commit 8fd0d4aed4b7934a3a704fe938614685df988305 Author: Michael Zingale Date: Mon Jul 15 17:13:08 2024 -0400 rework the unit test docs (#1570) We split the current page into 3 separate pages and add descriptions for all of the unit tests sphinx_docs/source/comprehensive_tests.rst sphinx_docs/source/index.rst sphinx_docs/source/one_zone_tests.rst sphinx_docs/source/unit_tests.rst commit 24fc8547090297bacdefe30f14bc2c37e53069f4 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Jul 14 20:53:47 2024 -0400 include higher taylor terms for fast_atan (#1611) Pointed out by Eric: in screening, atan is used in cases like gamma - atan(gamma), so we should use a higher order term rather than simply letting atan(gamma) ~ gamma when gamma is small. unit_test/test_nse_net/ci-benchmarks/nse_net_unit_test.out unit_test/test_nse_net/make_table/burn_cell.H unit_test/test_nse_net/make_table/ci-benchmarks/nse_net_make_table_unit_test.out util/approx_math/approx_math.H commit a5408bad445e49e4b8c0622843905a4c08b1ed6d Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Jul 14 15:02:00 2024 -0400 update self-consistent NSE SDC update with Tabular NSE (#1569) the self-consistent and tabular code paths are now consistent -- both do an update that should be second-order accurate. integration/nse_update_sdc.H networks/CNO_extras/actual_rhs.H networks/ECSN/actual_rhs.H networks/He-C-Fe-group/actual_rhs.H networks/ase/actual_rhs.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/URCA-medium/actual_rhs.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/nova/actual_rhs.H networks/nova2/actual_rhs.H networks/partition_test/actual_rhs.H networks/sn160/actual_rhs.H networks/subch_base/actual_rhs.H networks/subch_simple/actual_rhs.H nse_solver/Make.package nse_solver/nse_eos.H commit b413290def9550c8fac7035ec614f90f68c12ba4 Author: Michael Zingale Date: Fri Jul 12 11:34:44 2024 -0400 remove some more Fortran comments (#1609) Make.Microphysics nse_solver/make_table/main.cpp nse_solver/nse_compatibility/main.cpp unit_test/burn_cell/main.cpp unit_test/burn_cell_primordial_chem/main.cpp unit_test/burn_cell_sdc/main.cpp unit_test/eos_cell/main.cpp unit_test/nse_table_cell/main.cpp unit_test/test_aprox_rates/README.md unit_test/test_eos/README.md unit_test/test_jac/main.cpp unit_test/test_linear_algebra/main.cpp unit_test/test_nse_interp/main.cpp unit_test/test_nse_net/main.cpp unit_test/test_nse_net/make_table/main.cpp unit_test/test_part_func/main.cpp unit_test/test_react/main.cpp unit_test/test_rhs/main.cpp unit_test/test_sdc/main.cpp unit_test/test_sdc_vode_rhs/main.cpp commit 448132f96834e1958e5fe38a10f08610ec665981 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Jul 12 07:30:45 2024 -0400 remove test_nse and rename test_ase -> test_nse_net (#1610) remove redundant test_nse and rename test_ase to test_nse_net for better clarity .github/workflows/cuda.yml .github/workflows/nse_net.yml .github/workflows/nse_test.yml unit_test/test_nse/GNUmakefile unit_test/test_nse/Make.package unit_test/test_nse/README.md unit_test/test_nse/_parameters unit_test/test_nse/ci-benchmarks/aprox21_ci.out unit_test/test_nse/inputs_aprox13 unit_test/test_nse/inputs_aprox19 unit_test/test_nse/inputs_aprox21 unit_test/test_nse/inputs_iso7 unit_test/test_nse/inputs_subch_full unit_test/test_nse/main.cpp unit_test/test_nse/nse_example.H unit_test/test_nse_net/GNUmakefile unit_test/test_nse_net/Make.package unit_test/test_nse_net/README.md unit_test/test_nse_net/_parameters unit_test/test_nse_net/burn_cell.H unit_test/test_nse_net/ci-benchmarks/nse_net_unit_test.out unit_test/test_nse_net/inputs_ase unit_test/test_nse_net/main.cpp unit_test/test_nse_net/make_table/GNUmakefile unit_test/test_nse_net/make_table/Make.package unit_test/test_nse_net/make_table/README.md unit_test/test_nse_net/make_table/_parameters unit_test/test_nse_net/make_table/burn_cell.H unit_test/test_nse_net/make_table/ci-benchmarks/nse_net_make_table_unit_test.out unit_test/test_nse_net/make_table/main.cpp commit 963ff00371ca38c271b82c96ccde9fbd17bb4952 Author: Michael Zingale Date: Thu Jul 11 15:07:04 2024 -0400 remove the old test_screening (#1608) the new templated version works with more networks 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/inputs unit_test/test_screening/main.cpp unit_test/test_screening/screening_util.cpp unit_test/test_screening/test_screen.H unit_test/test_screening/variables.H unit_test/test_screening/variables.cpp commit d791e67c65f623e0ee05b7458f6e6fae19668704 Author: Michael Zingale Date: Thu Jul 11 13:39:25 2024 -0400 Remove strang nse (#1549) Strang does not really allow us to do 2nd order easily because we can't capture the evolution of the state during the burn .github/workflows/nse_table.yml Make.Microphysics_extern integration/Make.package integration/nse_update_strang.H unit_test/test_nse_interp/GNUmakefile commit 4142d4fbff132040a405d0bc3759b5c99099334c Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Jul 11 11:05:53 2024 -0400 Update rhoX for nse_solver for SDC and discard strang (#1607) This is to address #1606 and partially addresses #1542 Also some clean-ups to nse-solver. It mainly stores state.y[SFS+n] at the end. nse_solver/nse_check.H nse_solver/nse_solver.H unit_test/test_ase/GNUmakefile unit_test/test_ase/burn_cell.H unit_test/test_ase/ci-benchmarks/ase_nse_net_unit_test.out unit_test/test_ase/make_table/GNUmakefile unit_test/test_ase/make_table/burn_cell.H unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out unit_test/test_nse/GNUmakefile unit_test/test_nse/ci-benchmarks/aprox21_ci.out unit_test/test_nse/nse_example.H commit 0b1a2310392f83adfee33c5a50da9fd90a2b5a7c Author: Michael Zingale Date: Tue Jul 9 08:30:51 2024 -0400 add NSE bailout to RKC (#1544) also clean up some VODE stuff integration/RKC/rkc.H integration/VODE/vode_type.H integration/integrator_data.H commit a3bc2465da68185084efc23383c55be90e426712 Author: Michael Zingale Date: Mon Jul 8 19:56:12 2024 -0400 add a second T check to tablular NSE (#1547) if we are larger than T_always_nse, then we ignore composition (density still matters) nse_tabular/_parameters nse_tabular/nse_table_check.H sphinx_docs/source/nse.rst unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out commit cd22d99e2473d8a8da8f2d5b83dee1bb4fcbfa7e Author: Michael Zingale Date: Mon Jul 8 15:57:13 2024 -0400 add SDC+NSE unit test example (#1548) .github/workflows/nse_table.yml unit_test/burn_cell_sdc/burn_cell.H unit_test/burn_cell_sdc/ci-benchmarks/aprox19_NSE_state_over_time.txt unit_test/burn_cell_sdc/inputs_aprox19.nse.ci commit f0a7fcef17fb589cd8555e58133be6a2d53e9e9d Author: Michael Zingale Date: Mon Jul 8 14:02:12 2024 -0400 some clang-tidy enum type fixes (#1582) these use smaller types now integration/integrator_data.H interfaces/eos_type.H networks/aprox19/actual_network.H unit_test/burn_cell_sdc/burn_cell.H commit f2ef85f71c1bffccd17ac75b5379844a0de3c39a Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jul 8 13:05:20 2024 -0400 Fast log and pow implementation (#1591) Fast log implementation by inverting fast_exp, roughly 10 times faster than std::log, but it doesn't check bounds like inf and 0. With additional if-statements, it would be slower, but still ~5 times faster than std::log This is discussed in: https://martin.ankerl.com/2007/10/04/optimized-pow-approximation-for-java-and-c-c/ Also adds fast_pow implementation by combining fast_exp and fast_log, this is the vfast_pow function. It is roughly 30 times faster than std::pow but poor accuracy when exponent is >> 1. If we combine the method of exponentiation by squaring for solving the integer part and only use approximation for the fraction part of the exponent, then we get overall ~3% relative error for all exponents, but its a lot slower than vfast_pow, but still ~5 times faster than std::pow. util/approx_math/approx_math.H util/approx_math/test_fast_log/GNUmakefile util/approx_math/test_fast_log/Make.package util/approx_math/test_fast_log/main.cpp util/approx_math/test_fast_log/test_fast_log.H util/approx_math/test_fast_pow/GNUmakefile util/approx_math/test_fast_pow/Make.package util/approx_math/test_fast_pow/main.cpp util/approx_math/test_fast_pow/test_fast_pow.H commit 8f0ce83cd3023d320a039c1a02d3a8ea0ad435e3 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Mon Jul 8 17:53:46 2024 +0200 updated to replace std::pow with a combo of std::exp and std::log for speedup (#1605) I replaced most calls to std::pow with a combination of std::exp and std::log to speedup chemistry. Also added free-free cooling, which was missing from the previous version. In the future, I will follow #1586 and #1591 to use fast_exp and fast_log. The unit test passes, with small differences in the number densities of H and H2 as compared to the reference solution (3.5% and 0.3% respectively). The difference in H is more likely due to free-free cooling. Co-authored-by: Piyush Sharda networks/primordial_chem/actual_rhs.H commit 52f71c84d198e0c2003b3896dfce0d7bfb7a6000 Author: Eric T. Johnson Date: Mon Jul 8 08:07:26 2024 -0400 Fix some errors in the aprox network rate derivatives (#1604) I found these while comparing against a version that I updated to use autodiff. rates/aprox_rates.H commit 523b4beec43c95f088a7eec74afbf32f430b0029 Author: Eric T. Johnson Date: Mon Jul 8 08:03:39 2024 -0400 Avoid dividing by zero in constexpr linear algebra routines (#1603) This fixes the crash in `Detonation-collision-retry-SDC` in the Castro test suite. integration/VODE/vode_dvjac.H networks/rhs.H commit 4fc88926c320a29681a91680ca6cb5ea96068b82 Author: Max Katz Date: Fri Jul 5 12:38:25 2024 -0400 Remove references to gamma_law_general (#1602) EOS/gamma_law/actual_eos.H unit_test/test_eos/GNUmakefile commit 0a96241b0f29b95347745ad74fd688dfd3d56660 Author: Eric T. Johnson Date: Tue Jul 2 02:49:41 2024 -0400 Enable FPE traps in all github actions (#1601) .github/workflows/burn_cell.yml .github/workflows/burn_cell_primordial_chem.yml .github/workflows/burn_cell_sdc.yml .github/workflows/eos_cell.yml .github/workflows/nse_net.yml .github/workflows/nse_table.yml .github/workflows/nse_test.yml .github/workflows/test_neutrinos.yml .github/workflows/test_nse_interp.yml .github/workflows/test_rhs.yml commit c2795ec391217dd0bb7d56044eaccac128d5112f Author: Michael Zingale Date: Tue Jul 2 02:46:39 2024 -0400 update changes for 24.07 (#1599) CHANGES.md commit 41c88a6bc7eeb8dc7a5741a4a64d478a59473609 Author: Eric T. Johnson Date: Mon Jul 1 18:18:39 2024 -0400 Fix FPE in templated networks (#1600) Also document `autodiff::detail::isDual` for checking templated types. I'm leaving this as a quiet NaN so it will show up in outputs if it ever gets used by accident, but won't immediately trigger a floating-point exception. screening/screen.H sphinx_docs/source/autodiff.rst commit 3ff348fe93ac2bab46422c2b33d4eb025ac66dc2 Author: Eric T. Johnson Date: Fri Jun 28 18:45:23 2024 -0400 Use autodiff in screening routines (#1588) This PR gives the same results for test_screening to within roundoff, and the performance is about the same or slightly better. It also adds a page to the docs about how to use the autodiff library. One notable change is that the templated networks don't calculate the derivative terms when screening is called from RHS::rhs() (this is also how the pynucastro networks behave). Previously, they would be calculated unnecessarily if integrator.jacobian was set to 1. interfaces/rhs_type.H networks/CNO_extras/actual_rhs.H networks/ECSN/actual_rhs.H networks/He-C-Fe-group/actual_rhs.H networks/aprox13/actual_network.H networks/aprox19/actual_network.H networks/aprox21/actual_network.H networks/ase/actual_rhs.H networks/ignition_chamulak/actual_network.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/URCA-medium/actual_rhs.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_simple/actual_network.H networks/iso7/actual_network.H networks/nova/actual_rhs.H networks/nova2/actual_rhs.H networks/partition_test/actual_rhs.H networks/powerlaw/actual_network.H networks/rhs.H networks/rprox/actual_network.H networks/sn160/actual_rhs.H networks/subch_base/actual_rhs.H networks/subch_simple/actual_rhs.H networks/triple_alpha_plus_cago/actual_network.H nse_solver/nse_solver.H screening/screen.H unit_test/burn_cell/ci-benchmarks/chamulak_VODE_unit_test.out unit_test/test_screening/screening_util.cpp unit_test/test_screening_templated/_parameters unit_test/test_screening_templated/screening_util.cpp commit 3641c24c0a9a86983b47116e52c099eaac1e7bc1 Author: Eric T. Johnson Date: Fri Jun 28 17:13:35 2024 -0400 Update check_powi.py to handle floats properly (#1598) Also check instances of admath::pow in addition to std::pow and gcem::pow. .github/workflows/check_powi.py networks/primordial_chem/actual_rhs.H commit ed417bc31c3b5062217419a9f44cb7fa9b733d2b Author: Eric T. Johnson Date: Fri Jun 28 17:12:31 2024 -0400 Add note about `autodiff::seed()` to the docs (#1597) sphinx_docs/source/autodiff.rst commit 01c244ad85a05469f696e53b46bb4f648d56390a Author: Eric T. Johnson Date: Thu Jun 27 07:35:16 2024 -0400 Add `autodiff::dual_array` (#1596) This can calculate derivatives with respect to multiple variables in a single pass. sphinx_docs/source/autodiff.rst util/microphysics_autodiff.H commit 6734dabf2aed32f58685b131c4d81b6cfd7da329 Author: Ryan Brady Date: Wed Jun 26 13:46:16 2024 -0400 update NSE table check docs (#1594) sphinx_docs/source/nse.rst commit bbe8723a11930d2f018b1d332e41377419fffb26 Author: Eric T. Johnson Date: Wed Jun 26 11:34:10 2024 -0400 Add autodiff machinery and docs (#1593) This adds a new header, microphysics_autodiff.H, which includes the autodiff library and sets things up for use with AMReX. It also provides the admath namespace, which is a drop-in replacement for std for functions from , and works on both autodiff types and normal numeric types. sphinx_docs/source/autodiff.rst sphinx_docs/source/index.rst sphinx_docs/source/refs.bib util/Make.package util/microphysics_autodiff.H commit 90adb0f90b28c39c5171ac2446c033afeb2f6f27 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Jun 25 13:17:52 2024 -0400 Fast exp algorithm implementation. (#1586) A fast exp algorithm implementation following: Ref: 1. A Fast, Compact Approximation of the Exponential Function by Schraudolph 1999 (https://doi.org/10.1162/089976699300016467). 2. On a Fast Compact Approximation of the Exponential Function by Cawley 2000 (https://doi.org/10.1162/089976600300015033). 3. https://gist.github.com/jrade/293a73f89dfef51da6522428c857802d 4. https://github.com/ekmett/approximate/blob/master/cbits/fast.c There are two versions: jrade_exp: Its roughly 6-times faster than std::exp. It has reasonable accuracy across all range (roughly ~2% relative error), we follow Ref (3) ekmett_exp: It is about twice as slow as jrade_exp, but still ~ 3 times faster than std::exp, but it gives much better accuracy, ~0.1% relative error for most cases. The main driver is fast_exp, which also included a simple taylor approximation, 1+x, when x < 0.1, currently it is defaulted to use jrade_exp but one can just switch to ekmett_exp for better accuracy. We also use memcpy approach to avoid undefined behavior from type-punning when using union (pointed out by Eric), and this approach is demonstrated in Ref 3, which we adapt for ekmett_exp. nse_solver/make_table/burn_cell.H unit_test/test_ase/make_table/burn_cell.H util/approx_math/approx_math.H util/approx_math/test_fast_exp/GNUmakefile util/approx_math/test_fast_exp/Make.package util/approx_math/test_fast_exp/main.cpp util/approx_math/test_fast_exp/test_fast_exp.H commit e27c00f66c5b72e9e2d362febba3f8cf6742c987 Author: Ben Wibking Date: Mon Jun 24 08:52:51 2024 -0400 robustify PrimordialChem unit test (#1590) Return exit code and check for the right input file. unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_primordial_chem/main.cpp commit 48149cdd24507eea98f4a5031261816c2abbffc3 Author: Eric T. Johnson Date: Sat Jun 22 15:05:46 2024 -0400 Use 4 make jobs in "Test compilation" workflow (#1589) .github/workflows/find_changed_files.py commit 134200e7a376b8709f438223208b9795a14aa3ee Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sat Jun 22 13:01:10 2024 -0400 implement a fast atan approximation function (#1583) implement a fast atan function using an approximate function for x in [-1, 1], for |x| > 1, the identity arctan(x) = sign(pi/2, x) - arctan(1/x) (Thanks to Eric) is used. Two versions of the approximate functions are included. 1. Efficient Approximations for the Arctangent Function by Rajan 2006: Equation 9: Max error ~0.0015 rad 2. https://stackoverflow.com/questions/42537957/fast-accurate-atan-arctan-approximation-algorithm: Max error ~0.00063 rad Generally I find the form from stackoverflow is more accurate and also faster. 1) is also discussed in 2). In general, from testing, atanf is roughly more than 2 times faster than std::atan. Make.Microphysics_extern screening/screen.H unit_test/test_ase/ci-benchmarks/ase_nse_net_unit_test.out unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out unit_test/test_nse/ci-benchmarks/aprox21_ci.out util/approx_math/Make.package util/approx_math/approx_math.H util/approx_math/test_fast_atan/GNUmakefile util/approx_math/test_fast_atan/Make.package util/approx_math/test_fast_atan/main.cpp util/approx_math/test_fast_atan/test_fast_atan.H commit 7d846d09de22af753dfe68712e3244516d3f38e6 Merge: e1a89f61 77240dd5 Author: Michael Zingale Date: Fri Jun 21 17:51:22 2024 -0400 Merge pull request #1587 from zingale/fix_test_conductivity_compilation fix compilation of test_conductivity commit 77240dd5fe5ab43f67e37f7ef5d7d1396d58dcee Author: Michael Zingale Date: Fri Jun 21 15:21:29 2024 -0400 fix compilation of test_conductivity unit_test/test_conductivity/conductivity_util.cpp commit e1a89f619ddfc8f3b2033d4cb673db4181f1f14e Merge: f9e2e1d6 c86a060b Author: Michael Zingale Date: Fri Jun 21 14:11:12 2024 -0400 Merge pull request #1585 from zhichen3/factor_out_terms_chabrier1998 Factor out some sqrt terms in chabrier1998 screening. commit f9e2e1d62dc75ec05ecf4d0b61e06fc05c63e83b Merge: 30469dd4 2d23ccef Author: Michael Zingale Date: Fri Jun 21 13:43:28 2024 -0400 Merge pull request #1584 from zingale/amrex_namespace remove using namespace amrex from aprox nets commit 2d23cceff56c923555031470490403ed7f8dfa4c Author: Michael Zingale Date: Thu Jun 20 16:57:28 2024 -0400 fix namespace networks/aprox19/nse_table_size.H commit c86a060b1c5eb4ff9e8c6a306852c60f01cb4eb8 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Jun 20 16:39:27 2024 -0400 give CBRT_2 its own name Co-authored-by: Eric T. Johnson screening/screen.H commit a5fa160ab731d8bdfd2ee8ba64b3551dcefb5338 Author: Zhi Date: Thu Jun 20 16:27:58 2024 -0400 update benchmnark again unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out commit d4c01840f92d81f35c27d58f7757cfce24cfbeca Author: Zhi Date: Thu Jun 20 16:19:05 2024 -0400 update benchmark unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out commit f361dc38c97d5a2c1c93edeacbaf3fa84054d431 Author: Zhi Date: Thu Jun 20 16:10:20 2024 -0400 factor out some terms to have less sqrt calls screening/screen.H commit a492a2461756a018a7d69583860c9926c21853a7 Author: Michael Zingale Date: Thu Jun 20 15:15:23 2024 -0400 more fixes integration/ForwardEuler/actual_integrator.H integration/ForwardEuler/fe_type.H networks/ignition_simple/actual_network.H util/linpack.H commit 91c312953994d6caee34c0f2309a007edf3788bb Author: Michael Zingale Date: Thu Jun 20 12:56:00 2024 -0400 more fixes util/hybrj/hybrj.H util/hybrj/hybrj_dogleg.H util/hybrj/hybrj_enorm.H util/hybrj/hybrj_qform.H util/hybrj/hybrj_qrfac.H util/hybrj/hybrj_r1mpyq.H util/hybrj/hybrj_r1updt.H commit eac88aea61e236a5c9df2c777cbeaca73fbc15ec Author: Michael Zingale Date: Thu Jun 20 12:49:18 2024 -0400 fix amrex networks/triple_alpha_plus_cago/actual_network.H commit b0c0344e08ee0ebadc881975a9e79ead52d09528 Author: Michael Zingale Date: Thu Jun 20 12:46:54 2024 -0400 more fixes unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_sdc/burn_cell.H 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 unit_test/test_ase/make_table/burn_cell.H unit_test/test_conductivity/conductivity_util.cpp unit_test/test_conductivity/test_cond.H unit_test/test_jac/jac_zones.H unit_test/test_linear_algebra/test_linear_algebra.H unit_test/test_neutrino_cooling/test_sneut.H unit_test/test_nse/nse_example.H unit_test/test_nse_interp/nse_cell.H unit_test/test_part_func/pf_cell.H unit_test/test_react/react_zones.H unit_test/test_rhs/rhs_zones.H unit_test/test_screening/test_screen.H unit_test/test_screening_templated/test_screen.H unit_test/test_sdc/react_zones.H unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit 099d94f1a03602953541c425477295cc63e488a6 Author: Michael Zingale Date: Thu Jun 20 12:33:55 2024 -0400 more fixes nse_tabular/nse_eos.H nse_tabular/nse_table_check.H commit 338c238bb3848195bafe49d681a76578cad3674c Author: Michael Zingale Date: Thu Jun 20 12:30:39 2024 -0400 more fixes nse_solver/make_table/burn_cell.H nse_solver/nse_check.H nse_solver/nse_compatibility/nse_network_compatibility.H nse_solver/nse_solver.H commit a714be80a8a0092921257dcc8039324f0108c723 Author: Michael Zingale Date: Thu Jun 20 12:23:55 2024 -0400 more fixes networks/aprox19/actual_network.H networks/aprox21/actual_network.H networks/ignition_chamulak/actual_network.H networks/ignition_simple/actual_network.H networks/iso7/actual_network.H networks/rprox/actual_network.H networks/triple_alpha_plus_cago/actual_network.H commit c3b138d2f6ac551e8fdb175ef23615f971ec8731 Author: Michael Zingale Date: Thu Jun 20 12:21:09 2024 -0400 more integrator fixes integration/BackwardEuler/be_integrator.H integration/ForwardEuler/actual_integrator.H integration/ForwardEuler/fe_type.H integration/QSS/actual_integrator.H commit 76470ffedfd019a4b76bbe75bb8204b2de60dbe0 Author: Michael Zingale Date: Thu Jun 20 12:16:40 2024 -0400 more nets networks/aprox19/actual_network.H networks/aprox19/nse_table_size.H networks/aprox21/actual_network.H networks/ignition_chamulak/actual_network.H networks/ignition_simple/actual_network.H networks/rprox/actual_network.H networks/triple_alpha_plus_cago/actual_network.H commit ef059f5dff310dde361db40120770cd2299979e7 Author: Michael Zingale Date: Thu Jun 20 12:09:16 2024 -0400 remove using namespace amrex from aprox nets 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/utils/jacobian_utilities.H interfaces/burner.H networks/aprox13/actual_network.H networks/rhs.H networks/rhs.cpp unit_test/burn_cell/burn_cell.H commit 30469dd4b2c8374b5a19708f95f6921748211366 Merge: e56bbf10 11fd505e Author: Michael Zingale Date: Fri Jun 14 16:54:45 2024 -0400 Merge pull request #1581 from yut23/add_autodiff Add autodiff library commit 11fd505ee74af2f9554614639c1468edd2b391dc Author: Eric T. Johnson Date: Fri Jun 14 15:08:05 2024 -0400 Add autodiff to Make.package and ignore it in linters .codespellrc .editorconfig .github/workflows/check_ifdefs.py .