-accelerated loop
unit_test/test_react/main.f90
commit 96c0ae64ea969633c99f7e52c62541fcc7b0afa6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 12 18:30:31 2016 -0400
deallocate state and pf % names
unit_test/test_react/main.f90
unit_test/test_react/variables.f90
commit a457676ba4a737cf7fa5885e1e03d0f0b7852e20
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Oct 12 12:42:38 2016 -0400
Fixed uninitialized state on GPU. ACC and OMP now agree to at least 1 part in 10^6
unit_test/test_react/main.f90
commit a811ee46661e81464241d9e9f3460778b0a75b0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Oct 6 18:02:21 2016 -0400
add testburn.f90 to f90sources to prevent the .o from being dropped
in the root directory
networks/ignition_simple/test/GNUmakefile
commit f2d0441e54bacd59a1e3e3c66fb4449a35cfb888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 3 10:57:15 2016 -0400
no 16.10 changes?
CHANGES
commit 875bbde96d2bf340213f7d741d5a69c46779d886
Merge: 74a5ec52 2f6740bc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Oct 3 10:53:43 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 2f6740bcd6a7a742482a221dff08fe8f4a8b32b6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Sep 21 10:24:37 2016 -0400
Remove the NSE stuff, it's not ready yet
NSE/Make.package
NSE/NSE_data.F90
NSE/README_emq
NSE/README_hmq
NSE/Readme_tables
NSE/_parameters
NSE/nse_dens_emq_table.txt
NSE/nse_pres_hmq_table.txt
README.md
networks/CONe2NSE/Make.package
networks/CONe2NSE/NETWORK_REQUIRES
networks/CONe2NSE/_parameters
networks/CONe2NSE/actual_burner.F90
networks/CONe2NSE/actual_network.F90
networks/CONe2NSE/eos_externalComputeAbarZbar.F90
commit 74a5ec52ba2005a23d9f98a86ff52b68bed34258
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 15 16:04:16 2016 -0400
add note about PGI_ACC_NOTIFY
Docs/openacc/openacc.tex
commit 7ccdd550be2a296d7e10d24228207a47801f4125
Merge: 07c93ba3 6bcd117d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 15 15:49:05 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 07c93ba33a8c9174feba1b17b1d5809a73af725e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 15 15:48:50 2016 -0400
don't init MPI twice
unit_test/microphysics.f90
commit 6bcd117d595c2050a036199119870020657a7fc7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 18:34:41 2016 -0400
Changed scaling method for urca net in unit test (BS).
unit_test/test_react/inputs_reaclib_urca.BS
commit 1ad874a2a189f4d18c427c0a9d46fb0c99ce8c6a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 18:17:43 2016 -0400
Added small X parameters and changed scaling method for cburn BS unit test.
unit_test/test_react/inputs_reaclib_cburn.BS
commit 97fd8eaec379620628bb92448a6a31de1b92ae29
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 18:16:30 2016 -0400
Added small_x for reaclib cburn network unit test (VODE).
unit_test/test_react/inputs_reaclib_cburn
commit cd22618064a0ebe0b58d6dfc848320d5f354dd56
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 17:35:18 2016 -0400
Added small_x to VODE inputs for ctest unit test.
unit_test/test_react/inputs_reaclib_ctest
commit 19c6b3d1b97462f84f39b3c204316bbf7e5bc7e1
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 17:07:42 2016 -0400
Updated test suite inputs for ignition_reaclib/C-test (BS).
unit_test/test_react/inputs_reaclib_ctest.BS
commit 43e7b2227bc8809c270d1c46024bab748d540eca
Merge: d90c7bb9 48e94e4d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 14:53:22 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit d90c7bb9f49aceedb008fbc0b77c547c9f8b3c1f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 14:52:53 2016 -0400
Added SMALL_X_SAFE probin parameter and set it to a working value for ctest.
unit_test/burn_cell/inputs_ctest.BS
commit 1f7990e36dd1a1034e3ad60d81723122afaf857d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 14:52:00 2016 -0400
Added SMALL_X_SAFE as a PROBIN parameter. Moved species renormalization option into clean_state.
integration/BS/_parameters
integration/BS/bs_rhs.F90
integration/BS/bs_type.F90
commit 90ab1f5822321164f05186213f935ab40ba9261d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 14:49:44 2016 -0400
Explicitly set jac(net_itemp, net_ienuc) = ZERO.
integration/temperature_integration.f90
commit ecd36301c6bcd0dd4f9b3a4b63e6192ae9214f75
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 00:56:58 2016 -0400
Added time, rho, T, X inputs file for ignition_reaclib/C-test network.
unit_test/burn_cell/init_ctest
commit 70e75d81f347cde2c8a5a2aa977245caf2fff385
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 00:56:35 2016 -0400
Added inputs file for ignition_reaclib/C-test network and BS integrator.
unit_test/burn_cell/inputs_ctest.BS
commit c0581a2a2ac7c5cf326859b3bdf83b2dda51eee3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Sep 12 00:54:32 2016 -0400
For burn_cell plotting, fixed data ordering bug, etc.
Also enabled plotting against file number.
unit_test/burn_cell/burn_cell.py
commit 78abba87f824760a29060feef10be77ef31d6384
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Sep 11 20:59:55 2016 -0400
Exit plotting script if no files to plot found.
unit_test/burn_cell/burn_cell.py
commit c34b4c4fee9574022610a9f42e882cdd11472594
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sun Sep 11 20:59:16 2016 -0400
Set initial state in time to zero for burn_cell.
unit_test/burn_cell/main.f90
commit 71ece23058359472a38263ad64c5652747b2ee33
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Sep 9 16:34:23 2016 -0400
Added more output plots.
Outputs png and eps
Changed X vs time to log X vs log time
Outputs T, edot vs time in log-log.
unit_test/burn_cell/burn_cell.py
commit 48e94e4d856f9065fe5b8e65a3e0b86e5cec6621
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Sep 8 22:10:34 2016 -0400
Fix typo
EOS/helmholtz/actual_eos.F90
commit af8279cc0acea22afd9d3cb800cf3e0e3ac9becb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 8 01:37:10 2016 -0400
Added testjacobian program for C-test network.
networks/ignition_reaclib/C-test/test/GNUmakefile
networks/ignition_reaclib/C-test/test/GPackage.mak
networks/ignition_reaclib/C-test/test/testjacobian.f90
commit cb9a14fa0983c634499fd30da4ee67dfbfd97a30
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 8 01:36:18 2016 -0400
Added testjacobian program for URCA-simple network.
networks/ignition_reaclib/URCA-simple/test/GNUmakefile
networks/ignition_reaclib/URCA-simple/test/GPackage.mak
networks/ignition_reaclib/URCA-simple/test/testjacobian.f90
commit e171a28de1f501aa853e1f94323b999cb5a6c94a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:57:20 2016 -0400
Updated test suite inputs files for reaclib networks.
They now test a slightly larger range in temp up to 6e8 K.
Tolerances are tighter for species, enuc, and temp.
ODE max steps are lower for BS integrator.
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_cburn.BS
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_ctest.BS
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/inputs_reaclib_urca.BS
commit c31c403eedea261527c5073151b0ef955db0d2c7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:26:08 2016 -0400
In burn_cell plotting script, fixed a bug with obtaining a time axis, etc.
Also added plotting for nuclide ydot.
unit_test/burn_cell/burn_cell.py
commit 829c75275271f52f43543ad95a553f6160523e3a
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:23:59 2016 -0400
Updated float output formatting for more exponent digit places in evaluate_rhs.
util/eval_rhs/evaluate_rhs.f90
commit 8738780f685dd19b5c1ad963e486d7be0be25779
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:18:31 2016 -0400
Fixed non-threadsafe bug in actual_rhs module for reaclib networks.
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
commit a9d23b5024c5e0dd13dc817c9957778b87a71710
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:17:15 2016 -0400
Updated pyreaclib generation scripts for the new pyreaclib module system.
networks/ignition_reaclib/C-burn-simple/c.py
networks/ignition_reaclib/C-test/c.py
networks/ignition_reaclib/URCA-simple/urca.py
commit 16f48dcee60bc0d82d60bedc2415e3ac54c13339
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:14:42 2016 -0400
Removed test-cpp for URCA-simple as it's no longer needed.
networks/ignition_reaclib/URCA-simple/test-cpp/.#out
networks/ignition_reaclib/URCA-simple/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
commit bb83c920011a6bb8a8e3074efbb4ec1c53b921fc
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 22:14:04 2016 -0400
Removed test-cpp for C-burn-simple as it's no longer needed.
networks/ignition_reaclib/C-burn-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/C-burn-simple/test-cpp/main.cpp
networks/ignition_reaclib/C-burn-simple/test-cpp/out_gnu
networks/ignition_reaclib/C-burn-simple/test-cpp/probin
networks/ignition_reaclib/C-burn-simple/test-cpp/testburn.f90
commit b2b97f3b6a6d7536ab41a16d7ae0ca94703eb79e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Sep 7 13:39:43 2016 -0400
remove the timestep estimator -- VODE always does this
unit_test/test_react/inputs_reaclib_ctest
commit 004340db2d30b53cd7f4e6b8e9c8f4dc7d2291cb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed Sep 7 12:27:37 2016 -0400
Modified and added inputs files for reaclib networks.
*.BS inputs have ode_max_steps and scaling_method, the others do not.
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_cburn.BS
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_ctest.BS
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/inputs_reaclib_urca.BS
commit c63351a132ac1a96b249b9439db81bd1fe480975
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 6 23:25:20 2016 -0400
Added a plotting script to make abundance vs time plots.
unit_test/burn_cell/burn_cell.py
unit_test/burn_cell/matplotlibrc
commit b4d979d660203e7904704c409eeae08207a7a9d4
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Sep 6 23:23:23 2016 -0400
Added output options, a sample input file, and a sample probin file for URCA.
Includes a subroutine for writing the contents of burn_t to a file.
unit_test/burn_cell/init_urca
unit_test/burn_cell/inputs_burn_urca
unit_test/burn_cell/main.f90
commit 98f50e81a7c25a057aa828677e60e38568c41c16
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Sep 2 18:06:48 2016 -0400
Test program to evolve a single rho, T, x over intervals in time.
unit_test/burn_cell/GNUmakefile
unit_test/burn_cell/GPackage.mak
unit_test/burn_cell/_inputs
unit_test/burn_cell/_parameters
unit_test/burn_cell/inputs_urca
unit_test/burn_cell/main.f90
commit 36fcea6d9571438b78ae119db6b1ecfbd1226b76
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Sep 1 18:26:15 2016 -0400
Fixed typo 'per nucleon' to 'per nucleus' for bion.
networks/ignition_simple/actual_network.f90
commit 578a34e17433e6c999f517d1aedbf2bdde664065
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Sep 1 13:19:09 2016 -0400
new tag
CHANGES
commit 5104de85aa3f0b8e94c49a24df41e79a234fd8ed
Merge: 8d68c187 a5ec24e8
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 30 18:44:36 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 8d68c1877be23ce80f0a011b4afb4ecd1231a14d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 30 18:44:05 2016 -0400
Added a test program to evaluate the RHS and print results.
util/eval_rhs/GNUmakefile
util/eval_rhs/GPackage.mak
util/eval_rhs/evaluate_rhs.f90
util/eval_rhs/inputs_reaclib_urca
commit a5ec24e8a74a5185476f4f727d54c25e668d7c75
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Aug 30 15:15:38 2016 -0400
Fix capitalization typo
networks/general_null/write_network.py
commit e0da8925a483f1b33d5b8c151cc296615882927f
Merge: 9f8a0140 ac298fbb
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Aug 29 16:43:25 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 9f8a0140f36c8294e44305ef8ed798d101b84df6
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Aug 29 16:42:50 2016 -0400
Updated networks to remove erroneous subroutine-level array declarations for dqweak and epart.
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
commit ac298fbb3b378789344df4d5078a687e42ccc9d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 27 21:50:00 2016 -0400
remove the scaling stuff
Docs/networks/networks.tex
commit fc1d206dc2618b94b5afedc23b5aa032e4e5d457
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Aug 26 15:52:07 2016 -0400
Updated reaclib test suite inputs. They work with the BS integrator now.
The cburn and urca test suite inputs cover a wide range of densities and temperatures suitable for a simmering WD.
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/inputs_reaclib_ctest.BS
unit_test/test_react/inputs_reaclib_urca
commit 30b44528542328a618d3d8f7a1127ba4baf56b64
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 26 14:47:34 2016 -0400
Remove rho/T/e scaling
integration/BS/actual_integrator.F90
integration/BS/bs_type.F90
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf_type.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_type.f90
integration/integration_data.f90
integration/integrator.f90
commit 69924d9d070735d7cb7c262a93a952260b562415
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Aug 26 14:35:21 2016 -0400
Remove references to scaling data
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-test/actual_burner.f90
networks/ignition_reaclib/URCA-simple/actual_burner.f90
commit fe43485dc09745314af7bd8aaaf36fa3b8015725
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Aug 26 12:31:10 2016 -0400
Updated reaclib networks so they do not use temp_scale or ener_scale.
Also changed proton species names to hydrogen-1.
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-test/actual_burner.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/actual_burner.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
commit 95b5ee3c014d71566b305b97ecff14418cca6624
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 23 18:28:40 2016 -0400
Added an inputs file for testing BS integrator with ctest net.
unit_test/test_react/inputs_reaclib_ctest.BS
commit b56b09ff45434ec6b6e4cdc41f26c3a2f20f06b5
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 23 16:33:08 2016 -0400
Added test_react inputs for the C-test reaclib network.
unit_test/test_react/inputs_reaclib_ctest
unit_test/test_react/xin.reaclib_ctest
commit 2a1e8a489d7c19e6d5b5027329f1f0b78f240c7d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 23 16:31:14 2016 -0400
Added a test reaclib network ctest.
C-test consists only of the he4+c12->o16 rate and those 3 nuclides and is useful for debugging the reaclib networks.
networks/ignition_reaclib/C-test/GPackage.mak
networks/ignition_reaclib/C-test/Make.package
networks/ignition_reaclib/C-test/NETWORK_REQUIRES
networks/ignition_reaclib/C-test/actual_burner.f90
networks/ignition_reaclib/C-test/actual_network.f90
networks/ignition_reaclib/C-test/actual_rhs.f90
networks/ignition_reaclib/C-test/c.py
networks/ignition_reaclib/C-test/physical_constants.f90
networks/ignition_reaclib/C-test/reaclib_rates.f90
networks/ignition_reaclib/C-test/table_rates.f90
commit 70af8ea1608397824469189e87084bb6f66ffbbd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 23 16:30:27 2016 -0400
Updated inputs for reaclib cburn and urca networks.
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_urca
commit 850a240e2acbcf7af98c003005d088ea832a9df2
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 23 16:28:34 2016 -0400
Added URCA tables to gitignore ala helm_table
.gitignore
commit f85c1baaaa356a453325e33ab1626ec37c8e018b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue Aug 23 16:25:30 2016 -0400
If using the URCA network and tables aren't present, link them.
GMicrophysics.mak
commit 2eca0621c0bdc4081ebec4c2c1944107e4bb1160
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Aug 22 02:12:02 2016 -0400
Changed some density and temperature ranges.
unit_test/test_react/inputs_reaclib_cburn
commit 9e0ed483cf336e655c831a9bc7fa9539b5016bc3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Aug 22 01:46:53 2016 -0400
Updated reaclib xin files.
unit_test/test_react/xin.reaclib_cburn
unit_test/test_react/xin.reaclib_urca
commit 569cb7b4734ef1de2724750c95c1ed0a7ddf3d00
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon Aug 22 01:02:49 2016 -0400
Added he4+c12->o16 to ignition_reaclib networks.
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/c.py
networks/ignition_reaclib/C-burn-simple/reaclib_rates.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.f90
networks/ignition_reaclib/URCA-simple/urca.py
unit_test/test_react/inputs_reaclib_cburn
unit_test/test_react/inputs_reaclib_urca
unit_test/test_react/xin.reaclib_cburn
unit_test/test_react/xin.reaclib_urca
commit b607fce107c1b17e4ef81304322df94233ac530b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Aug 20 21:13:10 2016 -0400
Make Helmholtz use eos_t % ye instead of overriding
EOS/helmholtz/actual_eos.F90
commit 3745c4ad2af3783c89417f562d85dc6a505cfe95
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Aug 18 15:37:07 2016 -0400
Added simple C-burning source files for reaclib network.
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/reaclib_rates.f90
networks/ignition_reaclib/C-burn-simple/table_rates.f90
commit 8aa1675b4c6a5d946e70040941de85547a2384ed
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Aug 18 15:36:25 2016 -0400
Added simple URCA network source files.
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/actual_burner.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/reaclib_rates.f90
networks/ignition_reaclib/URCA-simple/table_rates.f90
commit c8d2be621d049eb56632fd5c1eba54620fd03397
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 23:07:04 2016 -0400
this is challenging for VBDF
networks/aprox13/test/GNUmakefile
networks/aprox13/test/testburn.f90
commit 6291583f5373e228016824f1046691def0cae8ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 22:58:00 2016 -0400
remove the sum{X} - 1 if we fail to converge
integration/VBDF/actual_integrator.F90
commit 52901df142495aa0b9dc6ebe5372e7af0e444bd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 22:57:04 2016 -0400
this version works with VBDF -- we can't seem to get the low
density burns correct, but those may even be unphysical for this
net
unit_test/test_react/inputs_aprox13.VBDF
commit 4b32c6aa10e08a62eb06256a994d211d08494e0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 21:45:47 2016 -0400
fix normt
Docs/networks/networks.tex
commit 09b4436656e7f6a2a9c6d3c232ac0fc4ad227e9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 13 21:43:10 2016 -0400
document the VBDF error criteria
Docs/networks/networks.tex
commit ad273e74da8dfc1c20c70a3cd760b6d92aea4b63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 15:06:00 2016 -0400
fix the diagnostic output if integrate_molar_fraction = F
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.F90
commit f6174afedfcda4874d647e04175f08c79b3f2f62
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 15:05:28 2016 -0400
use a reasonable floor for the mass fractions of 1.e-10 -- this
helps the integration
unit_test/test_react/main.f90
commit fe54b6338a21fe8767410c820359d5da26bc2327
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 14:15:24 2016 -0400
this case is challenging for VBDF
networks/aprox13/test/testburn.f90
commit db999fa49e234ccaf221f7d7e23057021226ddae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 12:56:18 2016 -0400
some syncing with the version in LMC
integration/VBDF/bdf.f90
commit 8a9884183f9d0fccb4e18387e570d9dfdb4f6657
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 11:43:33 2016 -0400
remove unused variables
integration/VBDF/actual_integrator.F90
commit 0bd389d7ba05e158e8093dee80dd646c43847ac1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 11:26:01 2016 -0400
make the option of whether to reuse the Jacobian a runtime parameter
integration/VBDF/_parameters
integration/VBDF/actual_integrator.F90
commit 45f041cf143e08b53fdd06658e1357c0b10eda64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 09:57:03 2016 -0400
add VBDF section
Docs/runtime_parameters/runtime_parameters.tex
commit 966225cbbbc2b0aa02d9838d7f018614bf2093a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 09:47:42 2016 -0400
make some of these runtime parameters
integration/VBDF/_parameters
integration/VBDF/bdf.f90
commit 608b1048545b3093e8997d41a25843ff5a6c5433
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Aug 12 09:29:16 2016 -0400
update parameter list
Docs/runtime_parameters/runtime_parameters.tex
commit 64a20da35279618c6029eee68dac14ab7d7ddd25
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 19:54:40 2016 -0400
we were not using ener_offset or ener_scale
integration/VODE/actual_integrator.f90
commit 575129dc2b61bde6d6612a09390b03d2d62e56c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 19:01:47 2016 -0400
some comments
integration/VBDF/NOTES
commit 39e106ccbb45a7f2782c8b48334b0aa48f3a5320
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 18:18:58 2016 -0400
rename for consistency
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/bdf_rhs.f90
commit 50efc29dd3b65520d2cd9c68c302e37002c9d662
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 16:36:23 2016 -0400
change the check on dt_min to not depend on epsilon()
integration/VBDF/bdf.f90
commit e5228f356187b4e3c34bd0f50ee3cc498b856881
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 16:34:00 2016 -0400
make dt_min smaller -- this is consistent with BS
integration/VBDF/bdf.f90
commit ba060d2a34c6e2b8a66753f64547dcf3de807ce7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 15:30:46 2016 -0400
store the number of RHS and Jac evaluations in the burn_t output
integration/VBDF/actual_integrator.F90
commit 1aacdf2b7d6b7d0b8633b7eeedbac2dc9e492708
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 15:15:41 2016 -0400
T and molar fraction work fine now with the latest VBDF -- this is
for the test suite
unit_test/test_react/inputs_3alpha.VBDF
commit 7e421604a800c6777e85f8228dae5c708cfe7f76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 13:41:59 2016 -0400
add the VODE timestep estimator
integration/VBDF/actual_integrator.F90
commit 28920007f52c35b1b3108268260612e8e30f5a8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 13:41:39 2016 -0400
z0 -> z -- this seems to be a translation error from the original
source
integration/VBDF/bdf.f90
commit e37e1d06b9c4c9073f716eb4d6e09ef777facbf1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 12:15:33 2016 -0400
this works with VBDF now
unit_test/test_react/inputs_3alpha.VBDF
commit a6e9126756fefbde566cb5c0d090e69d7a0cd408
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 11:34:33 2016 -0400
we were looping over the LU decomposition for each addition into
the matrix A -- bad linear algebra!
integration/VBDF/bdf.f90
commit 4d964f5ca3b1972b105f9f532b03936495fbf3f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 11 10:23:45 2016 -0400
fix some compilation errors
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf_type.f90
commit 120c77fd8f1fbadade05e3b560ce8200ff90d9c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 20:39:37 2016 -0400
this version works with PGI + OpenACC
unit_test/test_react/inputs_3alpha.BS.ACC
commit e4e08fee217787c865bba6fb6f24b9883cd735d3
Merge: 6bf8dc5f 6e92f77f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 20:36:42 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 6bf8dc5f39deba521c7dbb4f7e973b073e6f6f02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 20:36:06 2016 -0400
some ACC reorg
unit_test/test_react/main.f90
commit 6e92f77fc734243af8232470d23c1ab8ffbac500
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 19:15:10 2016 -0400
remove ldt
unit_test/test_react/main.f90
commit cf2513fa9490acf21a8df82adc69e7b8f7d92e14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 19:14:23 2016 -0400
we don't need burn_state_in firstprivate anymore
also explicitly mark j as private since we wrote out those loops for
GPUs
unit_test/test_react/main.f90
commit ac588fc4094d45e80b1c4b2d6e9714b18fc223a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 15:08:43 2016 -0400
sync up with the Maestro version
networks/xrb_simple/test/testburn.f90
commit cdc9023552035fa19bb35689fb2ccdf2e1ed2d6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 13:48:22 2016 -0400
fix ACC compilation
integration/BS/stiff_ode.F90
commit 4c89e084ac9fced8d240324c62dcdea46d1585ef
Merge: 0b7ec847 f885aa4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 13:38:08 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 0b7ec847bb95783c01b97ff4b9b0f01d1acedc37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 13:36:38 2016 -0400
add some robustness to the BS integrator:
if we encounter a singular matrix, stop the semi-implicit extrapolation
and return the timestep
add a "safety factor" that can be used to check whether intermediate
values from extrapolation are reasonable. The default value of
safety_factor should make it not come into play.
integration/BS/_parameters
integration/BS/stiff_ode.F90
commit f885aa4a8cdde8b395535af25adc4d021cbf435a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 13:27:06 2016 -0400
define integer indices
Docs/data_structures/data_structures.tex
commit 77783f8b35e5436bd9ab0d36dd4f1a01f61f8b99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 13:06:39 2016 -0400
triple_alpha takes orders of magnitude fewer RHS evaluations with scaling_method = 2
unit_test/test_react/inputs_3alpha.BS
commit a0f49b629b9542331919b2277a31519841502f83
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 10:33:47 2016 -0400
update CHANGES
CHANGES
commit 7762064895ccf7f820b834efc32d68f8c52358de
Merge: 937f2e0e 04117510
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 09:34:29 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 937f2e0ec5b3494424c67b5ff86dd960b36039b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Aug 10 09:33:53 2016 -0400
a little debuggin
Docs/openacc/openacc.tex
commit 04117510b5d1e7a6bc2ba71a768d229724432830
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Aug 9 14:29:11 2016 -0400
Move EOS subroutines to actual_eos.f90
EOS/breakout/GPackage.mak
EOS/breakout/Make.package
EOS/breakout/actual_eos.f90
EOS/gamma_law_general/GPackage.mak
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/actual_eos.F90
EOS/helmholtz/GPackage.mak
EOS/helmholtz/Make.package
EOS/helmholtz/actual_eos.F90
EOS/multigamma/GPackage.mak
EOS/multigamma/Make.package
EOS/multigamma/actual_eos.f90
EOS/polytrope/GPackage.mak
EOS/polytrope/Make.package
EOS/polytrope/actual_eos.f90
EOS/stellarcollapse/GPackage.mak
EOS/stellarcollapse/Make.package
EOS/stellarcollapse/actual_eos.f90
EOS/ztwd/GPackage.mak
EOS/ztwd/Make.package
EOS/ztwd/actual_eos.f90
commit 288de2602780a25aee2ccf63078c94ac0a5c4836
Merge: a80ef514 d0cd5035
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 13:05:40 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit a80ef5140c28a2c035befb39366346bbfe75bf71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 13:05:22 2016 -0400
remove some unnecessary acc markup
integration/BS/stiff_ode.F90
commit d0cd50359c5632b558f3a91c7736b4bd05c9e59d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 13:03:53 2016 -0400
add more OpenACC compilation notes
Docs/openacc/openacc.tex
commit e292e85b1f7c79903d47f2ece56198ac166c8bea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 10:44:25 2016 -0400
fix final update
integration/BS/stiff_ode.F90
commit e7a540f8628f9d72d4182803a76c474568e24685
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 10:21:33 2016 -0400
new parameter: ode_method to select semi-implicit extrap BS or
Rosenbrock
integration/BS/_parameters
integration/BS/stiff_ode.F90
commit 7a3cbc709b23112aa0a1eb76b378e2a98a654feb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Aug 9 10:05:30 2016 -0400
some comments
integration/BS/stiff_ode.F90
commit 0cd65358fe54410cad258af1c05e21426e4eba93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 23:25:59 2016 -0400
add a rosenbock method as an alternative. Not yet called though
integration/BS/stiff_ode.F90
commit aa983a6853a0165d992fb7d5827db29f44a57851
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 21:32:45 2016 -0400
more integration parameters into stiff_ode_module
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/stiff_ode.F90
commit 0dce06760dec9e2cb79bd76dfcd9d439ce3f08c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 21:19:20 2016 -0400
rename single_step to single_step_bs
integration/BS/stiff_ode.F90
commit cc047c74015faeee926fb72ea49a7b98deba30f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 13:54:48 2016 -0400
remove ldt -- that seems to cause OpenACC problems
unit_test/test_react/main.f90
commit 6039f55373ca0e76819345605ab57f88c088fea8
Merge: 75c43d31 2f48ee68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 12:34:31 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 75c43d31163b7a6929cbec7ef63f925356e1a875
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 12:34:22 2016 -0400
get this OpenACC-ed
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
commit 2f48ee686023796c7b7a500a40b941e15fbd7d8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 12:24:09 2016 -0400
start docing OpenACC error messages
Docs/GNUmakefile
Docs/MicrophysicsUsersGuide.tex
Docs/openacc/openacc.tex
commit 0ef5500630c1b82470f3949a446b55b4e4efd9c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 12:05:56 2016 -0400
output RHS stats
unit_test/test_react/main.f90
commit 03ee21c16e99e6f5227b5e33531b71c2288ff612
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 11:26:35 2016 -0400
get the number of rhs evals from vode directly
integration/VODE/actual_integrator.f90
commit 845e08cc8ff223be4e06c055332da4e9a9053cd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 11:13:44 2016 -0400
make n_rhs and n_jac properties of burn_t
I've confirmed that BS accurately passes out the number of RHS
evaluations now.
integration/BS/actual_integrator.F90
integration/BS/actual_integrator_sdc.F90
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/stiff_ode.F90
interfaces/burn_type.F90
networks/triple_alpha_plus_cago/test/testburn.f90
commit 6097f96ac95f5c791c071a35d015f7d0b65eec05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 8 09:40:24 2016 -0400
re-remove species derivatives
interfaces/burn_type.F90
commit 5b7a63c2132a803c63381b57365a1c94d1fb4318
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Aug 7 21:57:40 2016 -0400
remove have_rates -- we don't do that anymore
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs_sdc.F90
commit 575c7874d0f03284123023de318a3015e6cc5139
Merge: 30df06f6 b5730c1c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Aug 7 00:11:55 2016 -0400
Merge branch 'development' into openacc
commit b5730c1c7c4c0413664f5bec48051319b0657008
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Aug 6 21:09:23 2016 -0400
Fix a divide-by-zero error in numerical_jac
integration/numerical_jacobian_sdc.f90
commit 30df06f6b646aa843b6d970655dab9ab9a36ec98
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 20:00:28 2016 -0400
Remove smallt/smalld from eos_t
interfaces/eos_type.f90
unit_test/eos.F90
commit 065dc91450b3720912bcf818c3a29c488c9e670c
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Aug 6 19:32:50 2016 -0400
Include module reference
networks/general_null/actual_rhs.f90
commit 3f6fa2c64400f207f6572381b855fc74436934e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Aug 6 18:17:27 2016 -0400
add note on input validation
Docs/EOS/eos.tex
commit 50b01686d4867871cfc156d8eb62c72f61ec1c72
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Aug 6 16:02:02 2016 -0400
Remove initializations from burn_t/eos_t and clean up
EOS/helmholtz/helmholtz.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/VBDF/bdf_type.f90
integration/VODE/vode_type.f90
interfaces/burn_type.F90
interfaces/eos_type.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
unit_test/eos.F90
unit_test/test_eos/main.f90
unit_test/test_react/main.f90
commit 9d379916decd767cf94044c92a8046c2cc50ac5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 12:20:44 2016 -0400
remove smallx
interfaces/eos_type.f90
commit 5d24194ef13fbece9c188d2902c2bee5d91232de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 11:08:15 2016 -0400
fix typo
Docs/networks/networks.tex
commit 2dcf14463b349b5254b640a872a4684de11d1344
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 10:40:58 2016 -0400
some updates
CHANGES
commit 5552c482e87283139bdd8800c9cf66fbd98823b3
Merge: 9273f858 320e5a02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 10:39:41 2016 -0400
Merge branch 'development' into development-next
commit 320e5a023262783648a1b1acdee26d98a9fefdbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 1 10:39:03 2016 -0400
reset changes since last time
CHANGES
commit 9273f85863c7b9a3c4135d7e6537ba8fe680e734
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jul 31 01:13:09 2016 -0400
Don't evolve rho/rho*u in the SDC burn
integration/BS/bs_type_sdc.F90
integration/BS/rpar.F90
integration/GPackage.mak
integration/Make.package
integration/numerical_jacobian_sdc.f90
integration/rpar.F90
commit d530503ccc7511e8036f414de8ec11dc384d8250
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 30 16:04:03 2016 -0400
Rescale all SDC variables on density reset
integration/BS/bs_type_sdc.F90
commit d44cba0eedab06f28ef008997f87647abf2d464b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 20:42:53 2016 -0400
add num_rate_groups
networks/general_null/network.template
commit da7660a0e10ad7d8bfeeafc28e2b2cc991b66f9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 20:40:18 2016 -0400
discuss num_rate_types
Docs/networks/networks.tex
commit ec635c3c1ed135187ae92d060e36d62fe64ae490
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 20:31:54 2016 -0400
make num_rate_types network-specific
networks/aprox13/actual_network.f90
networks/aprox19/actual_network.f90
networks/aprox21/actual_network.f90
networks/breakout/actual_network.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_simple/actual_network.f90
networks/iso7/actual_network.f90
networks/powerlaw/actual_network.f90
networks/rate_type.f90
networks/rprox/actual_network.f90
networks/triple_alpha_plus_cago/actual_network.f90
networks/xrb_simple/actual_network.f90
commit 465eb34bdc2e57bf3d4f3f9c7db7dd61dccd0892
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 15:17:34 2016 -0400
a little more doc
Docs/data_structures/data_structures.tex
Docs/networks/networks.tex
commit 15e1eaedce4ac5543f048bd59aceea60eed2ff7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 29 09:05:47 2016 -0400
accidently checked in bad code
unit_test/test_react/main.f90
commit 4857d6bfe7f24c70a641aedecea23f2882134492
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 28 22:44:59 2016 -0400
more changes since last time
CHANGES
unit_test/test_react/main.f90
commit e335f57d91bc70f6281684714cf9191472b7381f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 28 09:58:43 2016 -0400
Tell F make about the new module
integration/BS/GPackage.mak
commit 56a32cc7fa0fa4eaa98dc740e253e781850ef1e8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 28 03:51:26 2016 -0400
Expand the guards against invalid SDC data
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_type_sdc.F90
commit 1f1f31ea72842c206c5adc595025c5ea8e52f854
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 27 18:55:13 2016 -0400
Fix the EOS call in SDC
integration/BS/bs_type_sdc.F90
commit 18162c820ca9928658c52a972da340f00e08fba6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 27 17:35:13 2016 -0400
Add a file missed in a previous commit
integration/numerical_jacobian_sdc.f90
commit d33cc8b1a7ec320cc9a051f8ebcca7cddb58915d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 27 17:12:25 2016 -0400
Move the BS Jacobian to its own module
This avoids circular dependencies in the numerical Jac
integration/BS/Make.package
integration/BS/bs_jac.F90
integration/BS/bs_jac_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/stiff_ode.F90
commit c640ed042177c94a4a0d082b107d2aeafd152481
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 27 15:38:59 2016 -0400
Add a numerical Jacobian for SDC
integration/BS/bs_rhs_sdc.F90
integration/Make.package
commit 1466f77ab9b9ef39352b2f711a8981a4ffe58c30
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 27 04:25:19 2016 -0400
Copy the Jacobian to the bs_t
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_type_sdc.F90
commit 60f4cb9a9e428c6bb989424f2d0fd85c3f380a37
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 27 00:32:19 2016 -0400
Add SDC version of the BS integrator
integration/BS/Make.package
integration/BS/actual_integrator_sdc.F90
integration/BS/bs_rhs.F90
integration/BS/bs_rhs_sdc.F90
integration/BS/bs_type.F90
integration/BS/bs_type_sdc.F90
integration/BS/stiff_ode.F90
integration/Make.package
integration/integrator_sdc.f90
networks/aprox13/Make.package
networks/aprox19/Make.package
networks/aprox21/Make.package
networks/breakout/Make.package
networks/general_null/Make.package
networks/ignition_chamulak/Make.package
networks/ignition_simple/Make.package
networks/iso7/Make.package
networks/kpp/Make.package
networks/powerlaw/Make.package
networks/rprox/Make.package
networks/triple_alpha_plus_cago/Make.package
networks/xrb_simple/Make.package
commit 385f9fcbd4f12205b028642847dbf19d1e215816
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jul 26 03:36:25 2016 -0400
Move scaling vector computation to bs_rhs
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/bs_rhs.F90
integration/BS/bs_type.F90
integration/BS/stiff_ode.F90
commit 11c289f1e0817064e6d2d712e5abe5b9734c2fd2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 15:13:33 2016 -0400
fix URL
README.md
commit b204536c89729f43493a24ce5bbc1c69fef79a41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 15:12:34 2016 -0400
add link to user's guide PDF
README.md
commit 453fcaf93ba2629ad1842d2d54069f63dd2bea55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 25 14:56:37 2016 -0400
add openacc
networks/triple_alpha_plus_cago/actual_network.f90
commit 66a9c2b857337a50cff9bde2c022353b485ed570
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 24 21:57:16 2016 -0400
bs_t doesn't need i,j,k
integration/BS/bs_type.f90
commit 073e11d8cd8dfbdace2122a0b6f8314649c36a07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 24 20:54:11 2016 -0400
more doc on BS stuff
Docs/data_structures/data_structures.tex
Docs/networks/networks.tex
commit 9f073a6c0d475b9c1104da110e29f140bc9e10ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 24 20:54:03 2016 -0400
add intent
integration/BS/bs_type.f90
commit 727531b8047e28b0f467c7a700c43e806f01a340
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 24 19:26:43 2016 -0400
fix compilation
networks/rprox/actual_rhs.f90
commit 0cd806d00f33106f8a8595e790967f1e6f57caaf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 24 15:48:22 2016 -0400
2 fixes for C++ compilation
first, only define rate_type.f90 if we are reacting, and then
give the VPATH to it
second, we need to put the actual integrator first in the VPATH,
before integration/. This allows any integrator-specific overrides
to come into play.