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh util/Make.package commit 7864c0228ad2dd01629de434178622373b544a8e Merge: e56bbf10 9285df28 Author: Eric T. Johnson Date: Fri Jun 14 14:56:32 2024 -0400 Merge commit '9285df283ea57361606dd1adddf390c7c3546005' as 'util/autodiff' commit 9285df283ea57361606dd1adddf390c7c3546005 Author: Eric T. Johnson Date: Fri Jun 14 14:56:32 2024 -0400 Squashed 'util/autodiff/' content from commit cb2d6e8b git-subtree-dir: util/autodiff git-subtree-split: cb2d6e8b9fa98b7b8cf3ffaefa231943c56361ae .arquive/benchmarks/CMakeLists.txt .arquive/benchmarks/README.md .arquive/benchmarks/benchmark1.cpp .bazelrc .clang-format .github/workflows/bazel.yml .github/workflows/linux.yml .github/workflows/osx.yml .github/workflows/website.yml .github/workflows/windows.yml .gitignore .pre-commit-config.yaml BUILD CHANGELOG.md CMakeLists.txt LICENSE README.md WORKSPACE art/autodiff-header.svg art/autodiff-logo.svg art/autodiff.github.io.svg art/expression-tree-diagram.svg art/inkscape/autodiff-header.inkscape.svg art/inkscape/autodiff-logo.inkscape.svg art/logo.png autodiff/BUILD autodiff/CMakeLists.txt autodiff/common/binomialcoefficient.hpp autodiff/common/classtraits.hpp autodiff/common/eigen.hpp autodiff/common/meta.hpp autodiff/common/numbertraits.hpp autodiff/common/vectortraits.hpp autodiff/forward/dual.hpp autodiff/forward/dual/dual.hpp autodiff/forward/dual/eigen.hpp autodiff/forward/real.hpp autodiff/forward/real/eigen.hpp autodiff/forward/real/real.hpp autodiff/forward/utils/derivative.hpp autodiff/forward/utils/gradient.hpp autodiff/forward/utils/taylorseries.hpp autodiff/pybind11/eigen.hpp autodiff/reverse/var.hpp autodiff/reverse/var/eigen.hpp autodiff/reverse/var/var.hpp cmake/CCache.cmake cmake/CondaAware.cmake cmake/autodiffConfig.cmake.in cmake/autodiffInstallCMakeConfigFiles.cmake docs/CMakeLists.txt docs/mkdocs-macros.py docs/mkdocs.yml docs/website/about.md docs/website/css/extra.css docs/website/faq.md docs/website/fonts/Comfortaa-Bold.ttf docs/website/fonts/Comfortaa-Light.ttf docs/website/fonts/Comfortaa-Regular.ttf docs/website/img/autodiff-header.svg docs/website/img/autodiff-logo.svg docs/website/img/autodiff.github.io.svg docs/website/img/expression-tree-diagram.svg docs/website/index.md docs/website/installation.md docs/website/tutorials.md environment.devenv.yml examples/CMakeLists.txt examples/cmake-project/CMakeLists.txt examples/cmake-project/README.md examples/cmake-project/main.cpp examples/forward/BUILD examples/forward/CMakeLists.txt examples/forward/example-forward-directional-taylor-series-using-eigen.cpp examples/forward/example-forward-directional-taylor-series.cpp examples/forward/example-forward-gradient-derivatives-using-eigen-with-parameters.cpp examples/forward/example-forward-gradient-derivatives-using-eigen.cpp examples/forward/example-forward-gradient-derivatives.cpp examples/forward/example-forward-hessian-derivatives-using-eigen-with-parameters.cpp examples/forward/example-forward-hessian-derivatives-using-eigen.cpp examples/forward/example-forward-higher-order-cross-derivatives.cpp examples/forward/example-forward-higher-order-directional-derivatives-using-eigen.cpp examples/forward/example-forward-higher-order-directional-derivatives.cpp examples/forward/example-forward-jacobian-derivatives-using-eigen-map.cpp examples/forward/example-forward-jacobian-derivatives-using-eigen-with-parameters.cpp examples/forward/example-forward-jacobian-derivatives-using-eigen.cpp examples/forward/example-forward-multi-variable-combine-analytical-derivative.cpp examples/forward/example-forward-multi-variable-function-with-parameters.cpp examples/forward/example-forward-multi-variable-function.cpp examples/forward/example-forward-single-variable-function-custom-scalar.cpp examples/forward/example-forward-single-variable-function.cpp examples/reverse/BUILD examples/reverse/CMakeLists.txt examples/reverse/example-reverse-conditional.cpp examples/reverse/example-reverse-gradient-derivatives-using-eigen.cpp examples/reverse/example-reverse-hessian-derivatives-using-eigen.cpp examples/reverse/example-reverse-higher-order-derivatives-multi-variable-function.cpp examples/reverse/example-reverse-higher-order-derivatives-single-variable-function.cpp examples/reverse/example-reverse-multi-variable-function-with-parameters.cpp examples/reverse/example-reverse-multi-variable-function.cpp examples/reverse/example-reverse-single-variable-function.cpp python/CMakeLists.txt python/bindings/ArrayXdual0th.py.cxx python/bindings/ArrayXdual1st.py.cxx python/bindings/ArrayXdual2nd.py.cxx python/bindings/ArrayXdual3rd.py.cxx python/bindings/ArrayXdual4th.py.cxx python/bindings/ArrayXreal0th.py.cxx python/bindings/ArrayXreal1st.py.cxx python/bindings/ArrayXreal2nd.py.cxx python/bindings/ArrayXreal3rd.py.cxx python/bindings/ArrayXreal4th.py.cxx python/bindings/CMakeLists.txt python/bindings/MatrixXreal0th.py.cxx python/bindings/MatrixXreal1st.py.cxx python/bindings/MatrixXreal2nd.py.cxx python/bindings/MatrixXreal3rd.py.cxx python/bindings/MatrixXreal4th.py.cxx python/bindings/VectorXdual0th.py.cxx python/bindings/VectorXdual1st.py.cxx python/bindings/VectorXdual2nd.py.cxx python/bindings/VectorXdual3rd.py.cxx python/bindings/VectorXdual4th.py.cxx python/bindings/VectorXreal0th.py.cxx python/bindings/VectorXreal1st.py.cxx python/bindings/VectorXreal2nd.py.cxx python/bindings/VectorXreal3rd.py.cxx python/bindings/VectorXreal4th.py.cxx python/bindings/autodiff.py.cxx python/bindings/dual.py.cxx python/bindings/eigen.hxx python/bindings/pybind11.hxx python/bindings/real.py.cxx python/package/CMakeLists.txt python/package/autodiff/__init__.py python/package/autodiff/extensions/__init__.py python/package/setup.py.in tests/CMakeLists.txt tests/common/meta.test.cpp tests/forward/dual/dual.test.cpp tests/forward/dual/dual.test.cu tests/forward/dual/eigen.test.cpp tests/forward/real/eigen.test.cpp tests/forward/real/real.test.cpp tests/forward/real/real.test.cu tests/forward/utils/derivative.test.cpp tests/forward/utils/gradient.test.cpp tests/forward/utils/taylorseries.test.cpp tests/main.cpp tests/reverse/var/eigen.test.cpp tests/reverse/var/var.test.cpp tests/utils/catch.hpp commit e56bbf10f02424dd0897514aefd8443b35f51dff Author: Michael Zingale Date: Thu Jun 6 20:00:57 2024 -0400 some generalization of the NSE table stuff (#1580) this fixes table initialization and linking with nets other than aprox19. The instructions are also updated. Make.Microphysics_extern interfaces/network_initialization.cpp networks/aprox19/actual_network.H nse_tabular/README.md commit 094a26dac2a58fb35a95500ae84d6a630c6d5656 Author: Ryan Brady Date: Wed Jun 5 11:15:55 2024 -0400 make table check work for any arbitrary network (#1577) Previously, nse_table_check.H only worked for the aprox19 network. Now, we can pass in any arbitrary reaction network and complete the necessary NSE calculations. Co-authored-by: Eric T. Johnson nse_tabular/nse_table_check.H commit 16dfa439de1ff6ac0d70acc53835560b13d8979c Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jun 5 07:52:58 2024 -0400 fix compilation error when using NSE with null screening (#1579) nse_solver/nse_solver.H commit 70f231a5693a955a143adcb6b112e2fcaa8617e7 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Jun 4 12:31:30 2024 -0400 Delete subch_full and subch_approx networks. (#1578) .github/workflows/burn_cell.yml networks/He-C-Fe-group/README.md networks/subch networks/subch2 networks/subch_approx/Make.package networks/subch_approx/README.md networks/subch_approx/_parameters networks/subch_approx/actual_network.H networks/subch_approx/actual_network_data.cpp networks/subch_approx/actual_rhs.H networks/subch_approx/inputs.burn_cell.VODE networks/subch_approx/partition_functions.H networks/subch_approx/pynucastro.net networks/subch_approx/python_net_approx.ipynb networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.png networks/subch_approx/subch_approx.py networks/subch_approx/table_rates.H networks/subch_approx/table_rates_data.cpp networks/subch_approx/tfactors.H networks/subch_full/Make.package networks/subch_full/README.md networks/subch_full/_parameters networks/subch_full/actual_network.H networks/subch_full/actual_network_data.cpp networks/subch_full/actual_rhs.H networks/subch_full/inputs.burn_cell.VODE networks/subch_full/network_plot.py networks/subch_full/partition_functions.H networks/subch_full/pynucastro.net networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.png networks/subch_full/subch_full.py networks/subch_full/subch_network_explore.ipynb networks/subch_full/subch_plotting.ipynb networks/subch_full/table_rates.H networks/subch_full/table_rates_data.cpp networks/subch_full/tfactors.H networks/subch_simple/README.md sphinx_docs/source/networks.rst sphinx_docs/source/subch_base.png sphinx_docs/source/subch_simple.png unit_test/burn_cell/README.md unit_test/burn_cell/ci-benchmarks/subch_simple_BE_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_simple_unit_test.out unit_test/burn_cell/compare_networks.ipynb unit_test/burn_cell/inputs_subch_compare unit_test/burn_cell/inputs_subch_simple commit d928c2084d0096f5276f90c1dff00ed66025da30 Author: Michael Zingale Date: Mon Jun 3 11:30:58 2024 -0400 change how the retry tolerances work (#1573) they now default to -1, in which case the original (non-retry) tolerance will be used. This makes it easier for a user to use the retry mechanism without having to remember to explicitly set all of the tolerances integration/_parameters integration/integrator_setup_sdc.H integration/integrator_setup_strang.H sphinx_docs/source/ode_integrators.rst commit 4fc00a24cfeb1f1cd97292cfe9e7cb5bb6a08167 Author: Michael Zingale Date: Mon Jun 3 11:29:50 2024 -0400 add amrex namespace to nse_table_size.H (#1576) nse_tabular/make_nse_table.py commit 4be804a78ed8250015f6741406f2f5371f4c043a Author: Michael Zingale Date: Sat Jun 1 16:14:00 2024 -0400 update changes for 24.06 (#1571) CHANGES.md commit 1667a38742fec0880e40f40bfdad9efae5db5de1 Author: Michael Zingale Date: Thu May 30 19:06:51 2024 -0400 sort the entries in the runtime parameter struct by type (#1575) this reduces padding a lot util/build_scripts/write_probin.py commit 39cb2a4d875770682f8d73aac119032376b7fa4b Author: Michael Zingale Date: Wed May 29 12:34:57 2024 -0400 unify the SDC integrator code paths (#1546) This removes a lot of the redundancy in the various actual_integrator_sdc.H files integration/BackwardEuler/actual_integrator_sdc.H integration/Make.package integration/RKC/actual_integrator_sdc.H integration/VODE/actual_integrator_sdc.H integration/_parameters integration/integrator_setup_sdc.H commit db24f6f606a14e8b3f3d1fbc2fcc5d429e8a9e3a Author: Michael Zingale Date: Wed May 29 11:41:17 2024 -0400 a bit more cleaning / emphasis in the integrator docs (#1568) sphinx_docs/source/integrators.rst commit 0cc5a3789c28c3f8dbf5cc59c2d6bc4c7b15e76c Author: Michael Zingale Date: Wed May 29 11:31:36 2024 -0400 create a struct to hold the Microphysics runtime parameters (#1433) This now creates a header extern_type.H with a struct extern_t that holds all of the runtime parameters for Microphysics. The struct is filled on initialization and returned by init_extern_parameters(). This can replace the global version of the runtime parameters. This also revives the test_parameters unit test to show how to access things. Make.Microphysics 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/test_parameters.H unit_test/unit_test.H util/build_scripts/runtime_parameters.py util/build_scripts/write_probin.py commit 41df7b48794924143bdfa467a51d65e87fff43ed Author: Michael Zingale Date: Wed May 29 11:26:50 2024 -0400 copyright: 2012 -> 2024 (#1572) sphinx_docs/source/conf.py commit 7b1458be1988c663bd3a339b4e1c363e03d91ba9 Author: Michael Zingale Date: Mon May 27 15:26:39 2024 -0400 extract some common integrator infrastructure (#1515) integration/BackwardEuler/actual_integrator.H integration/Make.package integration/RKC/actual_integrator.H integration/RKC/rkc_type.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_sdc.H integration/VODE/vode_dvode.H integration/integrator_setup_strang.H commit 2adc854dcde1ef3d9a432a26be1985bf304e5126 Author: Michael Zingale Date: Sun May 26 12:29:30 2024 -0400 document use_number_densities (#1567) sphinx_docs/source/integrators.rst commit 8ac20475721f435204c2bd55383265797fbc66bb Author: Michael Zingale Date: Sat May 25 11:30:01 2024 -0400 remove duplicate renormalization section from docs (#1566) this was probably a merge issue sphinx_docs/source/ode_integrators.rst commit ed235802bf4ac67780eda850cb61f6586b7f8dde Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri May 24 18:43:41 2024 -0400 fix drhoauxdt declaration (#1565) NumSpec -> NumAux integration/nse_update_sdc.H commit 4d8c2e5a9ca653c5adad41928fd463d54c3f1fbf Author: Michael Zingale Date: Fri May 24 13:45:02 2024 -0400 add docs on Jacobian caching (#1561) sphinx_docs/source/ode_integrators.rst commit bc1bdda8da6995cc8fb848d4561d59220ad9f5ac Author: Michael Zingale Date: Fri May 24 13:44:22 2024 -0400 clean up some USE_CUDA bits in the makefiles (#1564) in particular, we don't need to reuire VODE if USE_CUDA=TRUE in unit tests also generalize the disabling of Jacobian caching for any GPU, not just CUDA integration/VODE/Make.package unit_test/burn_cell/GNUmakefile unit_test/burn_cell_primordial_chem/GNUmakefile unit_test/eos_cell/GNUmakefile unit_test/nse_table_cell/GNUmakefile unit_test/test_ase/GNUmakefile unit_test/test_ase/make_table/GNUmakefile unit_test/test_jac/GNUmakefile unit_test/test_linear_algebra/GNUmakefile unit_test/test_nse/GNUmakefile unit_test/test_nse_interp/GNUmakefile unit_test/test_part_func/GNUmakefile unit_test/test_react/GNUmakefile unit_test/test_rhs/GNUmakefile util/cj_detonation/GNUmakefile commit 7a4346d2eaac1fcf1b70172ac998639052753ec9 Author: Michael Zingale Date: Fri May 24 12:46:29 2024 -0400 document SMALL_X_SAFE and do_species_clip (#1562) sphinx_docs/source/ode_integrators.rst commit 6674a9d885ede8d6d1b3735097ccad710091b18f Author: Michael Zingale Date: Fri May 24 10:28:51 2024 -0400 fix a spelling pointed out by codespell update (#1563) EOS/helmholtz/actual_eos.H commit 21365f97162552b9975cddba82f5544c8b617121 Author: Michael Zingale Date: Fri May 24 09:30:33 2024 -0400 document the burn retry (#1560) sphinx_docs/source/ode_integrators.rst commit 6373156031ab2c6200042ee653a423de157df1a0 Author: Michael Zingale Date: Fri May 24 09:29:18 2024 -0400 some reorganization of the docs into sections (#1559) sphinx_docs/source/design.rst sphinx_docs/source/getting_started.rst sphinx_docs/source/index.rst sphinx_docs/source/integrators.rst sphinx_docs/source/ode_integrators.rst commit 0dd7c3c76005bb5fa05cf767caf23d24acecb3b1 Author: Eric T. Johnson Date: Wed May 22 19:12:46 2024 -0400 Rework runtime parameter docs (#1557) sphinx_docs/rp.py sphinx_docs/source/integrators.rst sphinx_docs/source/nse.rst sphinx_docs/source/rp_intro.rst commit f67da7d8a14d406ea81f659c49d748cb5af8565e Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed May 22 19:05:53 2024 -0400 update minimum T threshold for self-consistent NSE (#1558) * make T_min_nse a runtime parameter * update docs nse_solver/_parameters nse_solver/nse_check.H sphinx_docs/source/nse.rst commit dc758f7e509bbe11148f442e8b2c5fe2d0e08a7f Author: Michael Zingale Date: Wed May 22 16:14:32 2024 -0400 make some arrays const in the NSE table functions (#1554) nse_tabular/nse_table.H commit d99de4ab72d9cf453cff3643e3cc7d828f9831ac Author: Michael Zingale Date: Fri May 17 15:04:43 2024 -0400 fix some compiler warnings in ignition_simple (#1551) networks/ignition_simple/actual_network.H commit f988690f355ddb397573f9ae14c3ef9b2dcaf139 Author: Michael Zingale Date: Fri May 17 15:04:09 2024 -0400 remove some old CXX_REACTION stuff (#1553) unit_test/burn_cell_primordial_chem/GNUmakefile unit_test/test_ase/GNUmakefile commit 87d6e6929920bb299c302cf8713342cd55f05255 Author: Michael Zingale Date: Fri May 17 12:56:00 2024 -0400 add some linkcheck options (#1552) sphinx_docs/source/conf.py sphinx_docs/source/refs.bib commit 1028285f22156888357d79fbf05c56c64a110056 Author: Max Katz Date: Thu May 16 12:52:03 2024 -0400 Remove C++ language suffix from unit tests (#1309) 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_sdc/main.cpp commit 87839b7567858ac7dd8cb3fa2bacfffb9d3f0c6e Author: Michael Zingale Date: Sun May 12 18:31:53 2024 -0400 sync hip CI up with amrex (#1550) .github/workflows/dependencies/dependencies_hip.sh commit 02e71ba9ba38ae0d3f14770f589fe52095c6bd8c Author: Michael Zingale Date: Thu May 9 10:33:36 2024 -0400 standardize names for # of rhs calls, Jac evals, and steps (#1541) this will make it easier to merge a lot of integrator logic integration/RKC/actual_integrator.H integration/RKC/actual_integrator_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_sdc.H integration/VODE/vode_dvjac.H integration/VODE/vode_dvnlsd.H integration/VODE/vode_dvode.H integration/VODE/vode_dvstep.H integration/VODE/vode_type.H integration/utils/rkc_util.H commit ca9e53204090ff26e641eff03606bccd99700fe9 Author: Michael Zingale Date: Mon May 6 19:03:29 2024 -0400 add an eos_rh_t for MAESTROeX (#1539) interfaces/eos_type.H commit a6de6080baff73da337a6abb104bdda14e62eaa6 Author: Michael Zingale Date: Mon May 6 19:02:35 2024 -0400 some fixes to actions (#1538) don't cache pip if we don't pip install anything fix check_powi action name .github/workflows/check_powi.yml .github/workflows/docs-test.yml commit adba4f92b85f1fed14bf87ae01c02d91dfa66e36 Author: Michael Zingale Date: Mon May 6 19:00:18 2024 -0400 silence clang-tidy in conductivity (#1537) conductivity/stellar/actual_conductivity.H commit c89e33409e8c6bd35764dbb0f457a10e72a5af7b Author: Michael Zingale Date: Wed May 1 08:25:04 2024 -0400 update changes CHANGES.md commit 8e7e375014208c41403b304789a305e92ff757a6 Author: Michael Zingale Date: Mon Apr 29 15:43:59 2024 -0400 allow for bool in _parameters again, integer -> int, character -> string (#1536) many int parameters were changed to bool -- this will help when we go all-in on a struct also replace all the X.dY with C++ style Co-authored-by: Eric T. Johnson EOS/breakout/_parameters EOS/gamma_law/_parameters EOS/helmholtz/_parameters EOS/multigamma/_parameters EOS/polytrope/_parameters EOS/primordial_chem/_parameters EOS/rad_power_law/_parameters conductivity/constant/_parameters conductivity/constant_opacity/_parameters integration/BackwardEuler/_parameters integration/QSS/_parameters integration/RKC/_parameters integration/_parameters networks/_parameters networks/powerlaw/_parameters networks/rprox/_parameters networks/triple_alpha_plus_cago/_parameters nse_solver/_parameters nse_solver/make_table/_parameters nse_solver/nse_compatibility/_parameters nse_tabular/_parameters opacity/rad_power_law/_parameters screening/_parameters unit_test/_parameters unit_test/burn_cell/_parameters unit_test/burn_cell_primordial_chem/_parameters unit_test/burn_cell_sdc/_parameters unit_test/eos_cell/_parameters unit_test/test_aprox_rates/_parameters unit_test/test_ase/_parameters unit_test/test_ase/make_table/_parameters unit_test/test_conductivity/_parameters unit_test/test_eos/_parameters unit_test/test_jac/_parameters unit_test/test_neutrino_cooling/_parameters unit_test/test_nse/_parameters unit_test/test_react/_parameters unit_test/test_rhs/_parameters unit_test/test_screening/_parameters unit_test/test_screening_templated/_parameters unit_test/test_sdc/_parameters unit_test/test_sdc_vode_rhs/_parameters util/build_scripts/runtime_parameters.py commit 4ad225b74fc2ec970bf1f556de64702205b03515 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue Apr 16 17:29:25 2024 -0400 Bump peaceiris/actions-gh-pages from 3 to 4 (#1534) Bumps [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) from 3 to 4. - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](https://github.com/peaceiris/actions-gh-pages/compare/v3...v4) --- updated-dependencies: - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/gh-pages.yml commit b130fa5b2f4ccc6992dad2a368aaa3d282c40654 Author: Michael Zingale Date: Tue Apr 