networks/Make.package
commit 144592d9a4eff99d1745e8949c1bc8357ec4ceb6
Merge: e1b7e09c 171b6160
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 20:36:16 2016 -0400
Merge branch 'development' into BS-refactor
commit 171b6160b764443aac92d6655bda14e7065ec070
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 14:07:34 2016 -0400
more stuff to doc
Docs/networks/networks.tex
commit d41ee15fd5cf52d7f730c230375d63702a1c2f12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 14:02:34 2016 -0400
remove note about state % rates
Docs/networks/networks.tex
commit 0e869e8191bdbbf4b84ff76d8d9e64a5c90c8bf4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 14:01:37 2016 -0400
more docs on the data structures
Docs/data_structures/data_structures.tex
commit e1b7e09c123ae6585b2fdbcc6381e5de58f2750a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 12:07:44 2016 -0400
undo unintended option changes
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_aprox13
commit 86c4193d4c29b7e3d0cca5f26317b416a6f21988
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 11:36:46 2016 -0400
had y_init allocated with too few entries
integration/BS/rpar.f90
commit 8308e94c4906f4e05946d1ea0882d4d046212099
Merge: dc2564e5 fcb12f3b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 10:45:19 2016 -0400
Merge branch 'development' into BS-refactor
commit dc2564e5dfa7851301cb39e8f8540a9a05805c18
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 23 10:40:48 2016 -0400
add a T_eval field to rate_t
in the future, we can use this to do safe temperature factor
caching
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_simple/actual_rhs.f90
networks/ignition_simple/test/GNUmakefile
networks/iso7/actual_rhs.f90
networks/rate_type.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/xrb_simple/actual_rhs.f90
commit fcb12f3b3a4c8597355b120bb4ae05c1fb3c9cbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 21:51:11 2016 -0400
go back to using t = 0 as the start of integration but store
the simulation time in the rpar (irp_t0) -- this is the offset
to convert from integration time to simulation time
integration/BS/actual_integrator.F90
integration/BS/rpar.f90
integration/VBDF/actual_integrator.F90
integration/VODE/actual_integrator.f90
integration/rpar.f90
commit 813056b206b98c6126c9c06d1196b2bd64266165
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 15:19:41 2016 -0400
fix indexing
networks/triple_alpha_plus_cago/actual_rhs.f90
commit d60a165345587d7f2b07b7432cd8510f51438275
Merge: 983c18c6 54eaa279
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 14:41:40 2016 -0400
Merge branch 'development' into BS-refactor
commit 983c18c66f4ca87d5264441096ccb41c2f30b332
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 14:05:48 2016 -0400
fix compilation issues
integration/BS/rpar.f90
networks/aprox21/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
commit c6101f6ce4b767e1c8eed6a0e85e8cb2c87b22a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 13:52:32 2016 -0400
... actually, hold off on the FPE stuff
unit_test/microphysics.f90
commit 248b64aeaf295e8252f1f2a08fabaa20cf07045b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 13:52:04 2016 -0400
initialize BoxLib and enable FPE stuff
unit_test/microphysics.f90
unit_test/test_react/GNUmakefile
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_aprox13
commit ab85f459c817863a2129cf2bd894e2861c4cf61b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 12:55:27 2016 -0400
new file -- the rate_t
networks/rate_type.f90
commit 850574f8426df79a8d937d7f3253d013825a4564
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 22 12:47:40 2016 -0400
more work on eliminating rates from the burn_t
this change also has every network's Jac reevaluate the rates rather
than rely on cached rates. We can reintroduce caching later if desired
through an optional argument to actual_jac
integration/BS/bs_type.f90
integration/VODE/vode_type.f90
integration/rpar.f90
networks/GPackage.mak
networks/Make.package
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_simple/actual_rhs.f90
networks/iso7/actual_rhs.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/xrb_simple/actual_rhs.f90
commit 54eaa279d469f3675243e05efebe3de9c696bb8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 22:30:17 2016 -0400
this version of rprox works
unit_test/test_react/inputs_rprox
commit 6d54b34393485e4316f8dd62dfbad15b23a71727
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 22:22:13 2016 -0400
this works
unit_test/test_react/inputs_aprox21
commit 4b55ccc405d8266d14ce170e840bcb6498ba5cc3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 22:11:14 2016 -0400
start removing the rate storage
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/BS/rpar.f90
integration/BS/stiff_ode.F90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
integration/rpar.f90
interfaces/burn_type.F90
commit d7b7128e525ca9a01634b4cb831fcff5294576ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 21:36:01 2016 -0400
reset T_old and dcvdT/dcpdT for resets
closes issues #4
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.F90
commit a850dd6b656f04072e9ca918a4a5ba17d78bd6e3
Merge: 8ac34c42 2b3ad6b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 20:17:02 2016 -0400
Merge branch 'BS-refactor' into development
commit 2b3ad6b86d4cf8a3422bba60810f55b3209ea917
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 20:06:48 2016 -0400
add a unnecessary conversion from X to Y to get tests passing
-- this is just a roundoff issue
integration/BS/bs_type.f90
commit ea4d39c64d38981363257f3f51b76e0647c33d9c
Merge: 03c56ed6 7e67876d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 18:08:11 2016 -0400
Merge branch 'BS-refactor' of ssh://github.com/BoxLib-Codes/Microphysics into BS-refactor
commit 8ac34c428a26eb1339228a9490bd829432a19c9c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 14:21:30 2016 -0400
clean up and output runtime params
networks/triple_alpha_plus_cago/test/testburn.f90
commit 7e67876d022ecfaea81aa9755ce9de80797b5528
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 13:23:59 2016 -0400
more challenging state + dump out runtime parameters
networks/aprox13/test/testburn.f90
commit 5cd58845b3e0d95f6efb7878bd54e5328b0d3d4d
Merge: 3e5e78ea c3c108da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 21 10:12:40 2016 -0400
Merge branch 'development' into BS-refactor
commit 03c56ed6ff33dbe8c9b30c9aca31f9a1eefa7b92
Merge: 3e5e78ea c3c108da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 22:15:03 2016 -0400
Merge branch 'development' into BS-refactor
commit c3c108da658359f6fa6096da5def2ee606a8dc42
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 22:14:36 2016 -0400
better printing
networks/aprox13/test/GNUmakefile
networks/aprox13/test/testburn.f90
commit 3e5e78ea9564d6e8a3d95cf43a1d316cac246de1
Merge: cad386f6 a6eb47c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 21:33:46 2016 -0400
Merge branch 'development' into BS-refactor
commit a6eb47c7f6026604f17d8f424fde18c4aa7a136e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 21:31:22 2016 -0400
fix compilation
integration/VBDF/bdf_type.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_type.f90
commit cad386f643334f1e8ca1ae7d5945b69a45f59d86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 21:24:07 2016 -0400
remove the species derivatives
integration/VBDF/bdf_type.f90
integration/VODE/vode_type.f90
integration/rpar.f90
commit 41ab5f716677d35da5fc6536f642b0cf7c1109f3
Merge: 53543021 d94f904b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 21:15:44 2016 -0400
Merge branch 'development' into BS-refactor
commit d94f904b137b9c5458eca0ca373748fc2cde804d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 21:15:03 2016 -0400
use n_not_evolved + fix output for VODE error
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf_type.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_type.f90
commit 53543021e684d41a8341d22a4601f991b335b771
Merge: 1847290d 819102b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 20:54:11 2016 -0400
Merge branch 'development' into BS-refactor
commit 1847290d70eb80f975d58830d122b2c832843d9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 20:53:11 2016 -0400
use debug mode
networks/aprox13/test/GNUmakefile
commit 819102b9dcd2d49b1f04f5147514744c36b4f7c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 20:47:14 2016 -0400
this version runs in debug mode w/o error
networks/aprox13/test/testburn.f90
commit 61ac4fb953e8983c7a9e8a05e852afe043b7ea71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 20:35:49 2016 -0400
remove loop
networks/aprox13/test/testburn.f90
commit 65160d6965abb88d77204007b08c9357e3c93b70
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 19:18:36 2016 -0400
fix the initialization of T in eos_to_bs
this now gives exactly the same result on ignition simple as the old BS
integration/BS/bs_type.f90
commit 01417bbfa5ad8beea83f0767c77d244f4eaef03b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 17:14:06 2016 -0400
explicitly use bl_error_module -- PGI complains if we inherit it
unit_test/network.f90
commit e2e2d2d0a313deeb32a549f73e232f94e8d0ee12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 17:08:01 2016 -0400
remove unused variables
integration/BS/actual_integrator.F90
integration/BS/bs_type.f90
commit 0307ba2cb504e7e73c82d485a2b4684b79f7bd7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 16:43:39 2016 -0400
fix rpar use
integration/BS/actual_integrator.F90
integration/BS/bs_type.f90
commit 6f71371adf1e492360e69c9ba33fdc5966ad1b61
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 16:38:50 2016 -0400
switch ordering of integrator/ and integrator/INTEGRATOR_DIR/
so VPATH overrides work
networks/GNetwork.mak
networks/ignition_chamulak/test/testburn.f90
commit 9cbb40ea6aee57fbb35814b6b354229d33d3697b
Merge: 5ead0f38 f13c6cfb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 14:23:02 2016 -0400
Merge branch 'development' into BS-refactor
commit 5ead0f38fce5847864e52037454c974b522208e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 14:17:32 2016 -0400
this seems to work
integration/BS/actual_integrator.F90
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/BS/stiff_ode.F90
commit cc4dbf6c1254fdd3959d1e972920f2532ffc1d9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 12:20:35 2016 -0400
compiles but crashes
integration/BS/actual_integrator.F90
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/BS/stiff_ode.F90
integration/BS/test/GNUmakefile
commit f13c6cfb849c0533e735a9bf23ad22a8689521d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 20 09:38:16 2016 -0400
a little more on the usage
Docs/basics/basics.tex
commit 61b72f91afe4b6a19bb459394a4b30de6eb88364
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 22:16:18 2016 -0400
burn_s
integration/BS/bs_type.f90
commit 60d1ce9ac171c0182fa48539e93cd2a2e11f90f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 22:15:33 2016 -0400
remove the species derivatives
interfaces/burn_type.F90
commit eee414b88af4d17b99c2b6878f6935014f4103a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 22:14:26 2016 -0400
more progress on integrating burn_t into bs_t
integration/BS/bs_type.f90
integration/BS/rpar.f90
commit 92ffc70b7a67c6f43e9503317a535ec4d682e26d
Merge: 7a3ada4c 4ef1a3fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 19:08:07 2016 -0400
Merge branch 'development' into BS-refactor
commit 4ef1a3fa44de909f6a3779e908c9e7dc77bf9ed0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 19:07:19 2016 -0400
define n_not_evolved to make things cleaner
integration/BS/actual_integrator.F90
integration/BS/bs_type.f90
integration/rpar.f90
commit 7a3ada4c2e8fb47e1ba306fc27055a9d7bb483ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 18:57:29 2016 -0400
start working on the refactor
integration/BS/bs_type.f90
integration/BS/rpar.f90
commit cd8ee6bf2afa301d37d22c6e26a67e4cc8e76ef0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 16:16:20 2016 -0400
use normalize_abundances_burn
integration/VBDF/actual_integrator.F90
integration/VODE/actual_integrator.f90
commit 28519432db2f31e1509ac278a925da87173c68b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 16:14:06 2016 -0400
document how we call the RHS
Docs/networks/networks.tex
commit 4fa302b86678efc124f55e46594921e2a7ff87ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 15:57:49 2016 -0400
define a normalize_abundances_burn() that operates on burn_t
integration/BS/actual_integrator.F90
interfaces/burn_type.F90
commit 3ddf16e5c9f58a486fb092c51ff0ec169e665e05
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 15:34:07 2016 -0400
add a flow chart
Docs/networks/networks.tex
commit a923f6683904d7b2ae6a0fb86b5e1485408d1e51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 15:08:58 2016 -0400
document BS
Docs/networks/networks.tex
Docs/refs.bib
commit 840e31dd9891aca619c8ba5ad6c17e7512020746
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 14:52:46 2016 -0400
enable the timestep estimator
unit_test/test_react/inputs_3alpha.BS
commit e6d17862413d5f44b40a959528eea90f1fa687b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 11:21:42 2016 -0400
finish up to the ODE solvers
Docs/networks/networks.tex
commit ebfd2b38781834de7008eb904f221181a445ccf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 19 10:18:39 2016 -0400
add burning_mode_factor
Docs/networks/networks.tex
commit e2d105f309116612bdbece3eb5ac9f2ca2b7c6e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 22:36:36 2016 -0400
sync clean_state up with BS
integration/VBDF/bdf_type.f90
commit 4e45fb30f0f501beb757edca2626abff8df7b3be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 22:28:31 2016 -0400
update VBDF to integrate_molar_fraction
integration/BS/bs_type.f90
integration/VBDF/bdf_type.f90
commit c2f2631b8779bc37289e85e69c1e038e14962281
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 22:08:16 2016 -0400
typo
Docs/networks/networks.tex
commit 9fef44e0e2a0334409a4599406bfaf55607d72c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 22:05:11 2016 -0400
add section
Docs/networks/networks.tex
commit c8b82a93e8cbb2ce18ee0360aec7bf638d0aa2bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 22:04:29 2016 -0400
fix VODE integrate_molar_fraction
integration/BS/bs_type.f90
integration/VODE/vode_type.f90
commit d17662406758f9eff538a42894e8170cdf73efd7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 20:57:46 2016 -0400
use update_unevolved_species
networks/ignition_simple/actual_rhs.f90
commit 76d6a9343dc175f1fe6e81a2ccf18f314f3dcec8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 20:09:06 2016 -0400
fix the integrate_molar_fraction = F stuff
integration/BS/bs_type.f90
commit 3295b0716d8a995fa2026f58d5641a7ed47a445e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 19:08:57 2016 -0400
more docing
Docs/networks/networks.tex
commit 7f9df291b07a75993e2c441d5ef90c544767092f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 18:10:30 2016 -0400
document update_unevolved_species
Docs/networks/networks.tex
commit b07fab135588fb1a6f069009e06a6841d140fdf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 16:56:20 2016 -0400
more clarity on the internal energy
Docs/networks/networks.tex
commit 6655d411c062c34f7e3bafbd0f97a8d1fab18a53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 16:52:43 2016 -0400
clarify the 2 meanings of e in burn_t
Docs/data_structures/data_structures.tex
Docs/networks/networks.tex
commit 09b5c91798ac3cca64850a7eae999ea7f35e50f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 16:09:31 2016 -0400
typo
Docs/networks/networks.tex
commit 7e4d8512679088b06c651dd6613324e5de40f638
Merge: 92f1023b 69156246
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 16:08:32 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 92f1023bd594f521324a7266fda2fdbca68086c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 16:07:02 2016 -0400
some energy stuff
Docs/networks/networks.tex
commit 69156246a86a14c7d51729f7ab6d377ec5eaf14b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jul 18 16:03:21 2016 -0400
Clarify burning_mode 3
Docs/networks/networks.tex
Docs/runtime_parameters/runtime_parameters.tex
integration/_parameters
commit 2ceac0e7ccdf8fbcec04c1edda33ceed4d2df98b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 15:54:56 2016 -0400
clarify burn_state % e
Docs/data_structures/data_structures.tex
Docs/networks/networks.tex
commit 3d3260d5d1832b5e43350ae1788a0fc53abbe085
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 15:52:55 2016 -0400
fix comment
integration/_parameters
commit 5e3eb6b30bc5a883978109eb1e56ab72774d72ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 15:43:43 2016 -0400
no need for enthalpy in the burn state -- we can get what we need from
the internal energy`
interfaces/burn_type.F90
commit e4ee335eca5f178611968a21489a95fd04522d14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 14:40:50 2016 -0400
finish T evolution section
Docs/networks/networks.tex
commit 8eaafda0c768073aa5b9fad2c805931d832644ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 14:32:58 2016 -0400
add a comment
integration/BS/bs_type.f90
commit 91ee40b2183646ca205b2ea1d6e8f57c979175b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 14:21:59 2016 -0400
a bit about use_eos_in_rhs
Docs/networks/networks.tex
commit c8a8cd47214f87920a36b5824cd5537665992e5d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 13:24:34 2016 -0400
some T evolution
Docs/networks/networks.tex
commit 7c6b3b42d3d6d9ac513738dd442a05555724000f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 12:06:12 2016 -0400
add a section explaining rhs and jac
Docs/networks/networks.tex
commit 4d988d3e6bd72326982891c629594f261c186e59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 11:59:47 2016 -0400
loop in numerical Jac should be over nspec_evolve, not nspec
integration/numerical_jacobian.f90
commit 775e819029fca2747f7f19e2505b97cd0f51cb7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 10:48:17 2016 -0400
add comment
networks/triple_alpha_plus_cago/actual_rhs.f90
commit 212be1ec7462a2e2d58a103b29f5ddb1d979618c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 10:01:26 2016 -0400
tweak
Docs/networks/networks.tex
commit c3d728c3296ca7848cb139b5e5cf5b54554a080a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 18 09:55:09 2016 -0400
add a description of xrb_simple from notes with Stan & Chris
Docs/networks/networks.tex
commit b1027a7540667bacb074f753a9eed6dd0d1bf24e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jul 17 18:42:24 2016 -0400
Default aprox19/aprox21 to numerical Jacobian
networks/aprox19/_parameters
networks/aprox21/_parameters
commit 729377e388ac20612c58c4477f7d13680d8e5560
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jul 17 15:10:24 2016 -0400
more cleaning
networks/rprox/test/GNUmakefile
networks/rprox/test/testburn.f90
commit 7047c4d712629d2c521a299c07d27c96d8884bf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 20:59:02 2016 -0400
we are using the programs macro, so we don't need to copy the
executable rule
GMicrophysics.mak
commit 2ddc952d922d1e1f73b387f0dff5cd0984974df9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 18:22:32 2016 -0400
remove some redundant code
Docs/runtime_parameters/rp.py
commit 3138698bc811a2fce4d86138a36ebc085a2ac992
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 18:16:23 2016 -0400
some cleaning
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit 6c1869d039bf8d78fb002e8ce1aa9a970dc55d10
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 16 17:11:43 2016 -0400
fix the way we find descriptions -- reset after each blank line
this works with or without a first header
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
commit e4b9e38d62b2e16cdbb39ceff3f34d89028d7b1b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 16 02:59:06 2016 -0400
Disable printing of T+H=T message unless verbose
integration/VODE/actual_integrator.f90
integration/VODE/vode_source/dvode.f
commit 0848ed152f61730fc0edaec65bb18f84e2b3d362
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 16 02:58:50 2016 -0400
Pull in local VODE source for C++ build
integration/VODE/Make.package
integration/VODE/vode_source/Make.package
commit 86a3466152bcef910078dd9e698c26ec7839b061
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 16:18:48 2016 -0400
no need to initialize the jacobian from the bs type
integration/BS/bs_type.f90
commit 786f50c8fc42a2809dcf7b9bccba011c99db193c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 14:02:30 2016 -0400
this works -- very small tmax
+ remove some BS-specific stuff
unit_test/test_react/inputs_aprox19
commit 1008661dad58f4dc8d9f46305f8c3880c3ab7ba8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 13:57:41 2016 -0400
new inputs
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_ignition_chamulak
unit_test/test_react/inputs_ignition_chamulak.BS
commit 982cc024a7a1ac1e213a9e504aa7d795edd92f17
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 13:54:57 2016 -0400
remove print
networks/ignition_chamulak/actual_rhs.f90
commit c5be7b415482e50d623d5c7c6f96f6bdc4d308e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 12:50:01 2016 -0400
fix compilation
networks/xrb_simple/actual_rhs.f90
commit a157843e511010924264c9137580dac516774222
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 15 12:39:46 2016 -0400
rebreak OpenACC -- these need to be set to get good results
interfaces/eos_type.f90
commit 3e82dd7eebe1dae16876af5a1c62148b2abb554d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 22:13:40 2016 -0400
a little more docs
Docs/networks/networks.tex
commit 5f04b360bab126546449ef628fc5fa9c0ab7d713
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 21:36:07 2016 -0400
pass time through to the burn_t into the RHS
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf_type.f90
commit a260ed8b9f45440fd3013ac1aae46a2f391e22a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 19:47:11 2016 -0400
pass the time into the rhs and jac through burn_state
integration/VODE/actual_integrator.f90
integration/VODE/vode_rhs.f90
commit 290a8e83a66e053f4a3e6e416752de2aa3ca15a7
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date: Thu Jul 14 18:21:40 2016 -0400
turn implied loop into explicit to keep GPU happy
unit_test/test_react/main.f90
commit dcd01deb3c83c419c153b95145f73ea009f3b307
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 15:10:31 2016 -0400
this does a final call to update_unevolved_species() after
the integration but before the normalization. This ensures
that the composition is correct with nspec_evolve < nspec.
Testing ignition_chamulak against Maestro shows great agreement
now.
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.F90
integration/VODE/actual_integrator.f90
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_rhs.f90
commit 186c43af55cdf28481bc774d713ebeefa6a4b1e4
Merge: 06f80a8a ec270323
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 14:36:04 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 06f80a8af041cb167de5df2457e2489c7a3ed42a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 14:35:46 2016 -0400
add stub update_unevolved_species()
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/breakout/actual_rhs.f90
networks/general_null/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_simple/actual_rhs.f90
networks/iso7/actual_rhs.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/xrb_simple/actual_rhs.f90
commit ec27032313093f9156b4d93c5d986caebdd7f7ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 14:04:38 2016 -0400
add the @@acc@@ clause to get the device update
unit_test/dummy.probin.template
commit ba8bfaed62d3bb3bdfa98e31ef65f0d9b614720b
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 14 13:37:54 2016 -0400
Make the acc collapse cromulent
unit_test/test_react/main.f90
commit 9614f7931b0e7d4169a081b095ef38d54ab5e8e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 13:10:12 2016 -0400
more doc
Docs/networks/networks.tex
Docs/unit_tests/unit_tests.tex
commit abbc993abc8267f914237878e22d8824b3317156
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 14 13:06:39 2016 -0400
Do some markup for OpenACC
GMicrophysics.mak
interfaces/burn_type.F90
interfaces/eos_type.f90
unit_test/GPackage.mak
unit_test/eos.F90
commit 43dfce47b62c95e9e5842c7e826a964db4ad97ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 14 11:35:52 2016 -0400
more net docs
Docs/maestrosymbols.tex
Docs/networks/networks.tex
Docs/refs.bib
commit 059b7c33107bcc60e662760ec30d0b79c9d2bf7b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 14 02:47:24 2016 -0400
Fix bug: min, not max, in mazurek
There was a bug in the mazurek subroutine for the electron capture
rates on nickel 56. This had the effect of resetting any temperature
below the maximum for that routine (T9 = 14) to the maximum. The fix
replaces a max with a min so that any temperature in the allowed range
of (2 < T9 < 14) is correctly fit, and any temperature above T9 = 14
is reset to T9 = 14. This has been corrected in the main releases of
the aprox* networks as well as MESA.
rates/aprox_rates.f90
commit 7de9752f64d8bd489569f3a297d901a9b7a4b7ce
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 14 02:42:57 2016 -0400
Avoid some unused variable issues in BS
integration/BS/actual_integrator.F90
integration/BS/stiff_ode.F90
commit 3806615bbe32aa5d34f9854fb2cfd7a0b870462b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 14 02:26:58 2016 -0400
Remove some unused density derivatives
networks/aprox21/actual_rhs.f90
commit 00244a88ad9fa60e5864ca5efc73242440452630
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 14 00:42:59 2016 -0400
Remove some unused density derivatives
networks/aprox19/actual_rhs.f90
commit d2b8fb26b8480bff7b04659cdf0a1e7a7622dee0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 23:07:42 2016 -0400
add spec names to print
networks/rprox/test/eval.f90
commit 8d021e444fa5748451adbc25a1b2c1663c463713
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 22:55:06 2016 -0400
update for this net
networks/triple_alpha_plus_cago/test/eval.f90
commit dd53e7bd1134c76ecf8ef45844a469e3716555b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 22:46:32 2016 -0400
update for this net
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
commit d947305ff7331c59311fc1ee5b382a15a5bf634e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 21:29:11 2016 -0400
a little more notes on networks
Docs/networks/networks.tex
commit 71cab162cd53bda9c308899364fbb96cef514817
Merge: 67a98d68 576c4de0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 19:20:40 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 67a98d68f9865a2924a70a6557cb7210809264c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 19:20:02 2016 -0400
this atleast works
unit_test/test_react/inputs_aprox19
commit 576c4de06d8ac51b68f625a8cba2acb6cc99b70b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 15:40:00 2016 -0400
more sections
Docs/networks/networks.tex
commit 3f3a83effbcf5afbcf23b4aaad1212fcaeb41328
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 15:34:23 2016 -0400
update
Docs/runtime_parameters/runtime_parameters.tex
commit 033ed240cfd77a062d0a2032843794dbc7a730d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 15:33:29 2016 -0400
due to a quirk in the doc script, the first lines (till empty)
are considered comments on the parameter file itself
integration/_parameters
commit d96def36b37f85cd5dafcf3c54c5ea4d2d0caaed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 15:27:30 2016 -0400
actually set the xn(:) according to how we evolve
networks/ignition_chamulak/actual_rhs.f90
commit a0ebdf8953c8443627280cbde6119de53029c2f4
Merge: 252ed551 f242fe46
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 15:11:07 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 252ed551ef6038122640b9dee06f79dc91514439
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 15:09:00 2016 -0400
get this working + using nspec_evolve
previously, it was not considering the ash update at all. Now
we switch to nspec_evolve = 1, and algebraically compute the
update to the ash from the mass fractions.
The energy output from this now agrees very well with Maestro,
but the ash mass fraction is off by 2x -- not sure what's up
yet.