16 17:17:19 2024 -0400 fix some header issues identified by clang-tidy (#1533) most adding inline to avoid ODR issues nse_solver/make_table/burn_cell.H unit_test/burn_cell/burn_cell.H unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_sdc/burn_cell.H unit_test/eos_cell/eos_cell.H unit_test/nse_table_cell/nse_cell.H unit_test/test_ase/burn_cell.H unit_test/test_ase/make_table/burn_cell.H unit_test/test_linear_algebra/test_linear_algebra.H unit_test/test_nse/nse_example.H unit_test/test_nse_interp/nse_cell.H unit_test/test_part_func/pf_cell.H unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit d4312a6c85fa2da99f62e2e33e46d067cd8f65d5 Author: Michael Zingale Date: Wed Apr 10 19:26:45 2024 -0400 add clang-tidy build CI for burn_cell_sdc (#1530) .github/workflows/clang-tidy.yml .github/workflows/dependencies_clang-tidy-apt-llvm.sh networks/aprox13/actual_network.H networks/aprox19/actual_network.H networks/rhs.H unit_test/burn_cell_sdc/burn_cell.H commit 983c8e674d64834a0ad3b382410b8b05fa3a12ce Author: Michael Zingale Date: Wed Apr 10 18:53:15 2024 -0400 have clang-tidy warn about recursion (#1532) CUDA doesn't seem to like it .clang-tidy commit 43dc7a53ce866eb41391a8c4a8f759d771f33a0b Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Apr 9 10:05:07 2024 -0400 change quickSort to not use recursion (#1531) this is intended to address AMReX-Astro/Castro#2818 as suggested by @WeiqunZhang nse_solver/nse_check.H util/microphysics_sort.H commit e5fecb7a81f0263128a417e1d02d15691e55594a Author: Max Katz Date: Fri Apr 5 19:10:49 2024 -0400 Add CI test that fails if a PR is issued to main (#1356) The `edited` activity type includes changes to the base branch, so we need to add that to the trigger types. It also needs to run on development as well as main, so the workflow can succeed once the base branch is changed. Do the check in bash, so we get "Successful" instead of "Skipped" Co-authored-by: Eric T. Johnson .github/workflows/check_pr_branch.yml commit d82c8c88afb55e8ad4386897d5f9c4a41d81ebd3 Author: Eric T. Johnson Date: Thu Apr 4 16:32:47 2024 -0400 Update pynucastro networks for derived rate speedup (#1529) Includes improvements from pynucastro/pynucastro#726. networks/CNO_extras/partition_functions.H networks/ECSN/partition_functions.H networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/reaclib_rates.H networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/partition_functions.H networks/ignition_reaclib/URCA-medium/partition_functions.H networks/ignition_reaclib/URCA-simple/partition_functions.H networks/nova/partition_functions.H networks/nova2/partition_functions.H networks/partition_test/partition_functions.H networks/partition_test/reaclib_rates.H networks/sn160/partition_functions.H networks/subch_approx/partition_functions.H networks/subch_base/partition_functions.H networks/subch_base/reaclib_rates.H networks/subch_full/partition_functions.H networks/subch_simple/partition_functions.H commit 45f59b17c9c11179f93fb623a82bd21ad45b76e8 Author: Michael Zingale Date: Thu Apr 4 14:55:48 2024 -0400 remove some references to Fortran in the docs (#1528) sphinx_docs/source/unit_tests.rst commit ab9345c22c6171eae0e94f59bde2342055a88329 Author: Eric T. Johnson Date: Wed Apr 3 15:10:28 2024 -0400 Fix some compiler warnings with SDC+NSE (#1527) .github/workflows/compiler-warnings.yml integration/nse_update_sdc.H nse_solver/nse_check.H commit dfc746f5f35ab0e9a32025ca325f83232826f420 Author: Michael Zingale Date: Mon Apr 1 10:22:45 2024 -0400 update changes CHANGES.md commit 3112c13a1cd0a2d7219e1652bac4640cc54d446e Author: Michael Zingale Date: Wed Mar 27 14:57:56 2024 -0400 enable more clang-tidy checks (#1525) also modernize typedefs .clang-tidy integration/integrator_data.H interfaces/burn_type.H commit f47a7fcc6de52925a3cf7f23078a3aa6f1bfb891 Author: Eric T. Johnson Date: Tue Mar 26 17:59:21 2024 -0400 Add a version of test_screening that works on any templated network (#1524) I've been using this to test out autodiff on the screening implementations. unit_test/test_screening_templated/GNUmakefile unit_test/test_screening_templated/Make.package unit_test/test_screening_templated/README unit_test/test_screening_templated/_parameters unit_test/test_screening_templated/inputs unit_test/test_screening_templated/main.cpp unit_test/test_screening_templated/screening_util.cpp unit_test/test_screening_templated/test_screen.H unit_test/test_screening_templated/variables.H unit_test/test_screening_templated/variables.cpp commit 81de2adb1afd40444611dd57fd6b903c68e507fd Author: Michael Zingale Date: Thu Mar 21 14:53:59 2024 -0400 don't link on the missing default for spin (#1522) networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/CNO_extras/partition_functions.H networks/ECSN/partition_functions.H networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/partition_functions.H networks/ase/ase.png networks/ase/partition_functions.H networks/ignition_reaclib/C-burn-simple/partition_functions.H networks/ignition_reaclib/URCA-medium/partition_functions.H networks/ignition_reaclib/URCA-medium/urca_medium.png networks/ignition_reaclib/URCA-simple/partition_functions.H networks/nova/nova.png networks/nova/partition_functions.H networks/nova2/nova.png networks/nova2/partition_functions.H networks/partition_test/partition_functions.H networks/sn160/partition_functions.H networks/subch_approx/partition_functions.H networks/subch_approx/subch_approx.png networks/subch_base/partition_functions.H networks/subch_base/subch_base.png networks/subch_full/partition_functions.H networks/subch_full/subch_full.png networks/subch_simple/partition_functions.H networks/subch_simple/subch_simple.png commit b934b16f2defbf90760f22a87d8efe130170ee2c Author: Michael Zingale Date: Wed Mar 20 13:52:03 2024 -0400 clang-tidy: modernize type traits in eos.H (#1518) interfaces/eos_type.H commit 27e85ad321e4961292bc9f596543c42a3f1536ec Author: Michael Zingale Date: Wed Mar 20 13:51:44 2024 -0400 some network_properties.H cleaning (#1516) put aion, zion, ... into an anonymous namespace instead of making them static also disable linting on the switch for lacking a default -- this is hard with the constexpr these were suggested by clang-tidy also remove an old Fortran template Co-authored-by: Eric T. Johnson networks/general_null/network_header.template networks/general_null/network_properties.template commit e0323a161dfed658310a3d8854473640f167fd2e Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Mar 20 12:59:09 2024 -0400 separate coulomb contribution calculation from nse solver (#1508) Separate out calculation of coulomb contribution from nse solver to make things faster. Even though coulomb contribution depends on electron fraction, y_e, but the y_e we use to evaluate the coulomb contribution does not change during iteration. We just use the input y_e. nse_solver/nse_solver.H unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out commit aa0a4ffeae7d60c7c9bf0557f4483ee2992f4d89 Author: Michael Zingale Date: Tue Mar 19 13:05:06 2024 -0400 rename f1 to tmp to avoid confusion with fl (#1519) clang-tidy: misc-confusable-identifiers neutrinos/sneut5.H commit 452b8b1ecfe1c7ecfedd8441b9f3fd9f25537500 Author: Michael Zingale Date: Tue Mar 19 13:04:43 2024 -0400 remove an unused compute of abar1_out in nse (#1520) also clean up the logic some so it is clear we are using the value from the last nse table call integration/nse_update_sdc.H commit c7ac125ffa235f3fc2789a95f47772b1d9e1d09d Author: Michael Zingale Date: Tue Mar 19 11:17:48 2024 -0400 fix compilation with amrex::Font (#1517) something changed upstream that we need to be more explicit now integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_sdc.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_sdc.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_sdc.H integration/VODE/vode_dvode.H commit d25543855d3470b5cbf848cb37d6e33cbbf9f5f2 Author: Michael Zingale Date: Sat Mar 16 15:05:48 2024 -0400 eliminate some divides in the helmholtz EOS (#1512) EOS/helmholtz/actual_eos.H commit c3587f5a4a5bc1b08dd7b4cde32f65d791cbe985 Author: Michael Zingale Date: Sat Mar 16 14:47:13 2024 -0400 sync up integrators (#1513) also fix a bug with the retry tolerances in the Strang RKC integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_sdc.H integration/BackwardEuler/be_integrator.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_sdc.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_sdc.H commit 834938b2432730c3240be7b8be97593b98e96b77 Author: Michael Zingale Date: Sat Mar 16 14:11:39 2024 -0400 add CI test for RKC+SDC (#1514) .github/workflows/burn_cell_sdc.yml unit_test/burn_cell_sdc/ci-benchmarks/aprox19_RKC_state_over_time.txt commit 07a186e9f0f8565f0ea537b387de33203bc8479f Author: Michael Zingale Date: Fri Mar 15 18:22:26 2024 -0400 remove reinterpret_cast in rhs.H (#1435) networks/rhs.H commit a5faa5f9ce96c6a1f23cc50dd5025a624ffd13d4 Author: Michael Zingale Date: Thu Mar 14 19:12:54 2024 -0400 some typo fixes to the SDC docs (#1509) sphinx_docs/source/sdc.rst commit bc1b27390b208d340bc0d42de0861ba67669c1e6 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Thu Mar 14 12:28:12 2024 +0100 Added quokka to codes using microphysics (#1511) README.md commit a33745d1c907a9a2f9ac4e1f4ace6f74e1534432 Author: Michael Zingale Date: Thu Mar 14 07:27:46 2024 -0400 add Ben and Piyush to .zenodo.json (#1510) .zenodo.json commit 124b71becfb95e1a0c7cdbc9b3a15e0e4be1096b Author: Michael Zingale Date: Tue Mar 12 17:43:16 2024 -0400 use a helper function to get the index into the NSE tables (#1495) nse_tabular/nse_table.H commit 95cb860c0cda929b91b883ce00e7c15189a4fd86 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Mar 10 10:35:38 2024 -0400 remove redundant rhs and ydot for NSE_NET (#1507) I think ydot was somehow needed before, but no longer the case. nse_solver/nse_check.H commit 886498d0db40396c5989e3b5815ba2894b7e156a Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sat Mar 9 20:09:50 2024 -0500 Optimize fill_merge_indices/nse_grouping for NSE_NET (#1506) To determine whether we're in NSE for the self-consistent NSE, we need some grouping process. And one of the criteria is to start grouping with the reaction rates that have the fastest (smallest) timescale. However, Kushnir defines the timescale using the molar fraction of the entire group, which complicates things, because the timescale changes after the last successful merge. I changed it so that we only use the actual molar fraction of the isotope involved in the reaction. This way, we can calculate and store the timescale of all reactions in the beginning and sort the order in which we do the merge by sorting the timescale array. nse_solver/nse_check.H nse_solver/nse_solver.H sphinx_docs/source/nse.rst unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out util/microphysics_sort.H commit 3169bfed5c07804b91f541b7637d68954f4eec62 Author: Michael Zingale Date: Sat Mar 9 11:19:35 2024 -0500 remove the is_jacobian_term_used logic in the linear algebra (#1502) this was wrong, but turns out, it had no effect because of a bug in the logic of the is_jacobian_term_used. That issue is also fixed here, and the function is kept for use in the future. note: nets with one species that was not evolved will see a change here. networks/rhs.H unit_test/burn_cell/ci-benchmarks/chamulak_VODE_unit_test.out commit d7e5b848b5e0f86cc746e632ac08371b6db7d478 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Mar 8 15:50:12 2024 -0500 remove fast reaction cycle check for NSE_NET check. (#1503) Fast reaction cycle is one of the check that Kushnir introduced in his paper. However this check only works with neutron present in the network. In the past, I would just skip this check whenever there is no neutron in the network, which is almost always and it worked fine. And I've tested with the network that does have neutron without this check, and it gives more or less the same. So I want to get rid of this. Also changed the indentation to 4 space to be consistent with the rest of the code. nse_solver/nse_check.H nse_solver/nse_solver.H commit 9dd9dbb619da9a210e5d453db502994cb844a846 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Mar 8 10:27:20 2024 -0500 add more unit test for testing NSE_NET (#1504) Added unit_test using make_table in test_ase, which gives output of the NSE_NET check on a wider variety of conditions. Just to ensure I don't break things in the later PRs. .github/workflows/nse_net.yml unit_test/test_ase/make_table/ci-benchmarks/ase_nse_net_make_table_unit_test.out commit ce331bc849de71dafa0d32e7f2ba0c09527ba1d5 Author: Michael Zingale Date: Sun Mar 3 18:19:42 2024 -0500 update test_linear_algebra to output the Jacobian mask (#1501) unit_test/test_linear_algebra/test_linear_algebra.H commit 02d46a67cf5852509cc35db7850e5f87da495679 Author: Michael Zingale Date: Fri Mar 1 08:19:40 2024 -0500 updated changelog for 24.03 (#1498) CHANGES.md commit 2359fab66cfb9a2cf2749a4c89005c5d5527bf54 Author: Michael Zingale Date: Fri Mar 1 08:19:20 2024 -0500 fix RKC integration with SDC (#1497) integration/RKC/actual_integrator_sdc.H integration/utils/circle_theorem.H commit 695b7118aa20023c7baa9b34fa0cba1049011fd2 Author: Michael Zingale Date: Fri Mar 1 08:19:05 2024 -0500 update test_linear_algebra to reflect pivot templating (#1496) unit_test/test_linear_algebra/test_linear_algebra.H commit e587300c654f9dc8a4be111a30b384dc269fab52 Author: Michael Zingale Date: Wed Feb 28 08:00:58 2024 -0500 some more cleaning of the runtime_parameters.py (#1448) this silences some clang-tidy warnings about string initialization util/build_scripts/runtime_parameters.py commit 8fc4cfeef47d78b056f7f1b3bcffb86a60f030b1 Author: Michael Zingale Date: Wed Feb 28 08:00:41 2024 -0500 template pivoting in the linear algebra (#1454) now we can do `integrator.linalg_do_pivoting=0` to disable pivoting integration/BackwardEuler/be_integrator.H integration/VODE/vode_dvjac.H integration/VODE/vode_dvnlsd.H integration/_parameters util/linpack.H commit adb26008165aecf183466ac9b1a2be19861689ef Author: Michael Zingale Date: Wed Feb 28 08:00:23 2024 -0500 work on addressing some issues with the Jacobian scaling (#1479) this applies if we run with scale_system=1 also as part of this change, allow the Circle theorem to use the numerical Jacobian. integration/integrator_rhs_strang.H integration/utils/circle_theorem.H integration/utils/jacobian_utilities.H integration/utils/numerical_jacobian.H unit_test/burn_cell/ci-benchmarks/aprox13_RKC_unit_test.out commit 48bf41c51a9da8dc9c654cfc4b9f461bf5b8e23b Author: Michael Zingale Date: Wed Feb 28 07:59:57 2024 -0500 remove some unused includes in test_nse_interp (#1494) unit_test/test_nse_interp/main.cpp unit_test/test_nse_interp/nse_cell.H commit f336cab4e612f032a60042e503dc571bfc38a182 Author: Michael Zingale Date: Mon Feb 26 15:21:51 2024 -0500 create a linear algebra unit test (#1493) this will test the rhs.H routines for solving a linear system as well as those in linpack.H. unit_test/test_linear_algebra/GNUmakefile unit_test/test_linear_algebra/Make.package unit_test/test_linear_algebra/README.md unit_test/test_linear_algebra/_parameters unit_test/test_linear_algebra/main.cpp unit_test/test_linear_algebra/test_linear_algebra.H commit 9a8c260b7af05cf09478d589e04f3c60f53e1ce2 Author: Michael Zingale Date: Mon Feb 26 15:01:26 2024 -0500 clean up some unused vars in unit tests (#1492) EOS/helmholtz/actual_eos.H unit_test/burn_cell/main.cpp unit_test/burn_cell_sdc/main.cpp unit_test/eos_cell/eos_cell.H unit_test/eos_cell/main.cpp unit_test/nse_table_cell/main.cpp unit_test/nse_table_cell/nse_cell.H commit 348dad9c7326fe14e9becec2ec5cd0584d20bee0 Author: Michael Zingale Date: Mon Feb 26 14:29:21 2024 -0500 remove redundant (and conflicting) typedefs in rhs.H (#1491) in particular, IArray1D was `int` here, but `short` in integrator_data.H networks/rhs.H commit 86807d6ba1bb4bc731cb7d7efb9518d56d6b8969 Author: Michael Zingale Date: Mon Feb 26 14:28:59 2024 -0500 update the SDC docs (#1469) including removing the vestiges of "starkiller" sphinx_docs/source/mathsymbols.tex sphinx_docs/source/sdc.rst commit 3df6ba0c56c5081088175691eb5853bd5c51f8c0 Author: Michael Zingale Date: Wed Feb 21 20:14:54 2024 -0500 if we are building with HIP, don't force inlining (#1490) this works around some issues with large kernels and ROCm .github/workflows/hip.yml Make.Microphysics_extern commit 4f2ee5fd050be9c2c84edf7b72720f7be26fd31b Author: Michael Zingale Date: Tue Feb 20 12:46:22 2024 -0500 fix compilation of nse_table_cell (#1486) unit_test/nse_table_cell/nse_cell.H commit 6ccf1811bc05c00e19f483a4addae94cee7ae5ca Author: Michael Zingale Date: Tue Feb 20 12:30:02 2024 -0500 address some clang-tidy issues in RKC (#1478) integration/RKC/actual_integrator.H integration/RKC/rkc.H commit 6b6842d2dc0ec025e0d0434c99606b46c3c391d6 Author: Eric T. Johnson Date: Tue Feb 20 11:22:15 2024 -0500 Disable force-inlining in HIP CI (#1487) Also remove COMP=gnu, since it's redundant, and bump up the number of parallel make jobs to 4. .github/workflows/hip.yml commit 32b2c42a6891a8587b1195154b79b242d230d7f9 Author: Michael Zingale Date: Mon Feb 19 14:31:23 2024 -0500 remove dabardt from the NSE output (#1484) we never use it and the interpolation can be expensive nse_tabular/nse_table.H nse_tabular/nse_table_type.H unit_test/nse_table_cell/nse_cell.H unit_test/test_nse_interp/ci-benchmarks/aprox19.out unit_test/test_nse_interp/nse_cell.H commit 940698ec2dd8dbcf9f282a94e76ae7e6d1bbc0e3 Author: Michael Zingale Date: Mon Feb 19 10:54:46 2024 -0500 add d/dt to the predictor for the NSE+SDC update (#1485) This is a small change, but makes us consistent with have a prediction for the energy evolution from NSE integration/nse_update_sdc.H commit eb1f853dbd45771719476d44a72576d29b2f163c Author: Michael Zingale Date: Sat Feb 17 12:51:08 2024 -0500 add missing weak rate energy to NSE update (#1483) This accounts for the fact that when we just do the binding energy, we don't capture the energy difference from converting protons to neutrons. That term looks like N_A (m_n - (m_p + m_e) c**2 dY_e/dt. This adds that to the SDC integration/nse_update_sdc.H commit 53d2621985f53e7b555ae52acba605c358717f89 Author: Michael Zingale Date: Tue Feb 13 09:06:12 2024 -0500 rate_type.H is no longer used (#1471) networks/Make.package networks/rate_type.H sphinx_docs/source/data_structures.rst commit be028dcabe7e83814a29130fb2c2e48cdfe5de9d Author: Eric T. Johnson Date: Tue Feb 13 08:00:29 2024 -0500 Don't force-inline actual_integrator() (#1481) This greatly reduces the compilation time. integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_sdc.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_sdc.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_sdc.H commit 191d0006070000afac18e5edcd04c4e66b189578 Author: Michael Zingale Date: Tue Feb 13 07:36:13 2024 -0500 don't include unless we are a new network type (#1467) integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H networks/rhs.cpp commit 5226a1f73110ba68ab4c18108ab27e64997b3ea8 Author: Eric T. Johnson Date: Mon Feb 12 19:37:06 2024 -0500 Turn Sphinx warnings into errors in CI (#1480) .github/workflows/docs-test.yml commit 2b623ab7c2c09c50f4bfcb11cec3a692b072252f Author: Michael Zingale Date: Mon Feb 12 10:37:31 2024 -0500 rename *_simplified_sdc.H -> *_sdc.H (#1475) since we've merged the code paths for true SDC and simplified SDC, this is a more accurate name integration/BackwardEuler/Make.package integration/BackwardEuler/actual_integrator_sdc.H integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/Make.package integration/RKC/Make.package integration/RKC/actual_integrator_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H integration/VODE/Make.package integration/VODE/actual_integrator_sdc.H integration/VODE/vode_dvhin.H integration/VODE/vode_dvjac.H integration/VODE/vode_dvode.H integration/VODE/vode_type.H integration/integrator.H integration/integrator_rhs_sdc.H integration/integrator_type_sdc.H integration/nse_update_sdc.H integration/utils/circle_theorem.H interfaces/burner.H unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit 348ca2f5801c8cf80fa5910efe5f036bf4f737fe Author: Michael Zingale Date: Thu Feb 8 19:45:52 2024 -0500 more amrex namespace removal (#1474) EOS/multigamma/eos_composition.H EOS/ztwd/actual_eos.H conductivity/stellar/actual_conductivity.H integration/BackwardEuler/be_type.H integration/RKC/rkc.H integration/RKC/rkc_type.