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_chamulak/burner_aux.f90
networks/ignition_chamulak/f_rhs.f90
networks/ignition_chamulak/test/GNUmakefile
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
commit f242fe4607f06bd26f4f13f0315e5347187bf458
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 13 14:58:47 2016 -0400
Fix bug: actually get data from the state
networks/aprox19/actual_rhs.f90
commit ab2ce3e5410b88f5c364fb550994ba81a4eba95d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 14:25:41 2016 -0400
more network documentation
Docs/GNUmakefile
Docs/maestrosymbols.tex
Docs/networks/networks.tex
commit 660627148f42b626e374d09b55c459eb569b92f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 14:09:15 2016 -0400
add a section on what is expected in a network
Docs/maestrosymbols.tex
Docs/networks/networks.tex
commit 15590810de630836f6dfe65f63288cbdefe4603f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 12:42:59 2016 -0400
a bit more organizatoin
Docs/MicrophysicsUsersGuide.tex
Docs/burners/burners.tex
Docs/networks/networks.tex
Docs/refs.bib
commit 323b3d76edd575f0daa97a82b42ed52428373995
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 11:30:56 2016 -0400
a little syncing with aprox13, but this still fails
unit_test/test_react/inputs_aprox21
commit 924fef1d752937089c3dfae33a1a84d5e43dbfd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 11:23:24 2016 -0400
update
Docs/runtime_parameters/runtime_parameters.tex
commit 024f92d822c942d45d3bf89b715e2e6a8b853dfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 13 11:22:43 2016 -0400
typos
Docs/data_structures/data_structures.tex
commit 58d9f1239830092c26b01475e2007cc67f8c631a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 13 10:33:49 2016 -0400
Fix a typo in aprox19 RHS
networks/aprox19/actual_rhs.f90
commit 5a284145bc6423b434fd90d5efb9a5295e636347
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 20:45:14 2016 -0400
some fixes
Docs/EOS/eos.tex
commit 3ec4e3e280df3fa78f6036ceb83f900021875ab5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 20:10:20 2016 -0400
more ztwd clarification
Docs/EOS/eos.tex
commit faa3ca08b85fd0f933941b8bc03bed7a9572ca96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 19:51:48 2016 -0400
fix some ztwd notation
Docs/EOS/eos.tex
commit 38535ccf30caea0caf18297c0d69c5c91e598bb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 19:46:44 2016 -0400
document the polytrope EOS
Docs/EOS/eos.tex
commit 1b1733e5055b431807a1661b61f44e7fc3483b1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 19:36:23 2016 -0400
add CGS note + document gamma_law_general
Docs/EOS/eos.tex
Docs/basics/basics.tex
commit f61e820cb4c0deb6358488bc9562c9795252c9cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 18:54:11 2016 -0400
separate preface, note external sources
Docs/GNUmakefile
Docs/MicrophysicsUsersGuide.tex
Docs/preface/preface.tex
commit 01fb16d97ed4cd4977208d44103ef647764cd7fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 18:50:45 2016 -0400
add note about User's Guide
README.md
commit b6ae67ffc532971de295073feafa4d8396cc85cd
Merge: 27599f15 b3e1cbac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 18:48:08 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 27599f151d6e38c1271601e19d9aa8be424a4583
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 18:47:43 2016 -0400
userguide.tex -> MicrophysicsUsersGuide.tex to be consistent with
the other codes
Docs/GNUmakefile
Docs/MicrophysicsUsersGuide.tex
commit b3e1cbac045b7319ebf9c765cb59235be9bfed51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 13:54:53 2016 -0400
more changes
CHANGES
commit 01b5f99bb63d1190f429440b42c145bece2e6e32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 13:52:45 2016 -0400
document the unit tests
Docs/unit_tests/unit_tests.tex
commit 0d30015e6b7f965b1b53e3dd99c0ef5aadc30d89
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 12 13:44:55 2016 -0400
dt -> tmax for clarity
unit_test/test_react/_parameters
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_3alpha.BS
unit_test/test_react/inputs_aprox13
unit_test/test_react/inputs_aprox19
unit_test/test_react/inputs_aprox21
unit_test/test_react/inputs_ignition
unit_test/test_react/inputs_ignition.BS
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_xrb_simple
unit_test/test_react/main.f90
commit 4c23c4e932039ef663091208f144b9310bdace50
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:55:01 2016 -0400
accidentally checked in centered diff
unit_test/test_react/inputs_xrb_simple
commit d8e663e21c9745a76d65709f117bb92319200f81
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:53:55 2016 -0400
lower the density max
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_xrb_simple
commit 9250d65a41572e1576cfd588701a873e12416a49
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:42:09 2016 -0400
fix the exclusion rule for helm_table.dat
.gitignore
commit 7aa4f41599fe6f4179d2455e18bf09527ef5e4c2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:41:51 2016 -0400
accidentally deleted this on the move
EOS/helmholtz/helm_table.dat
commit fa187907477012e4429dd80b56fd1e32b2b424d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:37:36 2016 -0400
revert change 8dd50d2 -- use VODE's numerical Jac
integration/VODE/actual_integrator.f90
integration/VODE/vode_rhs.f90
commit 612bb33974657d174b3a95f9f9dd90185c289c68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:28:33 2016 -0400
unit test stub
Docs/GNUmakefile
Docs/unit_tests/unit_tests.tex
Docs/userguide.tex
commit 627838cea80443f828dfcb48bd5767733bdf7598
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 15:17:34 2016 -0400
add call graph
Docs/networks/doxygen_network.png
Docs/networks/networks.tex
Docs/userguide.tex
commit 19fc03c4969f4d69906fc230267569f3d13a1e8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 14:15:38 2016 -0400
better philosophizing
Docs/basics/basics.tex
commit 161d42b0650b8a8e884b729782dc39b85ccf8c45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 13:45:01 2016 -0400
more docs -- some runtime parameter intro
Docs/GNUmakefile
Docs/runtime_parameters/rp_intro.tex
Docs/userguide.tex
commit b445bbadabbc8880567365940754728bb0c1951f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 13:27:28 2016 -0400
more data structure info
Docs/GNUmakefile
Docs/basics/basics.tex
Docs/data_structures/data_structures.tex
Docs/userguide.tex
commit eadd02122a9963548f06ac62e39945d6ba1b0d58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 12:10:01 2016 -0400
C++ macro
Docs/maestrosymbols.tex
commit 84938fc7ec0bde0c835b608c9d4b7f331cb5963f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 11:24:00 2016 -0400
updating the intro
Docs/GNUmakefile
Docs/basics/basics.tex
Docs/maestrosymbols.tex
Docs/userguide.tex
commit 032a88fc13c4f96ea443c4b8de68f92eee7ea7b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 11:12:11 2016 -0400
eos -> EOS
CHANGES
commit b70f280c6f63abcacf53f7b020b486ae9a24866d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 11:11:21 2016 -0400
eos -> EOS
README.md
commit 9f904ee72512c27da106e05fa6642aa281482103
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 11:11:11 2016 -0400
eos -> EOS
GMicrophysics.mak
commit 2aca3f0849ec29369661f3324086e1afe6ae6a91
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 11:03:23 2016 -0400
rename
EOS/GPackage.mak
EOS/Make.package
EOS/README.md
EOS/breakout/GPackage.mak
EOS/breakout/Make.package
EOS/breakout/_parameters
EOS/breakout/eos_stuff.f90
EOS/gamma_law_general/GPackage.mak
EOS/gamma_law_general/Make.package
EOS/gamma_law_general/_parameters
EOS/gamma_law_general/gamma_law_general.F90
EOS/helmholtz/GPackage.mak
EOS/helmholtz/Make.package
EOS/helmholtz/README
EOS/helmholtz/_parameters
EOS/helmholtz/helmholtz.F90
EOS/multigamma/GPackage.mak
EOS/multigamma/Make.package
EOS/multigamma/_parameters
EOS/multigamma/multigamma.f90
EOS/polytrope/GPackage.mak
EOS/polytrope/Make.package
EOS/polytrope/_parameters
EOS/polytrope/polytrope.f90
EOS/stellarcollapse/GPackage.mak
EOS/stellarcollapse/Make.package
EOS/stellarcollapse/README
EOS/stellarcollapse/_parameters
EOS/stellarcollapse/eos_aux_data.f90
EOS/stellarcollapse/stellarcollapse.f90
EOS/ztwd/GPackage.mak
EOS/ztwd/Make.package
EOS/ztwd/_parameters
EOS/ztwd/ztwd.f90
eos/helmholtz/helm_table.dat
commit 2d7c3f8ab3a53b4a28b8bfaac6fd5300be5b0027
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 11 10:21:59 2016 -0400
doxygen config
util/doxygen/Doxyfile
commit 1b4c695d803b838cb7cda40a51eec2d9a5a3519b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 22:06:26 2016 -0400
add some notes
networks/rprox/test/README
commit 37889f65526a410758ee3a87dfb817dad5e073f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:56:58 2016 -0400
update compilation
networks/xrb_simple/test/GNUmakefile
commit c23cd9606443d177e904126323d245176759b1aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:55:28 2016 -0400
get this compiling again
networks/ignition_simple/test/GNUmakefile
commit 112fb5d56cdcb2a4a462082e8405b2da3d85db07
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:53:17 2016 -0400
get this compiling again
networks/aprox13/test/GNUmakefile
commit fd20c6b64e9407b2ffe5ab91d57a7818ad2b63ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:50:51 2016 -0400
update GNUmakefile
networks/triple_alpha_plus_cago/test/GNUmakefile
commit 2038e0555ed90e4f4903208372e9d3b2b402b627
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:21:13 2016 -0400
/10.0**9 -> * 1.e-9_dp_t
networks/rprox/actual_burner.f90
commit 474b0ff9ab87a8f3cac5fcfbdb235c05dc230792
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:19:39 2016 -0400
here's a state that breaks
networks/rprox/test/GNUmakefile
networks/rprox/test/testburn.f90
commit 1728421df572b30f64443515bb06bf1e51ff5f4d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 20:06:00 2016 -0400
fix the build due to make changes
networks/rprox/test/GNUmakefile
commit 2d53851a05f01979287fab24020ea82cc92215f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 15:50:13 2016 -0400
new parameter
Docs/runtime_parameters/runtime_parameters.tex
commit 62be21f4f56b79cd866eadba595aa44fd4d767b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 15:48:28 2016 -0400
fix building after yesterday's build system changes
unit_test/test_eos/GNUmakefile
commit 9bf6bc72907e856e4f7c486455d2364afcd13842
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 15:42:43 2016 -0400
more Make fixes after yesterday's build-system change
GMicrophysics.mak
unit_test/test_react/GNUmakefile
commit 904cce9616403bd46eef721a5956b514f10e34a5
Merge: eba5c84f 1e5d402d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 15:35:14 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit eba5c84ffcb4ff71cd01c708509af2795f35a8cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 15:33:33 2016 -0400
something changed in the build system yesterday that we now need
the include at the very end. strange...
unit_test/test_react/GNUmakefile
commit 2965128a7ecdaabcb0b0ae829ca8d75c440405fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 15:30:47 2016 -0400
add a use_timestep_estimator parameter
if true, we use the VODE algorithm's initial timestep
integration/BS/_parameters
integration/BS/stiff_ode.F90
commit 1e5d402d76b220da4a52026017e163da713768d8
Merge: 0af8e792 fe7712de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 12:02:57 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 0af8e792190f2cd45ef997ff3537efac2a528ecd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 8 12:02:49 2016 -0400
new parameters
Docs/runtime_parameters/runtime_parameters.tex
commit fe7712dedac30af3a7413c31000acaee747e8a54
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 8 02:18:54 2016 -0400
Tell our numerical Jacobian about mass fraction integration
integration/numerical_jacobian.f90
commit ebfb2659be9c4fdfabaaf1cbc5f89f111f4561d3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 8 02:15:19 2016 -0400
Avoid some redundant operations for the numerical Jacobian
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
commit 8dd50d2a83da029c8428bd36ef170514f5b645b7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 8 02:07:36 2016 -0400
Use our version of the numerical Jacobian in VODE
integration/VODE/actual_integrator.f90
integration/VODE/vode_rhs.f90
commit c637cb84641e9c243bfb71d61c212bf0d244dac8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 8 02:01:52 2016 -0400
Add an option for integrating X instead of Y
Docs/runtime_parameters/runtime_parameters.tex
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
integration/_parameters
commit fd4a8ed5495fb3d040501f4cc99e94a6921ce736
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 8 01:28:49 2016 -0400
Allow disabling of temperature/energy integration
Docs/runtime_parameters/runtime_parameters.tex
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
integration/_parameters
commit 5332bdd42e4281430564cd646788bb466ee198d3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 7 22:42:40 2016 -0400
Fix the sound crossing time for burning_mode 3
Same logic as the last commit: this gives the most restrictive limiter.
integration/BS/actual_integrator.F90
integration/BS/bs_rhs.f90
integration/VBDF/actual_integrator.F90
integration/VBDF/vbdf_rhs.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_rhs.f90
integration/rpar.f90
commit a580dacd4a1b8277a5dc8de5ee875b5815df63f2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 7 22:25:08 2016 -0400
Fix the energy to be the initial zone energy for burning_mode 3
The logic here is that this gives the most restrictive condition on the
rate and ensures that we are matching the desired physical condition, that
over the course of the burn we don't increase the original energy too much.
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
commit 9ca0084612c836c55e46d2ef836518fb5e8d5716
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 7 22:24:48 2016 -0400
Save the initial integration vector in the rpar/upar
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.F90
integration/VODE/actual_integrator.f90
integration/rpar.f90
commit babba5cd42fb2a032560fa44014b141192dcd3e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 7 10:11:06 2016 -0400
/10.0**9 to * 1.e-9_dp_t
networks/rprox/actual_rhs.f90
commit 17a181628a0fb453c6cf903b6c81539354baaabc
Merge: 0603d4c1 c95e7a54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 7 09:59:12 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 0603d4c1725781e1957d4f9cd2a6e055ea4a8a6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 7 09:58:41 2016 -0400
simple driver just to output dydt
networks/rprox/test/eval.f90
commit c95e7a54790a9aa752cf31305d149a33705768fd
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu Jul 7 01:22:09 2016 -0400
Make max_steps and odescal into runtime parameters
integration/BS/_parameters
integration/BS/stiff_ode.F90
commit d28e5342b213afeb56a79de4fb6aa8a24b7362f9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 6 20:42:56 2016 -0400
rprox seems to need a numerical Jacobian
unit_test/test_react/inputs_rprox
commit 7393c85c48ed713e586585b547f6e55742b61d26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 6 20:09:49 2016 -0400
better settings, dt -- this convergese
unit_test/test_react/inputs_xrb_simple
commit 1d21eb73d4d70c91f65f18e9d03e801e3df45bc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 6 19:09:34 2016 -0400
fix attempt at OpenACC
unit_test/test_react/main.f90
commit 6f7759174f24b974b61cac56037e6f45ceb6acf0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 6 16:32:24 2016 -0400
Add OpenACC routine declarations
integration/BS/bs_type.f90
integration/VBDF/bdf_type.f90
commit 5039a863638be87c514646af28954eca68484296
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jul 5 14:33:51 2016 -0400
double precision -> real(dp_t)
integration/BS/actual_integrator.F90
commit 58e5b8e5b3e24796802bd069dd477cbef0731eea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 5 12:54:56 2016 -0400
update version number
CHANGES
commit 05b97420a8f39b6caf2b3f80d39eaa01b053b851
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 4 12:56:31 2016 -0400
new inputs file for test suite
unit_test/test_react/inputs_3alpha.BS
commit a0beff2cdaab4b141e06fbeb6f24c704abf457a4
Merge: f36b6973 26799e1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 4 10:22:08 2016 -0400
Merge branch 'development-next' of ssh://github.com/BoxLib-Codes/Microphysics into development-next
commit f36b69737ea05b2a49f2ec9a7eb304d0f15b7316
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jul 4 10:21:51 2016 -0400
for the test suite -- exercise scaling_method = 1
unit_test/test_react/inputs_ignition.BS
commit 26799e1d5641698e0466bd69257e3f42da873e7f
Merge: a53273a4 0199fec8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 2 20:05:54 2016 -0400
Merge branch 'development-next' of ssh://github.com/BoxLib-Codes/Microphysics into development-next
commit a53273a449bd71d9bbee463781ae8d3e135ba602
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 2 20:05:22 2016 -0400
eos_state needs FIRSTPRIVATE since the components in it
have save attributes
unit_test/test_eos/main.f90
commit b4aeb06fa7c18a20dbfac3b5fc35910b9bd28643
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 2 19:56:13 2016 -0400
FIRSTPRIVATE burn_state_in
unit_test/test_react/main.f90
commit 0199fec8212e7df420cacb7c8dcfcc72e41baffb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 2 19:23:01 2016 -0400
Explicitly initialize state % check_inputs
unit_test/test_eos/main.f90
commit 364b4d594b8fe59ffb1334b821b8abafcc262caf
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 2 19:07:40 2016 -0400
Avoid possibility of undefined value
unit_test/eos.f90
commit c9ed27016531e58bc2daf4dd17ce0701e00091cf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 2 18:46:56 2016 -0400
remove dynamic scheduling
unit_test/test_eos/main.f90
commit e64c7882a4a7a237e52038fdd06f15f215f8d801
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 13:40:25 2016 -0400
Fix a bug in indicating we want to compute the rates
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
commit 691da880bd3f1d31084ac783b3b10759597d931a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jul 2 12:58:03 2016 -0400
use small_temp as returned from the EOS as the T cutoff
also document some of the magic numbers in here
integration/BS/bs_type.f90
commit 096ffc5c8a2f10df393576dde79ba8fe47169d32
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 05:33:50 2016 -0400
Move thermodynamics update into separate subroutine
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/actual_integrator.F90
integration/BS/bs_convert.f90
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_convert.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/actual_integrator.f90
integration/VODE/vode_convert.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
commit fb4396f5c6e8ec0b675879623dd0ede5ca58139f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 04:34:31 2016 -0400
Tell local EOS module about check_inputs
unit_test/eos.f90
commit 81d7c8dd278956d7483dd6aae7b327838434d036
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 03:54:24 2016 -0400
Move the abundance/temp fixing to a new subroutine
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_rhs.f90
integration/VODE/vode_type.f90
commit 90db9c47914ee62698cae4fdad39b61927511133
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 03:42:04 2016 -0400
Add eos_state % reset in VODE and VBDF
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
commit 0b56770c6b200493b3014fb7a6fb65411bec3131
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 03:36:20 2016 -0400
Do not check validity of inputs in RHS EOS calls
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
interfaces/eos_type.f90
commit b772464bee102f0955cb3e0ecb016ead4c58eca1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jul 2 02:42:29 2016 -0400
Clean up unused variables
networks/aprox13/actual_rhs.f90
neutrinos/sneut5.f90
rates/aprox_rates.f90
screening/screen.f90
commit 891626ecc91c370a9c559ec97a61c9d4b11e33eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 21:31:10 2016 -0400
add OpenMP directives
unit_test/test_eos/main.f90
commit 8c1019e4495e2be8535b813d535f8171e79d1834
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 21:11:13 2016 -0400
add OpenMP directives
unit_test/test_react/main.f90
commit 5ea325ce6758c8606c62ab2d55cb6c3475b446cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 19:49:05 2016 -0400
change the scaling method used by the BS integrator
the default now no longer takes dydt into account
integration/BS/_parameters
commit e78ef5d1add36c6f4c46f14e282d3f8cfc575b8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 17:54:04 2016 -0400
update docs
Docs/runtime_parameters/runtime_parameters.tex
commit 61eba03a149ebde8d3cd90e3ea96cb48aa645fe3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 1 16:17:27 2016 -0400
add a centered-difference Jacobian option
integration/_parameters
integration/numerical_jacobian.f90
commit 22d1544b92430a766dd3e6b7fe59538705891bf3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 30 22:46:33 2016 -0400
Print out more time information when verbose
integration/BS/actual_integrator.F90
commit d3d539bc7737b6a8e108fb5c718fe3129c617a99
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 30 21:40:55 2016 -0400
density derivatives are not supported yet
networks/aprox21/actual_rhs.f90
commit c4cc61faf23ebaa1cfbb3fcb83d484148e2b393e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 30 20:52:30 2016 -0400
test for the aprox21 network
unit_test/test_react/inputs_aprox21
unit_test/test_react/xin.aprox21
commit c2cf75e219809cb2219a4de1d03e96990829c057
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 30 20:00:09 2016 -0400
add a list of changes since the last merge
CHANGES
commit 5725c927fb0ed9094d3f5d20e614aa19a1d7da97
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jun 29 04:21:54 2016 -0400
Pass in dx and cs explicitly rather than t_sound
integration/BS/actual_integrator.F90
integration/BS/bs_convert.f90
integration/BS/bs_rhs.f90
integration/VBDF/actual_integrator.F90
integration/VBDF/vbdf_convert.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_convert.f90
integration/VODE/vode_rhs.f90
integration/rpar.f90
interfaces/burn_type.F90
commit 2f23c494d3c0b94cb18667c828d36d9f1b024ee0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jun 29 00:43:34 2016 -0400
Add a burning mode that limits numerically unstable burning
Docs/runtime_parameters/runtime_parameters.tex
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
integration/_parameters
commit 1ece0018e5aaf1bdb2c8ba719581adaed575a048
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jun 28 23:44:08 2016 -0400
Add sound-crossing time to burn_t
integration/BS/actual_integrator.F90
integration/BS/bs_convert.f90
integration/VBDF/actual_integrator.F90
integration/VBDF/vbdf_convert.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_convert.f90
integration/rpar.f90
interfaces/burn_type.F90
commit 008108efa0dde580d29958d6a97467529bcad028
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:05:37 2016 -0400
MICROPHYSICS_DIR -> MICROPHYSICS_HOME
GMicrophysics.mak
README.md
integration/Make.package
networks/GNetwork.mak
networks/Make.package
networks/aprox13/test/GNUmakefile
networks/general_null/GPackage.mak
networks/general_null/Make.package
networks/ignition_simple/test/GNUmakefile
networks/rprox/test/GNUmakefile
networks/triple_alpha_plus_cago/test/GNUmakefile
networks/xrb_simple/test/GNUmakefile
unit_test/test_eos/GNUmakefile
unit_test/test_react/GNUmakefile
commit 9d4c144bed43feee04b6fb4e1929374f176667b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 28 13:04:56 2016 -0400
vddot is in LINPACK
util/BLAS/Make.package
util/LINPACK/Make.package
commit 674fed9c6f3dbd3f04c37fb8df392423363db6e4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jun 27 00:31:59 2016 -0400
Remove the BS check on a dt underflow
This was causing problems when the starting time was not zero,
and this check is also redundant with our check against dt < dt_min.
integration/BS/stiff_ode.F90
commit 70888819c8e074e267783b4fa7aab588eb57d806
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 26 03:21:49 2016 -0400
Initialize the Pascal matrix
integration/VBDF/actual_integrator.F90
commit 32a4f0e9c0767c63a422f043ecdf9a7f52529a7a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun Jun 26 00:33:02 2016 -0400
Simplify esum again
util/microphysics_math.F90
commit e1372307395400f61e4bf6196d051dba83d6bda5
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 25 22:42:03 2016 -0400
test_numerical_jac doesn't run on the GPU
integration/numerical_jacobian.f90
commit acdaf6577e513b1ab811f4e52b96990cf0c55fcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 17:23:46 2016 -0400
remove sdc debug
networks/aprox13/actual_rhs.f90
commit faa6fca72ea4f693777eb96840b498698e1468db
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 17:22:16 2016 -0400
don't store just yet
networks/aprox13/actual_rhs.f90.wdtest
commit 9e3454609b88847fa25562d2256471e42878b03f
Merge: ed9e4464 c1042ea2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 17:21:26 2016 -0400
Merge branch 'development' into sdc_diag
commit ed9e4464b4e01f0bdbf3ca00798ea9ddf7be4372
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 17:19:11 2016 -0400
port i,j,k, time from Castro
interfaces/burn_type.F90
commit af112bf2430e0fa5aa9a455e82d6728fd21de1ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 17:16:31 2016 -0400
move the setting of i,j,k to convert
integration/BS/bs_convert.f90
integration/BS/bs_rhs.f90
commit b915cb5795cdb96849079ede914068c4556a4729
Merge: d758f47f b385df14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 16:03:30 2016 -0400
Merge branch 'sdc_diag' of ssh://github.com/BoxLib-Codes/Microphysics into sdc_diag
commit d758f47ffde17b4de8eda3c022a42d09411badbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 24 16:03:16 2016 -0400
this is for SDC testing
networks/aprox13/actual_rhs.f90.wdtest
commit c1042ea2a330d411511b92dd81f64540216224f5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 23 17:23:17 2016 -0400
Add the energy offset technique to VBDF
integration/VBDF/actual_integrator.F90
commit b385df144533527e3df60b4957182313f62627df
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 14:11:08 2016 -0400
pass the actual time through all the tmeps to rhs
integration/BS/bs_rhs.f90
integration/BS/stiff_ode.F90
commit 92d44b4ade371eb291f2e9222491235d99d54e3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 13:54:35 2016 -0400
fix file openning
networks/aprox13/actual_rhs.f90
commit 5b6ddd52a81deaf1bde086de1009d1539ba2349b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 13:20:02 2016 -0400
add SDC diagnostics for the wd collision problem
integration/BS/actual_integrator.F90
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
networks/aprox13/actual_rhs.f90
commit f60bdf9f13fec3127643691e2f291c493eed3052
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 23 12:31:59 2016 -0400
initialize time propertly and pass it into the burn_t before the RHS call
integration/BS/actual_integrator.F90
integration/BS/bs_convert.f90
commit 5333d84f8d4db48773cfe332d23b228a33412649
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jun 22 13:18:04 2016 -0400
rename for consistency with the other codes
Docs/.gitignore
Docs/EOS/eos.tex
Docs/GNUmakefile
Docs/README.md
Docs/burners/burners.tex
Docs/maestrosymbols.tex
Docs/networks/networks.tex
Docs/refs.bib
Docs/runtime_parameters/rp.py
Docs/runtime_parameters/runtime_parameters.tex
Docs/userguide.tex
commit a22e1917afa9f850399ca777f9e04288070306c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 23:44:37 2016 -0400
update -- only allow the main helm_table.dat
.gitignore
networks/aprox13/test/testburn.f90
commit 29caa6e1a09d85fd9d3edef6506ef91159da1636
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 23:28:26 2016 -0400
tighten enuc and temp tolerances
networks/triple_alpha_plus_cago/_parameters
commit bfbbee740ef55f24b6ed2dc205a88b0e8a7b2300
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 23:28:02 2016 -0400
a troublesome state -- this needs good tolerances with BS to get
a good answer
networks/triple_alpha_plus_cago/test/testburn.f90
commit 212634146163c9709eb8636b6ab37149eead0733
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 22:58:36 2016 -0400
store both the old and new X
unit_test/test_react/main.f90
unit_test/test_react/variables.f90
commit 94aa73476d2fc2aeae72c96abead3ae18fbfa872
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 19:19:46 2016 -0400
more sanity checks
unit_test/test_react/main.f90
commit b7ad8b4d91de969b506735c300d4b3fbf9e341bf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 19:08:49 2016 -0400
add a small_dens and small_temp and initialize the EOS with them
unit_test/test_react/_parameters
unit_test/test_react/main.f90
commit cf1110c67c376229b4dcccfbfaa47cf2ee7a78f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 18:28:56 2016 -0400
more d0
unit_test/test_react/xin.rprox
unit_test/test_react/xin.xrb_simple
commit 164125a163e81a10ad2b45ca8eb810d5fb38d934
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 17:59:34 2016 -0400
more .d0
unit_test/test_react/xin.aprox13
unit_test/test_react/xin.aprox19
commit 44c7697f73f4d50e8d25b3b86a57539fbddeb4f0
Merge: ac9b9181 0a2ef134
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 16:54:11 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit ac9b9181376f732f2379c6535ad2fdc667fd7405
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 21 16:53:51 2016 -0400
need .d0 to get reliable results. Need to update the others
unit_test/test_react/xin.3alpha_plus_o
commit 0a2ef13412845d845b4d0e5a40eda606ad0e12e2
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 20 01:44:02 2016 -0400
Undo energy scaling from aprox networks
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
networks/iso7/actual_burner.f90
commit 4403b073e96b58218573bae325b04399e9a05ad9
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 20 01:32:10 2016 -0400
Use an offset when integrating the energy in BS
We use the zone energy as calculated in the call to the EOS
as our offset, and subtract it from the final amount of
energy generated. This seems to help quite a bit with convergence.
integration/BS/actual_integrator.F90
commit 2b9f15c7c01dc31833ca62c9b6236cb2d74ff6cb
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 19 18:00:52 2016 -0400
Remove an array zero'ing for performance
util/microphysics_math.F90
commit 90e23ee7589951114181aaa28665e22e3506dbec
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jun 17 20:00:47 2016 -0400
Eliminate a few more divisions
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
integration/numerical_jacobian.f90
commit 6dbf0080a6bbedd23f0f4d7a5e69377775c69bec
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jun 17 20:00:23 2016 -0400
Print out more information if verbose
integration/BS/actual_integrator.F90
commit c2dcd373621c684bc09c17dd504207d8e28ac014
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jun 17 00:27:01 2016 -0400
Update device data
integration/integrator.f90
commit 2dfdce1407f1a21573433f60787d14ec34b7c8dd
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 16 23:54:01 2016 -0400
Eliminate some common divisions
integration/BS/bs_convert.f90
integration/VBDF/vbdf_convert.f90
integration/VODE/vode_convert.f90
integration/integration_data.f90
integration/integrator.f90
commit 6e5072baf76128ca01720078fe8d4109d2b59829
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 16 23:41:57 2016 -0400
Enact recent changes in VODE, VBDF
integration/VBDF/vbdf_convert.f90
integration/VODE/vode_convert.f90
commit 9e14827832379402a7899c5d1fd37a3df37a905e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 16 23:33:20 2016 -0400
Some more better indexing
integration/BS/bs_convert.f90
commit 08888e7db344dfe29946dc9ffd4fff21dcd01122
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 16 23:05:01 2016 -0400
Remove a costly array initialization
util/microphysics_math.F90
commit d2efc1845ec444b50213111632c47303d5e6a688
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 16 22:02:32 2016 -0400
use F90 slice notation to speed-up a hotspot
integration/BS/bs_convert.f90
commit 4c04545bd815af1813c1129b9d65ed0efd38ce5c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jun 16 08:20:25 2016 -0400
fix a stray line continuation
GMicrophysics.mak
commit aad8b2075bda95093c43a75c891dbaee4dd52579
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 21:30:29 2016 -0400
add description of test_react and test_eos
README.md
commit 6759e58dfed789264f73006f64b12951115b9225
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 19:53:14 2016 -0400
extend the range of T and rho
unit_test/test_eos/input_eos
commit 9ff89d0566111441dfb6a3d13eb705a303f48a12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 19:44:02 2016 -0400
put the EOS name in the outfile + some cleaning
now we skip eos_input_th for gamma_law_general (it is not defined)
and make the input rho only slightly perturbed for that EOS
unit_test/test_eos/_parameters
unit_test/test_eos/input_eos
unit_test/test_eos/main.f90
commit 248fbdbf747f814b9fe8a86d3d8e5bc49e80ab84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 15:13:13 2016 -0400
allow for small_temp and small_dens
unit_test/test_eos/_parameters
unit_test/test_eos/main.f90
commit a750555d210cb271cd81fe3d44d51f60a1852bf0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 15:04:22 2016 -0400
add a copy of the constants for testing and allow small to eos_init()
unit_test/GPackage.mak
unit_test/constants_cgs.f90
unit_test/microphysics.f90
commit 15c713c5465d70c6948eaacbf31bb8829e8cb9ca
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jun 14 14:12:05 2016 -0400
Correct the expression for dh/drho in Helmholtz
This was introduced when the expression for dh/drho was originally
introduced into Castro, the commit with git hash:
cd49a4189b7e42fab0f336c881e1d6cca7cf06e0
eos/helmholtz/helmholtz.F90
commit 923f0d57f1203798bbba8f59cfaf77c6f1f24ba0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 13:13:39 2016 -0400
fix a variable name
unit_test/test_eos/variables.f90
commit 144f6c65cc9d327902c50c9f3c4abde844b5a0e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 13:12:03 2016 -0400
test_eos seems to work
unit_test/test_eos/GNUmakefile
unit_test/test_eos/GPackage.mak
unit_test/test_eos/_parameters
unit_test/test_eos/gr0_3d.small
unit_test/test_eos/input_eos
unit_test/test_eos/main.f90
commit d49fe6956cd871f2175bdd21da48c46582a5c5ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 13:04:11 2016 -0400
more progress
unit_test/test_eos/_parameters
unit_test/test_eos/main.f90
unit_test/test_eos/variables.f90
commit 7aad1660086958a372013759f1f4434fa7ef5a65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 12:17:39 2016 -0400
remove unused parameters
unit_test/test_react/_parameters
commit 121f5df0293c2a4ef12d98dc745f9b5b44dd007c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 12:14:33 2016 -0400
start of the EOS test:
unit_test/test_eos/variables.f90
commit f7b939169de708bc9bb2679fce1bd0392d3a05a9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 11:56:40 2016 -0400
a test driver
networks/rprox/test/GNUmakefile
networks/rprox/test/GPackage.mak
networks/rprox/test/testburn.f90
commit 091e61d4ef1d6e290e6ec6490361426402c335b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 10:33:46 2016 -0400
test driver for this net
networks/xrb_simple/test/GNUmakefile
networks/xrb_simple/test/testburn.f90
commit f01dd46bee446396aad2dda785a413c3a043218c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 10:29:39 2016 -0400
use microphysics_init()
networks/triple_alpha_plus_cago/test/testburn.f90
commit 642fa52c0796506b4ec9beb908ffd6d298b0487b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 10:27:54 2016 -0400
use relative path for MICROPHYSICS_DIR
networks/triple_alpha_plus_cago/test/GNUmakefile
commit 453cae48d9498f6ad1b5e92ebd460aecf1224f9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 10:19:31 2016 -0400
make testjacobian work
networks/triple_alpha_plus_cago/test/testjacobian.f90
commit 12030c37b48f76fd9312b1484a8308be5693cda1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 10:04:12 2016 -0400
add comment about eps
integration/numerical_jacobian.f90
commit f27a5bf07e6cb8ec7185aa12102eedce9ee78ca1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jun 14 08:43:59 2016 -0400
reorder
README.md
commit 2a8844aeb0b2a95134e7843a5e0b3392fdc957fb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 01:45:58 2016 -0400
Add a missing use statement
integration/BS/stiff_ode.F90
commit b4fa2ced5408e98c082efaad3912fda85bd2a0bb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 01:37:49 2016 -0400
Add a change I missed in the last commit
networks/GNetwork.mak
commit 9c8157701c0c82a22a222da176b6439d2b8eff4d
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 01:35:14 2016 -0400
Rename rates.f90 -> aprox_rates.f90; reorganize
README.md
aprox_rates/GPackage.mak
aprox_rates/Make.package
networks/Make.package
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
rates/GPackage.mak
rates/Make.package
rates/aprox_rates.f90
rates/tfactors.f90
commit d6af2e9179ab5387a3bff4ea44a38e121ebcf7d6
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 14 01:25:22 2016 -0400
Permit another scaling method in BS
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/_parameters
integration/BS/stiff_ode.F90
commit 8dd245b2e00c53274739424db19a09a6406a8774
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 23:08:07 2016 -0400
add the integrator to the output file name
this is needed for the test suite so the output file names are distinct
when running the same problem with different integrators
unit_test/test_react/main.f90
commit a1b19a45a7b32c4fa15bc531cc9096d920c31fae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 22:38:40 2016 -0400
make a routine test_numerical_jac() that automates comparing to analytic
integration/numerical_jacobian.f90
networks/aprox13/test-cpp/testjacobian.f90
commit 71a07278265104e864ff302c09512d3d2312cba8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 20:44:00 2016 -0400
add a call to microphysics_finalize()
unit_test/test_react/main.f90
commit 59de76401b7366f37e5d85a09a4f437fd4a8c980
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 20:43:12 2016 -0400
get this working again
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 7b3d3a99dbd4c7cb810ffb60b8007654ac35d3be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 20:29:13 2016 -0400
make realclean should deal with helm_table.dat
GMicrophysics.mak
commit a7e4422d3a7c6a264e9212406ce7f73ce5694390
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 20:22:42 2016 -0400
update description
README.md
commit 61572ef1de0579bcfa0266d335ce3ffaeb1848e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 15:54:34 2016 -0400
deallocate xn_zone
unit_test/test_react/main.f90
commit ec3ef327fddf1c77c1deddee290f4621ee71c4b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 15:30:46 2016 -0400
hook in the integrator to build_info
GMicrophysics.mak
commit 9994ffd04722a1a14cb1b50b80f6f82693e8aaba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 15:01:46 2016 -0400
create a new GNetwork.mak that is used to handle all of the make stuff for F90
This can simply be included now. It will add to a MICROPHYS_CORE variable
that can the be processed in the usual way we do for F90 BoxLib
GMicrophysics.mak
integration/GPackage.mak
integration/VODE/GPackage.mak
networks/GNetwork.mak
networks/GPackage.mak
commit 6bd1a6ef2e1b5a4c8d9a54299c83dc824094ce44
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 14:58:49 2016 -0400
vddot.f is LINPACK, not BLAS
util/BLAS/GPackage.mak
util/LINPACK/GPackage.mak
util/LINPACK/vddot.f
commit 0fa184c45b95ba675a2f8649661e75bf28e92ebd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 14:39:35 2016 -0400
add a TODO
unit_test/test_react/TODO
commit d985b26074743ef721e314db1f3573f4948e04a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 13:30:55 2016 -0400
increased T range
unit_test/test_react/inputs_aprox13
commit f47de3cbfa60b9c2755f64b3a4de83fe01b73279
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 13:22:31 2016 -0400
first cut at an aprox19 test
unit_test/test_react/inputs_aprox19
unit_test/test_react/xin.aprox19
commit 4c6ab513a6633b0dfb0ef7b8091c01b68507a19a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 13:01:08 2016 -0400
not used
unit_test/test_react/inputs_approx8
unit_test/test_react/xin.approx8
commit b146e1dd68894e2100603f13bdba61a79b87b36b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:59:41 2016 -0400
not used
unit_test/test_react/xin.ignition.64
commit 4b58e4ae4a08a51e2af6313a37ab4ba4ce1fb4a0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:53:02 2016 -0400
echo SUCCESS if we build -- for the test suite
GMicrophysics.mak
commit 9f37098d278741624be67aa10786cf5941bbd6e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:38:25 2016 -0400
need to explicitly set MICROPHYSICS_DIR to ../..
if we don't do this, then the environment variable is chosen, and this
can break the test suite
unit_test/test_react/GNUmakefile
commit 5094883c7e2aee10ceac866e80812823d5f8f47d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:23:51 2016 -0400
rates/ -> aprox_rates/
networks/Make.package
commit 5e7068959f5dbc77cba53a7f8f6658b0cbc65c38
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:20:28 2016 -0400
use NETWORK_REQUIRES to indicate what is needed by the net
this fixes the F90 build system for the networks. Now any stuff
explicitly needed (like screening, etc.) should be indicated here
GMicrophysics.mak
networks/CONe2NSE/NETWORK_REQUIRES
networks/MESA/NETWORK_REQUIRES
networks/aprox13/GPackage.mak
networks/aprox13/NETWORK_REQUIRES
networks/aprox19/GPackage.mak
networks/aprox19/NETWORK_REQUIRES
networks/aprox21/GPackage.mak
networks/aprox21/NETWORK_REQUIRES
networks/breakout/NETWORK_REQUIRES
networks/general_null/NETWORK_REQUIRES
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/NETWORK_REQUIRES
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-burn-simple/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/NETWORK_REQUIRES
networks/ignition_simple/GPackage.mak
networks/ignition_simple/NETWORK_REQUIRES
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/NETWORK_REQUIRES
networks/iso7/GPackage.mak
networks/iso7/NETWORK_REQUIRES
networks/kpp/NETWORK_REQUIRES
networks/powerlaw/NETWORK_REQUIRES
networks/rprox/NETWORK_REQUIRES
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/NETWORK_REQUIRES
networks/xrb_simple/NETWORK_REQUIRES
commit dc88b6ff9bf06570b285388afb1282078f624d6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:20:10 2016 -0400
clean this up -- remove the old Maestro stuff
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_approx8
unit_test/test_react/inputs_aprox13
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_xrb_simple
commit d831ea39280b67bd79cc4537608ed2dae610ebeb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:05:10 2016 -0400
rename
aprox_rates/GPackage.mak
aprox_rates/Make.package
aprox_rates/rates.f90
aprox_rates/tfactors.f90
commit 92e1f2a856585c6edc1a07d9e0d661f8305ec652
Merge: 5db044ac 4397867b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:03:09 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 5db044ac3b949192f218f381e92832afc156b892
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 12:03:03 2016 -0400
network requires
GMicrophysics.mak
networks/triple_alpha_plus_cago/test/eval.f90
networks/triple_alpha_plus_cago/test/testburn.f90
commit 4397867b16b31fa1fb2487f1341dd9863e5b3cd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 09:14:47 2016 -0400
add integrator to job_info
unit_test/write_job_info.f90
commit 83d876132fa57191cdabb9141cf4f07f183b2671
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 08:29:57 2016 -0400
more inputs / xin
unit_test/test_react/inputs_3alpha
unit_test/test_react/inputs_approx8
unit_test/test_react/inputs_aprox13
unit_test/test_react/inputs_rprox
unit_test/test_react/inputs_xrb_simple
unit_test/test_react/xin.3alpha_plus_o
unit_test/test_react/xin.approx8
unit_test/test_react/xin.aprox13
unit_test/test_react/xin.ignition.64
unit_test/test_react/xin.rprox
unit_test/test_react/xin.xrb_simple
commit 6652db259cf7da0065947c1508e4e9609c616f58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 08:29:24 2016 -0400
add job_info to the output
GMicrophysics.mak
unit_test/GPackage.mak
unit_test/dummy.probin.template
unit_test/test_react/main.f90
unit_test/write_job_info.f90
commit c5a3a24b904e6522215cc9cd9add0b30bba6bbed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 08:07:25 2016 -0400
a few more ignores
.gitignore
commit c5971b5d7ef1f15fee7afd131ca375f0d9ab42e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Jun 13 08:03:28 2016 -0400
simplify the makefiles a bit
GMicrophysics.mak
networks/aprox13/test/GNUmakefile
networks/triple_alpha_plus_cago/test/GNUmakefile
unit_test/test_react/GNUmakefile
commit b3739df536cf564bea7d613a75d2793d06d864b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 21:06:19 2016 -0400
fix the energy -- we don't care about e it seems
unit_test/test_react/main.f90
commit 2d7cfe3f8bee5a037cc57d40696e55b40597b613
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 20:59:29 2016 -0400
this should work now, but gives negative energy
unit_test/test_react/GNUmakefile
unit_test/test_react/inputs_ignition
unit_test/test_react/main.f90
commit 991aa8f24f3f07c509424a8a4bb3e2e8a4a50635
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 20:38:40 2016 -0400
first example
unit_test/test_react/gr0_3d
unit_test/test_react/gr0_3d.small
unit_test/test_react/inputs_ignition
unit_test/test_react/varden.f90
unit_test/test_react/xin.ignition
commit 6329396d742382332e0cff07b44c9043a2e4ac34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 20:36:40 2016 -0400
add support for reading an inputs file
unit_test/dummy.probin.template
commit e9835ed13a171650d9045055e04573165a559c11
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 19:26:30 2016 -0400
remove dupe init_variables
unit_test/test_react/varden.f90
commit 1695c97761313c586785bb6a2f9ceb217bb9e2c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 19:13:57 2016 -0400
add the boxlib init and finalize. This compiles now, but doesn't work
unit_test/test_react/_parameters
unit_test/test_react/varden.f90
unit_test/test_react/variables.f90
commit c9397907da49f27a39dc5507293da494c6d451e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 19:06:03 2016 -0400
don't explictly add varden -- we don't like (dupe main) this way
unit_test/test_react/GPackage.mak
commit e71bd589210919e2ecccaedb2ad328b153bf58f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:34:17 2016 -0400
allow for PROBIN_PARAMETER_DIRS to be appended
GMicrophysics.mak
commit 123e48d1e3d6ce8d9c8ad688fe5dac8261c65a01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:32:45 2016 -0400
add parameters
unit_test/test_react/_parameters
commit b23a930cbb87014ffcf176310a6d91d7db4ab71c
Merge: 456fd2bc 7815a310
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:30:49 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 456fd2bc60510d0536d5ca30958e37237c92ba67
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:29:47 2016 -0400
some compilation fixes
unit_test/test_react/varden.f90
commit 7815a3100698c7232dec7fa1faf7d21c1f532f01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:22:48 2016 -0400
use the microphysics module
networks/aprox13/test/testburn.f90
commit 3a77eeaa954e7ca73982c724bcf4f6f4b20d2e5e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:22:05 2016 -0400
seems that not every network has a finalize?
unit_test/microphysics.f90
commit 37ddd5e677588a9958de715d05936f9a6f32293b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:17:57 2016 -0400
fix typo
unit_test/microphysics.f90
unit_test/test_react/varden.f90
commit b9f2f1758510631ba8c97d515d1efe0be78b689a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 18:15:46 2016 -0400
make it easier to init and finalize
unit_test/GPackage.mak
unit_test/microphysics.f90
unit_test/network.f90
commit a27923836ef00193f3576e6ef1ccfb2b09399a7b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 16:44:19 2016 -0400
a bit more progress
unit_test/test_react/GNUmakefile
unit_test/test_react/util.f90
unit_test/test_react/varden.f90
unit_test/test_react/variables.f90
commit 75a7676a97110f1127684758fbbcebc9463f1dc1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 16:19:30 2016 -0400
start of a standalone unit test
unit_test/test_react/GNUmakefile
unit_test/test_react/GPackage.mak
unit_test/test_react/gr0_3d
unit_test/test_react/util.f90
unit_test/test_react/varden.f90
unit_test/test_react/variables.f90
commit bf296b34959b87f10bbfcea590e7125adad524d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 13:24:50 2016 -0400
call init_rhs and init_burner actually
networks/aprox13/test/GNUmakefile
unit_test/network.f90
commit 3807577bb231fd562c6a3e451e5b463ab1a5ed6c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 13:09:35 2016 -0400
a standalone unit test
networks/aprox13/test/GNUmakefile
networks/aprox13/test/testburn.f90
commit 8d7f8d71f55d8f3ea0673280dca958073203ba96
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 12:36:15 2016 -0400
this seems to work now
networks/triple_alpha_plus_cago/test/testburn.f90
commit f9d279091914c2160f8666bc3270dcc4f7134dea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 12:00:01 2016 -0400
remove unnecessary file
networks/triple_alpha_plus_cago/make.out
commit 10a4bfdd440023a9112c51b9472800217d0e965d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 11:58:31 2016 -0400
closer to compiling, but I don't understand what the problem is
networks/triple_alpha_plus_cago/test/GNUmakefile
networks/triple_alpha_plus_cago/test/testburn.f90
commit 5f3cd5a3194a9ddfd1e2dfb1e598110cf0062aff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 10:31:41 2016 -0400
some cleaning
UsersGuide/runtime_parameters/rp.py
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 422879af22a30272851f156e13291b3f7f01a78b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 12 10:14:02 2016 -0400
make the runtime parameter script smarter
it now does a latex-compatible label
UsersGuide/GNUmakefile
UsersGuide/runtime_parameters/rp.py
UsersGuide/runtime_parameters/runtime_parameters.tex
commit 1301d043c9988d98de5214065cd9b548851e4a17
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 12 00:48:37 2016 -0400
Add a chapter about the burner
UsersGuide/burners/burners.tex
UsersGuide/networks/networks.tex
UsersGuide/refs.bib
UsersGuide/userguide.tex
commit 579612dec515dd6ea4bbebd8cc4ce8efd92d823f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 11 21:02:16 2016 -0400
change eos_gamma default to 5.d0/3.d0
this won't change any functionality, since previously we reset the
default of 0 to 5/3 in the init
eos/gamma_law_general/_parameters
eos/gamma_law_general/gamma_law_general.F90
commit 2e19ba3fa1d3b8edd9031517efb23f309d4526d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 11 16:37:49 2016 -0400
1.e-30 -> 1.d-30
networks/_parameters
commit ac7699414dcba999ca0c4d99c562141bab06b2d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 10 15:38:52 2016 -0400
almost there...
interfaces/burn_type.F90
interfaces/eos_type.f90
unit_test/eos.f90
commit 1648f1649d326303a423acf1862c7654aa21dd54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 10 15:34:39 2016 -0400
add GPackage.mak
interfaces/GPackage.mak
commit d43eff5b6cb6198b3671d7180d87c0ac8db975b0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jun 10 15:27:51 2016 -0400
all your small_x are belong to network
networks/_parameters
unit_test/_parameters
commit cd53272b744b9444655c95fca6a9cbbc0cc86d11
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jun 10 00:17:13 2016 -0400
Get some networks compiling again
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
commit d561d47f9ef63bf9ebdbdc384f3a7013df5795b9
Merge: 9f69779c 44b5241f
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date: Tue Jun 7 14:52:30 2016 -0400
Merge branch upstream changes into Adam's local changes
commit 9f69779cabda791383ed8868674e3fd39dd68349
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date: Tue Jun 7 14:49:50 2016 -0400
Move Pascal matrix out of bdf_ts_build
integration/VBDF/bdf.f90
integration/VBDF/bdf_type.f90
commit 44b5241f354cf72edae0b8f98cfd3f53d130c04c
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 13:49:48 2016 -0400
Port over xrb_simple to our framework
networks/README
networks/xrb_simple/GPackage.mak
networks/xrb_simple/Make.package
networks/xrb_simple/_parameters
networks/xrb_simple/actual_burner.f90
networks/xrb_simple/actual_network.f90
networks/xrb_simple/actual_rhs.f90
networks/xrb_simple/burner_aux.f90
networks/xrb_simple/f_rhs.f90
networks/xrb_simple/network_indices.f90
networks/xrb_simple/xrb_simple_burner.f90
commit 71d085b6e7c979caeaa476b3448e60b69487ca86
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 03:21:43 2016 -0400
Add some parameters for rprox
networks/rprox/_parameters
commit a5a1debccbc3ffb6a611c48d768c4c49c9989e11
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jun 7 03:02:05 2016 -0400
Fix bugs in rprox
networks/rprox/actual_rhs.f90
commit 0290118bbc1d874fb109adba58db1d315d92b494
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 6 23:03:51 2016 -0400
Include a copy of the original VODE source
integration/VODE/GPackage.mak
integration/VODE/vode_source/GPackage.mak
integration/VODE/vode_source/dacopy.f
integration/VODE/vode_source/dewset.f
integration/VODE/vode_source/dumach.f
integration/VODE/vode_source/dvhin.f
integration/VODE/vode_source/dvindy.f
integration/VODE/vode_source/dvjac.f
integration/VODE/vode_source/dvjust.f
integration/VODE/vode_source/dvnlsd.f
integration/VODE/vode_source/dvnorm.f
integration/VODE/vode_source/dvode.f
integration/VODE/vode_source/dvset.f
integration/VODE/vode_source/dvsol.f
integration/VODE/vode_source/dvsrco.f
integration/VODE/vode_source/dvstep.f
integration/VODE/vode_source/iumach.f
integration/VODE/vode_source/ixsav.f
integration/VODE/vode_source/test/GNUmakefile
integration/VODE/vode_source/test/tvode.f
integration/VODE/vode_source/vode.H
integration/VODE/vode_source/xerrwd.f
integration/VODE/vode_source/xsetf.f
integration/VODE/vode_source/xsetun.f
commit ae077c4e50fb51c6bb4c46aa41a1b24935f63b49
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Jun 6 21:53:33 2016 -0400
Make triple_alpha behave like in MAESTRO
networks/triple_alpha_plus_cago/_parameters
networks/triple_alpha_plus_cago/actual_network.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
commit da236b70a674913b1018c3ae90e59cd74b63f8e4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jun 6 00:45:56 2016 -0400
Fix an indexing error in the tolerances
This would only have caused an issue if nspec_evolve < nspec - 2,
which is not the case for any of the current networks.
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.F90
integration/VODE/actual_integrator.f90
commit bad9d390c6eb6b924ea9c6fdd6d71c02c943c045
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 17:42:38 2016 -0400
need the interfaces
GMicrophysics.mak
commit 6a3d23b2b1c408a87ee6be64597249249eac0928
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 17:42:04 2016 -0400
this is a more up-to-date version, from Castro
unit_test/eos.f90
commit 149e0805222147b7b169e857361f604cedcc81eb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 17:16:56 2016 -0400
update to reflect recent changes
README.md
commit e3e20fd3eb37daed55f456b0997a05c3fff87c32
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 5 16:55:12 2016 -0400
Copy the breakout network from CastroRadiation
networks/breakout/GPackage.mak
networks/breakout/Make.package
networks/breakout/actual_burner.f90
networks/breakout/actual_network.f90
networks/breakout/actual_rhs.f90
commit f1cd85e36f1e88b8cfc5e48a8218b4470306010a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 5 16:32:35 2016 -0400
Copy the breakout EOS from CastroRadiation
eos/breakout/GPackage.mak
eos/breakout/Make.package
eos/breakout/_parameters
eos/breakout/eos_stuff.f90
commit b4b84cb2585a992fb3d06294f56927eb286ae3dc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 5 16:28:14 2016 -0400
Allow the radiation component of Helmholtz to be disabled
eos/helmholtz/GPackage.mak
eos/helmholtz/Make.package
eos/helmholtz/helmholtz.F90
commit 0ac9810e236c5e1d32baceb2c9e303f205bc950a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 5 14:45:39 2016 -0400
Hook in a network routine
eos/multigamma/multigamma.f90
commit 216a0df303bc2698c7fd1a0fef64134199b15177
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jun 5 12:35:01 2016 -0400
Create new directory for derived types
eos/GPackage.mak
eos/Make.package
interfaces/README.md
interfaces/burn_type.F90
interfaces/eos_type.f90
networks/GPackage.mak
networks/Make.package
commit 59c39154d114b8363a51eb7083411348ae00aa4b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 11:24:41 2016 -0400
most of the build stuff here seems to be using the C++ BoxLib conventions,
even for F90, so switch to that.
GMicrophysics.mak
commit 0eb24e09c7dfb697dbe6db10d7afc13a1e989683
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 11:12:36 2016 -0400
forgot to add these
unit_test/_parameters
unit_test/dummy.probin.template
unit_test/eos.f90
unit_test/network.f90
commit 76a3c265ff4d81adc66243b60a28e03826e9120a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 11:10:56 2016 -0400
more work getting this to compile
networks/triple_alpha_plus_cago/test/GNUmakefile
networks/triple_alpha_plus_cago/test/_parameters
commit 1d77b58f12121d76b6f743271f08291fea5e083b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 11:10:31 2016 -0400
we need eos.f90
unit_test/GPackage.mak
commit 4d906170b42098c5ddf640cb749b0fe198506661
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 11:10:17 2016 -0400
more work getting this all put together
GMicrophysics.mak
commit 61d88f0ac6c8ce7b730bbafa832d9169fec65315
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Jun 5 11:06:04 2016 -0400
much more ignoring
.gitignore
commit fcbf03901f5731cb8857cc436951f9c9911ddc76
Merge: 0e64821e 4a36142a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 4 23:01:29 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 0e64821e107c16d6e7eca1bd2d639f83370240f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 4 23:01:13 2016 -0400
start of the stub makefile for building in Microphysics/
GMicrophysics.mak
commit 4a36142a8671499f52d9a0bfdbcaf1039d734018
Merge: 917fb2c0 993ec116
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Jun 4 22:17:29 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 917fb2c0393a5d99c3ef78da95cbc1b95bdd7758
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Jun 4 22:16:26 2016 -0400
Updated reaclib networks to use sneut module directory.
Removed testing reaclib network directories.
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-local/GPackage.mak
networks/ignition_reaclib/URCA-simple-sneut-local/Make.package
networks/ignition_reaclib/URCA-simple-sneut-local/actual_burner.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_network.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_network_data.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_rhs.f90
networks/ignition_reaclib/URCA-simple-sneut-local/net_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-local/physical_constants.f90
networks/ignition_reaclib/URCA-simple-sneut-local/sneut5.f90
networks/ignition_reaclib/URCA-simple-sneut-local/table_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-local/terminator.f90
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/out_pgi
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/out_pgi-acc
networks/ignition_reaclib/URCA-simple-sneut-moduledir/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_burner.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_network.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_network_data.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_rhs.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/na23--ne23-toki
networks/ignition_reaclib/URCA-simple-sneut-moduledir/ne23--na23-toki
networks/ignition_reaclib/URCA-simple-sneut-moduledir/net_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/physical_constants.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/table_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/terminator.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/.#out
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/out_pgi
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/out_pgi-acc
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/probin
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/urca.py
networks/ignition_reaclib/URCA-simple/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple/na23--ne23-toki
networks/ignition_reaclib/URCA-simple/ne23--na23-toki
networks/ignition_reaclib/URCA-simple/test-cpp/.#out
networks/ignition_reaclib/URCA-simple/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple/urca.py
commit 993ec1161878d6414a12bfacf32a22868a956b76
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 4 21:57:53 2016 -0400
NETWORK_REQUIRES no longer makes sense
since the integration is decoupled from the net, we don't specify
the linear algebra in the net anymore. Note: Castro never used
NETWORK_REQUIRES anyway, so nothing should be affected
networks/MESA/NETWORK_REQUIRES
networks/aprox13/NETWORK_REQUIRES
networks/aprox19/NETWORK_REQUIRES
networks/aprox21/NETWORK_REQUIRES
networks/general_null/NETWORK_REQUIRES
networks/ignition_chamulak/NETWORK_REQUIRES
networks/ignition_reaclib/C-burn-simple/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-commented/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-local/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-moduledir/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple/NETWORK_REQUIRES
networks/ignition_simple/NETWORK_REQUIRES
networks/ignition_simple_SDC/NETWORK_REQUIRES
networks/iso7/NETWORK_REQUIRES
networks/kpp/NETWORK_REQUIRES
networks/powerlaw/NETWORK_REQUIRES
networks/rprox/NETWORK_REQUIRES
networks/triple_alpha_plus_cago/NETWORK_REQUIRES
networks/xrb_simple/NETWORK_REQUIRES
commit 58bb2e2b6472d999ce051044527b87b0cc5aa7e7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Sat Jun 4 21:05:49 2016 -0400
undataified sneut module fixes local vs moduledir differences.
networks/ignition_reaclib/URCA-simple-sneut-commented/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/GPackage.mak
networks/ignition_reaclib/URCA-simple-sneut-commented/Make.package
networks/ignition_reaclib/URCA-simple-sneut-commented/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_burner.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_network.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_network_data.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_rhs.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/na23--ne23-toki
networks/ignition_reaclib/URCA-simple-sneut-commented/ne23--na23-toki
networks/ignition_reaclib/URCA-simple-sneut-commented/net_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/physical_constants.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/sneut5.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/table_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/terminator.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/.#out
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/out_pgi
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/out_pgi-acc
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/probin
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/urca.py
networks/ignition_reaclib/URCA-simple-sneut-local/sneut5.f90
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple/na23--ne23-toki
networks/ignition_reaclib/URCA-simple/ne23--na23-toki
networks/ignition_reaclib/URCA-simple/test-cpp/.#out
networks/ignition_reaclib/URCA-simple/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple/urca.py
commit ffc8cd381f77069448754a2fb3333953560a8aa9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 19:43:15 2016 -0400
Add a copy of eos_t and burn_t
eos/GPackage.mak
eos/Make.package
eos/eos_type.f90
networks/GPackage.mak
networks/Make.package
networks/burn_type.F90
commit 6941b703f5c85cc4af5877c98b482470ac0d4472
Merge: 027ae663 3f52f45d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 19:31:56 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 027ae663b9443533ba2bf470ed5b104d7a0eec14
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 16:44:18 2016 -0400
Remove reliance on eos_data_module
eos/gamma_law_general/gamma_law_general.F90
eos/helmholtz/helmholtz.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/eos_aux_data.f90
eos/stellarcollapse/stellarcollapse.f90
eos/ztwd/ztwd.f90
networks/kpp/actual_burner.f90
commit 3f52f45d97f9cd3eaab6d6162ff3cb77423ccd67
Merge: f8a14dfd 5fc643ec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 4 17:43:27 2016 -0400
Merge branch 'master' into development
commit 5fc643ecbb0317e65ba496e23d4bfc2076495b57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Jun 4 17:40:20 2016 -0400
add a README
screening/README
commit f8a14dfdf6b2a46551d48d716c9f265475b32159
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 15:41:38 2016 -0400
Initialize RHS in the test script
networks/aprox13/test-cpp/testburn.f90
networks/aprox13/test-cpp/testjacobian.f90
commit e94f253c0e2c1dbb66807b1f908100b9acde2c8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 15:40:30 2016 -0400
Clarify the file layout in a network
UsersGuide/networks/networks.tex
commit 487c9a527b069468ecb2b48235ab3af9c4cc12d3
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 15:10:00 2016 -0400
Move some routines into an actual_rhs_init call
networks/aprox13/actual_burner.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_burner.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_burner.f90
networks/aprox21/actual_rhs.f90
networks/general_null/actual_rhs.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_simple/actual_rhs.f90
networks/iso7/actual_burner.f90
networks/iso7/actual_rhs.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
commit 9180f82f4883be5a28ef5aa86730f6d15fc5a25b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 15:00:46 2016 -0400
Initialize reaction names inside network
networks/aprox13/actual_burner.f90
networks/aprox13/actual_network.f90
networks/aprox19/actual_burner.f90
networks/aprox19/actual_network.f90
networks/aprox21/actual_burner.f90
networks/aprox21/actual_network.f90
networks/iso7/actual_burner.f90
networks/iso7/actual_network.f90
networks/rprox/actual_burner.f90
networks/rprox/actual_network.f90
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_network.f90
commit 1c04c2206b235149ac0836cfeacd64587a3a1efb
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 14:52:45 2016 -0400
Centralize the rpar indices
integration/BS/GPackage.mak
integration/BS/Make.package
integration/GPackage.mak
integration/Make.package
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/vbdf_rpar.f90
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/actual_integrator.f90
integration/VODE/vode_rpar.f90
integration/rpar.f90
commit 960074ac7aeac22036df168daa16931476e8d063
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 14:23:24 2016 -0400
Remove actual_network_data module
integration/VODE/vode_rpar.f90
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_network.f90
networks/aprox13/actual_network_data.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox19/actual_network.f90
networks/aprox19/actual_network_data.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/aprox21/actual_network.f90
networks/aprox21/actual_network_data.f90
networks/aprox21/actual_rhs.f90
networks/general_null/GPackage.mak
networks/general_null/Make.package
networks/general_null/actual_network_data.f90
networks/general_null/network.template
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_chamulak/actual_network_data.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_network_data.f90
networks/iso7/GPackage.mak
networks/iso7/Make.package
networks/iso7/actual_network.f90
networks/iso7/actual_network_data.f90
networks/iso7/actual_rhs.f90
networks/powerlaw/GPackage.mak
networks/powerlaw/Make.package
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_network_data.f90
networks/rprox/GPackage.mak
networks/rprox/Make.package
networks/rprox/actual_network.f90
networks/rprox/actual_network_data.f90
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_network.f90
networks/triple_alpha_plus_cago/actual_network_data.f90
commit 2dd9266c3c756ecea84e323305ccd25e88455df8
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 14:05:08 2016 -0400
Remove actual_burner_data module
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_burner.f90
networks/aprox13/actual_burner_data.f90
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox19/actual_burner.f90
networks/aprox19/actual_burner_data.f90
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/aprox21/actual_burner.f90
networks/aprox21/actual_burner_data.f90
networks/general_null/GPackage.mak
networks/general_null/Make.package
networks/general_null/actual_burner.f90
networks/general_null/actual_burner_data.f90
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_burner_data.f90
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_burner_data.f90
networks/iso7/GPackage.mak
networks/iso7/Make.package
networks/iso7/actual_burner.f90
networks/iso7/actual_burner_data.f90
networks/powerlaw/GPackage.mak
networks/powerlaw/Make.package
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_burner_data.f90
networks/rprox/GPackage.mak
networks/rprox/Make.package
networks/rprox/actual_burner.f90
networks/rprox/actual_burner_data.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_burner_data.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
commit 92ac02293ff18b3a9968e031e3f24ca129883b53
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 13:52:21 2016 -0400
Move rate tabulation data to actual_rhs module
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_rhs.f90
commit 32c7e1837b67df28e7bbf570c4d49f00f07961f9
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 13:11:28 2016 -0400
Move ener_gener_rate to actual_rhs module
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_burner_data.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_burner_data.f90
networks/aprox21/actual_rhs.f90
networks/ignition_chamulak/actual_burner_data.f90
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_simple/actual_burner_data.f90
networks/ignition_simple/actual_rhs.f90
networks/iso7/actual_burner_data.f90
networks/iso7/actual_rhs.f90
networks/powerlaw/actual_burner_data.f90
networks/powerlaw/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_burner_data.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
commit b97937d3385e3b7475c3f4d641049e07cf2c4b5a
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 12:55:37 2016 -0400
Use the neutrino module in aprox*
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_rhs.f90
networks/aprox13/sneut5.f90
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox19/actual_rhs.f90
networks/aprox19/sneut5.f90
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/aprox21/actual_rhs.f90
networks/aprox21/sneut5.f90
networks/iso7/GPackage.mak
networks/iso7/Make.package
networks/iso7/actual_rhs.f90
networks/iso7/sneut5.f90
commit ca4a602bcc07eea4139713eaeed8c837fe36211b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 12:53:51 2016 -0400
Avoid data statements in neutrino module
neutrinos/sneut5.f90
commit a7769dbf61100e1c09183f10105b98f61107e6a6
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 01:06:46 2016 -0400
Quiet used-before-defined compiler warnings
networks/aprox13/sneut5.f90
networks/aprox19/sneut5.f90
networks/aprox21/sneut5.f90
networks/iso7/sneut5.f90
neutrinos/sneut5.f90
screening/screen.f90
commit 2e557c06bbc3327d97cd2cd59f2c728cf505499d
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 00:35:25 2016 -0400
Initialize burn energy release to zero
networks/aprox13/test-cpp/testburn.f90
commit 216b47a5f30b0577ae58d73d6496e543472a657b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jun 4 00:22:01 2016 -0400
Shorten line length to make gfortran happy
networks/aprox13/test-cpp/testjacobian.f90
commit a6eebc1610ffbe25f3c77cc991c154560c383c8d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 3 23:04:49 2016 -0400
Removing an incorrect factor of 1 / aion
networks/ignition_simple/actual_rhs.f90
commit 44de546fb2aa8b33a7fc8da191cfbce49127660b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 3 22:55:57 2016 -0400
Rewrite testjacobian.f90 to use the numerical_jacobian routine
networks/aprox13/test-cpp/testjacobian.f90
commit 43bba37561d2ae753183d75b57414691219c9a4e
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 3 22:32:39 2016 -0400
Insert a missing factor of 1 / aion
networks/ignition_simple/actual_rhs.f90
commit a9944af7bac62eb25980a0df4e700d4bea8decf8
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 3 22:13:41 2016 -0400
Insert a missing factor of 1/2 in the energy release
networks/ignition_simple/actual_burner_data.f90
commit 53adacee7ecaf0c45e46e97ecb4be2a88508c568
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jun 3 18:05:38 2016 -0400
Zero out temporary array to avoid illegal accesses
integration/VBDF/bdf.f90
commit 7ceb77179d55db6790828e584c12513d7bb5341b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jun 3 18:03:53 2016 -0400
Fix the call to dgemm
integration/VBDF/bdf.f90
commit 83653c072e627e0e71dc0efedddbfa9ac93c913f
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jun 3 15:05:31 2016 -0400
Quiet some unused variable warnings
eos/helmholtz/helmholtz.f90
integration/BS/actual_integrator.F90
integration/BS/stiff_ode.f90
integration/temperature_integration.f90
screening/screen.f90
commit 9ebd6cb1e97c6f9069a4323a05a9f1c393d525e3
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Jun 3 13:49:57 2016 -0400
Added checks for ACC so burner verbose is ignored if ACC is true.
integration/BS/actual_integrator.F90
commit a500b2642aa0a6073ba5d2986faf0a7cb9ab5228
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri Jun 3 13:47:06 2016 -0400
Put sneut5 in its own directory.
Modified the make system so sneut5 is in its own directory
Made sneut5 into a module
Added test cases for URCA-simple with different sneut5 locations.
networks/GPackage.mak
networks/Make.package
networks/ignition_reaclib/URCA-simple-sneut-commented/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/GPackage.mak
networks/ignition_reaclib/URCA-simple-sneut-commented/Make.package
networks/ignition_reaclib/URCA-simple-sneut-commented/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_burner.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_network.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_network_data.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/actual_rhs.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/na23--ne23-toki
networks/ignition_reaclib/URCA-simple-sneut-commented/ne23--na23-toki
networks/ignition_reaclib/URCA-simple-sneut-commented/net_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/physical_constants.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/sneut5.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/table_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/terminator.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/.#out
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/out_pgi
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/out_pgi-acc
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/probin
networks/ignition_reaclib/URCA-simple-sneut-commented/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple-sneut-commented/urca.py
networks/ignition_reaclib/URCA-simple-sneut-local/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-local/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-local/GPackage.mak
networks/ignition_reaclib/URCA-simple-sneut-local/Make.package
networks/ignition_reaclib/URCA-simple-sneut-local/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-local/actual_burner.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_network.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_network_data.f90
networks/ignition_reaclib/URCA-simple-sneut-local/actual_rhs.f90
networks/ignition_reaclib/URCA-simple-sneut-local/na23--ne23-toki
networks/ignition_reaclib/URCA-simple-sneut-local/ne23--na23-toki
networks/ignition_reaclib/URCA-simple-sneut-local/net_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-local/physical_constants.f90
networks/ignition_reaclib/URCA-simple-sneut-local/sneut5.f90
networks/ignition_reaclib/URCA-simple-sneut-local/table_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-local/terminator.f90
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/.#out
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/out_pgi
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/out_pgi-acc
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/probin
networks/ignition_reaclib/URCA-simple-sneut-local/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple-sneut-local/urca.py
networks/ignition_reaclib/URCA-simple-sneut-moduledir/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/GPackage.mak
networks/ignition_reaclib/URCA-simple-sneut-moduledir/Make.package
networks/ignition_reaclib/URCA-simple-sneut-moduledir/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_burner.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_network.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_network_data.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/actual_rhs.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/na23--ne23-toki
networks/ignition_reaclib/URCA-simple-sneut-moduledir/ne23--na23-toki
networks/ignition_reaclib/URCA-simple-sneut-moduledir/net_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/physical_constants.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/table_rates.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/terminator.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/.#out
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/out_gnu
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/out_pgi
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/out_pgi-acc
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/probin
networks/ignition_reaclib/URCA-simple-sneut-moduledir/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple-sneut-moduledir/urca.py
neutrinos/GPackage.mak
neutrinos/Make.package
neutrinos/sneut5.f90
commit 925cedec3d94f6b54c47e1b4ee68c2221f2a8bae
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 2 17:06:32 2016 -0400
Specify that we want a rate calculation in the RHS
integration/VODE/vode_rhs.f90
commit bfbcb1ba00a58d0537c2351fe56ad630f853de80
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jun 2 16:26:30 2016 -0400
Fix typo in GPackage.mak for rprox
networks/rprox/GPackage.mak
commit 09002a44c7c48120542577073108f075f4bb47fa
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Jun 2 15:38:08 2016 -0400
Changed verbose flag to F to avoid GPU errors.
networks/ignition_reaclib/C-burn-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
commit 88628728404717067fb695d1f1331dad375e454c
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Jun 2 11:47:46 2016 -0400
Added EOS consistency call using re after burn.
networks/ignition_reaclib/C-burn-simple/test-cpp/testburn.f90
commit abb1b9ab30377ba9e62f69f74a0ae8fb65c42386
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Jun 2 11:33:10 2016 -0400
Changed EOS rt update to re to use burn energy released.