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_type.H integration/integrator.H integration/integrator_data.H integration/integrator_rhs_simplified_sdc.H integration/integrator_rhs_strang.H integration/integrator_type.H integration/integrator_type_simplified_sdc.H integration/integrator_type_strang.H integration/nse_update_simplified_sdc.H integration/nse_update_strang.H integration/utils/circle_theorem.H integration/utils/initial_timestep.H integration/utils/numerical_jacobian.H integration/utils/rkc_util.H interfaces/conductivity.H neutrinos/sneut5.H nse_tabular/nse_table.H nse_tabular/nse_table_data.H rates/aprox_rates.H unit_test/burn_cell/main.cpp unit_test/react_util.H util/esum.H util/hybrj/hybrj_type.H commit b5d1a91a99bcbd68bc3b864392fe103f61b76e3a Author: Michael Zingale Date: Thu Feb 8 15:10:37 2024 -0500 start moving away from "using namespace amrex" (#1465) EOS/breakout/actual_eos.H EOS/eos_composition.H EOS/gamma_law/actual_eos.H EOS/helmholtz/actual_eos.H EOS/multigamma/actual_eos.H EOS/polytrope/actual_eos.H EOS/primordial_chem/actual_eos.H EOS/tillotson/actual_eos.H interfaces/burn_type.H interfaces/eos.H interfaces/rhs_type.H interfaces/tfactors.H networks/rhs.H networks/rhs.cpp networks/rprox/rprox_rates.H screening/screen.H screening/screen_data.H commit f222253552d9c05bd26b387e35c484e5e176a749 Author: Michael Zingale Date: Thu Feb 8 13:48:43 2024 -0500 update the pynucastro nets to version 2.2.0 (#1470) Co-authored-by: Eric T. Johnson networks/CNO_extras/actual_network.H networks/CNO_extras/actual_rhs.H networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/CNO_extras/partition_functions.H networks/CNO_extras/reaclib_rates.H networks/CNO_extras/table_rates.H networks/CNO_extras/tfactors.H networks/ECSN/actual_network.H networks/ECSN/actual_rhs.H networks/ECSN/partition_functions.H networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H networks/ECSN/table_rates_data.cpp networks/ECSN/tfactors.H networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/actual_network.H networks/He-C-Fe-group/actual_rhs.H networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/reaclib_rates.H networks/He-C-Fe-group/table_rates.H networks/He-C-Fe-group/table_rates_data.cpp networks/He-C-Fe-group/tfactors.H networks/ase/actual_network.H networks/ase/actual_rhs.H networks/ase/ase.png networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ase/table_rates.H networks/ase/tfactors.H networks/ignition_reaclib/C-burn-simple/actual_network.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/C-burn-simple/partition_functions.H networks/ignition_reaclib/C-burn-simple/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/table_rates.H networks/ignition_reaclib/C-burn-simple/tfactors.H networks/ignition_reaclib/URCA-medium/actual_network.H networks/ignition_reaclib/URCA-medium/actual_rhs.H networks/ignition_reaclib/URCA-medium/partition_functions.H networks/ignition_reaclib/URCA-medium/reaclib_rates.H networks/ignition_reaclib/URCA-medium/table_rates.H networks/ignition_reaclib/URCA-medium/table_rates_data.cpp networks/ignition_reaclib/URCA-medium/tfactors.H networks/ignition_reaclib/URCA-medium/urca_medium.png networks/ignition_reaclib/URCA-simple/actual_network.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/partition_functions.H networks/ignition_reaclib/URCA-simple/reaclib_rates.H networks/ignition_reaclib/URCA-simple/table_rates.H networks/ignition_reaclib/URCA-simple/table_rates_data.cpp networks/ignition_reaclib/URCA-simple/tfactors.H networks/nova/actual_network.H networks/nova/actual_rhs.H networks/nova/nova.png networks/nova/partition_functions.H networks/nova/reaclib_rates.H networks/nova/table_rates.H networks/nova/tfactors.H networks/nova2/actual_network.H networks/nova2/actual_rhs.H networks/nova2/nova.png networks/nova2/partition_functions.H networks/nova2/reaclib_rates.H networks/nova2/table_rates.H networks/nova2/tfactors.H networks/partition_test/actual_network.H networks/partition_test/actual_rhs.H networks/partition_test/partition_functions.H networks/partition_test/reaclib_rates.H networks/partition_test/table_rates.H networks/partition_test/tfactors.H networks/sn160/actual_network.H networks/sn160/actual_rhs.H networks/sn160/partition_functions.H networks/sn160/reaclib_rates.H networks/sn160/table_rates.H networks/sn160/tfactors.H networks/subch_approx/actual_network.H networks/subch_approx/actual_rhs.H networks/subch_approx/partition_functions.H networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.png networks/subch_approx/table_rates.H networks/subch_approx/tfactors.H networks/subch_base/actual_network.H networks/subch_base/actual_rhs.H networks/subch_base/partition_functions.H networks/subch_base/reaclib_rates.H networks/subch_base/subch_base.png networks/subch_base/table_rates.H networks/subch_base/tfactors.H networks/subch_full/actual_network.H networks/subch_full/actual_rhs.H networks/subch_full/partition_functions.H networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.png networks/subch_full/table_rates.H networks/subch_full/tfactors.H networks/subch_simple/actual_network.H networks/subch_simple/actual_rhs.H networks/subch_simple/partition_functions.H networks/subch_simple/reaclib_rates.H networks/subch_simple/subch_simple.png networks/subch_simple/table_rates.H networks/subch_simple/tfactors.H commit 0e2e8f13f0364d5d975b573bec336dd8ecec7140 Author: Eric T. Johnson Date: Thu Feb 8 07:12:46 2024 -0500 Fix exit code check in VODE error message (#1472) integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H commit 0ad950aa98fb1ec91364050bedceb184e7a2b0b7 Author: Michael Zingale Date: Wed Feb 7 16:11:27 2024 -0500 some doc fixes (#1468) this adds dollar math and copybutton also removes the vestiges of "starkiller" requirements.txt sphinx_docs/rp.py sphinx_docs/source/basics.rst sphinx_docs/source/conf.py sphinx_docs/source/preface.rst commit 49fba8d71543f42e44cfd426a591dba4fc4f4c9f Author: Michael Zingale Date: Mon Feb 5 13:49:24 2024 -0500 add retry framework to burn (#969) This adds the ability to retry the burn in a zone if it fails, without having to return to the application code. It provides a few new parameters: * use_burn_retry * retry_swap_jacobians (this will use the other Jacobian type for the retried burn) * retry_rtol_spec, retry_rtol_enuc (the relative tolerance to use on the retry) * retry_atol_spec, retry_atol_enuc (the absolute tolerance to use on the retry) This works well near NSE where sometimes the other Jacobian type can get past a stubborn burn. The cost of this change is that we need to store an old copy of the burn_t, but this is templated out if we don't run with use_burn_retry=1 integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/RKC/actual_integrator.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/_parameters integration/integrator.H commit 56253c933f790548e2667e97d25f8a2bc505e0fe Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Feb 4 16:22:31 2024 -0500 fix nse_eos.H include (#1466) integration/nse_update_simplified_sdc.H commit 29b594fde58759787fe32a52daa08bc825ba0009 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Feb 1 08:51:12 2024 -0500 Bump actions/cache from 3 to 4 (#1462) Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/castro-development.yml .github/workflows/castro.yml .github/workflows/check_powi.yml commit 050b530d192fbd4c7ac5b53772d0e5441c601c78 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Feb 1 08:50:56 2024 -0500 Bump actions/upload-artifact from 3 to 4 (#1463) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/castro-development.yml .github/workflows/castro.yml commit effc4ea534e511dfd2bc9cdcfb6f1860e8ec0128 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Feb 1 08:50:41 2024 -0500 Bump actions/checkout from 3 to 4 (#1464) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/check_powi.yml commit f1992a2ba1fd17f97d30f61a73ba12ccb9fa7599 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Feb 1 07:44:52 2024 -0500 Bump actions/setup-python from 4 to 5 (#1461) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/check_powi.yml commit 649063a33f1ef83dd9acc457d7a79ceebcf3b60c Author: Michael Zingale Date: Thu Feb 1 07:15:28 2024 -0500 update for 24.02 CHANGES.md commit 6d5a4e1a71268a2bc558051d6c80cb428e8700c4 Author: Michael Zingale Date: Mon Jan 29 11:16:07 2024 -0500 add dependabot config for github actions and pip (#1447) .github/dependabot.yml commit c2186ed568b568786b7a174233c2bab61df0ae69 Author: Michael Zingale Date: Mon Jan 29 11:15:45 2024 -0500 add some more clang-tidy checks (#1450) .clang-tidy commit ccf197c0fa0575fdab5da1b85f78ff32a0f9d6c9 Author: Michael Zingale Date: Mon Jan 29 11:15:24 2024 -0500 some clang-tidy modernize-type-traits (#1452) is_same<>::value -> is_same_v<> EOS/breakout/actual_eos.H EOS/gamma_law/actual_eos.H EOS/helmholtz/actual_eos.H EOS/multigamma/actual_eos.H EOS/polytrope/actual_eos.H EOS/primordial_chem/actual_eos.H EOS/rad_power_law/actual_eos.H EOS/tillotson/actual_eos.H EOS/ztwd/actual_eos.H interfaces/eos.H nse_tabular/nse_table_check.H commit 9a240cd199ca418e05a9ca4e91163f44c0a0b484 Author: Michael Zingale Date: Mon Jan 29 11:15:06 2024 -0500 replace asctime -> strftime (#1453) asctime is unsafe unit_test/write_job_info.cpp commit cdb8b3734e9b5303a7787eb2aa59f79628640891 Author: Michael Zingale Date: Sun Jan 28 16:53:00 2024 -0500 initialize the components of burn_t (#1460) this makes the code safer interfaces/burn_type.H commit 2f3edcb2a7c3c03c4d577b801bb79058ba081dd9 Author: Michael Zingale Date: Sun Jan 28 15:10:21 2024 -0500 fix some issues pointed out by coverity (#1459) neutrinos/sneut5.H unit_test/burn_cell/burn_cell.H commit 4cc66f3d08f5b4e2f976ded18a3a3a1c1496e588 Author: Michael Zingale Date: Sun Jan 28 08:29:47 2024 -0500 add some const / initialization to VODE integration (#1457) integration/VODE/actual_integrator.H 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 commit 6b5785d1ba177d0ed0df81c08af0012f14b70482 Author: Michael Zingale Date: Sun Jan 28 08:29:30 2024 -0500 fix a narrowing in the linpack pivoting (#1458) util/linpack.H commit 0e28d42b4b030c198044bca3efc13ef942f73dda Author: Max Katz Date: Sat Jan 27 17:33:18 2024 -0500 Move pivot into the VODE state (#1456) This addresses #1451, which was caused by the pivot array being reused for the first time in a new step when the Jacobian had been cached without keeping the corresponding values of the pivot array in scope. integration/VODE/vode_dvjac.H integration/VODE/vode_dvnlsd.H integration/VODE/vode_dvstep.H integration/VODE/vode_type.H commit 0c58dd519b949961d8153966753c3e48583eb82f Author: Michael Zingale Date: Sat Jan 27 15:32:26 2024 -0500 remove some more Fortran vestiges (#1455) networks/general_null/Make.package networks/general_null/network.template commit a4d7ab4d4fc8528ebdb335181bfe7843751f4da3 Author: Simon Guichandut <40605210+simonguichandut@users.noreply.github.com> Date: Tue Jan 9 14:09:34 2024 -0500 Adding reverse rates to CNO_extras (#1445) networks/CNO_extras/.DS_Store networks/CNO_extras/CNO_extras.py networks/CNO_extras/actual_network.H networks/CNO_extras/actual_network_data.cpp networks/CNO_extras/actual_rhs.H networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/CNO_extras/reaclib_rates.H commit 518b421f0f4265a0fb9427c0cacad34272021440 Author: Michael Zingale Date: Fri Jan 5 20:43:08 2024 -0500 AMREX_USE_CUDA -> AMREX_USE_GPU (#1443) integration/BackwardEuler/actual_integrator.H commit fc7221426f4bbe079b65c4298218a5a077850962 Author: Eric T. Johnson Date: Fri Jan 5 17:27:19 2024 -0500 Disable SVML AVX-512 routines in the pyna update script (#1444) networks/update_pynucastro_nets.py commit fbeddb367c6ef7d71052e23c20deda164243e643 Author: Michael Zingale Date: Fri Jan 5 15:42:03 2024 -0500 update pynucastro nets to have bion/mion constexpr (#1437) networks/CNO_extras/actual_network.H networks/CNO_extras/actual_network_data.cpp networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/ECSN/actual_network.H networks/ECSN/actual_network_data.cpp networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/actual_network.H networks/He-C-Fe-group/actual_network_data.cpp networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/reaclib_rates.H networks/ase/actual_network.H networks/ase/actual_network_data.cpp networks/ase/ase.png networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/actual_network.H networks/ignition_reaclib/C-burn-simple/actual_network_data.cpp networks/ignition_reaclib/URCA-medium/actual_network.H networks/ignition_reaclib/URCA-medium/actual_network_data.cpp networks/ignition_reaclib/URCA-medium/urca_medium.png networks/ignition_reaclib/URCA-simple/actual_network.H networks/ignition_reaclib/URCA-simple/actual_network_data.cpp networks/nova/actual_network.H networks/nova/actual_network_data.cpp networks/nova/nova.png networks/nova2/actual_network.H networks/nova2/actual_network_data.cpp networks/nova2/nova.png networks/partition_test/actual_network.H networks/partition_test/actual_network_data.cpp networks/partition_test/partition_functions.H networks/sn160/actual_network.H networks/sn160/actual_network_data.cpp networks/subch_approx/actual_network.H networks/subch_approx/actual_network_data.cpp networks/subch_approx/subch_approx.png networks/subch_base/actual_network.H networks/subch_base/actual_network_data.cpp networks/subch_base/partition_functions.H networks/subch_base/reaclib_rates.H networks/subch_base/subch_base.png networks/subch_full/actual_network.H networks/subch_full/actual_network_data.cpp networks/subch_full/subch_full.png networks/subch_simple/actual_network.H networks/subch_simple/actual_network_data.cpp networks/subch_simple/subch_simple.png commit 3700590cd0dfb4c8e85c0814f97f69d38534c303 Author: Michael Zingale Date: Thu Jan 4 15:03:39 2024 -0500 constexpr some helm EOS table parameters (#1440) EOS/helmholtz/actual_eos.H EOS/helmholtz/actual_eos_data.H EOS/helmholtz/actual_eos_data.cpp commit 6fceeecf5fffcb28334790159cfaee93852be307 Author: Michael Zingale Date: Wed Jan 3 11:04:41 2024 -0500 update tols for Urca test_react so it runs (#1438) the relative tolerances were very tight unit_test/test_react/inputs_reaclib_urca commit 6dc51ad9e22e3c6e8ae2d26e6c84e1bca4819a8c Author: Michael Zingale Date: Mon Jan 1 15:26:37 2024 -0500 fix NSE+SDC when we are doing drive_initial_convection (#1431) The abar that we were getting was not consistent with NSE. Now we are sure to use the correct abar integration/nse_update_simplified_sdc.H commit d99cee07ad28935a9d061d685bed08afc76ca0a4 Author: Michael Zingale Date: Mon Jan 1 14:59:44 2024 -0500 update github actions to latest versions (#1429) also use the cache built into setup_python .github/workflows/burn_cell.yml .github/workflows/burn_cell_primordial_chem.yml .github/workflows/burn_cell_sdc.yml .github/workflows/c-linter.yml .github/workflows/castro.yml .github/workflows/check-ifdefs.yml .github/workflows/cmake_build_cell_primordial_chem.yml .github/workflows/codespell.yml .github/workflows/compile_action.yml .github/workflows/compiler-warnings.yml .github/workflows/create_release.yml .github/workflows/cuda.yml .github/workflows/docs-test.yml .github/workflows/eos_cell.yml .github/workflows/gh-pages.yml .github/workflows/hip.yml .github/workflows/macos_build_cell_primordial_chem.yml .github/workflows/nse_net.yml .github/workflows/nse_table.yml .github/workflows/nse_test.yml .github/workflows/style.yml .github/workflows/test_neutrinos.yml .github/workflows/test_nse_interp.yml .github/workflows/test_rhs.yml commit a0deaaed6397a83598f1096bbe414e828917f169 Author: Michael Zingale Date: Mon Jan 1 13:30:05 2024 -0500 add struct support for runtime_parameters.py (#1422) this will be used to make runtime parameters no longer managed util/build_scripts/runtime_parameters.py util/build_scripts/write_probin.py commit 9d0655b75c2d7c0690fe637f8491fa572227a1dc Author: Michael Zingale Date: Mon Jan 1 13:28:35 2024 -0500 update for 24.01 CHANGES.md commit 3185974142008f9504ebeca06dd9d37f3ff4dddc Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jan 1 10:00:55 2024 -0500 optional quantum correction terms for chabrier1998 (#1428) added a runtime parameter to make quantum correction terms in chabrier1998 screening optional. This is because in NSE_solver quantum terms are not included. Also fixed some inconsistent indentations This should also speed up this screening a little bit (issue #1396), although we already switched integer pows to powi. screening/_parameters screening/screen.H screening/screen_data.H sphinx_docs/source/screening.rst commit a83fe0040339307ee0a358b1c403a076a4f9eba6 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jan 1 09:30:24 2024 -0500 [WIP] fix powi script and bug in chugunov2009 screening (#1432) .github/workflows/check_powi.py screening/screen.H commit 32fa759848dab6e7314ed69ce9c04ba8de11b858 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Dec 31 14:58:35 2023 -0500 Replace std::pow with integer powers to amrex::Math::powi (#1426) With updated network to reflect changes in pynucastro/pynucastro#709. Added a script and CI to detect cases where we can potentially use powi instead of std::pow for integer powers. .github/workflows/check_powi.py .github/workflows/check_powi.yml EOS/ztwd/actual_eos.H conductivity/stellar/actual_conductivity.H integration/RKC/rkc.H integration/utils/initial_timestep.H integration/utils/rkc_util.H networks/CNO_extras/actual_rhs.H networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/ECSN/actual_rhs.H networks/He-C-Fe-group/actual_network.H networks/He-C-Fe-group/actual_network_data.cpp networks/He-C-Fe-group/actual_rhs.H networks/He-C-Fe-group/table_rates.H networks/He-C-Fe-group/table_rates_data.cpp networks/ase/actual_rhs.H networks/ase/ase.png networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/URCA-medium/actual_rhs.H networks/ignition_reaclib/URCA-medium/urca_medium.png networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/iso7/actual_network.H networks/nova/actual_rhs.H networks/nova/nova.png networks/nova2/actual_rhs.H networks/nova2/nova.png networks/partition_test/partition_functions.H networks/primordial_chem/actual_rhs.H networks/sn160/actual_rhs.H networks/subch_approx/actual_rhs.H networks/subch_approx/subch_approx.png networks/subch_base/actual_rhs.H networks/subch_full/actual_rhs.H networks/subch_full/subch_full.png networks/subch_simple/actual_rhs.H networks/subch_simple/subch_simple.png neutrinos/sneut5.H screening/screen.H screening/screen_data.H unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_unit_test.out util/hybrj/hybrj.H util/hybrj/hybrj_dogleg.H util/hybrj/hybrj_enorm.H commit fd59277613ff7736d2b04a92607a2f7e57423e4f Author: Michael Zingale Date: Fri Dec 29 14:29:05 2023 -0500 generalize in_nse() to work with an eos_t (#1424) nse_tabular/nse_table_check.H commit 0c3a1d020ea380f2343e92f474fe4fee114147a9 Author: Michael Zingale Date: Fri Dec 29 08:47:57 2023 -0500 add NSE EOS interfaces for finding a consistent density (#1430) these mirror the existing interfaces for temperature nse_tabular/nse_eos.H nse_tabular/nse_table.H unit_test/test_nse_interp/ci-benchmarks/aprox19.out unit_test/test_nse_interp/nse_cell.H commit b8815845b0edbd2451c08715d88567442f77a8fc Author: Michael Zingale Date: Thu Dec 28 21:11:07 2023 -0500 create an NSE table with finer spacing in rho and Ye (#1427) networks/aprox19/nse_aprox19.tbl networks/aprox19/nse_table_size.H nse_tabular/make_nse_table.py unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out unit_test/test_nse/ci-benchmarks/aprox21_ci.out unit_test/test_nse_interp/ci-benchmarks/aprox19.out commit 2ea84b91b7515f182fc11f45426737df4e2851ea Author: Michael Zingale Date: Thu Dec 28 20:43:12 2023 -0500 a version of SDC+NSE RK2 with the NSE EOS (#1415) This implements the SDC+NSE table update as a 2nd order Runge-Kutta. It uses the new NSE EOS interface to get an Abar / T consistent with the updated e integration/_parameters integration/nse_update_simplified_sdc.H commit a38a1eeab538ce317f70de334d44c5f379d6cdd9 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Dec 20 12:59:55 2023 -0800 add additional molar fraction check for NSE_NET (#1417) I was playing around with the NSE compatibility script and found the original molar fraction check a bit too strict, where the mass fractions might be already sufficient for the forward and reverse equilibrium conditions but still don't pass the molar fraction check. Here I added another one comparing the molar fraction of each species. nse_solver/_parameters nse_solver/nse_check.H sphinx_docs/source/nse.rst commit 7de212422501a88c1c1f536b93217721e3dc6701 Author: Michael Zingale Date: Wed Dec 20 14:29:03 2023 -0500 an EOS interface with NSE (#1405) solving for T(e) or T(p) in NSE is trickier than our standard interface because Abar and Zbar are also a function of rho, T, Ye through the NSE table. This does a self-consistent inversion of the EOS together with the NSE table. nse_tabular/nse_eos.H unit_test/test_nse_interp/ci-benchmarks/aprox19.out unit_test/test_nse_interp/main.cpp unit_test/test_nse_interp/nse_cell.H commit 4a44497fa0e72e0135ea28b0a246aa6d788ed654 Author: Michael Zingale Date: Wed Dec 20 13:33:14 2023 -0500 initialize nse_table_t members (#1418) this syncs up with eos_t nse_tabular/nse_table_type.H commit 925e0ce0f99140121954cad98b71398292f47b67 Author: Michael Zingale Date: Tue Dec 19 14:34:11 2023 -0500 fix concurrency for castro-development (#1423) .github/workflows/castro-development.yml commit d7428160359fb550276a80b51d2fa425b499b348 Author: Michael Zingale Date: Tue Dec 19 13:12:36 2023 -0500 add another Castro action that tests against AMReX development (#1421) .github/workflows/castro-development.yml commit 8a61b961d953ea1c54c2e01a1556ac13481deed2 Author: Michael Zingale Date: Tue Dec 19 12:51:45 2023 -0500 a simpler fix for constexpr_for in amrex (#1420) interfaces/rhs_type.H networks/rhs.H commit 4d7d0299fb39281eaac7c4d66bca1976d62c07b3 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Dec 18 17:38:24 2023 -0800 add a script to test network compatibility with NSE_NET (#1416) This script is based on burn_cell. This script does constant temperature evolution and compares it to the NSE results. It prints out tables at the end that show the absolute and relative errors of mass fractions. There are three cases for ye: <0.5, =0.5, >0.5 Both temperature and density are set at runtime. Since we didn't set a reference cell size, we should let nse.nse_dx_independent=1, if we want to see whether the burn_state would enter NSE. If nse.nse_dx_independent=1, then the script only prints out cases when burn_state failed to enter NSE. nse_solver/nse_compatibility/GNUmakefile nse_solver/nse_compatibility/Make.package nse_solver/nse_compatibility/README.md nse_solver/nse_compatibility/_parameters nse_solver/nse_compatibility/inputs_nse_compatibility nse_solver/nse_compatibility/main.cpp nse_solver/nse_compatibility/nse_network_compatibility.H commit 5757fb59a11e4a53dcabe71f0fadc9c221fb5af6 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Dec 18 17:00:37 2023 -0800 make sure const T evolution (#1408) make sure const temperature evolution when call_eos_in_rhs=false this makes sure we don't update the T in this case after the burn integration/VODE/actual_integrator.H commit 01577f32112fc8ad4c6ccc509c222d0e41fee062 Author: Michael Zingale Date: Mon Dec 18 16:42:45 2023 -0500 Revert "Start moving towards zero-based indexing with linpack (#536)" (#1412) This reverts commit 1f0c666f18c0418a3ab0aa817de00f8fd52ebac7. Co-authored-by: Max Katz util/linpack.H commit 43b5138dcecd92aa919a26afca9ef15f6937b22d Author: Michael Zingale Date: Mon Dec 18 14:37:06 2023 -0500 add a method to compute the T derivative of an NSE table quantity (#1407) this works by differentiating the cubic interpolant nse_tabular/nse_table.H unit_test/test_nse_interp/ci-benchmarks/aprox19.out unit_test/test_nse_interp/nse_cell.H commit 96f4c7efb1adbc6e653ed6966580b6e947735f1a Author: Michael Zingale Date: Sun Dec 17 20:29:39 2023 -0500 update hip install for ROCm 6.0 (#1413) .github/workflows/dependencies/dependencies_hip.sh commit 1e5c78eca7d99c2e9c298b38a415d37180f4664e Author: Michael Zingale Date: Fri Dec 15 12:34:34 2023 -0500 remove esum.H include (#1410) screening/screen_data.H util/microphysics_math.H commit bdf6a18e55fe67acbdcf4eb0c41f9e57006f8999 Author: Michael Zingale Date: Fri Dec 8 13:09:54 2023 -0500 start of a new NSE table interface (#1404) integration/nse_update_simplified_sdc.H integration/nse_update_strang.H nse_tabular/Make.package nse_tabular/nse_table.H nse_tabular/nse_table_type.H unit_test/test_nse_interp/nse_cell.H commit 49c97127a43700ac5d7f9ac5c3aa296a0c9695a7 Author: Michael Zingale Date: Fri Dec 1 08:13:01 2023 -0500 update changes for new release CHANGES.md commit cebf6af5e813f62ae4a453b0a36c76abc0c30071 Author: Eric T. Johnson Date: Thu Nov 30 14:40:58 2023 -0800 Update C++ linter settings to speed up cppcheck (#1403) We were previously testing a bunch of invalid preprocessor configurations, which we can now exclude. Installing all the build tools is unnecessary since the linter step runs inside its own Docker container. .github/workflows/c-linter.yml commit f104eff31026ebaef3a4c2056c3ca1b49e3f2178 Author: Eric T. Johnson Date: Tue Nov 28 16:33:34 2023 -0800 Add constants for the allowed values of SCREEN_METHOD (#1401) An enum would be much nicer here, but the preprocessor doesn't understand those. Make.Microphysics_extern nse_solver/nse_solver.H screening/screen.H screening/screen_data.H commit f03189021b9d0411f9c9479050ac1e5794cd6282 Author: Michael Zingale Date: Tue Nov 28 19:13:09 2023 -0500 fix a factor in chug2009 screening (#1402) screening/screen.H commit 635c36c6ff74638fd5275b356eb719fa6e359cf1 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Nov 28 17:10:08 2023 -0500 organize screening, put z1 z2 related pow vars to screen_factors_t (#1397) screening/screen.H screening/screen_data.H commit 0c5ef6a7a1583af997fd123ce285ae959b278aca Author: Michael Zingale Date: Tue Nov 28 13:13:16 2023 -0500 wrap SDC+NSE neutrino calls with NEUTRINOS (#1400) this will allow them to be disabled at compile-time just like we do for a network integration/nse_update_simplified_sdc.H commit 38fbee239a26634810236684e532c075196719c5 Author: Michael Zingale Date: Tue Nov 28 10:18:35 2023 -0500 make the default NSE interp tricubic (#1399) this works a lot better than trilinear nse_tabular/_parameters unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out unit_test/test_nse_interp/ci-benchmarks/aprox19.out commit 819a67913ecb6b658444040117d1ed67ba859772 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Nov 28 07:24:57 2023 -0500 Enforce chabrier1998 or null screening with NSE_NET (#1398) Make.Microphysics_extern nse_solver/make_table/GNUmakefile nse_solver/nse_solver.H unit_test/test_nse/GNUmakefile commit 965a061ac8275bdd3f07e0c5b8ddae6b55a80f47 Author: Michael Zingale Date: Sat Nov 25 19:57:33 2023 -0500 work around a CUDA linker issue with the NSE table (#1395) networks/aprox19/nse_table_size.H nse_tabular/nse_table.H commit 5ab809ab37f153721227c5c45b204344bae7645d Author: Michael Zingale Date: Wed Nov 22 13:05:52 2023 -0500 add neutrino loses to NSE + SDC (#1357) this works for both tables and self-consistent NSE integration/nse_update_simplified_sdc.H commit 4533640a19152306798cbd89c2e604a754367d35 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Nov 22 12:50:58 2023 -0500 Add subch base network (#1393) This network is a further simplification of subch_simple by excluding N14, F18, Ne21, and Na22. These nuclei were added to include n14(a, g)f18(a, p)ne21 rate sequence, which allows an enhancement to the c12(p, g)n13(a, p)o16 rate due to the proton release. However, we find that the effect is not very significant, and they also caused an artificial endpoint at Na22. networks/subch_base/Make.package networks/subch_base/README.md networks/subch_base/_parameters networks/subch_base/actual_network.H networks/subch_base/actual_network_data.cpp networks/subch_base/actual_rhs.H networks/subch_base/inputs.burn_cell.VODE networks/subch_base/partition_functions.H networks/subch_base/pynucastro.net networks/subch_base/reaclib_rates.H networks/subch_base/subch_base.png networks/subch_base/subch_base.py networks/subch_base/table_rates.H networks/subch_base/table_rates_data.cpp networks/subch_base/tfactors.H networks/subch_full/README.md commit e9e31f40650c768a489bb632a99d14358b201723 Author: Michael Zingale Date: Fri Nov 17 09:50:02 2023 -0500 make some helmeos stuff constexpr (#1384) EOS/helmholtz/actual_eos.H EOS/helmholtz/actual_eos_data.H EOS/helmholtz/actual_eos_data.cpp commit bbb78e68b06c88358e2dbe72a63b1d7580068374 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Nov 15 08:21:27 2023 -0500 sync run_prefix for burn cell input files (#1387) unit_test/burn_cell/inputs_aprox13_mott unit_test/burn_cell/inputs_aprox19.nse 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_ecsn unit_test/burn_cell/inputs_ignition_chamulak unit_test/burn_cell/inputs_subch_approx unit_test/burn_cell/inputs_subch_compare unit_test/burn_cell/inputs_vode_example commit 1cb55ecb0527db93b0e2474c931025b03beda475 Author: Michael Zingale Date: Wed Nov 15 08:05:46 2023 -0500 a new, slightly larger Urca net (#1365) networks/ignition_reaclib/URCA-medium/23mg-23na_electroncapture.dat networks/ignition_reaclib/URCA-medium/23na-23ne_electroncapture.dat networks/ignition_reaclib/URCA-medium/23ne-23na_betadecay.dat networks/ignition_reaclib/URCA-medium/Make.package networks/ignition_reaclib/URCA-medium/_parameters networks/ignition_reaclib/URCA-medium/actual_network.H networks/ignition_reaclib/URCA-medium/actual_network_data.cpp networks/ignition_reaclib/URCA-medium/actual_rhs.H networks/ignition_reaclib/URCA-medium/inputs.burn_cell.VODE networks/ignition_reaclib/URCA-medium/n-p_betadecay.dat networks/ignition_reaclib/URCA-medium/p-n_electroncapture.dat networks/ignition_reaclib/URCA-medium/partition_functions.H networks/ignition_reaclib/URCA-medium/pynucastro.net networks/ignition_reaclib/URCA-medium/reaclib_rate_metadata.dat networks/ignition_reaclib/URCA-medium/reaclib_rates.H networks/ignition_reaclib/URCA-medium/table_rates.H networks/ignition_reaclib/URCA-medium/table_rates_data.cpp networks/ignition_reaclib/URCA-medium/tfactors.H networks/ignition_reaclib/URCA-medium/urca.py networks/ignition_reaclib/URCA-medium/urca_medium.png commit 2383aa27bd7dc5466d7e4b91e3e233a4a1b0f90f Author: Michael Zingale Date: Tue Nov 14 10:24:38 2023 -0500 don't allow logical runtime parameters (#1385) when we originally did the Fortran -> C++ conversion, we passed all of the Fortran logicals into C++ ints. But now that we are completely C++, it doesn't make sense to have logical anymore. There are some places where we implicitly pass an int to a C++ bool. This will help track those down and eliminate things. EOS/gamma_law/_parameters EOS/helmholtz/_parameters Make.Microphysics integration/_parameters networks/_parameters nse_solver/_parameters util/build_scripts/write_probin.py commit 3fe63e82865cd4b57cbded0c2c697863c6b978c2 Author: Michael Zingale Date: Sat Nov 11 12:25:34 2023 -0500 update network pynucastro scripts to new RateCollection plot interface (#1383) networks/CNO_extras/CNO_extras.py networks/He-C-Fe-group/He-C-Fe-group.py networks/ase/ase.py networks/nova/network_plot.py networks/nova/nova.py networks/nova2/nova2.py networks/subch_approx/subch_approx.py networks/subch_full/network_plot.py networks/subch_full/subch_full.py networks/subch_simple/subch_simple.py commit 05a8bc2b952632c603180e8485965d8dae3c170b Author: Michael Zingale Date: Fri Nov 10 11:52:58 2023 -0500 fix some minor clang-tidy warnings for SDC+NSE (#1382) integration/VODE/actual_integrator_simplified_sdc.H integration/nse_update_simplified_sdc.H unit_test/burn_cell_sdc/burn_cell.H commit 6ceeb5d1fb4c24bfbc8a64b5c47390a1a575fbe9 Author: Michael Zingale Date: Thu Nov 9 15:55:45 2023 -0500 new NSE table (#1350) A new NSE table for aprox19 created with pynucastro replaces the original NSE table. This has mostly the same range of validity, but has finer dlogT spacing and also tabulates dAbar/dt, d/dt, and e_nu. This also contains a notebook that can be used to inspect the true NSE result from pynucastro at an arbitrary thermodynamic point. Finally, we include the python script that generates the table. Make.Microphysics_extern integration/nse_update_simplified_sdc.H integration/nse_update_strang.H networks/aprox19/Make.package networks/aprox19/README.md networks/aprox19/nse.tbl networks/aprox19/nse_aprox19.tbl networks/aprox19/nse_table_size.H nse_tabular/README.md nse_tabular/make_nse_table.py nse_tabular/nse_table.H nse_tabular/nse_table.ipynb nse_tabular/nse_table_data.H nse_tabular/nse_table_data.cpp unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out unit_test/nse_table_cell/GNUmakefile unit_test/nse_table_cell/Make.package unit_test/nse_table_cell/README.md unit_test/nse_table_cell/_parameters unit_test/nse_table_cell/main.cpp unit_test/nse_table_cell/nse_cell.H unit_test/test_nse_interp/README.md unit_test/test_nse_interp/ci-benchmarks/aprox19.out unit_test/test_nse_interp/nse_cell.H commit c31730833d4a6ada64d851a8ff6674e3874bb85f Author: Michael Zingale Date: Thu Nov 9 15:54:23 2023 -0500 fix some comments in sneut5 (#1381) neutrinos/sneut5.H commit 39a0f40188bc424a7e52d855378031d27e20cde6 Author: Eric T. Johnson Date: Tue Nov 7 08:32:12 2023 -0500 Fix swapped sin and cos in sneut (#1380) This reverts all the benchmark updates made in #1379, as the actual changes should be very minor. neutrinos/sneut5.H unit_test/burn_cell/ci-benchmarks/aprox13_QSS_unit_test.out unit_test/burn_cell/ci-benchmarks/aprox13_RKC_unit_test.out unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_unit_test.out unit_test/burn_cell_sdc/ci-benchmarks/aprox19_BE_state_over_time.txt unit_test/burn_cell_sdc/ci-benchmarks/aprox19_state_over_time.txt unit_test/test_neutrino_cooling/ci-benchmarks/test_sneut5.out unit_test/test_rhs/ci-benchmarks/aprox13.out unit_test/test_rhs/ci-benchmarks/aprox19.out unit_test/test_rhs/ci-benchmarks/aprox21.out unit_test/test_rhs/ci-benchmarks/ecsn.out unit_test/test_rhs/ci-benchmarks/iso7.out commit 2821e18a68fb8fe2c0f9d9536bb819d711cf6233 Author: Michael Zingale Date: Wed Nov 1 09:12:27 2023 -0400 update changes for 23.11 CHANGES.md commit 153fbf87bc2f16722105811e2bee7da77b6424d9 Author: Michael Zingale Date: Mon Oct 30 14:19:32 2023 -0400 use multiple angle formula in sneut to speed up sin/cos (#1379) Co-authored-by: Eric T. Johnson neutrinos/sneut5.H unit_test/burn_cell/ci-benchmarks/aprox13_QSS_unit_test.out unit_test/burn_cell/ci-benchmarks/aprox13_RKC_unit_test.out unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_unit_test.out unit_test/burn_cell_sdc/ci-benchmarks/aprox19_BE_state_over_time.txt unit_test/burn_cell_sdc/ci-benchmarks/aprox19_state_over_time.txt unit_test/test_neutrino_cooling/ci-benchmarks/test_sneut5.out unit_test/test_rhs/ci-benchmarks/aprox13.out unit_test/test_rhs/ci-benchmarks/aprox19.out unit_test/test_rhs/ci-benchmarks/aprox21.out unit_test/test_rhs/ci-benchmarks/ecsn.out unit_test/test_rhs/ci-benchmarks/iso7.out commit 04ba99af58522437f7d0f7ad33b551486653bebb Author: Michael Zingale Date: Sun Oct 29 19:20:59 2023 -0400 move pair neutrinos into it's own function in sneut5 (#1378) neutrinos/sneut5.H commit 5f987dd130b3fed27c045f67dd6c9752bff8fc6e Author: Michael Zingale Date: Sun Oct 29 18:03:11 2023 -0400 move plasma neutrino contribution into its own function (#1377) neutrinos/sneut5.H commit 53d979817c87aeeb0c7007bc20de7fdadf2b7b63 Author: Michael Zingale Date: Sun Oct 29 16:25:50 2023 -0400 move sneut photo section into its own function (#1375) neutrinos/sneut5.H commit 9066232c3a6b3c1e94f1de2020d879a61cdd7cf7 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Oct 29 15:22:16 2023 -0400 add weak rate neutrino loss for self-consistent nse check (#1369) nse_solver/nse_check.H commit df21ae5a4491625d1d6835f1b2c7cafb4e1330fc Author: Michael Zingale Date: Sat Oct 28 19:21:47 2023 -0400 move sneut bremsstrahlung into its own function (#1374) neutrinos/sneut5.H commit fc40d670ae0e09e303eb4b4558a634a4926fe742 Author: Michael Zingale Date: Sat Oct 28 18:45:17 2023 -0400 move sneut5 recombination section into its own function (#1373) neutrinos/sneut5.H commit 6f60462ff9ea041d44e24ec9d09a813d76b9d282 Author: Michael Zingale Date: Sat Oct 28 13:48:16 2023 -0400 SDC+NSE predictor-corrector update: make number of iters a runtime param (#1370) integration/_parameters integration/nse_update_simplified_sdc.H commit e052f6eaaef09bd58ff25540d8fcc814a9087eae Author: Michael Zingale Date: Sat Oct 28 13:44:53 2023 -0400 move common sneut factors into a struct (#1372) neutrinos/sneut5.H commit 8b48c0281d9f18eac6a6ed167871bbb2bd433d37 Author: Michael Zingale Date: Sat Oct 28 13:09:04 2023 -0400 move some Fermi integral coefficients to static arrays (#1371) no need to set these each time we enter the function neutrinos/sneut5.H commit 5dd1a910e5d662c94108cc29964be51071cbbfdb Author: Michael Zingale Date: Tue Oct 24 11:09:24 2023 -0400 update Urca network with the p -> n e-capture rate from Langanke (#1359) networks/ignition_reaclib/URCA-simple/actual_network.H networks/ignition_reaclib/URCA-simple/actual_network_data.cpp networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/n-p_betadecay.dat networks/ignition_reaclib/URCA-simple/p-n_electroncapture.dat networks/ignition_reaclib/URCA-simple/reaclib_rates.H networks/ignition_reaclib/URCA-simple/table_rates.H networks/ignition_reaclib/URCA-simple/table_rates_data.cpp networks/ignition_reaclib/URCA-simple/urca.py commit 7974a0d126fff28c05e0e1e3811b3feaed1e832e Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Oct 23 15:19:57 2023 -0400 update networks, benchmarks, and NSE_index due to specie name capitalization (#1362) corresponding update due to pynucastro/pynucastro#652 networks/CNO_extras/actual_network.H networks/CNO_extras/actual_rhs.H networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/CNO_extras/pynucastro.net networks/CNO_extras/reaclib_rates.H networks/CNO_extras/table_rates.H networks/ECSN/actual_network.H networks/ECSN/actual_rhs.H networks/ECSN/pynucastro.net networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H networks/ECSN/table_rates_data.cpp networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/actual_network.H networks/He-C-Fe-group/actual_rhs.H networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/pynucastro.net networks/He-C-Fe-group/reaclib_rates.H networks/He-C-Fe-group/table_rates.H networks/He-C-Fe-group/table_rates_data.cpp networks/aprox13/actual_network.H networks/aprox19/actual_network.H networks/aprox21/actual_network.H networks/ase/_parameters networks/ase/actual_network.H networks/ase/actual_rhs.H networks/ase/ase.png networks/ase/partition_functions.H networks/ase/pynucastro.net networks/ase/reaclib_rates.H networks/ase/table_rates.H networks/ignition_reaclib/C-burn-simple/actual_network.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/C-burn-simple/pynucastro.net networks/ignition_reaclib/C-burn-simple/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/table_rates.H networks/ignition_reaclib/URCA-simple/actual_network.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/pynucastro.net networks/ignition_reaclib/URCA-simple/reaclib_rates.H networks/ignition_reaclib/URCA-simple/table_rates.H networks/ignition_reaclib/URCA-simple/table_rates_data.cpp networks/ignition_simple/actual_network.H networks/iso7/actual_network.H networks/nova/actual_network.H networks/nova/actual_rhs.H networks/nova/nova.png networks/nova/pynucastro.net networks/nova/reaclib_rates.H networks/nova/table_rates.H networks/nova2/actual_network.H networks/nova2/actual_rhs.H networks/nova2/nova.png networks/nova2/pynucastro.net networks/nova2/reaclib_rates.H networks/nova2/table_rates.H networks/partition_test/actual_network.H networks/partition_test/actual_rhs.H networks/partition_test/partition_functions.H networks/partition_test/pynucastro.net networks/partition_test/reaclib_rates.H networks/partition_test/table_rates.H networks/sn160/actual_network.H networks/sn160/actual_rhs.H networks/sn160/pynucastro.net networks/sn160/reaclib_rates.H networks/sn160/table_rates.H networks/subch_approx/_parameters networks/subch_approx/actual_network.H networks/subch_approx/actual_rhs.H networks/subch_approx/pynucastro.net networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.png networks/subch_approx/table_rates.H networks/subch_full/_parameters networks/subch_full/actual_network.H networks/subch_full/actual_rhs.H networks/subch_full/pynucastro.net networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.png networks/subch_full/table_rates.H networks/subch_simple/_parameters networks/subch_simple/actual_network.H networks/subch_simple/actual_rhs.H networks/subch_simple/pynucastro.net networks/subch_simple/reaclib_rates.H networks/subch_simple/subch_simple.png networks/subch_simple/table_rates.H nse_solver/nse_check.H nse_solver/nse_solver.H unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_unit_test.out unit_test/test_ase/ci-benchmarks/ase_nse_net_unit_test.out commit e8749f94d270c76c4b833eaf8a57195eb947ed96 Author: Michael Zingale Date: Mon Oct 23 14:31:21 2023 -0400 update ECSN to latest pynucastro (#1368) networks/ECSN/actual_rhs.H networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out unit_test/test_rhs/ci-benchmarks/ecsn.out commit 8ec4f0831c8f21a2169bbf55f4862b78b65ee755 Author: Michael Zingale Date: Sun Oct 22 08:19:09 2023 -0400 update He-C-Fe-group with new pynucastro (#1364) we now need to remove duplicates before the RateCollection networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/He-C-Fe-group.py networks/He-C-Fe-group/actual_rhs.H networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/reaclib_rates.H networks/He-C-Fe-group/table_rates.H commit b6838d22dec2309713a769f9a7520d4270511188 Author: Michael Zingale Date: Sun Oct 22 08:18:42 2023 -0400 rely on short-circuiting to avoid valgrind complaints (#1363) unit_test/react_util.H commit b28cd4e2d618cdc7c1245161bc0a670697f45535 Author: Michael Zingale Date: Fri Oct 20 09:57:12 2023 -0400 fix CI diffs due to AMReX change (#1361) .github/workflows/burn_cell.yml .github/workflows/eos_cell.yml .github/workflows/nse_net.yml .github/workflows/nse_table.yml .github/workflows/nse_test.yml .github/workflows/test_nse_interp.yml commit 9744551f6eaa366ba860765455d0b13ba1ce56b0 Author: Michael Zingale Date: Thu Oct 19 17:58:06 2023 -0400 update He-C-Fe-group to include the positron parts of table rates (#1360) now we include positron-capture and positron-decay we also include n -> p and p -> n from Langanke. networks/He-C-Fe-group/55co-55fe_electroncapture.dat networks/He-C-Fe-group/55fe-55co_betadecay.dat networks/He-C-Fe-group/55fe-55mn_electroncapture.dat networks/He-C-Fe-group/55mn-55fe_betadecay.dat networks/He-C-Fe-group/56co-56fe_electroncapture.dat networks/He-C-Fe-group/56co-56ni_betadecay.dat networks/He-C-Fe-group/56fe-56co_betadecay.dat networks/He-C-Fe-group/56ni-56co_electroncapture.dat networks/He-C-Fe-group/57co-57ni_betadecay.dat networks/He-C-Fe-group/57ni-57co_electroncapture.dat networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/actual_network.H networks/He-C-Fe-group/actual_network_data.cpp networks/He-C-Fe-group/actual_rhs.H networks/He-C-Fe-group/n-p_betadecay.dat networks/He-C-Fe-group/p-n_electroncapture.dat networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/reaclib_rates.H networks/He-C-Fe-group/table_rates.H networks/He-C-Fe-group/table_rates_data.cpp commit ebdb5b8184ce1943934d38980f17a96ebb0d30cd Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Oct 19 07:36:41 2023 -0400 fix make clean logic (#1358) fixes the nse table cleaning instead of relying on NET_TABLES, we now delete *electroncapture.dat and *betadecay.dat Make.Microphysics_extern commit 8b2c485452b861614ddd906bd67b6b071ec4403c Merge: 9a858fec 4e4764d3 Author: Michael Zingale Date: Sun Oct 15 18:22:35 2023 -0400 Merge branch 'main' into development commit 9a858fecc733d8e1dd64bc81c45dc1e043d5061a Author: Michael Zingale Date: Fri Oct 13 19:38:53 2023 -0400 make sure we are actually getting lines from helm_table.dat (#1355) EOS/helmholtz/actual_eos.H commit 4e4764d3e67b24bbca667d2ca6a9d999d3fd5b21 Author: Ben Wibking Date: Fri Oct 13 11:53:11 2023 -0400 workaround macOS CI bug (#1353) Fixes https://github.com/AMReX-Astro/Microphysics/issues/1352. .github/workflows/macos_build_cell_primordial_chem.yml commit bf999d59657bb1b13db09b265a475b671e73c6b8 Author: Michael Zingale Date: Fri Oct 13 07:58:50 2023 -0400 add new H-C-Fe-group network (#1322) this is based on subch_simple but adds a lot of Fe group networks/He-C-Fe-group/55co-55fe_electroncapture.dat networks/He-C-Fe-group/55fe-55co_betadecay.dat networks/He-C-Fe-group/56co-56fe_electroncapture.dat networks/He-C-Fe-group/56co-56ni_betadecay.dat networks/He-C-Fe-group/56fe-56co_betadecay.dat networks/He-C-Fe-group/56ni-56co_electroncapture.dat networks/He-C-Fe-group/57co-57ni_betadecay.dat networks/He-C-Fe-group/57ni-57co_electroncapture.dat networks/He-C-Fe-group/He-C-Fe-group.png networks/He-C-Fe-group/He-C-Fe-group.py networks/He-C-Fe-group/Make.package networks/He-C-Fe-group/README.md networks/He-C-Fe-group/_parameters networks/He-C-Fe-group/actual_network.H networks/He-C-Fe-group/actual_network_data.cpp networks/He-C-Fe-group/actual_rhs.H networks/He-C-Fe-group/inputs.burn_cell.VODE networks/He-C-Fe-group/partition_functions.H networks/He-C-Fe-group/pynucastro.net networks/He-C-Fe-group/reaclib_rates.H networks/He-C-Fe-group/table_rates.H networks/He-C-Fe-group/table_rates_data.cpp networks/He-C-Fe-group/tfactors.H commit 657406dcaf546a5601c8388ef1a2b34a0016edb5 Author: Eric T. Johnson Date: Fri Oct 6 10:42:23 2023 -0400 Add AMReX style CI and EditorConfig file (#1349) https://editorconfig.org/ has instructions on setting up your editor to follow the configured style. .editorconfig .git-blame-ignore-revs .github/workflows/style.yml .