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
commit eaacef3da3e9b06af36cd02fde1e37c932006639
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu Jun 2 09:06:54 2016 -0400
EOS sync with rt after burn (for debugging)
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
commit f3d49be61a2131f90080fb811aa7d3fef9b32f55
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jun 1 15:17:35 2016 -0400
Update triple alpha for nrates change
networks/triple_alpha_plus_cago/actual_network.f90
commit 3c7e8ef9487ea12eca559b694db8f62ff45723b7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jun 1 09:41:58 2016 -0400
Update module reference
integration/VODE/vode_rpar.f90
commit 359795be95fc9cd0c0ebdef04a561d45109a76eb
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 23:08:46 2016 -0400
Get the VBDF integrator compiling with OpenACC
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/actual_integrator.F90
integration/VBDF/bdf.f90
integration/VBDF/bdf_type.f90
commit a8fc7bc3d855379ceb945d2fd948604f7f6dc85b
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 23:07:40 2016 -0400
Check in OpenACC-aware dgemm routine
util/BLAS/GPackage.mak
util/BLAS/Make.package
util/BLAS/dgemm.f
commit ffa9a45797ff180067622dc6bd1375f95c6ad7ae
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 21:55:24 2016 -0400
Move RHS and Jac into a module
integration/VBDF/bdf.f90
integration/VBDF/vbdf_rhs.f90
commit 05210caec210ec4b41fcd2807f5656b0a23c8241
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 18:04:10 2016 -0400
Fix some OpenACC issues in VBDF
integration/VBDF/vbdf_rhs.f90
integration/VBDF/vbdf_rpar.f90
commit 1b36ce070591ab0f82874ff4e3d2feef52cdbf6a
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 16:18:20 2016 -0400
Allow printing of verbose info on GPU
integration/BS/actual_integrator.F90
commit 22a76c4af4144b3963df06e3e5db5589caca44a5
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 31 16:16:54 2016 -0400
Use a more acc-friendly approach to the Jacobian choice
integration/BS/bs_rhs.f90
commit 92949b666afeefb890f9d8873a54343c4362ea57
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue May 31 15:44:05 2016 -0400
Protect against invalid Jacobian value
integration/BS/bs_rhs.f90
commit 348a2e3b2cd65b09f4ff15ae5e38f6ff2e66cb16
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue May 31 15:26:09 2016 -0400
Fix variable dependency
networks/aprox13/actual_burner_data.f90
commit 2b999f605e9da5572846e54d14ee769a09c4bb01
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue May 31 15:16:52 2016 -0400
Move nrates from burner to network data
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_network_data.f90
networks/aprox19/actual_burner_data.f90
networks/aprox19/actual_network_data.f90
networks/aprox21/actual_burner_data.f90
networks/aprox21/actual_network_data.f90
networks/general_null/actual_burner_data.f90
networks/general_null/actual_network_data.f90
networks/ignition_chamulak/actual_burner_data.f90
networks/ignition_chamulak/actual_network_data.f90
networks/ignition_simple/actual_burner_data.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_network_data.f90
networks/iso7/actual_burner_data.f90
networks/iso7/actual_network_data.f90
networks/powerlaw/actual_burner_data.f90
networks/powerlaw/actual_network_data.f90
networks/rprox/actual_burner_data.f90
networks/rprox/actual_network_data.f90
networks/triple_alpha_plus_cago/actual_burner_data.f90
networks/triple_alpha_plus_cago/actual_network_data.f90
networks/triple_alpha_plus_cago/make.out
commit fbb630cbc0a4ea3d97275cffca9fdf4355b6fc4f
Merge: 21c39f83 98a08218
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue May 31 13:38:37 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 21c39f8386c1cfd55298f780a0f87397e4cb3b22
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Tue May 31 13:37:39 2016 -0400
Updated Makefiles to include sneut5.
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/Make.package
commit 98a08218b1c2122f51ffdc7c14bb7c9a442c5075
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue May 31 13:17:50 2016 -0400
Default to a numerical Jacobian for powerlaw
networks/powerlaw/_parameters
commit ba3c89630abf68870bef7822df898e3e46bedce7
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 17:12:14 2016 -0400
Fix sign on energy release
networks/ignition_simple/actual_burner_data.f90
commit cad87cb061bbff0e2cb8ca27f884ecab2376c437
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 15:31:42 2016 -0400
Fix error in subroutine argument list
integration/VODE/actual_integrator.f90
commit 0473161fc184873b8036823a9b1c64a71a661bdd
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 15:24:37 2016 -0400
Add actual_network_finalize to all networks
networks/aprox13/actual_network.f90
networks/aprox19/actual_network.f90
networks/aprox21/actual_network.f90
networks/general_null/network.template
networks/ignition_chamulak/actual_network.f90
networks/ignition_simple/actual_network.f90
networks/iso7/actual_network.f90
networks/powerlaw/actual_network.f90
networks/rprox/actual_network.f90
networks/triple_alpha_plus_cago/actual_network.f90
commit 56cd5d2410e12493aea04a180be544c1af987a4b
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 15:03:30 2016 -0400
Remove the final EOS call from the burn.
The code that is calling this is now responsible for that.
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.f90
integration/VODE/actual_integrator.f90
commit 55f731ddd0fc9bf2c072a1b7c395ee5f83e60411
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 29 14:12:28 2016 -0400
Don't try to alter the initial burn state
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.f90
integration/VODE/actual_integrator.f90
commit a8dd108836e4fc297c28f0bd4c7dbae93bc3e14c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat May 28 16:35:07 2016 -0400
Correct an EOS call input type
integration/BS/bs_rhs.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/vode_rhs.f90
commit 8f80674b7f4de334e20e7f2a7feb07f779dda251
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 26 17:24:29 2016 -0400
Re-introduced source files I accidentally deleted.
networks/ignition_reaclib/C-burn-simple/.gitignore
networks/ignition_reaclib/C-burn-simple/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple/.gitignore
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
commit f072ab246cc0a7816853105eb1747c53d5ae5e8f
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 26 14:22:18 2016 -0400
Added needed files for URCA python script.
networks/ignition_reaclib/URCA-simple/na23--ne23-toki
networks/ignition_reaclib/URCA-simple/ne23--na23-toki
commit 6d6815a5e9b4a4617b6138ad17adf3a957bf5c61
Merge: 14e49dde 30a7a942
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 26 12:43:05 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 14e49dde138e846d6c8a5661c208c5de79ff880b
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 26 12:41:38 2016 -0400
Revised reaclib networks to contain the script to call pyreaclib.
Removed source files output from pyreaclib.
.gitignore
networks/ignition_reaclib/C-burn-simple/.gitignore
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_burner_data.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_network_data.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/c.py
networks/ignition_reaclib/C-burn-simple/net_rates.f90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/table_rates.f90
networks/ignition_reaclib/C-burn-simple/terminator.f90
networks/ignition_reaclib/C-burn-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/C-burn-simple/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple/.gitignore
networks/ignition_reaclib/URCA-simple/actual_burner.f90
networks/ignition_reaclib/URCA-simple/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_network_data.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/net_rates.f90
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/table_rates.f90
networks/ignition_reaclib/URCA-simple/terminator.f90
networks/ignition_reaclib/URCA-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
networks/ignition_reaclib/URCA-simple/urca.py
commit 30a7a9422bfcede623f2b2baec43cfa30f648fe8
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 26 10:15:36 2016 -0400
Assume that (rho, T) are valid going into the burn
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.f90
integration/VODE/actual_integrator.f90
commit 8b9d8506a6e461d5cf3363dee70e9db725faae24
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Thu May 26 02:42:54 2016 -0400
Reaclib networks clear sanity checks.
Automatically generated Reaclib networks for simple C burning and URCA both give the same answers on the CPU and GPU and the same answers as with the sundials cvode integrator version of the networks.
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_network_data.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/net_rates.f90
networks/ignition_reaclib/C-burn-simple/table_rates.f90
networks/ignition_reaclib/C-burn-simple/test/GNUmakefile
networks/ignition_reaclib/C-burn-simple/test/GPackage.mak
networks/ignition_reaclib/C-burn-simple/test/dummy.probin.template
networks/ignition_reaclib/C-burn-simple/test/eval.f90
networks/ignition_reaclib/C-burn-simple/test/testburn.f90
networks/ignition_reaclib/C-burn-simple/test/testjacobian.f90
networks/ignition_reaclib/URCA-simple/GPackage.mak
networks/ignition_reaclib/URCA-simple/Make.package
networks/ignition_reaclib/URCA-simple/NETWORK_REQUIRES
networks/ignition_reaclib/URCA-simple/actual_burner.f90
networks/ignition_reaclib/URCA-simple/actual_burner_data.f90
networks/ignition_reaclib/URCA-simple/actual_network.f90
networks/ignition_reaclib/URCA-simple/actual_network_data.f90
networks/ignition_reaclib/URCA-simple/actual_rhs.f90
networks/ignition_reaclib/URCA-simple/net_rates.f90
networks/ignition_reaclib/URCA-simple/physical_constants.f90
networks/ignition_reaclib/URCA-simple/table_rates.f90
networks/ignition_reaclib/URCA-simple/terminator.f90
networks/ignition_reaclib/URCA-simple/test-cpp/.#out
networks/ignition_reaclib/URCA-simple/test-cpp/23Na-23Ne_electroncapture.dat
networks/ignition_reaclib/URCA-simple/test-cpp/23Ne-23Na_betadecay.dat
networks/ignition_reaclib/URCA-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/URCA-simple/test-cpp/helm_table.dat
networks/ignition_reaclib/URCA-simple/test-cpp/main.cpp
networks/ignition_reaclib/URCA-simple/test-cpp/probin
networks/ignition_reaclib/URCA-simple/test-cpp/testburn.f90
commit b8ed4945c50befd1e93622a5fedfd99281444996
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Wed May 25 15:52:53 2016 -0400
Removed wayward present_or_copyin.
integration/BS/bs_rhs.f90
commit 3f6faaafa2900c4d996e18289eed3b73aaad8df9
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 14:24:58 2016 -0400
Make the Jacobian analytical by default again
integration/_parameters
commit 13a4aa8fa52c1be1d34b55ff1d204fe69ae11a87
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 14:04:13 2016 -0400
Resolve some makefile issues for Maestro
networks/GPackage.mak
rates/GPackage.mak
commit d6bf01785741183bc060039751a9037bf0ad7e9d
Merge: 0157285a 354035b2
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:57:16 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 0157285a6475751760fbb60045d8fb7a4215c4b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:57:10 2016 -0400
Remove unnecessary acc statement
networks/ignition_simple/actual_burner_data.f90
commit 9890598a085415c9bc2ac989708c7ab2353a615b
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:55:58 2016 -0400
Fix missing module include
integration/VBDF/vbdf_rhs.f90
commit 437b7ade33b9195d99092a6867a92e83e4834685
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:55:38 2016 -0400
Fix broken logic for Maestro build
integration/GPackage.mak
networks/GPackage.mak
commit f16e5e5cba383e9738ace2542a2f7f62099199ac
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 25 09:54:59 2016 -0400
Allow the EOS call at the end of the burn to be disabled
integration/BS/actual_integrator.F90
integration/VBDF/actual_integrator.f90
integration/VODE/actual_integrator.f90
commit 354035b2210596f3a6b8f908f7b4a693a3a651a5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 23:26:59 2016 -0400
just a bit of cleaning of constants -- no answers should change
screening/screen.f90
commit cf6c174c9481b801cd2509fa7f4bec9129f342fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 23:07:36 2016 -0400
some comments
networks/aprox13/actual_burner.f90
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
commit 4bdb8eb77d91b1388a7eb50e75d0046bad32af58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 23:03:24 2016 -0400
we'll need this to define small_x
networks/triple_alpha_plus_cago/test/_parameters
commit 18707c2062c996f1fe73e9a51973acbb7516a18c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 22:07:29 2016 -0400
state -> pstate for clarity for the plasma state
networks/iso7/actual_burner.f90
networks/iso7/actual_rhs.f90
commit 364afa2f4afc2a7850a1e525588fd54aa2cc2829
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue May 24 21:55:32 2016 -0400
a few comments
networks/iso7/actual_burner.f90
commit ac75e8589613bf7a3c61d9bcba3af5873663469f
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 24 09:27:53 2016 -0400
Print out an initialization message
networks/aprox13/actual_burner.f90
commit fcc537eeef12c882fcf4d16b95ce7a0309122b71
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue May 24 09:26:40 2016 -0400
Remove automatic arrays from screenz
networks/ignition_chamulak/actual_rhs.f90
networks/ignition_chamulak/f_rhs.f90
networks/ignition_simple/actual_rhs.f90
networks/ignition_simple_SDC/f_rhs_instantaneous.f90
networks/triple_alpha_plus_cago/screen_module.f90
screening/screen.f90
commit f42c89fc1e42799b55d2d9ac2cf06eba3ebff555
Merge: 8b2aa971 7764a153
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 23 09:13:27 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 8b2aa97157152aed97586a031ba0260ebc33c9ec
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Mon May 23 09:11:18 2016 -0400
Reaclib network compiles and runs with OpenACC markup.
The test-cpp case is working.
This runs together with Castro's test_react setup as well.
integration/BS/bs_rhs.f90
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_burner_data.f90
networks/ignition_reaclib/C-burn-simple/net_rates.f90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/table_rates.f90
networks/ignition_reaclib/C-burn-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/C-burn-simple/test-cpp/probin
commit 7764a153f81104289987f5052ff78236f20508a0
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 22 15:08:21 2016 -0400
Enable a tabulated rates option for aprox13
networks/aprox13/_parameters
networks/aprox13/actual_burner.f90
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_rhs.f90
commit 11a04b07985053f21a463c7d875eed0c43561f70
Author: Max Katz <maxpkatz@gmail.com>
Date: Sun May 22 14:27:14 2016 -0400
Fix incorrect variable type
util/microphysics_math.F90
commit e7b07afe29cb436b15d78df93f70fdee86686376
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 22 04:47:27 2016 -0400
Hack around conflicting parameter definitions
eos/helmholtz/helmholtz.f90
commit 1ddef4adfe0ee6bccfc0b79a06cc102fc807dead
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 22 02:59:43 2016 -0400
Reduce some parameter redundancy in the networks
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_network.f90
networks/aprox13/actual_network_data.f90
networks/aprox19/actual_burner_data.f90
networks/aprox19/actual_network.f90
networks/aprox19/actual_network_data.f90
networks/aprox21/actual_burner_data.f90
networks/aprox21/actual_network.f90
networks/aprox21/actual_network_data.f90
networks/iso7/actual_burner_data.f90
networks/iso7/actual_network.f90
networks/iso7/actual_network_data.f90
commit eed9340b52ec06a298d05a89d3b78a391f871566
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 22 02:46:49 2016 -0400
Hardcode the maximum partial sum array size in esum
util/microphysics_math.F90
commit 5d9f90f0395ac0f5d1f3b1a510b0456d591d9eb1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 22 02:30:23 2016 -0400
Use a hardcoded initial timestep for now
integration/BS/stiff_ode.f90
commit 82d397e2702671ee2a2ac07db8d932847dec6bcc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 22 02:27:59 2016 -0400
Remove an unnecessary automatic array computation
integration/BS/stiff_ode.f90
commit 486a68241127ba5e74659ecd3994ace5c675cdc5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu May 19 19:49:46 2016 -0400
Use dp_t kind rather than double precision in integrators
integration/BS/actual_integrator.F90
integration/BS/bs_rhs.f90
integration/VBDF/actual_integrator.f90
integration/VBDF/vbdf_rhs.f90
integration/VODE/actual_integrator.f90
integration/VODE/vode_convert.f90
integration/VODE/vode_rhs.f90
integration/integration_data.f90
integration/integrator.f90
integration/numerical_jacobian.f90
integration/temperature_integration.f90
commit e6b9dd5b3cf1cc54b306792672b9ea4af54f436a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu May 19 18:26:48 2016 -0400
Mark up gamma_law_general for OpenACC
eos/gamma_law_general/GPackage.mak
eos/gamma_law_general/Make.package
eos/gamma_law_general/gamma_law_general.F90
commit cb8e7da6379e9c3f8c39ef42ca9fc59ae9290750
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu May 19 11:38:34 2016 -0400
Revert the addition of temp/energy scalings to the networks
These seem to cause trouble in certain cases without providing obvious benefit.
networks/aprox13/actual_burner.f90
networks/ignition_simple/actual_burner.f90
networks/rprox/actual_burner.f90
commit 4fa1539528292d0742eaa56b3354ab3b3a193c00
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 18 10:54:50 2016 -0400
Add OpenACC markup to remaining VBDF routines
integration/VBDF/actual_integrator.f90
integration/VBDF/vbdf_convert.f90
integration/VBDF/vbdf_rhs.f90
integration/VBDF/vbdf_rpar.f90
commit 6a99c6ca4f67a7e96dbd605cc5fb47c43f20d7c8
Merge: 5dbea4d7 b2b0177d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri May 13 18:12:34 2016 -0400
Merge pull request #2 from dwillcox/development
Reaclib
commit b2b0177d384ffe83a7014d2686c53fef810552fd
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri May 13 17:43:23 2016 -0400
Renamed reaclib stuff for clarity and to make it easier to add new reaclib networks.
networks/ignition_reaclib/C-burn-simple/GPackage.mak
networks/ignition_reaclib/C-burn-simple/Make.package
networks/ignition_reaclib/C-burn-simple/NETWORK_REQUIRES
networks/ignition_reaclib/C-burn-simple/actual_burner.f90
networks/ignition_reaclib/C-burn-simple/actual_burner_data.f90
networks/ignition_reaclib/C-burn-simple/actual_network.f90
networks/ignition_reaclib/C-burn-simple/actual_network_data.f90
networks/ignition_reaclib/C-burn-simple/actual_rhs.f90
networks/ignition_reaclib/C-burn-simple/net_rates.f90
networks/ignition_reaclib/C-burn-simple/physical_constants.f90
networks/ignition_reaclib/C-burn-simple/table_rates.f90
networks/ignition_reaclib/C-burn-simple/terminator.f90
networks/ignition_reaclib/C-burn-simple/test-cpp/GNUmakefile
networks/ignition_reaclib/C-burn-simple/test-cpp/main.cpp
networks/ignition_reaclib/C-burn-simple/test-cpp/probin
networks/ignition_reaclib/C-burn-simple/test-cpp/testburn.f90
networks/ignition_reaclib/C-burn-simple/test/GNUmakefile
networks/ignition_reaclib/C-burn-simple/test/GPackage.mak
networks/ignition_reaclib/C-burn-simple/test/dummy.probin.template
networks/ignition_reaclib/C-burn-simple/test/eval.f90
networks/ignition_reaclib/C-burn-simple/test/testburn.f90
networks/ignition_reaclib/C-burn-simple/test/testjacobian.f90
commit 9cea205915d9a69eccd3247f4256f98973db1f2a
Merge: b1e62601 5dbea4d7
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri May 13 17:31:34 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit b1e626016807dce0dc80960df5b0932468b9c44d
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri May 13 17:30:22 2016 -0400
ignition_reaclib compiles, runs, and gets the right answer.
Isothermal so far.
networks/ignition_reaclib/GPackage.mak
networks/ignition_reaclib/Make.package
networks/ignition_reaclib/actual_burner.f90
networks/ignition_reaclib/actual_burner_data.f90
networks/ignition_reaclib/actual_network.f90
networks/ignition_reaclib/actual_network_data.f90
networks/ignition_reaclib/actual_rhs.f90
networks/ignition_reaclib/burn_type.f90
networks/ignition_reaclib/net_rates.f90
networks/ignition_reaclib/table_rates.f90
networks/ignition_reaclib/terminator.f90
networks/ignition_reaclib/test-cpp/GNUmakefile
networks/ignition_reaclib/test-cpp/probin
networks/ignition_reaclib/test-cpp/testburn.f90
networks/ignition_reaclib/test/GNUmakefile
networks/ignition_reaclib/test/eval.f90
commit 66d3a4292d1c84c575a9172ef2e73b5388cd492b
Author: Donald Willcox <dwillcox@electra.iacs.stonybrook.edu>
Date: Mon May 9 15:00:28 2016 -0400
Got the reaclib stuff to compile.
networks/ignition_reaclib/GPackage.mak
networks/ignition_reaclib/Make.package
networks/ignition_reaclib/actual_burner_data.f90
networks/ignition_reaclib/actual_network.f90
networks/ignition_reaclib/actual_rhs.f90
networks/ignition_reaclib/net_rates.f90
networks/ignition_reaclib/test-cpp/GNUmakefile
networks/ignition_reaclib/test-cpp/testburn.f90
commit 5dbea4d724be8413b0d2f89b676ebf25a637f7f8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 8 14:42:19 2016 -0400
Write out array data assignments to appease Cray
networks/aprox13/sneut5.f90
commit 5043994aec89dad6126a3eb03abc4e44271fb549
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 8 02:51:53 2016 -0400
Floor the mass fractions at a slightly larger value
integration/BS/bs_rhs.f90
commit 7edd27aa31ce5ee6c1c35c7d18485d2e99807be3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 8 02:51:17 2016 -0400
Fix recently created array initialization issue
networks/aprox13/actual_rhs.f90
commit 61abd4ae8c28b2c2465c9d9174df1a15f2f49072
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat May 7 23:04:45 2016 -0400
Fix recently introduced indexing error
integration/BS/stiff_ode.f90
commit 0383494f01bed8fa3c72ec9ff1197a9abc288e90
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat May 7 21:25:01 2016 -0400
OpenACC-ify aprox13 network
This required various changes like accelerating the rates
and changing the get_tfactors to be a subroutine.
networks/aprox13/actual_burner.f90
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_network.f90
networks/aprox13/actual_network_data.f90
networks/aprox13/actual_rhs.f90
networks/aprox13/sneut5.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
rates/rates.f90
rates/tfactors.f90
util/GPackage.mak
util/Make.package
util/microphysics_math.F90
commit bb75798175ad57f472c81f69edfaad44fc6b6644
Author: Donald Willcox <eugene.willcox@gmail.com>
Date: Fri May 6 16:08:07 2016 -0400
Added ignition_reaclib for testing reaclib network.
networks/ignition_reaclib/GPackage.mak
networks/ignition_reaclib/Make.package
networks/ignition_reaclib/NETWORK_REQUIRES
networks/ignition_reaclib/actual_burner.f90
networks/ignition_reaclib/actual_burner_data.f90
networks/ignition_reaclib/actual_network.f90
networks/ignition_reaclib/actual_network_data.f90
networks/ignition_reaclib/actual_rhs.f90
networks/ignition_reaclib/burn_type.f90
networks/ignition_reaclib/net_rates.f90
networks/ignition_reaclib/physical_constants.f90
networks/ignition_reaclib/table_rates.f90
networks/ignition_reaclib/test-cpp/GNUmakefile
networks/ignition_reaclib/test-cpp/main.cpp
networks/ignition_reaclib/test-cpp/probin
networks/ignition_reaclib/test-cpp/testburn.f90
networks/ignition_reaclib/test/GNUmakefile
networks/ignition_reaclib/test/GPackage.mak
networks/ignition_reaclib/test/dummy.probin.template
networks/ignition_reaclib/test/eval.f90
networks/ignition_reaclib/test/testburn.f90
networks/ignition_reaclib/test/testjacobian.f90
commit d56442c513ff41eefba030da1f421b24b19b9fec
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 00:35:20 2016 -0400
Let the generic wrapper update the OpenACC device data
integration/integrator.f90
networks/ignition_simple/actual_burner.f90
commit b0765c10755a01aa7ee8cb4779f7794959ad4470
Author: Max Katz <maxpkatz@gmail.com>
Date: Thu May 5 00:33:17 2016 -0400
Replace some exit statements we previously removed
integration/BS/stiff_ode.f90
commit 87141d6bde9f962eeafcac4f4784a1c16e220281
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 15:11:11 2016 -0400
Use the new smallt and smalld components of the EOS type
eos/helmholtz/helmholtz.f90
commit 7fa247c91d00896253201927454863e8c3c4cdfe
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 14:40:20 2016 -0400
Remove more obsolete OpenACC stuff
eos/helmholtz/helmholtz.f90
commit c8ec9da7ed565cb46a086ce351c149a491d2d5b6
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 14:39:12 2016 -0400
Remove obsolete OpenACC parameters from Helmholtz
eos/helmholtz/_parameters
commit 21c3b8911226358759b0debb7d8e4e3abc6261bc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 12:49:24 2016 -0400
Check in ignition_simple test
networks/ignition_simple/test-cpp/GNUmakefile
networks/ignition_simple/test-cpp/main.cpp
networks/ignition_simple/test-cpp/probin
networks/ignition_simple/test-cpp/testburn.f90
commit c6c8a33c69383d82615ade30884b4a2c39ff23c1
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 12:26:40 2016 -0400
Fix some OpenACC issues in LINPACK/BLAS
util/BLAS/daxpy.f
util/BLAS/vddot.f
util/LINPACK/dgefa.f
util/LINPACK/dgesl.f
commit 05e664e47afac65cf5c6b5fd26c4133a3006db73
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 10:23:54 2016 -0400
Fix typo
util/BLAS/Make.package
commit 600413fe7aacccc9a9fed9a14b25ca3479309f40
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 10:23:07 2016 -0400
Only hook in LINPACK and BLAS if doing reactions
networks/GPackage.mak
networks/Make.package
commit 59cf3e1e22f270a79a68b48af81a4c55481baf94
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 04:46:07 2016 -0400
OpenACCify the BS integrator
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/actual_integrator.F90
integration/BS/bs_convert.f90
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/BS/stiff_ode.f90
commit 5e774819fa8876a7117a60a02f1825500a37822a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 04:45:04 2016 -0400
Resolve possible circular dependencies in many nets
networks/aprox13/actual_burner.f90
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_burner.f90
networks/aprox19/actual_burner_data.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_burner.f90
networks/aprox21/actual_burner_data.f90
networks/aprox21/actual_rhs.f90
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_burner_data.f90
networks/ignition_chamulak/actual_rhs.f90
networks/iso7/actual_burner.f90
networks/iso7/actual_burner_data.f90
networks/iso7/actual_rhs.f90
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_burner_data.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_rhs.f90
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_burner_data.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
commit 21cef43dd65973c84741d4cd436003be7b978bba
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:58:41 2016 -0400
OpenaCCify the generic integration wrapper routines and data
integration/integration_data.f90
integration/integrator.f90
integration/temperature_integration.f90
commit 0002ec656124d72d3314ca8659c4e116cd25dadc
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:57:25 2016 -0400
OpenACCify the numerical Jacobian
integration/numerical_jacobian.f90
commit 39eadf5287aa151d02c7a101d14280d71887528f
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:52:57 2016 -0400
Remove unintentionally committed temp file
util/BLAS/.#GPackage.mak
commit 498a1b193c85d6878ef78a7f2c7aee4e3bf8b100
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:51:06 2016 -0400
OpenACCify the ignition_simple network
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_burner_data.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_network_data.f90
networks/ignition_simple/actual_rhs.f90
commit e67b5be7015042b876d2898459a0bccb27397531
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:48:11 2016 -0400
Insert our own copies of LINPACK and BLAS
networks/GPackage.mak
networks/Make.package
util/BLAS/.#GPackage.mak
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/BLAS/vddot.f
util/LINPACK/GPackage.mak
util/LINPACK/Make.package
util/LINPACK/dgbfa.f
util/LINPACK/dgbsl.f
util/LINPACK/dgefa.f
util/LINPACK/dgesl.f
commit bf4b70c6ddfb2dcf317e03ea0671b315962c6475
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:46:58 2016 -0400
ACC-ify the screening functions
screening/screen.f90
commit e663fcea087ed6e10abc4a246b90199f9858559a
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed May 4 02:46:21 2016 -0400
Update ACC-ification of the Helmholtz EOS
eos/helmholtz/helmholtz.f90
commit 35cb9ee865aada3802be8bf45636456f13361935
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon May 2 18:47:12 2016 -0400
Do a temperature reset inside the BS RHS
integration/BS/bs_rhs.f90
commit 66d971956f820b4d84c657218f53d5334e829733
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 1 23:57:54 2016 -0400
Add comment explaining BS tolerances
integration/BS/actual_integrator.f90
commit 8ad029dcd56f5e9a7260974e0f31c4ad0c8a4e57
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 1 17:45:27 2016 -0400
Use the VODE initial timestep predictor in BS
integration/BS/bs_type.f90
integration/BS/stiff_ode.f90
commit 8b15b077416b836fc46b15bef2938d33cc3ab959
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 1 03:29:57 2016 -0400
Inform the temperature sanity check with the scaling
integration/BS/bs_rhs.f90
commit 6d6fe8c22005ca7c2f9f581606114a61fa750cba
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 1 03:24:53 2016 -0400
Shrink the initial BS timestep to be safe
integration/BS/stiff_ode.f90
commit ae5502752a4add5fb8715f5b6dc68a78b6e1f647
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 1 03:23:08 2016 -0400
Insert some sanity checks into the BS RHS routine
We need to ensure that the abundances never go larger than one,
and that the temperature stays within a reasonable range. We use
(10**4, 10**11). This seems to be necessary to prevent craziness.
integration/BS/bs_rhs.f90
commit 580200e2c8e09b1818501d21513da62deeb7a40e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun May 1 01:19:58 2016 -0400
Add a function evaluation counter to the bs_t
integration/BS/actual_integrator.f90
integration/BS/bs_rhs.f90
integration/BS/bs_type.f90
integration/BS/stiff_ode.f90
commit 2d89d9ac751e3444819c3a11bce01fa9d0d2b836
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Apr 30 23:59:33 2016 -0400
Resolve the same bug in VBDF
integration/VBDF/vbdf_convert.f90
commit c0c52a1adaad81d4729b28b3dbccdd5aaae42917
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Apr 30 23:57:09 2016 -0400
Resolve a bug in the derived type conversions
We were copying the RHS and Jac from the burn_t into the bs_t,
but forgetting to copy them back out afterward. This meant we
were unintentionally zeroing out the RHS when we, say, called
the Jacobian routine.
integration/BS/bs_convert.f90
commit f945d6b9120a717e7aff96cd58a56e66b1c8015f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Apr 30 23:56:40 2016 -0400
Fix an indexing error in BS
Also, add a comment and pre-empt a possible uninitialized value error.
integration/BS/stiff_ode.f90
commit 80544bb01e2ec0ea362dfa8620e32b723544135b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Apr 29 18:39:21 2016 -0400
Rectify storage of final change in energy for VODE
integration/VODE/actual_integrator.f90
commit b1ed0f2f125555d25dbedeeab5970f1937cc6914
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Apr 29 18:00:58 2016 -0400
Do energy scaling for RHS/Jac in VODE
integration/VODE/vode_convert.f90
commit 1c725c2f69268c88f817508a0da7804dfdcf958b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Apr 29 17:59:35 2016 -0400
Convert the BS integrator to the Microphysics interface
The major limitation is that we can only use one (relative) tolerance,
so for now we default we use the largest relative tolerance.