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh commit 0ad0ab251562fb5eda9255c958fce8e0b1f6669b Author: Michael Zingale Date: Thu Oct 5 17:59:03 2023 -0400 remove sdc_burn_to_eos (#1347) it is not used interfaces/burn_type.H commit 5a2247f598f88f80ad8b186188fccfd5537b18d3 Author: Eric T. Johnson Date: Thu Oct 5 17:58:41 2023 -0400 Clean up whitespace (#1348) Replace tabs with spaces and trim trailing whitespace. .github/workflows/burn_cell_primordial_chem.yml .github/workflows/create_release.yml .github/workflows/find_changed_files.py .github/workflows/get_release_txt.py CMakeLists.txt EOS/breakout/actual_eos.H EOS/eos_composition.H EOS/helmholtz/actual_eos.H EOS/polytrope/actual_eos.H EOS/ztwd/actual_eos.H conductivity/stellar/actual_conductivity.H constants/fundamental_constants.H deploy_docs_action.sh integration/VODE/actual_integrator.H integration/VODE/vode_dvstep.H integration/integrator_type.H interfaces/burn_type.H interfaces/burner.H interfaces/eos_type.H interfaces/tfactors.H networks/aprox13/actual_network.H networks/aprox19/actual_network.H networks/aprox21/actual_network.H networks/ase/ase.py networks/ignition_chamulak/notes.txt networks/rhs.H networks/rprox/reaclib/make_rates_module.py networks/triple_alpha_plus_cago/actual_network.H nse_solver/make_table/burn_cell.H nse_solver/nse_check.H nse_solver/nse_solver.H rates/aprox_rates.H rates/aprox_rates_data.H screening/screen.H sphinx_docs/notes.txt sphinx_docs/source/basics.rst sphinx_docs/source/integrators.rst sphinx_docs/source/networks-overview.rst sphinx_docs/source/networks.rst sphinx_docs/source/nse.rst sphinx_docs/source/sdc.rst sphinx_docs/source/templated_networks.rst sphinx_docs/source/unit_tests.rst unit_test/burn_cell/burn_cell.H unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_sdc/burn_cell.H unit_test/test_aprox_rates/aprox_rates_util.cpp unit_test/test_aprox_rates/variables.cpp unit_test/test_ase/burn_cell.H unit_test/test_ase/main.cpp unit_test/test_ase/make_table/burn_cell.H unit_test/test_nse/nse_example.H unit_test/test_react/main.cpp unit_test/test_react/test_network_combinations.py unit_test/test_screening/screening_util.cpp unit_test/test_sdc/react_zones.H unit_test/test_sdc/variables.cpp unit_test/write_job_info.cpp util/code_checker/code_checker.py util/hybrj/hybrj.H util/hybrj/hybrj_dogleg.H util/hybrj/hybrj_enorm.H util/hybrj/hybrj_r1mpyq.H util/microphysics_sort.H util/skynet/burn.py util/skynet/compare.py commit e3e866c003cf511a0195ca30fcff43a1e02c7414 Merge: 4803fc8b 8e44dfdb Author: Michael Zingale Date: Tue Oct 3 09:10:00 2023 -0400 Merge branch 'main' into development commit 4803fc8b84d976022653cc63cd67ce4e616d6f7b Author: Michael Zingale Date: Mon Oct 2 20:46:48 2023 -0400 update due to codespell release (#1345) CHANGES.md util/gcem/README.md util/gcem/docs/source/index.rst util/skynet/README.md commit 8e44dfdbed1e83629bbcade8307bff4cdb367ded Author: Michael Zingale Date: Mon Oct 2 20:46:10 2023 -0400 remname initial_dt() to initial_react_dt() (#1344) this avoids a name conflict with Castro integration/BackwardEuler/be_integrator.H integration/utils/initial_timestep.H commit bef0d65d06c4818f2cf1e2e01429761c1e537b63 Author: Michael Zingale Date: Sun Oct 1 12:49:41 2023 -0400 update changes for 23.10 CHANGES.md commit 5d93c2a3c0c5e338cb2773c5ef44bc46258c5e89 Author: Michael Zingale Date: Fri Sep 29 09:38:28 2023 -0400 start of a merge of simplified and true SDC (#1341) from the point of view of the ODE integrator, they are the same .github/workflows/good_defines.txt Make.Microphysics_extern integration/BackwardEuler/Make.package integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/Make.package integration/RKC/Make.package integration/RKC/rkc.H integration/RKC/rkc_type.H 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_type.H integration/integrator.H integration/utils/circle_theorem.H integration/utils/nonaka_plot.H interfaces/burner.H commit 973a84c1d8c8edf42137a53ed3dc3e8b30cae44b Author: Michael Zingale Date: Thu Sep 28 11:09:03 2023 -0400 add some breaks in the valid step logic (#1342) no need to keep checking if we already failed integration/VODE/vode_dvstep.H commit 2261118f5c2ff89d66cab543f819076d11a6e707 Author: Eric T. Johnson Date: Wed Sep 27 16:43:11 2023 -0400 Update pynucastro networks (#1287) these were regenerated with pynucastro 2.1.0 networks/CNO_extras/actual_network.H networks/CNO_extras/actual_network_data.cpp networks/CNO_extras/actual_rhs.H networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/CNO_extras/partition_functions.H networks/CNO_extras/reaclib_rates.H networks/CNO_extras/table_rates.H networks/ECSN/actual_rhs.H networks/ECSN/table_rates.H networks/ase/actual_network.H networks/ase/actual_network_data.cpp networks/ase/actual_rhs.H networks/ase/ase.png networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ase/table_rates.H 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.H networks/ignition_reaclib/C-burn-simple/partition_functions.H networks/ignition_reaclib/C-burn-simple/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/table_rates.H networks/ignition_reaclib/URCA-simple/23Na-23Ne_electroncapture.dat networks/ignition_reaclib/URCA-simple/23Ne-23Na_betadecay.dat 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.H networks/ignition_reaclib/URCA-simple/actual_network_data.cpp networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/partition_functions.H networks/ignition_reaclib/URCA-simple/reaclib_rates.H networks/ignition_reaclib/URCA-simple/table_rates.H networks/ignition_reaclib/URCA-simple/table_rates_data.cpp networks/nova/actual_network.H networks/nova/actual_network_data.cpp networks/nova/actual_rhs.H networks/nova/nova.png networks/nova/partition_functions.H networks/nova/reaclib_rates.H networks/nova/table_rates.H networks/nova2/actual_network.H networks/nova2/actual_network_data.cpp networks/nova2/actual_rhs.H networks/nova2/nova.png networks/nova2/partition_functions.H networks/nova2/reaclib_rates.H networks/nova2/table_rates.H networks/partition_test/actual_network.H networks/partition_test/actual_network_data.cpp networks/partition_test/actual_rhs.H networks/partition_test/partition_functions.H networks/partition_test/reaclib_rates.H networks/partition_test/table_rates.H networks/sn160/Make.package networks/sn160/actual_network.H networks/sn160/actual_network_data.cpp networks/sn160/actual_rhs.H networks/sn160/partition_functions.H networks/sn160/reaclib_rates.H networks/sn160/table_rates.H networks/sn160/tfactors.H networks/subch_approx/_parameters networks/subch_approx/actual_network.H networks/subch_approx/actual_network_data.cpp networks/subch_approx/actual_rhs.H networks/subch_approx/partition_functions.H networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.png networks/subch_approx/table_rates.H networks/subch_full/_parameters networks/subch_full/actual_network.H networks/subch_full/actual_network_data.cpp networks/subch_full/actual_rhs.H networks/subch_full/partition_functions.H networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.png networks/subch_full/table_rates.H networks/subch_simple/_parameters networks/subch_simple/actual_network.H networks/subch_simple/actual_network_data.cpp networks/subch_simple/actual_rhs.H networks/subch_simple/partition_functions.H networks/subch_simple/reaclib_rates.H networks/subch_simple/subch_simple.png networks/subch_simple/table_rates.H networks/update_pynucastro_nets.py unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out unit_test/test_rhs/ci-benchmarks/ecsn.out commit 9c08d809b6798df9798691174e2fc3a64c41360c Author: Michael Zingale Date: Sat Sep 23 21:30:35 2023 -0400 some more true-SDC simplication (#1340) we can basically do what simplified-SDC does now integration/RKC/rkc_type.H integration/VODE/vode_type.H integration/integrator_data.H commit d55561ce3f5728f8b21e24e1902d07aa9feef1df Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Sat Sep 23 16:57:21 2023 +0200 remove general_null from primordial chem (#1339) CMakeLists.txt commit ffae4da80aff8b391b0b934151d4723388ba2fb5 Author: Michael Zingale Date: Thu Sep 21 08:19:44 2023 -0400 update true-SDC to be in sync with upcoming Castro cleaning (#1338) this will make it more in line with how simplified-SDC works integration/VODE/vode_dvhin.H integration/VODE/vode_dvode.H integration/VODE/vode_dvstep.H integration/integrator_data.H interfaces/burn_type.H commit 5ddd146e5efd3c0d22cb2a3941cf65e0fa40fb1c Author: Michael Zingale Date: Tue Sep 19 19:31:11 2023 -0400 add some comments on the Fermi integrals (#1328) neutrinos/sneut5.H commit 790ee200f193c79b22a070b05c6ab3f3c1b3f236 Author: Michael Zingale Date: Tue Sep 19 17:28:33 2023 -0400 template out the plasma neutrino derivatives (#1329) networks/CNO_extras/actual_rhs.H networks/ECSN/actual_rhs.H networks/ase/actual_rhs.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/nova/actual_rhs.H networks/nova2/actual_rhs.H networks/partition_test/actual_rhs.H networks/rhs.H networks/sn160/actual_rhs.H networks/subch_approx/actual_rhs.H networks/subch_full/actual_rhs.H networks/subch_simple/actual_rhs.H neutrinos/sneut5.H nse_solver/nse_check.H unit_test/test_neutrino_cooling/neutrino_util.cpp commit dfc865b794737af185cc257f49f398bda08b0c12 Author: Michael Zingale Date: Thu Sep 14 12:46:29 2023 -0400 fix test name for test_neutrinos (#1336) .github/workflows/test_neutrinos.yml commit 171e787ff40dfce771ae71528f397585a5559077 Author: Michael Zingale Date: Wed Sep 13 20:51:59 2023 -0400 add a sneu5 CI test (#1335) .github/workflows/test_neutrinos.yml unit_test/test_neutrino_cooling/ci-benchmarks/test_sneut5.out commit 5e38c703e51d69c285d025e1f9c908e2007e8fd3 Author: Eric T. Johnson Date: Wed Sep 13 07:55:16 2023 -0400 Move Helmholtz free energy from chabrier1998 into a helper function (#1334) This reduces code duplication and lets us reuse it in the NSE solver. Also pull some common subexpressions into variables so we only calculate them once. nse_solver/nse_solver.H screening/screen.H commit 94b016d2ac0243dc3cb06f10daf4704b827c7c9a Author: Michael Zingale Date: Tue Sep 12 12:28:02 2023 -0400 we don't need NUM_EXTRA_SPECIES in the preprocessor (#1321) we already have it as a constexpr networks/general_null/network_header.template commit f22678704e0d49f67299ca86af5c93f3af40b94a Author: Michael Zingale Date: Tue Sep 12 12:23:44 2023 -0400 add a neutrino cooling unit test (#1331) unit_test/test_neutrino_cooling/GNUmakefile unit_test/test_neutrino_cooling/Make.package unit_test/test_neutrino_cooling/README.md unit_test/test_neutrino_cooling/_parameters unit_test/test_neutrino_cooling/inputs unit_test/test_neutrino_cooling/main.cpp unit_test/test_neutrino_cooling/neutrino_util.cpp unit_test/test_neutrino_cooling/test_sneut.H unit_test/test_neutrino_cooling/variables.H unit_test/test_neutrino_cooling/variables.cpp commit 2c408a9c725a37a1717551433aed92f90992bf13 Author: Michael Zingale Date: Sun Sep 10 19:02:22 2023 -0400 sqrt() -> std::sqrt() and exp() -> std::exp() (#1330) EOS/breakout/actual_eos.H neutrinos/sneut5.H commit 3c755386955b2dd8e26c4d9e9e365e67e4fba58a Merge: a7d59904 743d388a Author: Michael Zingale Date: Sun Sep 10 12:52:18 2023 -0400 Merge branch 'development' of github.com:amrex-astro/Microphysics into development commit 743d388a0244688c82003ae35c8ce3ed9691fb76 Author: Michael Zingale Date: Sun Sep 10 12:32:14 2023 -0400 initialize ye, mu's for NSE_NET in burn_cell_sdc (#1325) this fixes some valgrind issues unit_test/burn_cell_sdc/_parameters unit_test/burn_cell_sdc/burn_cell.H commit c24487bdc3500141f9e4d7ddd7ee4a56a7044ee4 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sat Sep 9 11:15:22 2023 -0400 change initial guess from 1e6 to T_in (#1323) integration/nse_update_simplified_sdc.H commit a7d5990428d856bc39b74c34e54c6f1ae1b0b6eb Author: Michael Zingale Date: Fri Sep 1 07:59:14 2023 -0400 updates for 23.09 CHANGES.md commit bb8d2a2b5683c56eaf27812da778449898cad6d8 Author: Michael Zingale Date: Wed Aug 30 15:24:46 2023 -0400 update ECSN with latest pynucastro (#1320) this will help us with the diffs in the pynucastro C++ CI networks/ECSN/actual_network.H networks/ECSN/actual_network_data.cpp networks/ECSN/actual_rhs.H networks/ECSN/partition_functions.H networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H commit 5825917700e3b4c1671c1ab653238b991674cb0b Author: Eric T. Johnson Date: Tue Aug 29 10:42:08 2023 -0400 Update test_rhs/inputs_ecsn to cover tabular rates (#1319) Also add it to the test_rhs CI workflow. These inputs cover all the different interpolation/extrapolation cases in the tabular rate evaluation code. This should cause a failure in the nightly regression tests, and the benchmark will need to be updated on groot. .github/workflows/test_rhs.yml unit_test/test_rhs/ci-benchmarks/ecsn.out unit_test/test_rhs/inputs_ecsn commit 5e6104538bb5783b8aada2d78d3ef9f7aaa3c34f Author: Michael Zingale Date: Sat Aug 26 08:26:32 2023 -0400 fix the sphinx css includes (#1318) this syncs up with Castro sphinx_docs/source/conf.py commit 49d804e67c46a9cf81613b610eab582502cdebbe Author: Eric T. Johnson Date: Thu Aug 24 13:46:38 2023 -0400 Remove Sphinx version constraint (#1317) Sphinx 7.2.3 was released today, which includes a fix for the Breathe incompatibility. requirements.txt commit ced7cc41dbafae11ed587c1d446d80e442b9b967 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Aug 22 11:11:12 2023 -0500 CMake: do not generate network_properties twice (#1315) * remove duplication * change AMREX --> AMReX --------- Co-authored-by: Ben Wibking .github/workflows/cmake_build_cell_primordial_chem.yml .github/workflows/macos_build_cell_primordial_chem.yml CMakeLists.txt commit 00c8a99cf62ed2e2b3025af921bb3cc5b03bb5b3 Author: Eric T. Johnson Date: Mon Aug 21 19:05:18 2023 -0400 Constrain Sphinx version to fix docs build (#1316) Breathe is currently incompatible with Sphinx >= 7.2: see breathe-doc/breathe#943. requirements.txt commit 01724c98b1d36c6147ecf5505aa0b08e6325f7c0 Author: Michael Zingale Date: Sat Aug 19 10:31:39 2023 -0400 improve the docs on general_null (#1312) sphinx_docs/source/networks.rst commit c6df73528293b5de75f69c5befd1668be4704eb0 Author: Michael Zingale Date: Fri Aug 18 13:37:10 2023 -0400 update the README.md (#1313) it was a bit out of date README.md commit 9ecfd8d22f8e6ccbbd2fa1ab923373f17931307b Author: Michael Zingale Date: Tue Aug 15 15:38:47 2023 -0400 move the NSE table docs into its README (#1311) networks/aprox19/README.md nse_tabular/README.md commit f981413fe4cc53e4de9a69b57790df54693fcab0 Author: Max Katz Date: Tue Aug 15 07:44:58 2023 -0400 Remove obsolete NETWORK_PROPERTIES file (#1310) The last remaining entry in this file, NSCREEN, was made unnecessary by conversion of all of the networks to use the modern (compile-time) screening factor calculation. .github/workflows/find_changed_files.py .github/workflows/good_defines.txt CHANGES.md CMakeLists.txt networks/CNO_extras/NETWORK_PROPERTIES networks/ECSN/NETWORK_PROPERTIES networks/Make.package networks/aprox13/NETWORK_PROPERTIES networks/aprox19/NETWORK_PROPERTIES networks/aprox21/NETWORK_PROPERTIES networks/ase/NETWORK_PROPERTIES networks/general_null/Make.package 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/URCA-simple/NETWORK_PROPERTIES networks/ignition_simple/NETWORK_PROPERTIES networks/iso7/NETWORK_PROPERTIES networks/nova/NETWORK_PROPERTIES networks/nova2/NETWORK_PROPERTIES networks/partition_test/NETWORK_PROPERTIES networks/powerlaw/NETWORK_PROPERTIES networks/primordial_chem/NETWORK_PROPERTIES networks/rprox/NETWORK_PROPERTIES networks/sn160/NETWORK_PROPERTIES networks/subch_approx/NETWORK_PROPERTIES networks/subch_full/NETWORK_PROPERTIES networks/subch_simple/NETWORK_PROPERTIES networks/triple_alpha_plus_cago/NETWORK_PROPERTIES networks/update_headers.py networks/vode_example/NETWORK_PROPERTIES commit 255c3999891084274428e4d63419649320b388c7 Author: Max Katz Date: Mon Aug 14 17:06:46 2023 -0700 Remove legacy screening interface (#1304) All networks using this legacy approach have now been converted to use the new interface that doesn't rely on the vector of screening factors. screening/Make.package screening/screen.H screening/screen_data.H screening/screen_data.cpp commit 7a08c7a490cfdfdc0f57d62789937884f2c0502a Author: Andy Nonaka Date: Mon Aug 14 11:36:46 2023 -0700 fix inputs file so this runs again (#1308) unit_test/burn_cell/inputs_ignition commit 783d1a020274f53b7bd6b92778af22f10f8b032c Author: Eric T. Johnson Date: Sat Aug 12 13:02:04 2023 -0400 Checkout the correct AMReX tag in Castro CI (#1306) .github/workflows/castro.yml commit 90cd09c5f983a311c9e153df663263cc602715a4 Author: Max Katz Date: Fri Aug 11 14:01:35 2023 -0400 Use development branch for Castro CI (#1305) .github/workflows/castro.yml commit b3d1571d8a906485b11e62be2930f960890c6d58 Author: Max Katz Date: Thu Aug 10 20:18:11 2023 -0400 Remove unneeded actual_rhs.H from new network scheme (#1290) integration/BackwardEuler/be_integrator.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/integrator_type_simplified_sdc.H integration/utils/initial_timestep.H networks/aprox13/Make.package networks/aprox13/actual_rhs.H networks/aprox19/Make.package networks/aprox19/actual_rhs.H networks/aprox21/Make.package networks/aprox21/actual_rhs.H networks/ignition_simple/Make.package networks/ignition_simple/actual_rhs.H networks/iso7/Make.package networks/iso7/actual_rhs.H networks/triple_alpha_plus_cago/Make.package networks/triple_alpha_plus_cago/actual_rhs.H nse_solver/nse_solver.H util/cj_detonation/main.cpp commit d32b1a076cd3a324f164d66792d5ccd8bf20df7d Author: Max Katz Date: Thu Aug 10 08:13:30 2023 -0400 Convert rprox to the new reactions scheme (#1300) There were errors in the analytic Jacobian for rprox related to the use of delta1 and delta2 for determining which reaction pathways we were taking. This means results will change; while the new Jacobian is more likely to be correct, it is still not successful for integrating test_react with integrator.jacobian = 1. interfaces/tfactors.H networks/rprox/Make.package networks/rprox/actual_network.H networks/rprox/actual_network_data.cpp networks/rprox/actual_rhs.H networks/rprox/rprox.net networks/rprox/rprox_rates.H networks/rprox/rprox_tfactors.H unit_test/test_rhs/ci-benchmarks/rprox.out commit 3d2714f8001a9203bf95d94f88c942a606c7e1f0 Author: Eric T. Johnson Date: Sun Aug 6 18:42:15 2023 -0400 Update CUDA compilation test to cover more cases (#1297) This adds CUDA coverage for both partition functions and self-consistent NSE. .github/workflows/cuda.yml commit effba81d241424a4497ef8ea882eb5836f894773 Author: Max Katz Date: Sun Aug 6 18:41:21 2023 -0400 Add has_G to check if G is in the EOS type (#1303) This fixes invocations of gamma_law with types other than eos_t. EOS/gamma_law/actual_eos.H EOS/primordial_chem/actual_eos.H interfaces/eos_type.H commit 2ebca1330f0f21de3fc1831745e65e638c99fdea Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Fri Aug 4 23:19:36 2023 +0200 Compute thermodynamic derivatives and implement dens+pres mode in primordial chem EOS (#1302) Add the eos_input_rp mode for primordial chem EOS. Also, compute the sound speed and stores it in state.cs if pressure is defined. EOS/gamma_law/actual_eos.H EOS/primordial_chem/actual_eos.H interfaces/eos_type.H commit 588beb9c1cb042861b54dce7e321ff10319e4921 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Thu Jul 27 00:55:18 2023 +0200 Compute pressure for primordial chem EOS (#1301) EOS/primordial_chem/actual_eos.H commit eb5189fa546da7b644850bb11d5639af0eb5f20d Author: Max Katz Date: Sun Jul 23 18:36:06 2023 -0400 Convert ignition_chamulak to new reactions scheme (#1296) networks/ignition_chamulak/Make.package networks/ignition_chamulak/actual_network.H networks/ignition_chamulak/actual_network_data.cpp networks/ignition_chamulak/actual_rhs.H networks/ignition_chamulak/actual_rhs_data.cpp unit_test/burn_cell/ci-benchmarks/chamulak_VODE_unit_test.out unit_test/test_rhs/ci-benchmarks/chamulak.out commit 765279677f8af09f97f04a78f8a7dcd4cd866bfa Author: Max Katz Date: Sun Jul 23 16:51:42 2023 -0400 Fix analytic Jacobian in ignition_chamulak (#1294) The conversion back to d/dY form was missing the multiplication by A for the d/dX terms. Also, the J(ash, net_ienuc) term was missing. networks/ignition_chamulak/actual_rhs.H unit_test/burn_cell/ci-benchmarks/chamulak_VODE_unit_test.out unit_test/test_rhs/ci-benchmarks/chamulak.out commit 9af506c9ec4ad4fc8842a28229f6d8639781706b Author: Max Katz Date: Sun Jul 23 13:57:28 2023 -0400 Switch to a simpler approx net for HIP CI (#1295) .github/workflows/hip.yml commit 28ceb480974b411f99c6f0f6340c678f5e0cc7e9 Author: Max Katz Date: Sun Jul 23 13:56:58 2023 -0400 Switch to a simpler pynucastro net for HIP CI (#1293) .github/workflows/hip.yml commit ea4204146eb2269605764e432a022cb1ae090398 Author: Max Katz Date: Sun Jul 23 10:38:25 2023 -0400 Convert rhs_t number of reactions from int to real (#1292) This supports conversion of ignition_chamulak to the new reactions scheme. It should also allow replacement of the branching ratio, at least in some cases, with a direct modification to the number of reactants consumed. interfaces/rhs_type.