integration/BS/GPackage.mak
integration/BS/Make.package
integration/BS/actual_integrator.f90
integration/BS/bl_types.f90
integration/BS/bs_convert.f90
integration/BS/bs_rhs.f90
integration/BS/bs_rpar.f90
integration/BS/bs_type.f90
integration/BS/stiff_ode.f90
commit f07f2a513ec47b8afc7dd36d2e15561723d63438
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 21:20:02 2016 -0400
some cleaning
integration/BS/stiff_ode.f90
commit 8f018530a54be113b481a97beda23de9112c0a96
Merge: b03f5095 3c06fc8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 17:41:58 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit b03f5095659938b8e767dcf5c8b3d7b81d50f0b7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 17:41:42 2016 -0400
this seems to work -- it gives the right answer to the VODE test
problem
integration/BS/stiff_ode.f90
integration/BS/test/GNUmakefile
integration/BS/test/f_rhs.f90
commit 3c06fc8e83fe5a6131d25b3ea0edd4f9a3c905a7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 28 13:41:09 2016 -0400
Add the numerical Jacobian option to VBDF
integration/VBDF/vbdf_rhs.f90
commit 266c1265783307a3bb2877084bb2cf32a94e8d77
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 28 13:40:40 2016 -0400
Make the numerical Jacobian available to all networks
integration/GPackage.mak
integration/Make.package
integration/numerical_jacobian.f90
networks/aprox13/actual_rhs_numjac.f90
commit f15108fa6b2bca479bf57d9d244589121dc8a618
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 09:07:24 2016 -0400
this compiles and links now for the VODE test problem
integration/BS/stiff_ode.f90
integration/BS/test/GNUmakefile
integration/BS/test/f_rhs.f90
integration/BS/test/test.f90
commit 69aa34575a0d1aad0a9b98125eda7cde665925ca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 08:29:22 2016 -0400
hook in linpack
integration/BS/stiff_ode.f90
commit 04b80c4dd2f33565b233fb11d98a90ef8ad74f9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Apr 28 08:23:29 2016 -0400
hook in Castro's LINPACK
integration/BS/test/GNUmakefile
commit 8b8793832b4e692306383cd4efa687e74604f5dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 27 21:36:47 2016 -0400
part of the LU decomposition
integration/BS/stiff_ode.f90
commit 02ce7666ab0986473e59616ecb4e3ce4f11ca97e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 27 21:25:39 2016 -0400
this compiles now but still needs the LU hooks
integration/BS/stiff_ode.f90
commit e242ef63d1e912821510e43c5c0ce55fbace5873
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 27 19:49:44 2016 -0400
a lot of cleaning towards getting this to compile
integration/BS/stiff_ode.f90
commit 4ad39e0c735bffa9d6c79662fb24932a4106a9e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Apr 27 15:40:30 2016 -0400
crude makefile just for initial testing
integration/BS/bl_types.f90
integration/BS/stiff_ode.f90
integration/BS/test/GNUmakefile
commit 45f791ddcb4e6b9cea15a900fe0e3aaf7c1370a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 26 22:57:44 2016 -0400
more progress
integration/BS/stiff_ode.f90
commit 9e52a70a360b10d54be493536300865f8b34d984
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 26 15:22:46 2016 -0400
add LAPACK files -- these will be moved eventually, but
this is the LU decomposition stuff
integration/BS/LAPACK/dgetf2.f
integration/BS/LAPACK/dgetrf.f
integration/BS/LAPACK/dlamch.f
integration/BS/LAPACK/dlaswp.f
integration/BS/LAPACK/ieeeck.f
integration/BS/LAPACK/ilaenv.f
integration/BS/LAPACK/iparmq.f
integration/BS/LAPACK/lsame.f
integration/BS/LAPACK/xerbla.f
commit a6ba18939cd06e7f386182daebcb95be478a7615
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Apr 26 12:50:50 2016 -0400
start of a new Burlish-Stoer integrator
integration/BS/stiff_ode.f90
commit 0f5eb71cc0a9a24ff63f620fe79453e81b2531cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Apr 25 21:00:55 2016 -0400
a numerical Jacobian
networks/aprox13/actual_rhs_numjac.f90
commit 2969dad321a9c91cbdbec322a6f0fb7771f21d6f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 25 16:59:38 2016 -0400
Update aprox13 test; this fails with VBDF
networks/aprox13/test-cpp/GNUmakefile
networks/aprox13/test-cpp/testburn.f90
commit fac512ad9192890c348e797a7345b3a66fff983c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 25 16:57:03 2016 -0400
Strip allocatables out of VBDF
integration/VBDF/actual_integrator.f90
integration/VBDF/bdf.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_rpar.f90
commit 9ce18a74c77874732917be0ac72e8d958d5042ba
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 25 16:06:43 2016 -0400
Use have_rates in some networks
integration/VBDF/vbdf_convert.f90
integration/VBDF/vbdf_rhs.f90
integration/VBDF/vbdf_rpar.f90
integration/VODE/vode_convert.f90
integration/VODE/vode_rpar.f90
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/ignition_simple/actual_rhs.f90
commit dc3d2277b18aeb3f28338dfb0831afc50b9e9272
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 25 15:07:49 2016 -0400
Add c**2 energy scaling
networks/aprox13/actual_burner.f90
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
networks/ignition_simple/actual_burner.f90
networks/iso7/actual_burner.f90
commit 1d2a5bde0101e860d6c9619395830a2f8197ee9b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 25 14:54:59 2016 -0400
Add an energy scaling parameter to the integrators
integration/VBDF/actual_integrator.f90
integration/VBDF/vbdf_convert.f90
integration/VODE/vode_convert.f90
integration/integration_data.f90
commit e2faf052d494ffdedc966bad17d460e0eb33dd7c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 25 13:57:02 2016 -0400
Fix subroutine reference missed in previous commit
networks/powerlaw/actual_burner.f90
commit b726c38d4eb5ae24edc64b9cb2d700604b308f93
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Apr 22 00:26:55 2016 -0400
Initiate the process of using the VBDF integrator
This comes from MAESTRO/Util/VBDF/dev/oac.bdf.f90, with appropriate
changes made for the syntax we use here in Microphysics. This
compiles, but no attempt has yet been made to debug the actual run
behavior. The OpenACC bits have been stripped out in anticipation
of the fact that we're eventually going to be calling this in
!$acc routine mode, not as a standalone driver from the CPU.
integration/VBDF/GPackage.mak
integration/VBDF/Make.package
integration/VBDF/actual_integrator.f90
integration/VBDF/bdf.f90
integration/VBDF/bdf_type.f90
integration/VBDF/vbdf_convert.f90
integration/VBDF/vbdf_rhs.f90
integration/VBDF/vbdf_rpar.f90
commit 68f60bfc8783b01dc9a634654c4230b275bfb209
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 23:54:25 2016 -0400
Remove duplicate module reference
integration/VODE/vode_rhs.f90
commit c615ef507b23fd67f57eaa3534560f64c9936925
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 23:54:07 2016 -0400
Fix obsolete reference to filename
integration/VODE/actual_integrator.f90
commit 85aadeb68c856f49b41f0ba4ba9834c170148a24
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 23:45:02 2016 -0400
Have the INTEGRATOR_DIR directly set the make path
integration/Make.package
commit 12a53c109784a036e705ec3c428058f908fa653e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 23:01:12 2016 -0400
Reset the dT_crit data if we retry the burn
integration/VODE/actual_integrator.f90
commit f4be0f27fa7e9a389f2949dd58b29e903f50d173
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 16:51:29 2016 -0400
Standardize the integrator interface
For networks that want to use the built-in integrators, they
now simply call integrator() from inside actual_burner().
integrator then calls actual_integrator, which will depend on
which integrator you chose at compile time. You can choose a
different one by setting INTEGRATOR_DIR appropriately, the same
way one would do this for EOS_DIR or NETWORK_DIR.
integration/GPackage.mak
integration/Make.package
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/actual_integrator.f90
integration/_parameters
integration/integration.f90
integration/integrator.f90
networks/aprox13/actual_burner.f90
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
networks/ignition_chamulak/actual_burner.f90
networks/ignition_simple/actual_burner.f90
networks/iso7/actual_burner.f90
networks/powerlaw/actual_burner.f90
networks/rprox/actual_burner.f90
networks/triple_alpha_plus_cago/actual_burner.f90
commit 48afe1a071461a8b13a8963fe919b155b2a1df00
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 11:25:36 2016 -0400
Fix another bug in dT_crit functionality
integration/temperature_integration.f90
commit 3f8fb217c8f81c101c08182751ea070ff019f2f0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 10:30:58 2016 -0400
Fix bug in recent dT_crit functionality
The last commit unsafely tested on the value of dcv/dt and dcp/dt
but this was an issue because of interconversions between derived
types that lost its value. Now we just use the value of dT_crit
to determine when to use the specific heat linear predictor.
integration/VODE/vode_module.f90
integration/temperature_integration.f90
commit 78f165eb45ae60ed983ed2e84c03996ac5d91fdc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 21 09:53:34 2016 -0400
Enable the dT_crit functionality for the VODE burner
This reproduces a piece of code that was in some of the burners
we used before the switch to Microphysics. dT_crit is a real
variable that expresses the fractional change in temperature
one would like between calls to the EOS to re-evaluate the
thermodynamic derivatives (i.e. c_v and c_p). One new thing is
that in between EOS calls we do a first-order prediction of those
specific heats using a numerical difference estimate of dc_v/dt
and dc_p/dt.
UsersGuide/runtime_parameters/runtime_parameters.tex
integration/VODE/vode_convert.f90
integration/VODE/vode_module.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_rpar.f90
integration/_parameters
integration/temperature_integration.f90
commit fc67351846439ebb9f5eb34d983d8dfb765962f5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Apr 19 14:01:08 2016 -0400
Remove the chemical potential from all equations
We have agreed that the chemical potential terms, including
de/dX and dh/dX from the equation of state, should vanish
identically. They don't numerically, though, due to the finite
numerical timesteps encountered in the burn. So we are removing
them to prevent them from creating unphysical errors.
UsersGuide/runtime_parameters/runtime_parameters.tex
integration/_parameters
integration/temperature_integration.f90
networks/ignition_simple/actual_rhs.f90
commit a13e5d6867e56abad0ee0c2899ee0c71bfca8fc2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Apr 17 15:58:46 2016 -0400
Use eos_input_burn for EOS calls
integration/VODE/vode_module.f90
integration/VODE/vode_rhs.f90
commit 4ddd0ca897503fe396307f18d57a22e8ffbfb096
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Apr 17 15:42:02 2016 -0400
Evolve only C12 in ignition_simple, as before
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_network_data.f90
networks/ignition_simple/actual_rhs.f90
commit 31e64902c110f2bda71430fae45b2276a5d484d9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 20:48:53 2016 -0400
add runtime parameters chapter that is automagically generated using
the _parameter files
UsersGuide/runtime_parameters/rp.py
UsersGuide/runtime_parameters/runtime_parameters.tex
UsersGuide/userguide.tex
integration/_parameters
commit 5051236b5b053d13593ce75d762dfbb4a01f4600
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 19:01:27 2016 -0400
use our standard symbols latex include
UsersGuide/GNUmakefile
UsersGuide/maestrosymbols.tex
UsersGuide/networks/networks.tex
UsersGuide/refs.bib
UsersGuide/userguide.tex
commit fb5087ff1ee7508883471aa4bb6eda3978e12c8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 18:53:18 2016 -0400
compartamentalize
UsersGuide/EOS/eos.tex
UsersGuide/GNUmakefile
UsersGuide/networks/networks.tex
UsersGuide/userguide.tex
commit 405931623e002a3d573c3f1dca0369f138ca9372
Merge: 9ba342df e00dcd7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 18:37:00 2016 -0400
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 9ba342dfb6c52a76c421f980472811e46d736fc2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 16 18:36:33 2016 -0400
rename, we have MAESTRO/docs and Castro/UsersGuide, no need for
a 3rd naming convention...
UsersGuide/.gitignore
UsersGuide/GNUmakefile
UsersGuide/README.md
UsersGuide/refs.bib
UsersGuide/userguide.tex
commit e00dcd7cc95497ec939738fb98e70c1391e77205
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Apr 16 18:02:53 2016 -0400
Permit the chemical potential terms in the temperature equation to be disabled
integration/_parameters
integration/temperature_integration.f90
commit 1663ad8ad0f38208dccae8b52ec3dcd6269e6b61
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Apr 14 21:45:32 2016 -0400
aprox13 test that gets tripped up in small timesteps with the analytical Jacobian.
networks/aprox13/test-cpp/probin
networks/aprox13/test-cpp/testburn.f90
commit d403ca7093569df73ea82155e81eb8f74033090f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 23:50:36 2016 -0400
Limit the Newton iteration changes logarithmically
eos/stellarcollapse/stellarcollapse.f90
commit bcf985b9fd9e657b1901062441991d4ae7a84550
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 23:47:58 2016 -0400
Save a conversion factor
eos/stellarcollapse/eos_aux_data.f90
commit cadbb9548163eb4b44203a1cee762ebb51ec85da
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 23:06:00 2016 -0400
Fix stellarcollapse so that it compiles and meaningfully runs
eos/stellarcollapse/eos_aux_data.f90
eos/stellarcollapse/stellarcollapse.f90
commit 7a15c43791a4a33184216fce112ef4316f928bf9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 16:49:54 2016 -0400
Forgot to update general_null in a previous commit
networks/general_null/network.template
commit e0668f9c02f8ad7790bf70b6e0dab4d4054cda1e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 16:48:08 2016 -0400
powerlaw now only explicitly evolves nspec_evolve = 2 components. The third (inert) species does not participate in the burning.
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_network_data.f90
networks/powerlaw/actual_rhs.f90
commit ba172960d4ebbcbba1802f5bc8c89e8c38b03656
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 16:46:57 2016 -0400
Evolve only nspec_evolve species, not the full nspec.
integration/VODE/vode_convert.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_rpar.f90
integration/temperature_integration.f90
commit 0a35c55834fe2ac81de418c3829904711e0049c1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 11:25:37 2016 -0400
Add an nspec_evolve parameter to each network. At present it is the same as the number of species in each case.
networks/aprox13/actual_network_data.f90
networks/aprox19/actual_network_data.f90
networks/aprox21/actual_network_data.f90
networks/ignition_chamulak/actual_network_data.f90
networks/ignition_simple/actual_network_data.f90
networks/iso7/actual_network_data.f90
networks/powerlaw/actual_network_data.f90
networks/rprox/actual_network_data.f90
networks/triple_alpha_plus_cago/actual_network_data.f90
commit f802e439a9d9680c99c39bd397667b79c5aea111
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 11 08:55:00 2016 -0400
Allow the burner part of the networks to be disabled in the GPackage.mak
networks/aprox13/GPackage.mak
networks/aprox19/GPackage.mak
networks/aprox21/GPackage.mak
networks/general_null/GPackage.mak
networks/ignition_chamulak/GPackage.mak
networks/ignition_simple/GPackage.mak
networks/ignition_simple_SDC/GPackage.mak
networks/iso7/GPackage.mak
networks/kpp/GPackage.mak
networks/powerlaw/GPackage.mak
networks/rprox/GPackage.mak
networks/triple_alpha_plus_cago/GPackage.mak
networks/xrb_simple/GPackage.mak
commit 4250ef6877724fdb80ab2d1d4ee3c1460ea4704b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Apr 4 19:58:25 2016 -0400
Updated test problem for aprox13; this currently breaks with a negative temperature.
networks/aprox13/test-cpp/probin
networks/aprox13/test-cpp/testburn.f90
commit 736fcd22a707c4bcec01d6fd7f22ca60d68ea289
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Mar 29 12:10:56 2016 -0400
add this for now -- it still needs to be updated to the new format
networks/xrb_simple/GPackage.mak
networks/xrb_simple/NETWORK_REQUIRES
networks/xrb_simple/burner_aux.f90
networks/xrb_simple/f_rhs.f90
networks/xrb_simple/network_indices.f90
networks/xrb_simple/test/GNUmakefile
networks/xrb_simple/test/GPackage.mak
networks/xrb_simple/test/testburn.f90
networks/xrb_simple/xrb_simple_burner.f90
networks/xrb_simple/xrb_simple_network.f90
commit d333befc41fc1655278386bf6ba7dde03b804eec
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Mar 28 14:26:31 2016 -0400
Add a renormalize_abundances parameter that, well, renormalizes abundances at each step. Off by default.
integration/VODE/vode_rhs.f90
integration/_parameters
commit cdfa14a2e02ccd2262a77daa7a887e6cc149fc81
Merge: 03dfee6a 23ce784e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Mar 28 10:18:55 2016 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 23ce784e70950d4e9f25258ca5da4b30824c0302
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Mar 26 13:25:01 2016 -0400
Ensure that mass fractions always stay at least slightly positive in the integration.
integration/VODE/vode_rhs.f90
commit 03dfee6a15e4d2a004a9b05e5f89c9f81d265115
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Mar 18 23:11:17 2016 -0400
Add some parameters that allow us to retry a burn when the integration fails, using looser tolerances. This feature is disabled by default.
integration/VODE/vode_module.f90
integration/_parameters
commit 45ed859b6c1dc80d831d93f9728986d6ad6e1ddc
Merge: 39f356cd 7c273308
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 11 12:53:46 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 39f356cdb45a7d012c78685be2ac21da85cfdc85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 11 12:53:39 2016 -0500
update README
eos/README.md
commit 6cfc7777daa4a0bf8ddec9c0eb0412bbea2d876a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 11 12:49:09 2016 -0500
update README
README.md
commit 7c2733089251fda9110da9b9eb770589b34eac58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 11 11:54:11 2016 -0500
do something for the entropy -- note that this is not completely correct for a multigamma
EOS.
eos/multigamma/multigamma.f90
commit 1fff9235c23b6953c79f7c877420588817cb0545
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Mar 11 09:57:59 2016 -0500
fix punctuation in comment :)
eos/gamma_law_general/gamma_law_general.f90
commit 0b85e5f0de65dbf647b8d6348e827e2f67f930e1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Mar 10 21:55:14 2016 -0500
Fix uninitialized variable issue that was causing the double iteration mode of Helmholtz to work incorrectly.
eos/helmholtz/helmholtz.f90
commit 6b0210ba85aca7c081a80dbb3137ee6ae41500dc
Merge: 3b7dbf23 fda4de0e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 10 11:43:48 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit 3b7dbf23ca255934af000fad13e9da244936b0d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 10 11:43:34 2016 -0500
remove trailing whitespace
eos/helmholtz/helmholtz.f90
commit fda4de0e346383dfac17c728c4fcfb7f557a7860
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Feb 13 23:23:09 2016 -0500
Remove unused variables
networks/aprox13/actual_rhs.f90
commit f1bba3ff359a8df54dd6e8ef54959ad24f8cb4a4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Feb 9 14:10:28 2016 -0500
Migrate ignition_chamulak to the new burner interface
networks/README
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_burner_data.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_chamulak/actual_network_data.f90
networks/ignition_chamulak/actual_rhs.f90
commit bc7a589e723dd87cc23eff14a1e94225745c0dd3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Feb 9 12:20:16 2016 -0500
Update triple_alpha_plus_cago to the new interface
networks/README
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_network.f90
networks/triple_alpha_plus_cago/actual_network_data.f90
networks/triple_alpha_plus_cago/actual_rhs.f90
networks/triple_alpha_plus_cago/burner_aux.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/f_rhs.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
commit d72844fde749a923f6eb914fdc305395d6a6e92a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 10:03:09 2016 -0500
We don't need to pass nrates/nspec to init_rpar_indices, we can get that from the appropriate modules.
integration/VODE/vode_module.f90
integration/VODE/vode_rpar.f90
commit 112e6f7d2e0b33cc3a9f28e46aab5f1b8bea0e7d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 10:00:50 2016 -0500
Add a generic integration_init routine that handles the call to the initialization for the specific integrator we're using. With this commit, there are no longer any reference to VODE in the actual burners themselves.
integration/VODE/vode_module.f90
integration/integration.f90
networks/aprox13/actual_burner.f90
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
networks/ignition_simple/actual_burner.f90
networks/iso7/actual_burner.f90
networks/powerlaw/actual_burner.f90
networks/rprox/actual_burner.f90
commit d9dd307f965a342ea1798b18da3d3cb418d17ae2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 09:47:44 2016 -0500
Always add in the integration module if we've got reactions enabled.
networks/GPackage.mak
networks/Make.package
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/iso7/GPackage.mak
networks/iso7/Make.package
networks/powerlaw/Make.package
networks/rprox/Make.package
commit a9286a5e9997ac2dc5daacc064e6fbf0a43945ca
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 09:41:02 2016 -0500
Create a wrapper interface, do_burn, so that we're not calling VODE directly from the actual_burner. This gives us flexibility to add other integration software in the future. Correspondingly, create an integrator parameter.
integration/GPackage.mak
integration/Make.package
integration/VODE/Make.package
integration/VODE/vode_convert.f90
integration/VODE/vode_module.f90
integration/VODE/vode_rhs.f90
integration/_parameters
integration/integration.f90
integration/integration_data.f90
integration/temperature_integration.f90
networks/aprox13/actual_burner.f90
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
networks/ignition_simple/actual_burner.f90
networks/iso7/actual_burner.f90
networks/powerlaw/actual_burner.f90
networks/rprox/actual_burner.f90
networks/rprox/actual_rhs.f90
commit 56c5583c561dbdcaa58441bdea2bb0d71475e3bc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 02:02:38 2016 -0500
Move all VODE-specific integration code to a VODE subdirectory in the top-level integration directory
integration/GPackage.mak
integration/Make.package
integration/VODE/GPackage.mak
integration/VODE/Make.package
integration/VODE/vode_convert.f90
integration/VODE/vode_data.f90
integration/VODE/vode_module.f90
integration/VODE/vode_rhs.f90
integration/VODE/vode_rpar.f90
integration/_parameters
commit 053e4e8c73c27e26830145e1e4abf0e290cf6526
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 01:55:36 2016 -0500
We do support general_null too!
networks/README
commit 288e9516e0a8f53e3b43ccc0ee07c21d3de754a8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 01:55:14 2016 -0500
Add an actual_rhs_module to general_null, for consistency
networks/general_null/Make.package
networks/general_null/actual_rhs.f90
commit 92e83c368f9ba68a7e0bfd60f38feb5dd32929b2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Feb 5 01:47:35 2016 -0500
Rewrite the currently-supported networks so that their RHS interfaces take a burn_t derived type, rather than VODE data. This allows more flexibility in the future, both in terms of using different integrators with these networks, and in terms of allowing the RHS routines to be called in other parts of the BoxLib codes.
integration/Make.package
integration/rhs.f90
integration/temperature_integration.f90
integration/vode_convert.f90
integration/vode_data.f90
integration/vode_module.f90
integration/vode_rhs.f90
integration/vode_rpar.f90
networks/aprox13/actual_burner.f90
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_rhs.f90
networks/aprox13/test-cpp/testburn.f90
networks/aprox13/test-cpp/testjacobian.f90
networks/aprox19/actual_burner.f90
networks/aprox19/actual_rhs.f90
networks/aprox19/test-cpp/testburn.f90
networks/aprox19/test-cpp/testjacobian.f90
networks/aprox21/actual_burner.f90
networks/aprox21/actual_rhs.f90
networks/aprox21/test-cpp/testburn.f90
networks/aprox21/test-cpp/testjacobian.f90
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_burner_data.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_rhs.f90
networks/iso7/actual_burner.f90
networks/iso7/actual_rhs.f90
networks/iso7/test-cpp/testburn.f90
networks/iso7/test-cpp/testjacobian.f90
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_rhs.f90
networks/rprox/actual_burner.f90
networks/rprox/actual_burner_data.f90
networks/rprox/actual_rhs.f90
commit 455ef4d4d4c9d99beb5f1000abe4b21240468a8f
Merge: 2d722a4d a737a25a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 14:55:20 2016 -0500
Merge branch 'master' into development
commit a737a25ade9cadec544d0859ee4d06dc24de1908
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Feb 4 14:55:01 2016 -0500
update instructions
README.md
commit 2d722a4d1a9dffdeeca42578290eef4cbaac74c9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Feb 3 15:54:17 2016 -0500
assign high priority to burning_mode so we can override the
default specified in integration/
networks/powerlaw/_parameters
commit 241f9ed3b594e256deaa99ede64f3cd57a32c7be
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Feb 2 19:23:01 2016 -0500
Restore commented line
networks/powerlaw/actual_rhs.f90
commit 37dc4672df2e73e75096b5c713bee06afceedda1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Feb 2 13:39:56 2016 -0500
Get the powerlaw energy generation format in sync with other networks
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_rhs.f90
commit 3d3869cfa57309298ac0013043dfd8caecddf8b7
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 2 11:55:45 2016 -0500
Get the energy generation for ignition_simple in sync with what we have in the other networks
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_network_data.f90
networks/ignition_simple/actual_rhs.f90
commit 0e4baf89ce5f2287108a862f5d59ac57484a47b8
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Feb 2 11:06:40 2016 -0500
Be a little more careful with EOS states in the VODE integration. Also, fixed a bug where we were forgetting to update the energy after an EOS call.
integration/vode_module.f90
commit d64aef68fd6146065d8953a5e49255e3b647b739
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 17:47:29 2016 -0500
Add a README with a note on which networks are actively supported
networks/README
commit 45c24447906fd271bb918f5bd7a23448e77c87d7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 17:37:43 2016 -0500
Delete some files that are no longer used
networks/powerlaw/burner_aux.f90
networks/powerlaw/f_rhs.f90
commit 8020cb20a7d3aad5aadf9526dd8040a9a43a843d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 17:34:40 2016 -0500
Switch ignition_simple over to the generic VODE burner interface.
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_burner_data.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_rhs.f90
networks/ignition_simple/f_rhs.f90
networks/ignition_simple/rpar_indices.f90
commit 2dc28f62d1f06040ff6bffd210c8a47c1d316c0b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 16:57:45 2016 -0500
Switch the active networks over to use the burn_t derived type rather than the eos_t derived type.
integration/vode_module.f90
networks/aprox13/actual_burner.f90
networks/aprox19/actual_burner.f90
networks/aprox21/actual_burner.f90
networks/general_null/actual_burner.f90
networks/ignition_simple/actual_burner.f90
networks/iso7/actual_burner.f90
networks/powerlaw/actual_burner.f90
networks/rprox/actual_burner.f90
commit 2fcd77edcc0ba7cdde4254a02708927969c72302
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 16:22:58 2016 -0500
Remove obsolete file
networks/THREADSAFE
commit f33e67b5f7e9c46eaf670da9c82dc8e04024f38f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 16:21:56 2016 -0500
Apply the new module changes to rprox
networks/rprox/GPackage.mak
networks/rprox/Make.package
networks/rprox/actual_burner.f90
networks/rprox/actual_burner_data.f90
networks/rprox/actual_network.f90
networks/rprox/actual_network_data.f90
networks/rprox/actual_rhs.f90
networks/rprox/network_indices.f90
commit 00dee7d48e4a345e331186ffbb450c7d1328ad89
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 16:12:42 2016 -0500
Add missing use statement
networks/powerlaw/actual_burner.f90
commit 50c9db3a87c1e30be096448018de6c5c9e67ab69
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Feb 1 15:55:24 2016 -0500
New network/burner requirement: each network directory should have modules called actual_burner_data and actual_network_data. This is where data like nspec, nrates, and naux should be stored, as well as species/rate indices, etc. It is mandatory in particular that those three are included in the respective modules, even if nrates == 0. Right now the only networks that have been changed are ones that are actually used in Castro, but we'll be expanding to the rest soon. With this change, we can avoid circular module dependencies in cases where external code needs information like the number of rates.
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_burner.f90
networks/aprox13/actual_burner_data.f90
networks/aprox13/actual_network.f90
networks/aprox13/actual_network_data.f90
networks/aprox13/actual_rhs.f90
networks/aprox13/test-cpp/testburn.f90
networks/aprox13/test-cpp/testjacobian.f90
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox19/actual_burner.f90
networks/aprox19/actual_burner_data.f90
networks/aprox19/actual_network.f90
networks/aprox19/actual_network_data.f90
networks/aprox19/actual_rhs.f90
networks/aprox19/test-cpp/testburn.f90
networks/aprox19/test-cpp/testjacobian.f90
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/aprox21/actual_burner.f90
networks/aprox21/actual_burner_data.f90
networks/aprox21/actual_network.f90
networks/aprox21/actual_network_data.f90
networks/aprox21/actual_rhs.f90
networks/aprox21/test-cpp/testburn.f90
networks/aprox21/test-cpp/testjacobian.f90
networks/general_null/GPackage.mak
networks/general_null/Make.package
networks/general_null/actual_burner.f90
networks/general_null/actual_burner_data.f90
networks/general_null/actual_network_data.f90
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/actual_burner_data.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple/actual_network_data.f90
networks/iso7/GPackage.mak
networks/iso7/Make.package
networks/iso7/actual_burner.f90
networks/iso7/actual_burner_data.f90
networks/iso7/actual_network.f90
networks/iso7/actual_network_data.f90
networks/iso7/actual_rhs.f90
networks/iso7/test-cpp/testburn.f90
networks/iso7/test-cpp/testjacobian.f90
networks/powerlaw/GPackage.mak
networks/powerlaw/Make.package
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_burner_data.f90
networks/powerlaw/actual_network.f90
networks/powerlaw/actual_network_data.f90
networks/powerlaw/actual_rhs.f90
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_burner_data.f90
networks/triple_alpha_plus_cago/actual_network.f90
networks/triple_alpha_plus_cago/actual_network_data.f90
networks/triple_alpha_plus_cago/burner_aux.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/f_rhs.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
networks/triple_alpha_plus_cago/test/testjacobian.f90
userguide/userguide.tex
commit 4ba2a90289ff3411368c4579731e2504d4f3a4b6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 29 00:49:21 2016 -0500
Fix incorrect variable in test module
networks/iso7/test-cpp/testjacobian.f90
commit b2420665cade298c75179efa85a3d98701236516
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jan 28 23:49:40 2016 -0500
Use the new esum routine in aprox13/aprox19/aprox21/iso7.
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
networks/aprox21/actual_rhs.f90
networks/iso7/actual_rhs.f90
commit 50072cd99e95ac551e72a57f051eb9351e2f4da5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jan 28 23:46:17 2016 -0500
Add a math module to Microphysics. Right now it contains an exact summation routine, which we will use in some of the networks where higher accuracy is needed.
networks/GPackage.mak
networks/Make.package
networks/aprox13/actual_rhs.f90
util/GPackage.mak
util/Make.package
util/microphysics_math.f90
commit e011991feb3198bb782c2ec4812135cf77b2dc79
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jan 28 23:22:33 2016 -0500
Fix logic for the case of hybrid burning
integration/vode_module.f90
commit e2e16a5300ede0eed74972b5a5769a3108ba67df
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 26 15:29:50 2016 -0500
Fix comment
integration/_parameters
commit 341e0da4569c377631819e927ca741134764f58b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 23 20:03:05 2016 -0500
Use msum routine
networks/aprox13/actual_rhs.f90
commit b484a25608b317e8b7154306d85bf728f1bc44ef
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 22 02:05:41 2016 -0500
The Helmholtz EOS turns off the Coulomb corrections if the pressure goes negative because of them, but this is not enough to keep the hydro happy; we also need a cutoff if the energy goes negative, which is now implemented.
eos/helmholtz/helmholtz.f90
commit 782de2cd1b58ac434c2c2172b868291081e6006b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 20 11:39:15 2016 -0500
Remove unused variable
integration/rhs.f90
commit f7ce25206213c2997637730dbf81e76f948f9389
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 17:50:39 2016 -0500
iso7 network
networks/iso7/GPackage.mak
networks/iso7/Make.package
networks/iso7/NETWORK_REQUIRES
networks/iso7/README
networks/iso7/actual_burner.f90
networks/iso7/actual_network.f90
networks/iso7/actual_rhs.f90
networks/iso7/network_indices.f90
networks/iso7/sneut5.f90
networks/iso7/test-cpp/GNUmakefile
networks/iso7/test-cpp/main.cpp
networks/iso7/test-cpp/probin
networks/iso7/test-cpp/testburn.f90
networks/iso7/test-cpp/testjacobian.f90
commit 8d0123b58253f794a89d5d58c387ff7409997977
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 15:26:54 2016 -0500
Use quad precision sums in the Jacobian
networks/aprox13/actual_rhs.f90
networks/aprox19/actual_rhs.f90
commit 0ce87184e50ba77e7d85a6cdbb3a1d6691b71316
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 15:26:36 2016 -0500
Add aprox21 network
networks/aprox21/GPackage.mak
networks/aprox21/Make.package
networks/aprox21/NETWORK_REQUIRES
networks/aprox21/README
networks/aprox21/actual_burner.f90
networks/aprox21/actual_network.f90
networks/aprox21/actual_rhs.f90
networks/aprox21/network_indices.f90
networks/aprox21/sneut5.f90
networks/aprox21/test-cpp/GNUmakefile
networks/aprox21/test-cpp/main.cpp
networks/aprox21/test-cpp/probin
networks/aprox21/test-cpp/testburn.f90
networks/aprox21/test-cpp/testjacobian.f90
rates/rates.f90
commit 640f4aea3768993e1eb55ece34fd749a937b7854
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 12:37:29 2016 -0500
Add Frank Timmes' aprox19 network
networks/aprox19/GPackage.mak
networks/aprox19/Make.package
networks/aprox19/NETWORK_REQUIRES
networks/aprox19/README
networks/aprox19/actual_burner.f90
networks/aprox19/actual_network.f90
networks/aprox19/actual_rhs.f90
networks/aprox19/network_indices.f90
networks/aprox19/sneut5.f90
networks/aprox19/test-cpp/GNUmakefile
networks/aprox19/test-cpp/main.cpp
networks/aprox19/test-cpp/probin
networks/aprox19/test-cpp/testburn.f90
networks/aprox19/test-cpp/testjacobian.f90
commit 5a8f643cc8f1e3924d56b18725d6f5aa905812d5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 12:33:08 2016 -0500
Add the extra rates needed for aprox19
rates/rates.f90
commit 4eb519ddf78577ddbb4afef36871bbed171e106e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 11:58:50 2016 -0500
Add eta and y_e to the rpar array -- we're going to need these for aprox19.
integration/rhs.f90
integration/rpar_indices.f90
commit 02b3deef9216ccee294b5a1c322c538591d21fe5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 15 09:37:06 2016 -0500
Forgot to commit a new file for rprox
networks/rprox/network_indices.f90
commit 7547f4859b325639bad173c5ec5209c66ba53d63
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jan 14 11:15:04 2016 -0500
Restore the deleted lines where we initialized enuc to zero
integration/vode_module.f90
commit b353e9af32a5dd8aa0856e562e5a022c8a04f00c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jan 14 10:06:47 2016 -0500
Add save attribute
integration/vode_data.f90
commit 931c79406fe40fc556d12b20039465322c5c2b7e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jan 14 09:46:27 2016 -0500
Fix module reference
networks/aprox13/test-cpp/testjacobian.f90
commit 2a981952b13adf186df4f94da3cb2e7ac18c5be6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 21:14:52 2016 -0500
Rewrite the rprox network using the new generic VODE interface
networks/rprox/GPackage.mak
networks/rprox/Make.package
networks/rprox/README
networks/rprox/actual_burner.f90
networks/rprox/actual_network.f90
networks/rprox/actual_rhs.f90
networks/rprox/burner_aux.f90
networks/rprox/f_rhs.f90
commit ea15f61427e7ceebaa699e9b3bce7ccaf257bafc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 20:16:22 2016 -0500
Individual burners should add their own rpar components, and store the indices locally, if they want more than the ones that are provided by default.
integration/rhs.f90
integration/rpar_indices.f90
networks/aprox13/actual_burner.f90
networks/aprox13/actual_network.f90
networks/aprox13/actual_rhs.f90
networks/aprox13/network_indices.f90
commit 96c07b68e18b23276438b92b7b8b06e518ec7bf2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 18:33:55 2016 -0500
Write generic routines that calculate the RHS and Jacobian values for the temperature equation, since this is something that will be re-used by many networks.
integration/rhs.f90
networks/aprox13/actual_burner.f90
networks/aprox13/actual_rhs.f90
commit 33ab9578de085dcc78e72a428e67f24eba27742a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 17:32:44 2016 -0500
Spacing
networks/aprox13/actual_rhs.f90
commit d8775bea56cc5baea80c13af92668fac66eaf07c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 17:10:26 2016 -0500
Permit scaling of the temperature and density inside the integration.
integration/GPackage.mak
integration/Make.package
integration/rhs.f90
integration/vode_data.f90
integration/vode_indices.f90
integration/vode_module.f90
networks/aprox13/actual_burner.f90
networks/aprox13/actual_rhs.f90
commit 31d014382303fe8452121d48cc6fd64094a74318
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 17:01:59 2016 -0500
Change the default tolerances for temperature and energy to be 1.d-6, as this is a more reasonable choice for networks like aprox13.
integration/_parameters
commit 40d469a750e379d857c950fa88451ae41a0a67e5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 16:46:57 2016 -0500
More consistent usage of the EOS versus VODE states
integration/rhs.f90
integration/rpar_indices.f90
integration/vode_module.f90
networks/aprox13/actual_rhs.f90
networks/aprox13/test-cpp/testjacobian.f90
commit 761ee1802c679beac4e4a73953f13777f4116f85
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 16:30:42 2016 -0500
Write subroutines that convert back and forth from rpar to the state array
integration/rhs.f90
commit 4f91ccd7174fa0a218caa16175c3bd9bd5a1f5b6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 16:08:23 2016 -0500
More tfactors!
rates/tfactors.f90
commit abeba63f346d8d4de65c5661d0ffaf4c96ed45ce
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 16:08:04 2016 -0500
Since the aprox13 and friends family of networks expresses things in molar fractions, we'll do the same for the networks that use the VODE burner. We convert back to mass fractions that Castro/Maestro use at the end of the integration.
integration/rhs.f90
integration/vode_module.f90
networks/aprox13/actual_rhs.f90
commit fd336fcfc610fc40860851ca762b603baef45c5a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 15:53:16 2016 -0500
Don't renormalize the abundances in each integration step. That makes it harder to converge. We'll rely on one call at the end to do this for us.
integration/rhs.f90
commit 362af6172a634f1373a809113367cca1221a84a3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 15:43:52 2016 -0500
Switch to a paradigm where each network says which component utilities (e.g. rates, screening, etc.) it wants to include in its local make package.
eos/GPackage.mak
eos/Make.package
integration/Make.package
networks/GPackage.mak
networks/Make.package
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/Make.package
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/Make.package
screening/Make.package
commit 180ab92075078946ee5dcff3976b9d27d4c28321
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 15:08:25 2016 -0500
More independent burner module stuff
integration/GPackage.mak
integration/Make.package
integration/rhs.f90
integration/vode_indices.f90
integration/vode_module.f90
networks/aprox13/Make.package
commit b5ba872aa02272e98ad61e8536bbaeaf79d61267
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 02:06:39 2016 -0500
Standardization: the primary files in each network directory should be actual_network.f90 and actual_burner.f90.
networks/CONe2NSE/Make.package
networks/CONe2NSE/actual_burner.F90
networks/CONe2NSE/actual_network.F90
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_burner.f90
networks/aprox13/actual_network.f90
networks/general_null/GPackage.mak
networks/general_null/Make.package
networks/general_null/actual_burner.f90
networks/general_null/actual_network.f90.test
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/actual_burner.f90
networks/ignition_chamulak/actual_network.f90
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/actual_burner.f90
networks/ignition_simple/actual_network.f90
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/Make.package
networks/ignition_simple_SDC/actual_burner.f90
networks/ignition_simple_SDC/actual_network.f90
networks/kpp/GPackage.mak
networks/kpp/Make.package
networks/kpp/actual_burner.f90
networks/kpp/actual_network.f90
networks/powerlaw/Make.package
networks/powerlaw/actual_burner.f90
networks/powerlaw/actual_network.f90
networks/rprox/GPackage.mak
networks/rprox/actual_burner.f90
networks/rprox/actual_network.f90
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/actual_burner.f90
networks/triple_alpha_plus_cago/actual_network.f90
commit d46bb685dec2e0f313f4b996c6e52057c892cd88
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 13 01:51:22 2016 -0500
We intend to use the same integration routines for multiple networks, not just aprox13, so let's make the code more reusable by moving all the generic integration code up to a new top-level directory called integration/. Now for codes that want to use the VODE interface for burning, they will all use the same call to vode_burner, and the network-specific code requirement is an actual_rhs and actual_jac routine that provides the RHS and Jacobian calculation.
integration/_parameters
integration/rpar_indices.f90
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/actual_rhs.f90
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/network_indices.f90
commit 3c71eb8b1d1507953210bf834748c58eb67e9211
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 12 15:55:30 2016 -0500
Make the numerical Jacobian the default until we can sort out what is wrong with the analytical Jacobian
networks/aprox13/_parameters
commit 6c222243cab6c1ac80802ac8b0e3c3f80b35358d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 11 22:55:57 2016 -0500
Add to aprox13 a test of the analytical Jacobian by comparing it to the numerical Jacobian. It's a clone of the Jacobian test in MAESTRO's rprox network.
networks/aprox13/test-cpp/GNUmakefile
networks/aprox13/test-cpp/main.cpp
commit c916f4000c73668eba757cf471ce060fe1c993c6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 11 20:52:12 2016 -0500
We should be passing the rates to the Jacobian, not the rate derivatives.
networks/aprox13/f_rhs.f90
networks/aprox13/rhs.f90
networks/aprox13/rpar_indices.f90
commit 8995e8225c6f290207870a3584f7c125bd47b3d6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 11 16:43:27 2016 -0500
Some aprox13 cleanup
networks/aprox13/Make.package
networks/aprox13/aprox13_network.f90
networks/aprox13/rhs.f90
commit fa0dfe1d7f789093df9f643fa43645ee9e96fad5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 11 16:07:25 2016 -0500
Move the tfactors module to the rates directory
rates/Make.package
rates/tfactors.f90
commit 3626eb7bb81d728e861dcebf88207508214a8b0b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 11 14:46:33 2016 -0500
Move the rates module to a separate top-level directory, since it will be used by multiple networks.
rates/GPackage.mak
rates/Make.package
rates/rates.f90
commit be87e3107bfdc51e8e1f4114c20265355248ce4e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 22:43:02 2016 -0500
Various initialization fixes
networks/CONe2NSE/CONe2NSE_burner.F90
commit 3b8786d4e04d7f14db8e37fe412c8548f9e1e917
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 22:15:28 2016 -0500
Move over the detonation parameters to the Flame directory in Castro
networks/CONe2NSE/_parameters
commit fedb1e0b2e9bafbc4c0f2096fce63bd980553620
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 22:15:10 2016 -0500
Fix switched indexing
networks/CONe2NSE/CONe2NSE_burner.F90
commit 0718d7001d461c22b805167d368f4a975ccc558a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 21:56:51 2016 -0500
Call detonation_init in the burner initialization
networks/CONe2NSE/CONe2NSE_burner.F90
commit f8469eb9aadec1878d96312a9ce62d2deaa2cb49
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 06:07:37 2016 -0500
Forgot to reset the max number of steps for the hybrid burn
networks/aprox13/aprox13_burner.f90
commit 22935f3fea3682cd6262189aa0ee02cddeeafe24
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 05:58:06 2016 -0500
Use the quad precision summation present in the latest version of aprox13. This should automatically reduce to the old double precision summation on architectures that don't support quad precision. As shown in the MESA 3 paper, summing up the terms in the RHS using quad precision can result in a significant reduction in the number of iterations needed.
networks/aprox13/rhs.f90
commit 4de8c88cc3d530160b9842c6c060e2ecb05294b7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 05:22:06 2016 -0500
Save on some flops by recognizing that even if the user has enabled call_eos_in_rhs, there's no point in calling the EOS for hydrostatic/non-self-heating calculations because by construction the temperature doesn't change.
networks/aprox13/_parameters
networks/aprox13/f_rhs.f90
commit 228d66506b34f87129b682c06646521281200bfe
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 05:09:46 2016 -0500
Update some of the comments in the parameters file
networks/aprox13/_parameters
commit 48834a307385d3968db8fa42ef870ef50dff30ea
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 05:02:29 2016 -0500
Move up the aprox13 screening module to the main screening/ subdirectory. Since not every network defines nrates, I hardcoded the size of the screen arrays to 500, which is big enough for the usual networks we use. We may want to dynamically allocate them though.
networks/aprox13/Make.package
networks/aprox13/screening.f90
networks/ignition_chamulak/f_rhs.f90
networks/ignition_simple/f_rhs.f90
networks/ignition_simple_SDC/f_rhs_instantaneous.f90
networks/triple_alpha_plus_cago/screen_module.f90
screening/screen.f90
commit e7a3036aaeeaca812aa6daaf3019b4d00e50f3da
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 04:51:44 2016 -0500
Use automatic arrays instead of allocated pointer arrays for the VODE work arrays; these are small enough that memory is not an issue, and it should play nicer with the GPUs in the future.
networks/aprox13/aprox13_burner.f90
commit 6d2510268dd79e27ca1d632b926541c21bcacd20
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 04:46:12 2016 -0500
Don't store smallx in rpar because we weren't using it anyway. If we ever need to, it's located elsewhere in the calling code. Also, utilize a normalize_abundances call after the integration is done, rather than write it in by hand.
networks/aprox13/aprox13_burner.f90
networks/aprox13/rpar_indices.f90
commit 04d90465c7f2d8183a23eae99343f245b4ca726e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 04:26:03 2016 -0500
Add a derived type that stores the data needed by the screening routine, and fill it once at the beginning of screen_aprox13. This saves us from recomputing the same factors many times redundantly.
networks/aprox13/README
networks/aprox13/rhs.f90
networks/aprox13/screening.f90
commit 911409a8a2cefb157a902fc3861f6bb16ad2416c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 03:48:25 2016 -0500
Test update
networks/aprox13/test-cpp/GNUmakefile
networks/aprox13/test-cpp/probin
networks/aprox13/test-cpp/testburn.f90
commit c6a9cdd425231164036885c0ce2f0b25efd59208
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 10 03:42:39 2016 -0500
Turn the screening file into a module, and write an initialization procedure that caches some of the screening parameters.
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/aprox13_burner.f90
networks/aprox13/rhs.f90
networks/aprox13/screen5.f90
networks/aprox13/screening.f90
networks/aprox13/test-cpp/Make.package
commit 77786b5a01d941f4590624f986328ccde7b45a1c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 9 22:09:13 2016 -0500
Add hooks for a burner initialization step, since that's done in Castro now.
networks/CONe2NSE/CONe2NSE_burner.F90
networks/aprox13/aprox13_burner.f90
networks/general_null/general_null_burner.f90
networks/ignition_chamulak/ignition_chamulak_burner.f90
networks/ignition_simple/ignition_simple_burner.f90
networks/ignition_simple_SDC/ignition_simple_SDC_burner.f90
networks/kpp/kpp_burner.f90
networks/powerlaw/powerlaw_burner.f90
networks/rprox/rprox_burner.f90
networks/triple_alpha_plus_cago/triple_alpha_plus_cago_burner.f90
commit 436f88bd2f8284fa139f2a80e83161de2002c572
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 9 21:37:50 2016 -0500
In general the analytical Jacobian should be faster than the numerical Jacobian since it requires fewer evaluations of the rates. So, make it the default.
networks/aprox13/_parameters
commit dee8dff2241d7c3085057a3879286d7859f12684
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 9 21:32:15 2016 -0500
In the hybrid burning mode, if we re-do the integration, reset rpar and y to be consistent with the original state.
networks/aprox13/aprox13_burner.f90
commit 638514c80f29835479017d5e0a6183e6936b989f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 9 16:28:53 2016 -0500
For hydrostatic burning we will want to evolve the energy, just not the temperature.
networks/aprox13/f_rhs.f90
networks/aprox13/rhs.f90
commit 869d7cbf5eee682f14c5b073a1d6cd6b176e5039
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 9 16:13:00 2016 -0500
Add a 'hybrid' burning_mode == 2. This is normally hydrostatic, i.e. we don't evolve the temperature equation, but switches to self-heating mode and re-does the integration if the hydrostatic burn yields a net energy release. Usually that only happens at NSE conditions.
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/rhs.f90
networks/aprox13/rpar_indices.f90
commit 4393f595bf5a989e5e9bbe2911259464c3473add
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 8 19:08:49 2016 -0500
Fix the issues that were causing the analytical Jacobian to give the wrong result for the energy integration
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/rpar_indices.f90
commit 9ade1299a7fe3f39498296a99ababfe57861b9f9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 8 13:14:48 2016 -0500
Minor changes to sync up with the current aprox13
networks/aprox13/screen5.f90
networks/aprox13/sneut5.f90
commit 704b1e7ba18aea1a30867a72e643325677e96225
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jan 8 00:28:13 2016 -0500
Revert a recent change to the sign of one of the RHS terms, it turns out this was a typo in the public version of aprox13.
networks/aprox13/README
networks/aprox13/rhs.f90
commit 34fcdcf8e061a182aa0ea5e4ebfa4ae9e6e9e131
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 13:58:09 2016 -0500
Updated test problem
networks/aprox13/test-cpp/probin
networks/aprox13/test-cpp/testburn.f90
commit 57e304af68397bd7bf85ad4e1a8d8113be17314d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 13:57:45 2016 -0500
Make the aprox13 error tolerances be runtime parameters
networks/aprox13/_parameters
networks/aprox13/aprox13_burner.f90
commit 2b155ebc7393d0fa53e39f92ad8a4a62513ccdf1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 13:07:39 2016 -0500
Add some probin parameters
networks/aprox13/test-cpp/probin
commit 896211c38cb45672abc2d3749d18c47658c3ea47
Merge: dd7dc916 c3af4052
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 13:02:44 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit dd7dc916cb025710b5f43bb6e597707ac83bfaf6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 13:02:37 2016 -0500
parse probin
networks/aprox13/test-cpp/probin
networks/aprox13/test-cpp/testburn.f90
commit c3af4052ba0f9744a9f9def600d7cf77d4a5e8d6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 12:56:25 2016 -0500
Replicate some more code from burner.f90
networks/aprox13/test-cpp/testburn.f90
commit a3c55d27010a4c1c337cd86aa56119b5b721da65
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 12:53:49 2016 -0500
Bypass the burner frontend and call actual_burner directory, since the frontend relies on some castro parameters that aren't being initialized.
networks/aprox13/test-cpp/testburn.f90
commit b7758b699b242f44e591f7d435b3dea49857fda5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 12:47:24 2016 -0500
More output
networks/aprox13/test-cpp/testburn.f90
commit 3d6537e8b0abe5f8e8e41cd53bee3e1266fa778b
Merge: e43035f1 d3afcd63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 12:23:24 2016 -0500
Merge branch 'development' of ssh://github.com/BoxLib-Codes/Microphysics into development
commit e43035f1b3cf23db5c57843d10d5c1fe0de5b7f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jan 6 12:22:47 2016 -0500
add a C++ BoxLib based unit test for aprox13 -- this compiles in pretty
much all of Castro, but replaces main() with a custom version that calls
our F90 driver.
networks/aprox13/test-cpp/GNUmakefile
networks/aprox13/test-cpp/Make.package
networks/aprox13/test-cpp/main.cpp
networks/aprox13/test-cpp/testburn.f90
commit d3afcd63bf221b1d256b1c396c980e8e0a570b8f
Merge: 677bd9b2 b5a2d954
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 11:34:43 2016 -0500
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit b5a2d9549331c133cd770446fc2dc62e3bb34687
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jan 6 09:19:06 2016 -0500
Energy generation rate routine expects molar fractions, not mass fractions
networks/aprox13/f_rhs.f90
commit 2da31e8dfb87c5f88f75661a886dff2e49af15a4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 23:10:30 2016 -0500
If aprox13 is in verbose mode, print out energy release
networks/aprox13/aprox13_burner.f90
commit 276a2e06e3f6d05cdad8c7f1efb2e45f8470de70
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 23:10:10 2016 -0500
Fix analytical Jacobian component indexing
networks/aprox13/f_rhs.f90
commit 8b1cf1fd79a5a2ff6a966f3cc0fa1e1a2e86eb37
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 22:10:55 2016 -0500
Flip the sign on one of the components of the RHS for He4 to be consistent with what is in aprox13/aprox19/aprox21.
networks/aprox13/rhs.f90
commit 5ba3f0b7bcfc556b8db5883938c630d57904b074
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 21:07:44 2016 -0500
Cut down on function evaluations by storing some data in rpar when we call aprox13, then pulling it out when we evaluate the Jacobian
networks/aprox13/f_rhs.f90
networks/aprox13/rhs.f90
networks/aprox13/rpar_indices.f90
commit 81300e7522a4257ee311f570a7e673de893c9ff7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 20:50:25 2016 -0500
Also use normalize_abundances in the Jacobian
networks/aprox13/f_rhs.f90
commit ff670c1e3c28e5fadc87f4fac3805b17b04a19a1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 20:08:11 2016 -0500
Get the screening rates consistent with what's currently in aprox13
networks/aprox13/rhs.f90
commit 7093acb387f367a35ef4aa0c593d2a21cac1fa24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jan 5 17:11:12 2016 -0500
fix the fix -- we need molar fractions for the energy generation
rate, but not for the T equation
networks/aprox13/rhs.f90
commit 77010b915a556b03e06ff4d3856a832c4ad1df23
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 16:57:18 2016 -0500
Use the eos_type normalize_abundances function
networks/aprox13/f_rhs.f90
commit 73d0455abb5c9c1cf7df4d0b6f52da98991f90fc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Jan 5 16:18:02 2016 -0500
Conversion from molar to mass fractions doesn't depend on burning mode
networks/aprox13/rhs.f90
commit 8985ad3550f0bc41434c9f0b7510535d4cd2f4b8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 23:24:21 2016 -0500
Get some implicit nones going on in aprox13
networks/aprox13/rates.f90
networks/aprox13/tfactors.f90
commit 4c3b8a6fb05d6c74075b42ed4fde6254114c9fe6
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 18:35:59 2016 -0500
If burner integration fails, print out how much energy was generated
networks/aprox13/aprox13_burner.f90
commit 8e225d5d4b244c9eb8db35c06a3ca890f2e1679e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 18:34:16 2016 -0500
Have verbosity in aprox13 be a runtime extern parameter
networks/aprox13/_parameters
networks/aprox13/aprox13_burner.f90
commit e47ba91ba99372d8ae17556cb4512e312bf13d2c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 17:39:24 2016 -0500
Also need the dedX / dhdX contributions to dT/dy.
networks/aprox13/f_rhs.f90
commit 4bbb4378d63e3efaaa3c6708022f96a912270dad
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 17:33:14 2016 -0500
Forgot the dedX / dhdX terms for dT/dT Jacobian elements
networks/aprox13/f_rhs.f90
commit e8b463844995bead2b85e46d72fba6442412a26d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 17:08:14 2016 -0500
Forgot to add analytical Jacobian elements for temperature
networks/aprox13/f_rhs.f90
commit 1bc69ec7f6d34d5f4bb29bea296639a90a37799e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 16:44:57 2016 -0500
Optionally at runtime we can set whether to use an analytical or numerical Jacobian.
networks/aprox13/_parameters
networks/aprox13/aprox13_burner.f90
networks/aprox13/rhs.f90
commit c0ef80d56cc806ba1399b51087acf699d5eec30b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 16:38:36 2016 -0500
Normally we run in self-heating mode where the temperature and energy evolve in response to the burning. By setting burning_mode to 0 we can now disable this and run in hydrostatic mode, where T/e stay fixed through the burning evolution. Under the covers, this just sets the Jacobian and RHS elements for T and e to zero.
networks/aprox13/_parameters
networks/aprox13/f_rhs.f90
networks/aprox13/rhs.f90
commit 4852f71de67a194e362c70b269af8a05f9027a87
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 15:50:17 2016 -0500
Use the species Jacobian elements from saprox13 instead of from daprox13
networks/aprox13/rhs.f90
commit 086eaa43011bead1c0b0e8ac12b89e267867b346
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 15:15:53 2016 -0500
Copy over the dense analytical Jacobian code from aprox13. This should help in overcoming some integration issues we've seen near NSE. It doesn't work correctly yet, so the analytical Jacobian is not used by default.
networks/aprox13/README
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/rhs.f90
commit 7f5a1c956f89c830e716b0d3cecd6cc75b7d1cf1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 15:04:42 2016 -0500
More uncommenting of temperature derivatives
networks/aprox13/screen5.f90
networks/aprox13/sneut5.f90
commit 777dc3b7ccbc2a7612abc6592d1e9aa45474c080
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Jan 4 14:46:30 2016 -0500
Uncomment the temperature derivatives in the reaction rates
networks/aprox13/rates.f90
commit 677bd9b2df6820be31cbded9927dd97bad10d6ae
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 3 02:42:09 2016 -0500
React_proximity logic is now in Castro
networks/CONe2NSE/CONe2NSE_burner.F90
commit 50baf0b6739f166fea480190f353351c9111a14c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 3 02:19:40 2016 -0500
Enable a default react_proximity, this is also something that's going to have to be pulled out of this burner if we want to use it.
networks/CONe2NSE/CONe2NSE_burner.F90
commit bea80dfd91174e9be3f7cceae1a88e36aee42bb8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 3 02:06:27 2016 -0500
Slight cleanup of the shock burning stuff. But if we want to use this option we're probably going to have to do it in the main ca_react_state interface and have it available for all burners. Which, in turn, will require a dimension agnostic shock detection routine.
networks/CONe2NSE/CONe2NSE_burner.F90
commit 9b0fe69b88693c7d466a6866ab53ffebde29499c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 3 01:49:47 2016 -0500
Add in the detonation logic to the burner now that the infrastructure exists in Castro
networks/CONe2NSE/CONe2NSE_burner.F90
commit e8a7dc51d6d0b08e377d1b5fef156302869f37a7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 3 01:26:46 2016 -0500
Fix typo
networks/CONe2NSE/CONe2NSE_network.F90
commit 6338fd21e14c043a740f60d0947fc656606f6999
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Jan 3 00:39:25 2016 -0500
Add sanity checks on negative density and pressure in the NSE calculation
NSE/NSE_data.F90
commit ca3c4fad3a798d78889180b8d9d91d900533df00
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 2 19:54:32 2016 -0500
Remove all the detonation stuff from the flame network since it's being moved to Castro
networks/CONe2NSE/CONe2NSE_burner.F90
networks/CONe2NSE/CONe2NSE_network.F90
commit e1c5ea754cdca0a9f4cea2ac689f3e573cae6247
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Jan 2 11:54:34 2016 -0500
Get rid of the detonation stuff, we're moving that to Castro
networks/CONe2NSE/bn_paraAllIgnite.F90
networks/CONe2NSE/bn_paraAllSpark.F90
networks/CONe2NSE/bn_paraInterface.F90
networks/CONe2NSE/bn_paraSpark.F90
commit 33a41ec73e1111b76ea13843722d227d098549f8
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Dec 30 23:41:38 2015 -0500
Print out state data if the integration fails in aprox13
networks/aprox13/aprox13_burner.f90
commit 81a14b6f5a44a9aa7c5b8c7643d5f3c6374ef933
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Dec 27 07:16:26 2015 -0500
Add the flame variables as auxiliary variables
networks/CONe2NSE/CONe2NSE_burner.F90
networks/CONe2NSE/CONe2NSE_network.F90
commit d4ead51f6275b8c3bf36a6f35700633618273c13
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Dec 26 16:37:56 2015 -0500
Wrong filename
NSE/NSE_data.F90
commit 82aef309f49087133a933a6768443b7fa710bef1
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Dec 26 16:23:01 2015 -0500
Call the NSE_init routine from the network_init routine
networks/CONe2NSE/CONe2NSE_network.F90
commit 7b4f2615e262de104ccfa100d63f52174b6c3690
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Dec 26 16:00:48 2015 -0500
A first cut at adding the SNIa DDT-themed network and burner. Right now the network is set up and the deflagration code is too, but all the detonation/thermally-activated burning stuff is commented out. We can't do that here at present because the burner interface is all local.
networks/CONe2NSE/CONe2NSE_burner.F90
networks/CONe2NSE/CONe2NSE_network.F90
networks/CONe2NSE/Make.package
networks/CONe2NSE/_parameters
networks/CONe2NSE/bn_paraAllIgnite.F90
networks/CONe2NSE/bn_paraAllSpark.F90
networks/CONe2NSE/bn_paraInterface.F90
networks/CONe2NSE/bn_paraSpark.F90
networks/CONe2NSE/eos_externalComputeAbarZbar.F90
commit ee0990a59ce4d366a22e963d3b6e5750f5321c97
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Dec 26 11:44:36 2015 -0500
Move the NSE directory up
NSE/Make.package
NSE/NSE_data.F90
NSE/README_emq
NSE/README_hmq
NSE/Readme_tables
NSE/_parameters
NSE/nse_dens_emq_table.txt
NSE/nse_pres_hmq_table.txt
commit ad3b59f1f8011cd44180968daeec04f15fdbca2b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sun Dec 20 20:15:54 2015 -0500
Polytrope needed some more thermodynamic derivatives
eos/polytrope/polytrope.f90
commit 919ae6f5d53fbd434d5e4c440b2e09f947e59a35
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Dec 18 12:42:12 2015 -0500
Fix module references and data types
material_properties/NSE/NSE_data.F90
commit 02a9dfba0cc55f283af9e71b49be432290b001fc
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Dec 18 12:38:34 2015 -0500
Move everything into the NSE_data module
material_properties/NSE/Make.package
material_properties/NSE/NSE_data.F90
material_properties/NSE/NSE_finalAtDens.F90
material_properties/NSE/NSE_finalAtPres.F90
material_properties/NSE/NSE_finalize.F90
material_properties/NSE/NSE_init.F90
commit 878c007a56bf66536a42b73340961c769e117e2a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Dec 18 12:27:54 2015 -0500
Copy over the NSE material properties
material_properties/NSE/Make.package
material_properties/NSE/NSE_data.F90
material_properties/NSE/NSE_finalAtDens.F90
material_properties/NSE/NSE_finalAtPres.F90
material_properties/NSE/NSE_finalize.F90
material_properties/NSE/NSE_init.F90
material_properties/NSE/README_emq
material_properties/NSE/README_hmq
material_properties/NSE/Readme_tables
material_properties/NSE/_parameters
material_properties/NSE/nse_dens_emq_table.txt
material_properties/NSE/nse_pres_hmq_table.txt
commit a4c494dbf8062acfda33ba0ec910461201e24ea2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Dec 18 01:55:52 2015 -0500
Add a C/O/Ne network.
networks/general_null/CONe.net
commit 3ab3e95df5204008933a8fbd35d8e0e64f8182d9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Dec 15 01:27:05 2015 -0500
When given rho in the polytrope EOS, calculate state variables from rho (rather than e).
eos/polytrope/polytrope.f90
commit f22b44c8187011096dfd286acafef2c21e5455b7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Dec 14 17:58:59 2015 -0500
Calculate and store the polytropic index based on gamma, for the polytrope EOS.
eos/polytrope/polytrope.f90
commit f6887ba3939c38920544c357d883203c5e0e7e47
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Dec 1 10:54:28 2015 -0500
We know the size of rpar so we can avoid using an assumed size array.
networks/ignition_simple/f_rhs.f90
commit a14844b8de4d335ffe3cb96b707c442c30d93be9
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Nov 30 15:29:39 2015 -0500
Move the ignition simple network to be more like what we have in MAESTRO and the other networks, by using the rpar functionality to pass variables around.
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/burner_aux.f90
networks/ignition_simple/f_rhs.f90
networks/ignition_simple/ignition_simple_burner.f90
networks/ignition_simple/ignition_simple_network.f90
networks/ignition_simple/rpar_indices.f90
commit bafd19cb9310d45a668951e99c7a99ebd6e7fa18
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Nov 4 20:26:37 2015 -0500
Need to still get the rpar stuff when compiling without reactions.
networks/aprox13/Make.package
networks/ignition_chamulak/Make.package
networks/ignition_simple/Make.package
networks/powerlaw/Make.package
networks/rprox/Make.package
networks/triple_alpha_plus_cago/Make.package
commit 36212bcbecfa74356b63b34e3e2856b2e7516c50
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Nov 4 17:17:18 2015 -0500
For CASTRO make packages, only include the burner functions if USE_REACT=TRUE.
networks/aprox13/Make.package
networks/general_null/Make.package
networks/ignition_chamulak/Make.package
networks/ignition_simple/Make.package
networks/ignition_simple_SDC/Make.package
networks/kpp/Make.package
networks/powerlaw/Make.package
networks/rprox/Make.package
networks/triple_alpha_plus_cago/Make.package
commit 8cdb927e53853a05309819dec501cdad0a33155b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Nov 2 08:43:15 2015 -0500
Remove some more obsolete vectorized EOS references
networks/kpp/kpp_burner.f90
networks/rprox/rprox_burner.f90
commit 9337b56647ab2880ccfbf835eb3b06eed18be66e
Merge: e38f91e0 e08af1e4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Oct 30 11:19:34 2015 -0400
Merge branch 'openacc' into development
commit e08af1e493e071cba94079f2e810a22aa083cc69
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Oct 30 11:17:53 2015 -0400
More reverting of multi-D EOS stuff.