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/powerlaw/actual_network.H networks/triple_alpha_plus_cago/actual_network.H sphinx_docs/source/templated_networks.rst commit 0256f8db87314fb4ec2ddb71a27f97a21a0f77b0 Author: Max Katz Date: Sun Jul 23 09:07:56 2023 -0400 Add rhs_state to ener_gener_rate interface (#1291) This prepares for the conversion of ignition_chamulak, which determines the energy release based on the current density. 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/powerlaw/actual_network.H networks/rhs.H networks/triple_alpha_plus_cago/actual_network.H commit d995247d5e82244b457fca90c3dc3f3ba7d43482 Author: Max Katz Date: Sat Jul 22 16:17:37 2023 -0400 Convert powerlaw to new reactions scheme (#1289) this now also has an analytic Jacobian .github/workflows/good_defines.txt networks/Make.package networks/powerlaw/Make.package networks/powerlaw/_parameters networks/powerlaw/actual_network.H networks/powerlaw/actual_network_data.cpp networks/powerlaw/actual_rhs.H networks/powerlaw/actual_rhs_data.cpp networks/rhs.H unit_test/test_rhs/ci-benchmarks/powerlaw.out commit 5eea678e2e99eb1e1a64e26380a1f4a6568d5daf Author: Max Katz Date: Sat Jul 22 12:19:37 2023 -0400 Convert triple_alpha_plus_cago to new reactions scheme (#1265) This will change the rates for this network by about 1% due to a different implementation of the triple alpha and C12(a,g)O16 rates in this network compared to the aprox rates we use for the other networks. networks/triple_alpha_plus_cago/Make.package 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/burn_cell/ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out unit_test/test_rhs/ci-benchmarks/triple_alpha_plus_cago.out commit 28ef7e586be5c0bb3b1243b0a3d8514db167d855 Author: Eric T. Johnson Date: Sat Jul 22 12:18:27 2023 -0400 Fix remaining clang-tidy warnings (#1288) Along with #1287, this resolves all the remaining warnings I could find with burn_cell and test_rhs. EOS/helmholtz/actual_eos.H integration/VODE/actual_integrator.H interfaces/ArrayUtilities.H interfaces/burn_type.H interfaces/eos_type.H interfaces/rhs_type.H networks/aprox13/actual_network.H networks/aprox21/actual_network.H networks/iso7/actual_network.H networks/rhs.H nse_solver/nse_solver.H screening/screen_data.H unit_test/test_react/main.cpp unit_test/test_rhs/rhs_zones.H commit 9edc7c1ffd42d84fbe445053a881c76d133cef6f Author: Eric T. Johnson Date: Fri Jul 21 15:29:55 2023 -0400 Renumber the screening methods so null is at index 0 (#1286) Make.Microphysics_extern nse_solver/nse_solver.H screening/screen.H sphinx_docs/source/screening.rst commit 5a7415fe3c996b49fbd1c7a08c00407ebc45aba7 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Fri Jul 21 18:52:07 2023 +0200 Use amu instead of 1/n_A for m_nucleon in gamma_law (#1240) this will cause small diffs for any problem that uses the gamma law EOS EOS/gamma_law/actual_eos.H EOS/primordial_chem/actual_eos.H unit_test/eos_cell/ci-benchmarks/eos_gamma_law.out commit fb8107b1ecbdaad8b932978346fb1b43423c0a77 Author: Max Katz Date: Fri Jul 21 12:48:06 2023 -0400 Add CI coverage for ignition_chamulak (#1284) .github/workflows/burn_cell.yml .github/workflows/test_rhs.yml unit_test/burn_cell/ci-benchmarks/chamulak_VODE_unit_test.out unit_test/burn_cell/inputs_ignition_chamulak unit_test/test_rhs/ci-benchmarks/chamulak.out commit 030cddbb22d37ffaefdf584d9b0aca0c83458b1a Author: Max Katz Date: Fri Jul 21 10:26:38 2023 -0400 Add a constructor for rhs_t to simplify initialization (#1285) interfaces/rhs_type.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 commit 0ef8cc66245bfebda2197e377a86939d6a3f3d61 Author: Max Katz Date: Tue Jul 18 08:47:30 2023 -0400 Make mion and bion inline functions for aprox nets (#1267) The goal of this change is to remove the global data from actual_network_data.cpp, which in turn allows elimination of that file. Rather than an array, this can be handled with a constexpr function emulating the array. The new function is templated to allow compile-time evaluation of the binding energy. However, not all locations in Microphysics will be readily available to switch to a compile-time evaluation, so a "legacy" interface which accepts the species index at runtime is also provided. (This requires constexpr_for to be available in the network, so it is moved to a separate utility location.) interfaces/rhs_type.H networks/aprox13/Make.package networks/aprox13/actual_network.H networks/aprox13/actual_network_data.cpp networks/aprox19/Make.package networks/aprox19/actual_network.H networks/aprox19/actual_network_data.cpp networks/aprox21/Make.package networks/aprox21/actual_network.H networks/aprox21/actual_network_data.cpp networks/ignition_simple/Make.package networks/ignition_simple/actual_network.H networks/ignition_simple/actual_network_data.cpp networks/iso7/Make.package networks/iso7/actual_network.H networks/iso7/actual_network_data.cpp networks/rhs.H nse_tabular/nse_table.H commit d9e75f94e45ff2b4332a37aca08fda8fec9bce3f Author: Alexander Smith <72695548+aisclark91@users.noreply.github.com> Date: Tue Jul 18 07:56:06 2023 -0400 New Ci-Benchmark for the burn_cell test (#1277) This updates ECSN with the latest pynucastro, which changes the rate tables to be log10. Due to differences in the units conversion factors and the number of decimals between the existing tabular rates and the ones of the pynucastro PR #550, the existing benchmark will differ. 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/actual_network.H networks/ECSN/actual_network_data.cpp networks/ECSN/actual_rhs.H networks/ECSN/partition_functions.H networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out commit 40bb827a7147842a97b70cb9ccb502b7378f9d19 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jul 17 16:39:21 2023 -0400 abort earlier if T_in < T_nse_net (#1283) abort earlier if T_in < T_nse_net to avoid unnecessary computing. nse_solver/nse_check.H commit 6af7154420ef3aee199787763c4b6b6f30513a30 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jul 17 12:20:44 2023 -0400 decompose get_nse_state into two separate functions (#1276) Here I separated get_nse_state into two separate functions, one that calculates the exponent part of the nse mass fraction (depends on chemical potentials) and the other calculates components that do not depend on chemical potentials. This way we don't have to compute unnecessary parts when we solve for chemical potentials, mu_p and mu_n during hybrid solver, which includes getting the partition function. Heres the new profile, it brings down # of calls for get_partition_functions from 900,000,000+ (from pr1274) to 200,000,000+ nse_solver/_parameters nse_solver/nse_solver.H commit 3576210fffc54c9f7143597b395f7dc9512b3c21 Author: Michael Zingale Date: Mon Jul 17 10:18:11 2023 -0400 fix compilation of application codes that use the NSE table (#1282) these include Make.Microphysics_extern but not Make.Microphysics Make.Microphysics_extern commit 2e96530247667c2f7689cb3bd01d899f90db3204 Author: Max Katz Date: Mon Jul 17 07:54:41 2023 -0400 Move tabular NSE implementation to its own directory (#1281) this still only works with aprox19 Make.Microphysics Make.Microphysics_extern networks/aprox19/Make.package networks/aprox19/_parameters networks/aprox19/actual_network.H networks/aprox19/actual_network_data.cpp networks/aprox19/nse.tbl networks/aprox19/table_preprocess/rewrite.f90 nse_tabular/Make.package nse_tabular/_parameters nse_tabular/nse_table.H nse_tabular/nse_table_check.H nse_tabular/nse_table_data.H nse_tabular/nse_table_data.cpp unit_test/test_nse_interp/nse_cell.H commit 5fc8333487d19e82ba6929ec937f26dcd409036c Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Jul 16 18:03:31 2023 -0400 a simple temperature threshold for NSE_NET (#1278) add a simple temperature threshold for NSE_NET that is controlled by T_nse_net. nse_solver/_parameters nse_solver/nse_check.H sphinx_docs/source/nse.rst commit 2c425aa1aff6e38a2240ea8d64e6a72d7776edaa Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sun Jul 16 18:03:06 2023 -0400 remove init_nse_net (#1279) we used to have init_nse_net to compute rate_indices, but now we generate them directly. Therefore, it is really not needed anymore. interfaces/network_initialization.cpp 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/ignition_simple/actual_network.H networks/ignition_simple/actual_network_data.cpp networks/iso7/actual_network.H networks/iso7/actual_network_data.cpp nse_solver/nse_solver.H commit 83e3b6986c35c83e31a4f8f93c6e07df2f1f8628 Author: Max Katz Date: Sun Jul 16 18:02:46 2023 -0400 Add CI for test_nse_interp (#1280) .github/workflows/test_nse_interp.yml unit_test/test_nse_interp/ci-benchmarks/aprox19.out unit_test/test_nse_interp/nse_cell.H commit e5c0f75c95c9b0cb9ee858869fa848b8672d488a Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jul 12 15:57:45 2023 -0400 reorganize is_fastest_rate function for NSE_NET (#1274) Based on pr#1269. I reorganized is_fastest_rate function to make it more readable and renamed it to fill_merge_indices, since it is more descriptive and accurate of what the function does. It also gives a slight improvement in the time it takes for this function. nse_solver/nse_check.H nse_solver/nse_solver.H commit 9cf00883dab6c09cbd0e328a94352a3de7e470b9 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jul 12 15:26:21 2023 -0400 update ase network and add unit test (#1275) this adds a unit test for test_ase .github/workflows/nse_net.yml networks/ase/actual_network.H networks/ase/actual_network_data.cpp networks/ase/actual_rhs.H networks/ase/table_rates.H unit_test/test_ase/ci-benchmarks/ase_nse_net_unit_test.out commit a801f2d006aadf111b1aa001c2e99e493ef26aba Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jul 12 13:46:14 2023 -0400 template rate indices and corresponding changes for NSE_NET (#1269) Based on Pr#1231. Added rate indices for aprox networks and iso7 to be compatible updated pynucastro c++ network template. Delete unnecessary files that declare and initialize rate indices since now we do it directly via pynucastro, or hard coded it for aprox networks. 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/ignition_simple/actual_network.H networks/ignition_simple/actual_network_data.cpp networks/iso7/actual_network.H networks/iso7/actual_network_data.cpp nse_solver/Make.package nse_solver/nse_check.H nse_solver/nse_index.H nse_solver/nse_index.cpp nse_solver/nse_solver.H commit a74734006fc2fb63886bad6e1ee9ddfea1ce710c Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Jul 11 07:38:47 2023 -0400 typo fix (#1272) util/hybrj/hybrj_dogleg.H commit ffe836cf6a5f6ce67e522cfaba9d1ae1377ca294 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jul 10 14:24:09 2023 -0400 make self-consistent nse compatible with non-neutron networks. (#1231) Due to the missing neutron rates, it is difficult to group isotopes together into a single group. This pr mainly adds another logic of defining a single_group for non-neutron networks. If isotopes fail to form a single group and there is no neutron in the network, then use a second check where we consider nse if isotopes past Z=14(Si) that have odd N or even N form two distinct groups. Most of the line changes are code formatting. nse_solver/nse_check.H nse_solver/nse_solver.H sphinx_docs/source/nse.rst commit 04ff2a3e3578134387c2cf2bb740b6823e967f76 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Jul 10 13:31:54 2023 -0400 update adsurl for refs.bib (#1270) sphinx_docs/source/refs.bib commit 4bea489acd72ecdec9ae2a20d37e45a7fe6081da Author: Max Katz Date: Sat Jul 8 10:41:18 2023 -0400 Expand test_rhs CI coverage to more networks (#1268) .github/workflows/test_rhs.yml unit_test/test_rhs/ci-benchmarks/aprox13.out unit_test/test_rhs/ci-benchmarks/aprox19.out unit_test/test_rhs/ci-benchmarks/aprox21.out unit_test/test_rhs/ci-benchmarks/iso7.out unit_test/test_rhs/ci-benchmarks/powerlaw.out unit_test/test_rhs/ci-benchmarks/rprox.out unit_test/test_rhs/ci-benchmarks/triple_alpha_plus_cago.out commit c04000480d42541987c32fe200f24570f23c3dcd Author: Eric T. Johnson Date: Fri Jul 7 19:45:51 2023 -0400 Make operator<< work for any subclass of eos_base_t (#1266) interfaces/eos_type.H commit 39bd40b4ddf5c4677197169907dc41af5d335689 Author: Michael Zingale Date: Fri Jul 7 17:46:05 2023 -0400 update the docs regarding scale_system and use_circle_theorem (#1263) sphinx_docs/source/integrators.rst commit b0b5c193b79634bec86c382a3e93e4dd712ff60f Author: Michael Zingale Date: Fri Jul 7 17:45:15 2023 -0400 silence an unused var warning (#1262) EOS/helmholtz/actual_eos.H commit a1d3dac37021dc6b773814f34413a895ba040db0 Author: Max Katz Date: Fri Jul 7 02:31:38 2023 -0400 Remove rate_type.H from files that don't use rate_t (#1264) integration/QSS/actual_integrator.H networks/general_null/actual_rhs.H networks/ignition_chamulak/actual_rhs.H commit d5726e5b8e31295c949c23ab6ddc7c571a599eae Author: Max Katz Date: Thu Jul 6 14:45:00 2023 -0400 Migrate ignition_simple to the new network implementation (#1255) This change involves roundoff-level differences due to the different implementation of the RHS and Jacobian. networks/ignition_simple/Make.package networks/ignition_simple/actual_network.H networks/ignition_simple/actual_rhs.H networks/ignition_simple/actual_rhs_data.cpp unit_test/test_rhs/ci-benchmarks/ignition_simple.out commit 9e2e17b5b21e1da05d44ee6de834ee2a9b17b5e4 Author: Michael Zingale Date: Thu Jul 6 12:52:43 2023 -0400 fix a few clang compiler warnings (#1260) integration/RKC/rkc.H integration/utils/rkc_util.H unit_test/burn_cell_sdc/burn_cell.H commit bc626e8fa22f6a78d1b2ef513377abb1e06c2543 Author: Michael Zingale Date: Wed Jul 5 21:15:31 2023 -0400 for RKC, default to scale_system=1 and use_circle_theorem=1 (#1259) this overrides the integrator/ default for scale_system integration/RKC/_parameters unit_test/burn_cell/ci-benchmarks/aprox13_RKC_unit_test.out commit 6678fe9070a371460a83840e655c92c1903068a9 Author: Max Katz Date: Tue Jul 4 18:53:23 2023 -0400 Fix errors in the analytic Jacobian for ignition_simple (#1256) This PR also updates the CI benchmark for test_rhs since these three Jacobian elements have now changed. networks/ignition_simple/actual_rhs.H unit_test/test_rhs/ci-benchmarks/ignition_simple.out commit f7f62efb307215c04930828d91596a88e57ca05e Author: Michael Zingale Date: Tue Jul 4 16:25:23 2023 -0400 scale energy in simplified-SDC with scale_system = 1 (#1253) integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/RKC/actual_integrator_simplified_sdc.H integration/VODE/actual_integrator_simplified_sdc.H integration/integrator_rhs_simplified_sdc.H integration/integrator_type_simplified_sdc.H commit 3db0f96250d3f334b9aa5ec14e4a27ad7fce224e Author: Max Katz Date: Tue Jul 4 16:06:40 2023 -0400 Add CI coverage for test_rhs (#1257) .github/workflows/test_rhs.yml unit_test/test_rhs/ci-benchmarks/ignition_simple.out commit a3fffe8676078b3df76cae957bd090ec986c72c4 Author: Michael Zingale Date: Tue Jul 4 13:36:36 2023 -0400 store the error code returned by the integrator in burn_t (#1254) this will allow the application code to be more descriptive about failures integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H interfaces/burn_type.H commit 2059cd813b92c5e4bced3ac1fbbc2a4aeaf65ff8 Author: Max Katz Date: Mon Jul 3 08:34:18 2023 -0400 Add an integrator type to ForwardEuler (#1251) integration/ForwardEuler/Make.package integration/ForwardEuler/actual_integrator.H integration/ForwardEuler/fe_type.H commit cd2e4d02f19726d18b416be970a98e9753479089 Author: Max Katz Date: Sun Jul 2 19:14:52 2023 -0400 Add burn_cell CI coverage of ForwardEuler (#1252) .github/workflows/burn_cell.yml unit_test/burn_cell/ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out commit 310ffb90dcdf44d53b57c6ab49e4f9b739a49b35 Author: Michael Zingale Date: Sun Jul 2 12:06:34 2023 -0400 fix the thermodynamics in the RKC simplified-SDC (#1249) we come in with a valid e this syncs us up with VODE integration/RKC/actual_integrator_simplified_sdc.H commit 0e1775f26261309e8e5189e5c2d1ee6938125359 Author: Max Katz Date: Sun Jul 2 11:37:04 2023 -0400 Add parameters to the Strang clean state interface to match SDC (#1246) integration/integrator_rhs_strang.H integration/integrator_type_strang.H commit 6feb7868779bfcf3072890a39427eb632bcd5a8a Author: Michael Zingale Date: Sun Jul 2 11:27:12 2023 -0400 fix circle theorem compilation with simplified-SDC (#1248) integration/utils/circle_theorem.H commit 7af73b14e5c6fa9fdc754558d1d12c3798e55eff Author: Max Katz Date: Sun Jul 2 09:44:06 2023 -0400 Update cococubed website references (#1247) EOS/helmholtz/actual_eos.H sphinx_docs/source/transport.rst util/skynet/README.md commit d820e1ffcd752062277e224e1aa2518a307bb228 Author: Max Katz Date: Sat Jul 1 11:53:17 2023 -0400 Merge renormalize_species into clean_state (#1245) integration/integrator_type_simplified_sdc.H integration/integrator_type_strang.H commit 37551260a0c17a85dd6d08fc289a64c38dfa46a6 Author: Michael Zingale Date: Sat Jul 1 10:44:08 2023 -0400 update changes CHANGES.md commit a5ee71bbb8db2ee62d17efcffe659388af5cb614 Author: Michael Zingale Date: Thu Jun 29 21:10:43 2023 -0400 simplify some logic in the SDC integrators (#1243) basically, once we convert back from the integrator type to the burn_t, we should not have to use the integrator type any more. This will make it easier to merge these code paths in the future. integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/RKC/actual_integrator_simplified_sdc.H integration/VODE/actual_integrator_simplified_sdc.H commit 946f07927f063f36fbe16c2915d57c3b4a0b305c Author: Michael Zingale Date: Thu Jun 29 21:08:00 2023 -0400 update the interface for update_density_in_time (#1244) we don't need int_state integration/integrator_rhs_simplified_sdc.H integration/integrator_type.H integration/integrator_type_simplified_sdc.H commit c8f51187e55c341b33e7e49228217010ffb53780 Author: Max Katz Date: Thu Jun 29 10:49:30 2023 -0400 Start merging integrator_type (#1239) We start with the functions that don't conflict, and will follow up in future PRs with changes that harmonize the analogous functions and move them into integrator_type.H. integration/BackwardEuler/actual_integrator.H integration/ForwardEuler/actual_integrator.H integration/Make.package integration/QSS/actual_integrator.H integration/RKC/actual_integrator.H integration/VODE/actual_integrator.H integration/integrator_type.H integration/integrator_type_simplified_sdc.H integration/integrator_type_strang.H commit 716dc7f9e1bbd56aedc456275fd397aced53d136 Author: Max Katz Date: Sat Jun 24 15:18:31 2023 -0400 Remove simplified SDC ifdefs in burn_type (#1232) This is a first step in merging the integrator code paths for Strang and simplified SDC, as in #1200. For now these components will remain uninitialized and unused for Strang burns. interfaces/burn_type.H commit 25258a9d5624619f8cd3c78551abcd069a11ca65 Author: Michael Zingale Date: Fri Jun 23 21:14:39 2023 -0400 standardize integrator error codes (#1234) this will allow us to more easily template the actual_integrator routines integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/BackwardEuler/be_integrator.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc_type.