eos/gamma_law_general/gamma_law_general.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/stellarcollapse.f90
eos/ztwd/ztwd.f90
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
commit e38f91e0a23363b3ea645810c7f22c7d549e37c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 27 20:13:58 2015 -0400
add an activation energy
networks/powerlaw/_parameters
networks/powerlaw/f_rhs.f90
commit 9e40af0278bf13421a52dc0f30109891c74b35bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 21 20:01:38 2015 -0400
more reasonable inert properties
networks/powerlaw/powerlaw_network.f90
commit 32b31015493e216d1240b2f228c395680475a673
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 16:44:22 2015 -0400
add network_finalize stub
networks/ignition_simple/ignition_simple_network.f90
commit 33b896b59b53ccf4e6c7e7720f2f9bbbb7b553cf
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 16:41:51 2015 -0400
forgot some parts
networks/ignition_simple/ignition_simple_burner.f90
commit 53a5347a2a25f44174fb8d50ac0695807f4f4793
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 16:40:33 2015 -0400
remove loop over eos_t % N
networks/ignition_simple/ignition_simple_burner.f90
commit 644021a4c5ecde1b363e4eb606c77392db300325
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 16:37:40 2015 -0400
maestro wants these
networks/general_null/NETWORK_REQUIRES
networks/ignition_simple/NETWORK_REQUIRES
networks/kpp/NETWORK_REQUIRES
networks/powerlaw/NETWORK_REQUIRES
commit 4dcc0828db9c2abb790a4195bb0314f366311dc7
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:51:44 2015 -0400
remove all traces of vector eos
networks/general_null/general_null_burner.f90
networks/ignition_chamulak/ignition_chamulak_burner.f90
networks/ignition_simple/ignition_simple_burner.f90
networks/kpp/kpp_burner.f90
networks/powerlaw/powerlaw_burner.f90
networks/rprox/rprox_burner.f90
networks/triple_alpha_plus_cago/triple_alpha_plus_cago_burner.f90
commit fd79942effdef3141394edfdf01f3ff35251d432
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:43:53 2015 -0400
remove vectorized eos
networks/aprox13/aprox13_burner.f90
commit 41785e206eb79a080d24d671f041868b91c258a4
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:24:00 2015 -0400
fix typo
networks/triple_alpha_plus_cago/Make.package
commit 70d7767fb11b74c3725f1b8b2bbe3ee4f71697f3
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:14:46 2015 -0400
use actual_*
networks/triple_alpha_plus_cago/triple_alpha_plus_cago_burner.f90
networks/triple_alpha_plus_cago/triple_alpha_plus_cago_network.f90
commit bd19d192f2e9528e9706a2780e30d324d76e1c4d
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:13:25 2015 -0400
update naming
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/Make.package
networks/triple_alpha_plus_cago/triple_alpha_plus_cago_burner.f90
networks/triple_alpha_plus_cago/triple_alpha_plus_cago_network.f90
commit ea26c0fed924adab83fd13168428283a5f56cff5
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:11:07 2015 -0400
no longer needed
networks/rprox/burner.f90
commit 80d8ac82a7b26992ab4c0df9ea09b11b77ef7e00
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:09:21 2015 -0400
use actual_*
networks/ignition_simple_SDC/ignition_simple_SDC_burner.f90
networks/ignition_simple_SDC/ignition_simple_SDC_network.f90
commit c4e17a25b86f7afd73e098b85d9512e7fb59e5c6
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:06:44 2015 -0400
update naming
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/Make.package
networks/ignition_simple_SDC/ignition_simple_SDC_burner.f90
networks/ignition_simple_SDC/ignition_simple_SDC_network.f90
commit f06b94b52b0c97dfbeb636bb06d6b95216e52866
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 14:00:05 2015 -0400
moved from MAESTRO/Microphysics/networks
networks/MESA/Do_One_Zone_Burn.f90
networks/MESA/GPackage.mak
networks/MESA/NETWORK_REQUIRES
networks/MESA/Net-Files/carbon_burning.net
networks/MESA/Net-Files/carbon_burning_extended.net
networks/MESA/Net-Files/test_16_null.net
networks/MESA/Net-Files/test_2.net
networks/MESA/Net-Files/test_3.net
networks/MESA/Net-Files/test_approx19.net
networks/MESA/Net-Files/test_approx8.net
networks/MESA/Net-Files/test_ignition_simple.net
networks/MESA/Net-Files/test_triple_alpha.net
networks/MESA/README
networks/MESA/burn_solout.f90
networks/MESA/burner.f90
networks/MESA/get_mesa_ebin.f90
networks/MESA/net_utils.f90
networks/MESA/network.template.mesa
networks/MESA/scripts/compile-all-mods.sh
networks/MESA/scripts/compile-one-mod.sh
networks/MESA/setup_mesa_net.f90
networks/MESA/shutdown_mesa_net.f90
networks/MESA/write_network.py
networks/THREADSAFE
networks/ignition_simple_SDC/GPackage.mak
networks/ignition_simple_SDC/NETWORK_REQUIRES
networks/ignition_simple_SDC/burner.f90
networks/ignition_simple_SDC/burner_aux.f90
networks/ignition_simple_SDC/f_rhs.f90
networks/ignition_simple_SDC/f_rhs_instantaneous.f90
networks/ignition_simple_SDC/network.f90
networks/triple_alpha_plus_cago/GPackage.mak
networks/triple_alpha_plus_cago/NETWORK_REQUIRES
networks/triple_alpha_plus_cago/burner.f90
networks/triple_alpha_plus_cago/burner_aux.f90
networks/triple_alpha_plus_cago/dydt.f90
networks/triple_alpha_plus_cago/f_rhs.f90
networks/triple_alpha_plus_cago/network.f90
networks/triple_alpha_plus_cago/rates_module.f90
networks/triple_alpha_plus_cago/screen_module.f90
networks/triple_alpha_plus_cago/test/GNUmakefile
networks/triple_alpha_plus_cago/test/GPackage.mak
networks/triple_alpha_plus_cago/test/eval.f90
networks/triple_alpha_plus_cago/test/testburn.f90
networks/triple_alpha_plus_cago/test/testjacobian.f90
commit 44199bd9a37c70e933d2cd3c6b86de6d3a1e0940
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 11:51:14 2015 -0400
move to a centralized screenz routine
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/screen.f
networks/ignition_simple/GPackage.mak
networks/ignition_simple/Make.package
networks/ignition_simple/screen.f
screening/GPackage.mak
screening/Make.package
screening/screen.f90
commit b78b05ffaedbd792b3aba6807601f5e2abdc0f7e
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 11:07:11 2015 -0400
undo all the vectorization changes
eos/helmholtz/helmholtz.f90
commit 32b040e00938d6df185296b590eaf8394ce04d4d
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Wed Oct 21 11:06:54 2015 -0400
maestro needs a network_finalize
networks/ignition_chamulak/ignition_chamulak_network.f90
commit 58c0a2c6fe9e261f3683809cd4c0c442b2948604
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Oct 21 09:56:18 2015 -0400
add an inert species
networks/powerlaw/f_rhs.f90
networks/powerlaw/powerlaw_burner.f90
networks/powerlaw/powerlaw_network.f90
commit 8cbe3b08d33b431af58445cfd53f12fae1dd1405
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Tue Oct 20 16:39:37 2015 -0400
remove the eos_vector functionality
networks/ignition_chamulak/ignition_chamulak_burner.f90
commit f5ab6f06bcd9c4fec60a81b4c1a6728dd3b5a775
Author: Chris Malone <chris.m.malone@gmail.com>
Date: Tue Oct 20 16:38:33 2015 -0400
add private block around constants to prevent name-clashing; this should be extracted or pulled in from a common code-wide location
eos/helmholtz/helmholtz.f90
commit 36956cd0098add6060f44b42caef418c65537ba7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Oct 20 15:29:00 2015 -0400
For general null, send in aion and zion to the GPU
networks/general_null/network.template
commit d4648886cf77fbe1a3972f8056121f21a18f27a3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Oct 20 05:07:07 2015 -0400
Port over ignition_chamulak from MAESTRO
networks/ignition_chamulak/GPackage.mak
networks/ignition_chamulak/Make.package
networks/ignition_chamulak/NETWORK_REQUIRES
networks/ignition_chamulak/burner_aux.f90
networks/ignition_chamulak/f_rhs.f90
networks/ignition_chamulak/ignition_chamulak_burner.f90
networks/ignition_chamulak/ignition_chamulak_network.f90
networks/ignition_chamulak/notes.txt
networks/ignition_chamulak/screen.f
networks/ignition_chamulak/test/GNUmakefile
networks/ignition_chamulak/test/GPackage.mak
networks/ignition_chamulak/test/eval.f90
networks/ignition_chamulak/test/testburn.f90
networks/ignition_chamulak/test/testjacobian.f90
commit d0f8b6135fb2718fa3d5dc1457fe59ebbca44f5b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Oct 19 20:48:27 2015 -0400
Make do_acc a probin parameter for helmholtz
eos/helmholtz/_parameters
eos/helmholtz/helmholtz.f90
commit 755f491aa0cc518339d1417a313c0192ab6fb2f7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Mon Oct 19 20:22:50 2015 -0400
Add some missing GPackage.mak
networks/ignition_simple/GPackage.mak
networks/kpp/GPackage.mak
networks/rprox/GPackage.mak
commit 4a3ad5b8944027abab772ffc55cdffa9f029ec4e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 18 21:06:22 2015 -0400
update this to reflect the form of the reaction rate in our
model paper
networks/powerlaw/f_rhs.f90
commit aaaaa5bdf7b356fd07c9d09699919a3b753602ce
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 18 21:02:57 2015 -0400
update comments
networks/powerlaw/_parameters
networks/powerlaw/powerlaw_network.f90
commit 7353970c634a32a8b1a81c286184a4491b0bb896
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Oct 18 20:47:38 2015 -0400
more notation updates
networks/powerlaw/_parameters
commit b65ba5d1948df0f880323344a8701f42ed8e1b0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 20:42:43 2015 -0400
q_burn -> specific_q_burn
networks/powerlaw/_parameters
networks/powerlaw/powerlaw_burner.f90
commit eec829788b9366d2c080aeac03103a8c7257e2c7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 20:31:33 2015 -0400
this was adding the energy release incorrectly for a vectorized call
networks/powerlaw/powerlaw_burner.f90
commit 5e26feeca31d559ef98ad8ec34920520b1e03865
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Oct 17 18:46:16 2015 -0400
upate
networks/powerlaw/_parameters
commit 83937730e29b43cfb621d7c1ea66935d6a174e03
Merge: 33398c3a 12017677
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Oct 16 16:16:41 2015 -0400
Merge branch 'development' of github.com:BoxLib-Codes/Microphysics into development
commit 33398c3ac8278e8b6d500179c5c2d230e8ea7e15
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Oct 16 16:16:38 2015 -0400
Port over the powerlaw network from Castro
networks/powerlaw/Make.package
networks/powerlaw/_parameters
networks/powerlaw/burner_aux.f90
networks/powerlaw/f_rhs.f90
networks/powerlaw/powerlaw_burner.f90
networks/powerlaw/powerlaw_network.f90
commit 12017677765a55a2aef1e6a48f42f6f105a3c439
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date: Fri Oct 16 10:56:24 2015 -0700
added some save
networks/general_null/network.template
commit e13c1883da566933f878b097c18a972f071b46c3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Oct 16 12:52:33 2015 -0400
Add back eos_assume_neutral to the gamma_law_general EOS, mirroring a change in Castro for the simpler gamma_law EOS.
eos/gamma_law_general/_parameters
eos/gamma_law_general/gamma_law_general.f90
commit d2c0f7bba58c08abf5445e6307006da4bc4d9d87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date: Fri Oct 9 15:58:22 2015 -0700
optimization of gamma_law_general
eos/gamma_law_general/gamma_law_general.f90
commit 3ae88d9b59781a924f309f86e46d4f5680859a5b
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Oct 6 10:49:05 2015 -0400
Port over the rprox network from Maestro
networks/rprox/Make.package
networks/rprox/NETWORK_REQUIRES
networks/rprox/README
networks/rprox/burner.f90
networks/rprox/burner_aux.f90
networks/rprox/f_rhs.f90
networks/rprox/rates_module.f90
networks/rprox/reaclib/c12-pg-n13-ls09
networks/rprox/reaclib/f17--o17-wc07
networks/rprox/reaclib/f17-gp-o16-ia08
networks/rprox/reaclib/f17-pg-ne18-cb09
networks/rprox/reaclib/he4-aag-c12-fy05
networks/rprox/reaclib/make_rates_module.py
networks/rprox/reaclib/n14-pg-o15-im05
networks/rprox/reaclib/ne18--f18-wc07
networks/rprox/reaclib/ne18-ap-na21-mv09
networks/rprox/reaclib/ne19--f19-wc07
networks/rprox/reaclib/ne19-pg-na20-il10
networks/rprox/reaclib/o14--n14-wc07
networks/rprox/reaclib/o14-ap-f17-Ha96c
networks/rprox/reaclib/o15--n15-wc07
networks/rprox/reaclib/o15-ag-ne19-dc11
networks/rprox/reaclib/o16-ag-ne20-co10
networks/rprox/reaclib/o16-pg-f17-ia08
networks/rprox/reaclib/reaclib.pdf
networks/rprox/reaclib/si26-ap-p29-ths8
networks/rprox/reaclib/ti44-ap-v47-rh10
networks/rprox/rprox_burner.f90
networks/rprox/rprox_network.f90
commit fb4d0ab23e00a5054d5477d28197bdcd655abd90
Merge: 29f60600 17491e18
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 5 10:32:36 2015 -0400
Merge branch 'master' into development
commit 17491e18954e125064da7aa12ef9e7ccd77dbb4f
Author: Max Katz <maxpkatz@gmail.com>
Date: Mon Oct 5 10:10:35 2015 -0400
Add a name to each EOS.
eos/gamma_law_general/gamma_law_general.f90
eos/helmholtz/helmholtz.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/stellarcollapse.f90
eos/ztwd/ztwd.f90
commit 29f606000b6c9db09c8bb4caf681f77927b0e204
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Oct 2 12:59:14 2015 -0400
Fix to account for recent EOS changes
networks/aprox13/f_rhs.f90
commit 19f94fdd10a38c7a65acc7e107c22898be03e5c2
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Sep 24 17:18:47 2015 -0400
Port over a network from CASTRO
networks/general_null/ignition_wdconvect.net
commit 4348bedc0c35e7c193b225837790d9f4b9e0f599
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Sep 24 15:52:22 2015 -0400
Fix some outdated module name references
networks/general_null/general_null_network.f90.test
networks/ignition_simple/f_rhs.f90
commit d95e60bf1c6435cfc96536ffb44aa31ff5d81b28
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Sep 15 17:28:08 2015 -0400
Fix typo
networks/aprox13/aprox13_network.f90
commit db303538f2839b3e3a3829aafc0ee072715be2a2
Merge: 8bbeac31 31b30f28
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Sep 12 23:04:40 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Microphysics
commit 8bbeac31e7f909253ec795bbd0bcf312746dcacf
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Sep 12 23:04:35 2015 -0400
Need to make imax and jmax private as they are used elsewhere in the code
eos/helmholtz/helmholtz.f90
commit 31b30f288d923edd768042530878d0d862a11c89
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Sat Sep 12 18:45:38 2015 -0400
Move kpp network to this repository
networks/kpp/Make.package
networks/kpp/_parameters
networks/kpp/f_rhs.f90
networks/kpp/kpp_burner.f90
networks/kpp/kpp_network.f90
commit c0ad58d17d85f0ef67236f48fa5ca9996df76878
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Tue Aug 25 11:55:42 2015 -0400
Add a network to general_null containing the same species as aprox13.
networks/general_null/aprox13.net
commit a884f8a79f395106bb2a817f64807988938e9c6a
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Aug 14 15:37:41 2015 -0400
A .gitignore for the userguide directory.
userguide/.gitignore
commit 8aded518a2bda404cae296c098a7091e722f4435
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Aug 14 15:36:20 2015 -0400
Mirror the change from the network where we use actual instead of specific.
eos/gamma_law_general/gamma_law_general.f90
eos/helmholtz/helmholtz.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/stellarcollapse.f90
eos/ztwd/ztwd.f90
commit 1c3510580c683c65fd382388b4078ac68b9e4225
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Aug 14 15:31:10 2015 -0400
Need to change an include statement
networks/aprox13/screen5.f90
commit 6d8cd0457037197bc9130eae0f63fe2f19eefa38
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Aug 14 15:30:43 2015 -0400
Bring the zero-temperature white dwarf equation of state over from Castro.
eos/ztwd/GPackage.mak
eos/ztwd/Make.package
eos/ztwd/_parameters
eos/ztwd/ztwd.f90
userguide/userguide.tex
commit fdba01ac2f1c517f32c52b58df166cdbbdc9712c
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 29 00:28:09 2015 -0400
Move up the initialized variable to the main EOS module.
eos/gamma_law_general/gamma_law_general.f90
eos/helmholtz/helmholtz.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/stellarcollapse.f90
commit 3967007a084524b3a0c45dc69ff5bfd4322ed968
Author: Max Katz <maxpkatz@gmail.com>
Date: Tue Jul 28 22:27:28 2015 -0400
A little more cleanup of the aprox13 interface.
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/rpar_indices.f90
commit 96732635b35d359537860759be549eb4997b9c20
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 24 15:52:24 2015 -0400
Fix an additional name change
networks/aprox13/rhs.f90
commit 638e32d36f199ba1156936b0ac5ae77ff1d40954
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 23 15:05:04 2015 -0400
Switch from specific_* to actual_*
networks/aprox13/aprox13_burner.f90
networks/aprox13/aprox13_network.f90
networks/general_null/general_null_burner.f90
networks/general_null/network.template
networks/ignition_simple/ignition_simple_burner.f90
networks/ignition_simple/ignition_simple_network.f90
commit 1027e952d6746d1c7cb3b71c761f01e91255235d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 23 14:57:43 2015 -0400
Port over the ignition_simple network.
networks/ignition_simple/Make.package
networks/ignition_simple/burner_aux.f90
networks/ignition_simple/f_rhs.f90
networks/ignition_simple/ignition_simple_burner.f90
networks/ignition_simple/ignition_simple_network.f90
networks/ignition_simple/screen.f
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
commit ac12e903dfc5b98ed151a9840f3b622cd6376420
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 22 14:53:43 2015 -0400
Create a user's guide for this repository.
userguide/GNUmakefile
userguide/README.md
userguide/refs.bib
userguide/userguide.tex
commit 4fee35779ff78fb0d9c58c9854826f81a1ad60e0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 22 02:18:41 2015 -0400
Move the interface out of here; it will live in the individual codes that use this. The EOS and networks are expected to take an eos_t_vector, which should be suitably defined in the calling code.
eos/GPackage.mak
eos/Make.package
eos/_parameters
eos/eos.f90
eos/eos_data.f90
eos/eos_type.f90
networks/GPackage.mak
networks/Make.package
networks/burner.f90
networks/general_null/general_null_burner.f90
networks/network.f90
commit bd27de8b6a5fbcfaa5b99764b4443f640d23a554
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 17 00:06:01 2015 -0400
Don't try to create a pointer to aux data if there isn't any.
eos/eos_type.f90
commit 7676ef42ebec281053bb184964ca465d0bc0e4c3
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 16 19:00:09 2015 -0400
Some more MAESTRO make packages
eos/GPackage.mak
eos/gamma_law_general/GPackage.mak
eos/helmholtz/GPackage.mak
eos/multigamma/GPackage.mak
eos/polytrope/GPackage.mak
eos/stellarcollapse/GPackage.mak
networks/GPackage.mak
commit 458df6e7bfe1233493f464e34b66bb14bce79573
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 16 14:37:07 2015 -0400
Some fixes to the Make packages so that MAESTRO can compile
networks/aprox13/GPackage.mak
networks/general_null/GPackage.mak
networks/general_null/Make.package
commit 720f8ccbfda1323da13b9bcff0dd659a9b05a6e0
Author: Max Katz <maxpkatz@gmail.com>
Date: Wed Jul 15 23:58:17 2015 -0400
The aprox13 work array should not have been a module component, that was making it non-threadsafe.
networks/aprox13/aprox13_burner.f90
commit 837fb680587e288afea565248aea2e6652e0fcea
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 15 21:37:28 2015 -0400
Switch from the array of structures approach to the structure of arrays approach. We now have eos_t_1D, eos_t_2D, and eos_t_3D types that are composed of 1D/2D/3D arrays for each EOS component. We retain the old scalar eos_t type for backwards compatibility.
eos/eos.f90
eos/eos_type.f90
eos/gamma_law_general/gamma_law_general.f90
eos/helmholtz/helmholtz.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/stellarcollapse.f90
networks/aprox13/aprox13_burner.f90
networks/aprox13/f_rhs.f90
networks/burner.f90
networks/general_null/general_null_burner.f90
commit 7aa4adddaeba71ea2a9b77570ee8b744761d8d33
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 00:53:58 2015 -0400
Add the general_null network
networks/general_null/H_He.net
networks/general_null/H_core.net
networks/general_null/Make.package
networks/general_null/README
networks/general_null/gammalaw.net
networks/general_null/general_null_burner.f90
networks/general_null/general_null_network.f90.test
networks/general_null/hotcno.net
networks/general_null/ignition.net
networks/general_null/network.template
networks/general_null/pphotcno.net
networks/general_null/simple.net
networks/general_null/simple3.net
networks/general_null/triple_alpha_plus_o.net
networks/general_null/write_network.py
commit e19dbf68eb257cc0540c48b2c36da4ed13ea4e69
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 00:53:23 2015 -0400
Clean up the aprox13 burner a bit, and make it compatible with the new vectorized burner interface.
networks/aprox13/Make.package
networks/aprox13/aprox13_burner.f90
networks/aprox13/aprox13_network.f90
networks/aprox13/burner.f90
networks/aprox13/castro_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/network.f90
networks/aprox13/network_indices.f90
networks/aprox13/rhs.f90
networks/aprox13/rpar_indices.f90
networks/aprox13/screen5.f90
commit 21ff524aeacb03ccb242dba0492e60c2d3d183b4
Author: Max Katz <maxpkatz@gmail.com>
Date: Sat Jul 11 00:51:45 2015 -0400
Add a network and burner interface analogous to the new EOS interface. The network calls a specific_network routine that initializes the species. The burner calls a specific_burner module that updates an eos_type based on the reactions. Like the EOS, the burner accepts a scalar or 1D/2D/3D array eos_type.
networks/Make.package
networks/burner.f90
networks/network.f90
commit ff493002eca4a3b6464c76b77417309420f67002
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 10 12:20:01 2015 -0400
Remove eosfail parameter as it was not being used anymore. We could replace it with error codes in the future if needed, but our strategy in general should be to clean up the data before it enters the specific EOS so that errors shouldn't happen there.
eos/eos.f90
eos/gamma_law_general/gamma_law_general.f90
eos/helmholtz/helmholtz.f90
eos/multigamma/multigamma.f90
eos/polytrope/polytrope.f90
eos/stellarcollapse/stellarcollapse.f90
commit d14146a07930cddbc930d84d50ca7bbd755477bd
Merge: 4a22726f ab3ed92b
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 10 11:53:45 2015 -0400
Merge branch 'master' of github.com:BoxLib-Codes/Microphysics
commit 4a22726f59ff5b0214c610cf7cea13bfb4b87391
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 10 11:53:21 2015 -0400
Port over stellarcollapse EOS, and have it now use the eos_type y_e instead of the aux quantity y_e.
eos/stellarcollapse/Make.package
eos/stellarcollapse/README
eos/stellarcollapse/_parameters
eos/stellarcollapse/eos_aux_data.f90
eos/stellarcollapse/stellarcollapse.f90
commit 29ffca7e37c1f3db217ae758ec6c826bbb7ad78d
Author: Max Katz <maxpkatz@gmail.com>
Date: Fri Jul 10 11:47:32 2015 -0400
Add y_e to the eos_type and explicitly construct it along with other composition quantities.
eos/eos.f90
eos/eos_data.f90
eos/eos_type.f90
commit ab3ed92b1acca24dffa969289ce4d0bdce307a5d
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 16:45:47 2015 -0400
Port the multigamma EOS over from Castro. It is not fully correct yet.
eos/multigamma/Make.package
eos/multigamma/_parameters
eos/multigamma/multigamma.f90
commit b7f2773f26d85c418d42185392444cb90fb4fd1f
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 15:04:13 2015 -0400
Port over the polytrope EOS from Castro
eos/polytrope/Make.package
eos/polytrope/_parameters
eos/polytrope/polytrope.f90
commit 271abc5215e9b433bfcbc1fff656f9d965fcac7c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 14:49:59 2015 -0400
Port the gamma_law_general EOS from CASTRO and make it vectorized.
eos/gamma_law_general/Make.package
eos/gamma_law_general/_parameters
eos/gamma_law_general/gamma_law_general.f90
commit f6d4b700fcf304f369d2e5681234f49b6f94314e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 14:49:15 2015 -0400
Make assume_neutral a global EOS parameter.
eos/_parameters
eos/eos.f90
eos/eos_type.f90
commit 3e89d29e3ae363b9d8cd6914feb3489c891da398
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 13:52:58 2015 -0400
Remove eos_diag parameter; we no longer assume that we can do real-time I/O while the EOS is calculating because it can be on an accelerator and thus unable to communicate.
eos/eos.f90
commit 430006f98db0e1de58288ba6336c1825fa41fb91
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 13:37:55 2015 -0400
A bit of cleanup on the Helmholtz EOS.
eos/helmholtz/helmholtz.f90
commit 6638972d1e6afa9547eaa2598e6b37f22a240fff
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 13:19:20 2015 -0400
We do not need to pass the size of the array to the specific EOS; it will treat it as an assumed shape array and we can work it out using size().
eos/eos.f90
eos/helmholtz/helmholtz.f90
commit 075bec83608fd87c9f8e2e9c8cc27ee680df65b0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 13:01:11 2015 -0400
Allow the EOS to modify small_temp and small_dens if they are smaller than the minimum possible EOS values.
eos/eos.f90
commit 69fe8a685a9df01f26fc9693506f7defb074efff
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 12:41:45 2015 -0400
Don't attempt to set smallt and smalld inside the EOS; instead, allow the calling code to optionally set this.
eos/eos.f90
eos/eos_data.f90
commit 671f63527c662dcf9ba0e8be6eedb4301754189c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 12:34:23 2015 -0400
Add min/max temp and min/max dens and allow the EOS to set it consistent with its own requirements.
eos/eos.f90
eos/eos_data.f90
eos/helmholtz/helmholtz.f90
commit cbd1d146ff868e010cb8655a7013065612bf38ef
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 12:14:21 2015 -0400
Transition to a structure where there is a general EOS interface in the main eos/ directory, and each subdirectory holds the details of each specific EOS. This is now self-consistent since we carried over the eos_type and eos_data modules.
eos/Make.package
eos/eos.f90
eos/eos_data.f90
eos/eos_type.f90
eos/helmholtz/Make.package
eos/helmholtz/helmholtz.f90
commit 43200d0a1e8fe793032bae03f01d627fb64868b4
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Thu Jul 9 04:03:43 2015 -0400
Rename eos interface file
eos/helmholtz/Make.package
eos/helmholtz/eos.f90
commit 26785b156eb864dd68003d80dcbe4f1bdd7e3fb5
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 8 13:53:00 2015 -0400
Remove pt_index entirely from the interface. Instead, use the new eos_state % loc variable if you want to specify location information for the state.
eos/helmholtz/eos_stuff.f90
commit dfc604c0bc54b1d0ea4b10c133362e182a4a742c
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 8 13:23:52 2015 -0400
Disable pt_index for rank > 1, as it is meaningless. However we may still consider index information in the future, perhaps by adding the index data to the eos_state array.
eos/helmholtz/eos_stuff.f90
commit 121958d9ec4c424ffc475d6fc593e8cd09440540
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Wed Jul 8 13:02:49 2015 -0400
Add interfaces for higher rank arrays to be sent to the EOS. This allows us to hide the reshaping that is used for the vectorized EOS inside the EOS code and keeps the hydro code cleaner. We have up to rank 5 right now; shouldn't need more than that in practice.
eos/helmholtz/eos_stuff.f90
commit f55fc09a6b51ff8abeed56e09beb3e873766f470
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date: Fri Jul 3 02:49:49 2015 -0400
Copy over the Helmholtz EOS from the OpenACC branch of CASTRO.
eos/helmholtz/Make.package
eos/helmholtz/README
eos/helmholtz/_parameters
eos/helmholtz/eos_stuff.f90
eos/helmholtz/helm_table.dat
eos/helmholtz/helmholtz.f90
commit a1346cc07623378b244585839834eaa068b80f6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 5 18:44:12 2015 -0400
update readme
networks/aprox13/README
commit 8ca63a97438d70370d2f5cbf0ba871cd134de55c
Merge: 1a0b1049 2e87e377
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 5 18:42:17 2015 -0400
Merge /home/zingale/development/AstroDev
commit 2e87e377b4b9bd2003d3a35cc7ab23342763ee6d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun Apr 5 18:41:55 2015 -0400
move aprox13
networks/aprox13/GPackage.mak
networks/aprox13/Make.package
networks/aprox13/NETWORK_REQUIRES
networks/aprox13/README
networks/aprox13/_parameters
networks/aprox13/burner.f90
networks/aprox13/castro_burner.f90
networks/aprox13/f_rhs.f90
networks/aprox13/network.f90
networks/aprox13/network_indices.f90
networks/aprox13/rates.f90
networks/aprox13/rhs.f90
networks/aprox13/rpar_indices.f90
networks/aprox13/screen5.f90
networks/aprox13/sneut5.f90
networks/aprox13/test/GNUmakefile
networks/aprox13/test/GPackage.mak
networks/aprox13/test/testburn.f90
networks/aprox13/tfactors.f90
commit 1a0b10495d2152875e8bd5cc3684673c810f5bbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sat Apr 4 20:47:51 2015 -0400
adda readme
README.md
commit 207d4ead457ba065621e6ec121dc1b2112104d2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Jul 4 15:58:46 2014 -0400
just comment lines
f_rhs.f90
commit 68d99a8745763b341580945a27c48e86dbcc25e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Jul 3 19:27:25 2014 -0400
add the optional ability to call the EOS in the RHS evaluation
_parameters
f_rhs.f90
commit 926023edbc49763f4763c6eb5b4dc8715d626a5a
Merge: 29bed59b ad456452
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 2 20:53:02 2014 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AstroDev
commit 29bed59bb43a652a44b806a101592c3bc5bcfabf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 2 20:52:51 2014 -0400
more steps, if necessary
castro_burner.f90
commit ad45645247c73a7c22e43ee5c004dc4ac0a28cf7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 2 14:57:54 2014 -0400
add the ability to do a constant volume burn if desired
_parameters
f_rhs.f90
commit cf465ad3e27cedfa848e1efc490c04375431c75a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Jul 2 14:38:57 2014 -0400
add some more thermodynamic info to rpar to allow for constant volume burns
instead of constant pressure burns
burner.f90
castro_burner.f90
rpar_indices.f90
commit 3b0a93857ef0862440810ccfa8a1336105e36040
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Jul 1 10:59:24 2014 -0400
comment out some unused quantities and private some constants to gte this
compiling
burner.f90
network.f90
screen5.f90
sneut5.f90
test/GNUmakefile
commit bdef8c8ed32face83ac367b06c391b4351bb0b37
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date: Wed Aug 7 14:56:35 2013 -0400
comment out the derivative of the neutrino stuff -- we are not doing
the analytic Jacobian, so this only slows us down...
sneut5.f90
commit 140b3d7ef0209a78df4783a2aab53f577a5d0899
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Jul 14 12:53:30 2013 -0400
fix some comments
burner.f90
commit 1e01af7a5559ac96b0b907084870360d9cefd325
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Jul 14 12:39:36 2013 -0400
comment out all of the derivative terms in the screening function
-- since we are not doing an analytic Jacobian, it doesn't make
sense to calculate these
screen5.f90
commit 30ac54e8a24ae59e6d3be625301299846e229651
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Sun Jul 14 12:39:12 2013 -0400
remove unneeded variable
test/testburn.f90
commit 7537215f9f666d3565d09aebf2f2c9bd3ace8366
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Jul 12 20:19:41 2013 -0400
comment out the derivatives of the screening factors
rhs.f90
commit 79b715e0eff1b3b9d354dff5386f285cc18b3eab
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Jul 12 20:11:41 2013 -0400
update README
README
commit 22dec7a9026a6c15de169a0d4ccb61cc8fc0a1d6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Jul 12 19:51:38 2013 -0400
comment out all the analytic derivative terms -- we are doing a
numerical Jacobian, so these just add expense
rates.f90
commit 90b9bed51e79049b66eaea830874672618c9789f
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Fri Jul 12 18:51:20 2013 -0400
require the table
test/GNUmakefile
commit 5ffada11bc15291aecb70b33f787fb1bd97a6932
Author: lijewski <mjlijewski@lbl.gov>
Date: Wed Jun 26 12:25:30 2013 -0700
Removed some trim() calls when involved in a string comparison.
network.f90
commit 260e582fe14d24b230c8e57e24f0ac892c5c28c3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 19:54:37 2013 -0400
remove some factors not needed
tfactors.f90
commit 83db2a6d0f238d8d001e20fae010dae279ac7266
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 16:44:29 2013 -0400
loosen tolerances a little
burner.f90
commit 03556072ed640669f4cfb92ad08bdb6def3063dd
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 16:43:20 2013 -0400
updates for Castro
Make.package
burner.f90
castro_burner.f90
network.f90
commit 1d1e62e789e275cab0ac0d624aa149231f60877a
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 15:48:24 2013 -0400
seems to work (i.e. doesn't crash when run with the testburn)
network.f90
test/GNUmakefile
test/GPackage.mak
test/testburn.f90
commit 7feafb213acff58fe9465c31e0a3dfb94776201e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 15:28:19 2013 -0400
needed for MAESTRO
NETWORK_REQUIRES
commit b219acb3e2c4fd06a0789ae0fc63caed1ed507d6
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 15:28:01 2013 -0400
get the VODE RHS coded up
GPackage.mak
burner.f90
f_rhs.f90
rpar_indices.f90
commit bdd1e482f491cabada89e00e73e13e06bcdc48e3
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 14:23:13 2013 -0400
compiles now. Still need to build the actual RHS
rhs.f90
sneut5.f90
commit 63558f3adb473f07ba85957c328f97b7061e41ab
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 13:04:16 2013 -0400
more compiling work
network.f90
screen5.f90
commit 2ba652423a7fc74c5492e8f0699b913ac1ac1c29
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 12:59:20 2013 -0400
get this compiling -- mostly declaring a lot of arguments that previously
magically came in through the commons
rhs.f90
commit c57dbd4d634d744ba9dbea89c179f7bc03d45545
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 11:53:14 2013 -0400
fix some energy stuff -- it is enuc that will be returned, not enucdot
README
burner.f90
network_indices.f90
commit 6633e7661ec4ca9e7e32747a64b8c8b20a765a99
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 11:44:20 2013 -0400
main burner
burner.f90
public_aprox13.f90
commit 793532e34a5e8bcb1253abf7c17a91a3db9b1c77
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 11:42:51 2013 -0400
make the screening threadsafe at the expense of operations. Add itemp and ienucdot
network_indices.f90
screen5.f90
commit b5031aaa8068e4e865739e032d636c64ec8d3109
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 10:23:00 2013 -0400
rates now use the tf_t type
rates.f90
commit 91282b4e2711a28ced82e931b637fc93e487e920
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Tue Mar 19 10:11:09 2013 -0400
more progress
GPackage.mak
network.f90
rates.f90
rhs.f90
tfactors.f90
commit e3be06cfe0bec98d3e36f355ef0fb154b2e71a97
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 20:07:05 2013 -0400
module
rhs.f90
commit 1fabee2f48a9880efe9437637b722cfc38ebd851
Merge: a56217b5 f470b0da
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 20:05:46 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AstroDev
commit a56217b59568d293406d363f2b01857d10a1daf4
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 20:05:22 2013 -0400
integer indices
network_indices.f90
commit f470b0da2d1b52a2e3f5d589b7840755df2e6d56
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 20:02:26 2013 -0400
formatting, moduling
rhs.f90
commit 5a96064e2caf090874982e1a49250ae445f54014
Merge: 52f32eef d543368d
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 19:24:54 2013 -0400
Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AstroDev
commit 52f32eefd86e1958a5ead9b770123e4c227de307
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 19:24:34 2013 -0400
initialization stuff
network.f90
commit d543368dfa62a15f38ae28ac75dfb8e10e64229b
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 18:56:20 2013 -0400
more progress -- still need to setup the points, (ihe4, ...), store aion, zion, the names, mion, etc.
Also a lot of data is probably not yet getting passed through argument
lists.
rhs.f90
commit faf8ed972ca3cd86728a54ae426bb9cf2c1ac44e
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 18:43:08 2013 -0400
more files
rhs.f90
sneut5.f90
commit ffb630860eb42f8b348ef2d7b4329da0fbaa8d12
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 17:04:24 2013 -0400
more progress
README
rates.f90
commit 2042149f58537326b626a97cb5c74bb02b6ff904
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 15:20:31 2013 -0400
more updates
README
public_aprox13.f90
tfactors.f90
commit 45b695e78364882f24d5e8e38d590d9144f6fffa
Author: Michael Zingale <zingale@localhost.localdomain>
Date: Mon Mar 18 14:44:29 2013 -0400
start of a cleaned up version of Frank's aprox13 to use with VODE
README
public_aprox13.f90
rates.f90
screen5.f90