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvode.H integration/VODE/vode_dvstep.H integration/VODE/vode_type.H integration/integrator_data.H commit a39c4ed5f88e26714579ec32b3a49a9e2663939e Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Fri Jun 23 03:41:03 2023 +0200 Remove eos_composition.H from primordial chem EOS (#1238) EOS/primordial_chem/eos_composition.H commit 70e08b65e5eeac8f8ceb89f548ca8acfdc8b4407 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Wed Jun 21 15:29:32 2023 +0200 Restructure CMakeLists to allow two EOS (#1237) Restructured the CMakeLists.txt file to allow building either gamma_law or primordial_chem EOS. With this change, we can now build different problems in Quokka with different EOSes. CMakeLists.txt commit de50574943b53fb9019f4b5c59074dc2747b7e9c Author: Max Katz Date: Mon Jun 19 12:30:34 2023 -0400 Replace EXTRA_THERMO with augmented eos_t (#1229) The preprocessor variable EXTRA_THERMO is removed. Use cases that depend on dpdA/dpdZ or dedA/dedZ should use eos_extra_t, which is a container that holds all of the entities in eos_t as well as these derivatives wrt A and Z. .github/workflows/good_defines.txt CHANGES.md EOS/eos_composition.H EOS/gamma_law/actual_eos.H EOS/helmholtz/actual_eos.H EOS/multigamma/actual_eos.H EOS/multigamma/eos_composition.H EOS/polytrope/actual_eos.H EOS/primordial_chem/eos_composition.H EOS/ztwd/actual_eos.H Make.Microphysics_extern integration/integrator_rhs_simplified_sdc.H integration/utils/numerical_jacobian.H interfaces/burn_type.H interfaces/eos_type.H unit_test/burn_cell_sdc/GNUmakefile unit_test/burn_cell_sdc/burn_cell.H unit_test/test_aprox_rates/GNUmakefile unit_test/test_aprox_rates/aprox_rates_util.cpp unit_test/test_conductivity/GNUmakefile unit_test/test_conductivity/conductivity_util.cpp unit_test/test_eos/GNUmakefile unit_test/test_eos/eos_util.cpp unit_test/test_jac/GNUmakefile unit_test/test_jac/jac_zones.H unit_test/test_screening/GNUmakefile unit_test/test_sdc/GNUmakefile unit_test/test_sdc/main.cpp unit_test/test_sdc/react_zones.H unit_test/test_sdc_vode_rhs/GNUmakefile unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit 89b3f840eafdb0f773e942c6d63b903264e581c0 Author: Michael Zingale Date: Mon Jun 19 11:22:44 2023 -0400 estimate the spectral radius via the Gershgorin circle theorem (#1222) integration/RKC/_parameters integration/RKC/rkc.H integration/utils/Make.package integration/utils/circle_theorem.H commit 3ec57b383412d84aca66556e5846d1286917e3df Author: Michael Zingale Date: Mon Jun 19 11:10:34 2023 -0400 add an action that builds Castro (#1230) this will build both a Strang and simplified-SDC problem .github/workflows/castro.yml .github/workflows/cuda.yml .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_ccache.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/hip.yml commit 1dd6fa6947994a408eb8be78c14750782516adc5 Author: Max Katz Date: Sun Jun 18 20:00:22 2023 -0400 Template remaining integrators on number of equations (#1228) integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/QSS/actual_integrator.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H commit 025e4e64014f0b24827df3281160b53f2c66ad2d Author: Michael Zingale Date: Sun Jun 18 15:31:15 2023 -0400 add the ability to scale energy in the integration (#1224) If we run with integrator.scale_system=1, then the internal energy that the ODE integrator works with is scaled by the initial internal energy. This makes all of the ODE variables O(1) and dimensionless. Right now this is for Strang only, and does not work with QSS or ForwardEuler. integration/BackwardEuler/actual_integrator.H integration/RKC/actual_integrator.H integration/VODE/actual_integrator.H integration/_parameters integration/integrator_rhs_strang.H integration/integrator_type_strang.H integration/utils/nonaka_plot.H integration/utils/numerical_jacobian.H interfaces/burn_type.H sphinx_docs/source/integrators.rst commit 017f02087a1c1479d72ff5c1f6a68e0498dfc01e Author: Michael Zingale Date: Sun Jun 18 15:30:48 2023 -0400 add more readable error codes for RKC (#1226) integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H commit 7d1f4ad521a7638d0b5e4a8ac609ac3634050eed Author: Max Katz Date: Sun Jun 18 15:18:40 2023 -0400 Update numerical Jacobian for recent templating changes (#1227) integration/utils/numerical_jacobian.H commit a099206c5150808fef5346e5c8ebb571d826e202 Author: Max Katz Date: Sun Jun 18 12:33:38 2023 -0400 Template VODE on number of integrator equations (#1223) With this change, the number of equations integrated by VODE is now counted from the components of the burn_t, rather than being hardcoded at compile time (at least for Strang; SDC will be handled in a future change). This sets up a possible future change where different burn state objects are passed to the integrator at different times. The motivating use case is Quokka's desire to integrate (xn, e) at some times and (e_gas, e_radiation) at other times. A future change could support the integration of an object other than burn_t, particularly an object that does not have xn but has (multigroup) radiation energy, as long as the integration tolerances (and any other auxiliary information) are made consistent. integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H 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_type.H integration/integrator_data.H commit ca12e803559cca4700148f428fe8e4bbb946ede5 Author: Michael Zingale Date: Sun Jun 18 12:33:05 2023 -0400 update the numerical Jacobian to support disabling e and boosting (#1225) remove this from BackwardEuler, since now it is handled for us integration/BackwardEuler/be_integrator.H integration/utils/numerical_jacobian.H commit 274e378beec153b176fce3980747928f7de2f2ee Author: Michael Zingale Date: Sat Jun 17 19:12:58 2023 -0400 move rkc_util.H into integrator/utils (#1221) this can then be used by other integrators more easily integration/RKC/Make.package integration/RKC/rkc.H integration/utils/Make.package integration/utils/rkc_util.H commit b2aee1c3cb28b7975e583c65cf0ab91b7095fb0d Author: Michael Zingale Date: Sat Jun 17 18:50:13 2023 -0400 abort in burn_cell if we have an integration failure (#1220) since we do many substeps by default, we can sometimes miss a failure in an early step .github/workflows/burn_cell.yml unit_test/burn_cell/burn_cell.H unit_test/burn_cell/ci-benchmarks/aprox13_RKC_unit_test.out commit e429fdaa359dfa323bd029bec81c5e807c25222c Author: Max Katz Date: Sat Jun 17 13:27:37 2023 -0400 Add a chem_eos_t that has the minimal quantities for Quokka (#1199) EOS/gamma_law/actual_eos.H interfaces/eos.H interfaces/eos_type.H commit 90ccabc3d7dc9dbe405032b6e83136339037af2f Author: Max Katz Date: Sat Jun 17 12:36:07 2023 -0400 Replace VODE_NEQS with INT_NEQS (#1219) 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_dvstep.H integration/VODE/vode_type.H commit b329c00ed35857efc34be4eecc28b39ab20b667d Author: Michael Zingale Date: Sat Jun 17 11:52:03 2023 -0400 rename rkc_t tend -> tout to sync with other integrators (#1218) integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H integration/RKC/rkc_util.H commit 48f54771f130f55c35593b32b282a414163b39cc Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Sat Jun 17 03:35:23 2023 +0200 do not need to create microphysics as a library (#1217) We do not need to create Microphysics as a library while compiling it with CMake. This became redundant after we modified CMakeLists to just build the primordial chem target directly. This will help build Microphysics on Setonix (for Quokka). Fixes #1185. CMakeLists.txt unit_test/burn_cell_primordial_chem/CMakeLists.txt commit a0d8db09414dad2e587800fd96bd4e153c0627b6 Author: Eric T. Johnson Date: Wed Jun 14 19:19:18 2023 -0400 Fix ccache misses due to generated files (#1216) Sort the runtime parameter namespaces in extern_parameters.H and extern_parameters.cpp. util/build_scripts/write_probin.py commit cfd8eaa18814be8d56a1b85bde03355e64cf33d9 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Jun 13 12:14:45 2023 +0200 Compare primordial chem CI output to reference solution (#1214) In addition to building the primordial chem unit test, we also want to make sure that the comparison to reference solution passes. The way we test this as follows: we compare a select number of lines from the test output to the stored output. These lines describe the final temperature, internal energy, density, and number densities of electrons, H, H2 and He. If the ratio of the test values to the reference values is larger than 2, the CI will return an exit code 1 and fail the github action. .github/workflows/burn_cell_primordial_chem.yml .github/workflows/macos_build_cell_primordial_chem.yml unit_test/burn_cell_primordial_chem/reference_solution.out commit 8c5b63da04424fb75978f7f1d1352d0e61783e46 Author: Max Katz Date: Mon Jun 12 10:01:34 2023 -0400 Silence unused variable warning (#1213) EOS/gamma_law/actual_eos.H commit b821efbf9845d139f80a1ffb3cb0cbd484d7513f Author: Michael Zingale Date: Mon Jun 12 10:00:09 2023 -0400 some cleaning of RKC (#1211) this moves the spectra radius and timestep functions into their own header. integration/RKC/Make.package integration/RKC/rkc.H integration/RKC/rkc_type.H integration/RKC/rkc_util.H commit 3b44dee2c2d86ea87c2be96642f4443c7b203e01 Author: Michael Zingale Date: Fri Jun 9 19:37:23 2023 -0400 have BackwardEuler and RKC just use INT_NEQS directly (#1209) there's no reason for them to define their own name. Also fix up some comments integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H commit c66615e87cb8506c7d74449f53e3038ae00000cd Author: Michael Zingale Date: Fri Jun 9 12:43:55 2023 -0400 add an RKC CI test (#1210) this adds a burn_cell test using the RKC integrator .github/workflows/burn_cell.yml unit_test/burn_cell/ci-benchmarks/aprox13_RKC_unit_test.out commit c129742345cb57a4021feafc2f55705c69d60d6c Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Jun 8 11:36:02 2023 -0400 update and simplify ase network. (#1206) networks/ase/_parameters networks/ase/actual_network.H networks/ase/actual_rhs.H networks/ase/ase.png networks/ase/ase.py networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ase/subch_simple.png commit 4ad49d9a703ec96d9c1f18f79849f0eebfcc4c28 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jun 7 18:48:00 2023 -0400 update nse codes (#1205) update nse codes and unit tests due to recent changes to pynucastro and microphysics. nse_solver/nse_check.H nse_solver/nse_solver.H unit_test/test_ase/burn_cell.H unit_test/test_ase/make_table/burn_cell.H commit 013a53f37b3c7cbf62dcac354ca515ced793140d Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jun 7 18:32:48 2023 -0400 simplified-sdc self-consistent nse compatibility (#1201) add simplified-sdc compatibility to self-consistent nse nse_solver/nse_check.H nse_solver/nse_solver.H commit f729a255b7c0cec5ca9d40c4bf370a482d672756 Author: Michael Zingale Date: Wed Jun 7 13:01:24 2023 -0400 template out the initial timestep estimation function (#1208) now it can be used by other integrators integration/BackwardEuler/be_integrator.H integration/utils/Make.package integration/utils/initial_timestep.H commit 775efe11a637eb1fc842591edfd061a38756c39d Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Jun 6 15:19:56 2023 +0200 Corrected argument spelling (#1207) CMakeLists.txt commit 5a590bf9a50f21e001d21b185c2624d30b6da146 Author: Michael Zingale Date: Tue Jun 6 08:36:50 2023 -0400 remove SDC_EVOLVE_ENTHALPY (#1204) this was not tested an has not kept pace with the latest work on SDC. Furthermore, the MAESTROeX SDC implementation is not being used. .github/workflows/good_defines.txt integration/RKC/actual_integrator_simplified_sdc.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvstep.H integration/integrator_type_simplified_sdc.H interfaces/burn_type.H unit_test/burn_cell_sdc/GNUmakefile unit_test/burn_cell_sdc/burn_cell.H unit_test/test_sdc/GNUmakefile unit_test/test_sdc/react_zones.H unit_test/test_sdc_vode_rhs/GNUmakefile unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit 726fe1e26094e018f2d11e53a5d22f0cfd0d0668 Author: Max Katz Date: Sat Jun 3 09:55:32 2023 -0400 Template integrator interfaces on burn_t (#1202) integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/BackwardEuler/be_integrator.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvhin.H integration/VODE/vode_dvjac.H integration/VODE/vode_dvnlsd.H integration/VODE/vode_dvode.H integration/VODE/vode_dvstep.H integration/integrator.H integration/integrator_rhs_simplified_sdc.H integration/integrator_rhs_strang.H integration/integrator_type_simplified_sdc.H integration/integrator_type_strang.H integration/nse_update_simplified_sdc.H integration/nse_update_strang.H integration/utils/jacobian_utilities.H integration/utils/nonaka_plot.H integration/utils/numerical_jacobian.H interfaces/burn_type.H interfaces/burner.H commit edce3571a71fc2a88af8bcc63df0e1e69fb81550 Author: Michael Zingale Date: Fri Jun 2 15:16:20 2023 -0400 implement the NSE+SDC update for the self-consistent / network NSE (#1188) integration/nse_update_simplified_sdc.H commit bcf06921ae6144e0f1d24ceb8181af43357e9f84 Author: Michael Zingale Date: Thu Jun 1 08:00:11 2023 -0400 update for 23.06 CHANGES.md commit 2652c955c331331107966eb1aee18c145bf964cd Author: Michael Zingale Date: Wed May 31 17:18:20 2023 -0400 add a Runge-Kutta-Chebyshev (RKC) integrator (#1191) This is a port of the integrator from Sommeijer et al. 1997. It is fully explicit, so no Jacobian is needed, but it does need an estimate of the spectral radius, which is computed internally. This seems to work for moderate temperatures (T < 2.e9 K) for example with XRBs. integration/RKC/Make.package integration/RKC/README.md integration/RKC/_parameters integration/RKC/actual_integrator.H integration/RKC/actual_integrator_simplified_sdc.H integration/RKC/rkc.H integration/RKC/rkc_type.H sphinx_docs/source/integrators.rst sphinx_docs/source/refs.bib commit f5b7933ec4fe3b1d1081c1a1e29ee7bf2cd67719 Author: Michael Zingale Date: Tue May 30 20:34:20 2023 -0400 vode_parameters does not exist (#1193) remove it from Make.package integration/VODE/Make.package commit bf80346094d2424703ee008e5f03f5016fb98584 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Sat May 27 02:08:12 2023 +0200 Use redshift as a runtime parameter in primordial chem (#1198) We have to assume a certain redshift for doing Pop III simulations with primordial chemistry. We use z = 30, but it is also common to use a value between z = 20-30. With this PR, the user can define the redshift they want as a runtime parameter. networks/primordial_chem/_parameters networks/primordial_chem/actual_rhs.H unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_primordial_chem/inputs_primordial_chem commit 1f8fd85f441ea6e0f6fbd36e0b7f5bbbe81d0d6f Author: Ben Wibking Date: Tue May 23 07:27:17 2023 +1000 update primordial chemistry CI (#1195) This runs the unit test for the primordial_chem network, rather than just building it. We also add a (Linux) CMake build and a macOS+CMake build and run the unit test for those builds. .github/workflows/burn_cell_primordial_chem.yml .github/workflows/cmake_build_cell_primordial_chem.yml .github/workflows/macos_build_cell_primordial_chem.yml commit cc889d2c98e2045bf4d4839f2a90c8ed77a9a145 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Mon May 22 21:35:38 2023 +0200 using namespaces in CMake (#1196) CMakeLists.txt commit 10fb84d2965b06956123b00a7da8a99b289463a7 Author: Michael Zingale Date: Fri May 19 13:41:55 2023 -0400 enforce namespaces for the runtime parameters (#1056) EOS/breakout/actual_eos.H EOS/gamma_law/actual_eos.H EOS/helmholtz/actual_eos.H EOS/multigamma/actual_eos.H EOS/polytrope/actual_eos.H EOS/primordial_chem/actual_eos.H EOS/rad_power_law/actual_eos.H EOS/tillotson/actual_eos.H Make.Microphysics conductivity/constant/actual_conductivity.H conductivity/constant_opacity/actual_conductivity.H conductivity/powerlaw/actual_conductivity.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/integrator_rhs_strang.H integration/integrator_type_simplified_sdc.H integration/integrator_type_strang.H integration/utils/jacobian_utilities.H integration/utils/nonaka_plot.H integration/utils/numerical_jacobian.H interfaces/burn_type.H networks/ECSN/actual_rhs.H networks/aprox13/actual_network.H networks/aprox19/actual_network.H networks/aprox19/nse_table.H networks/aprox21/actual_network.H networks/general_null/actual_rhs.H networks/ignition_chamulak/actual_rhs.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_simple/actual_rhs.H networks/nova/actual_rhs.H networks/nova2/actual_rhs.H networks/partition_test/actual_rhs.H networks/powerlaw/actual_rhs.H networks/primordial_chem/actual_rhs.H networks/rprox/actual_rhs.H networks/sn160/actual_rhs.H networks/subch_approx/actual_rhs.H networks/subch_full/actual_rhs.H networks/subch_simple/actual_rhs.H networks/triple_alpha_plus_cago/actual_rhs.H networks/vode_example/actual_rhs.H nse_solver/make_table/burn_cell.H nse_solver/nse_solver.H opacity/rad_power_law/actual_opacity.H rates/aprox_rates.H screening/screen.H unit_test/burn_cell/burn_cell.H unit_test/burn_cell/main.cpp unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_primordial_chem/main.cpp unit_test/burn_cell_sdc/burn_cell.H unit_test/burn_cell_sdc/main.cpp unit_test/eos_cell/eos_cell.H unit_test/eos_cell/main.cpp unit_test/react_util.H unit_test/test_aprox_rates/aprox_rates_util.cpp unit_test/test_aprox_rates/main.cpp unit_test/test_conductivity/conductivity_util.cpp unit_test/test_conductivity/main.cpp unit_test/test_eos/eos_util.cpp unit_test/test_eos/main.cpp unit_test/test_nse/nse_example.H unit_test/test_part_func/pf_cell.H unit_test/test_react/react_zones.H unit_test/test_rhs/rhs_zones.H unit_test/test_screening/main.cpp unit_test/test_screening/screening_util.cpp unit_test/test_sdc/react_zones.H unit_test/test_sdc_vode_rhs/vode_rhs_test.H util/build_scripts/runtime_parameters.py util/build_scripts/write_probin.py util/cj_detonation/main.cpp commit cd53da1ea72733a2f2da970cdd671f5d0c29ee75 Author: Eric T. Johnson Date: Thu May 18 20:01:05 2023 -0400 Exclude AMReX sources when running clang-tidy (#1190) Make.Microphysics commit b9656434c677051c537b0be55fe2fc34d30bb832 Author: Michael Zingale Date: Thu May 18 20:00:37 2023 -0400 update comments that refer to Castro or gamma_law_general (#1189) EOS/README.md nse_solver/make_table/GNUmakefile unit_test/burn_cell/GNUmakefile unit_test/burn_cell_primordial_chem/GNUmakefile unit_test/burn_cell_sdc/GNUmakefile unit_test/eos_cell/GNUmakefile unit_test/test_aprox_rates/GNUmakefile unit_test/test_ase/GNUmakefile unit_test/test_ase/make_table/GNUmakefile unit_test/test_conductivity/GNUmakefile unit_test/test_eos/GNUmakefile unit_test/test_jac/GNUmakefile unit_test/test_nse/GNUmakefile unit_test/test_nse_interp/GNUmakefile unit_test/test_part_func/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 util/hybrj/test/GNUmakefile commit 600b619db6b9782d2f7ff354d75791d843b42842 Author: Michael Zingale Date: Tue May 16 13:51:57 2023 -0400 modify the SDC+NSE update to not include the advective part in enuc (#1092) This removes the advection component from rho (B/A) and computes the energy update as: [rho (B/A)]^{n+1} - [rho (B/A)]^n integration/nse_update_simplified_sdc.H interfaces/burn_type.H interfaces/burner.H commit 92832268bcca4f8b0f459b57d26611a802d5f24f Author: Ben Wibking Date: Wed May 17 01:31:45 2023 +1000 cmake: compile with warnings as errors (#1187) This sets the CMake build to also compile treating warning as errors. CMakeLists.txt EOS/primordial_chem/actual_eos.H networks/primordial_chem/actual_rhs.H commit 7f2a04bb6850b1084cf18cba52bff1f880649c1b Author: Michael Zingale Date: Tue May 16 11:31:18 2023 -0400 add a compiler warning action (#1186) this is based on Castro and will fail if we generate warnings .github/workflows/compiler-warnings.yml EOS/helmholtz/actual_eos.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H networks/subch_simple/actual_rhs.H unit_test/burn_cell/burn_cell.H commit 0685d31f9951099f74fcd8654dc9b9dbc95bad51 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue May 9 20:52:24 2023 +0200 Store mean molecular weight in primordial chem test (#1181) Added a line to store the mean molecular weight in the burn_t object state, so that it is accessible as a part of this object when it is called by external codes. EOS/primordial_chem/actual_eos.H commit 3a9cad19fc625ad80f68268b03c9d2c6e211e2c2 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Sun May 7 18:25:42 2023 +0200 Fully optimized primordial chem RHS (#1180) Optimized the remaining bit (ydots) in primordial chem RHS using sympy's CSE. This further reduces the file size from 241 to 213 kB, and reduces compilation time and memory required to build and run primordial chem. networks/primordial_chem/actual_rhs.H commit afec4c3801e68980b39206f32ce1177967a56c9f Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri May 5 12:51:55 2023 -0400 fix cuda compile error with nse_net (#1178) this refactors hybrj to no longer take the function and Jacobian as argument nse_solver/nse_index.H nse_solver/nse_index.cpp nse_solver/nse_solver.H util/hybrj/hybrj.H util/hybrj/hybrj_dogleg.H util/hybrj/hybrj_enorm.H util/hybrj/hybrj_qform.H util/hybrj/hybrj_qrfac.H util/hybrj/hybrj_r1mpyq.H util/hybrj/hybrj_r1updt.H util/hybrj/test/main.cpp util/hybrj/test/test_func.H util/microphysics_sort.H commit 513c26b507f45df9e7df7930300fcd0c0c6d3089 Author: Michael Zingale Date: Fri May 5 12:16:30 2023 -0400 add primordial chem back into the CI (#1179) now that it is optimized, it no longer times out .github/workflows/burn_cell_primordial_chem.yml .github/workflows/find_changed_files.py commit ac4fffe4824dd7712703e029bb293c1ed9c5bbc6 Author: Michael Zingale Date: Sun Apr 30 18:31:20 2023 -0400 remove abort_on_failure (#1174) it is now the responsibility of the application code to check the success flag in burn_t. This is because we were not aborting when on GPUs, so it is better if the application code makes these decisions. CHANGES.md integration/_parameters integration/integrator.H interfaces/burner.H sphinx_docs/source/integrators.rst commit 6d199a7e17f015c978f8200587d3f35465064caa Author: Michael Zingale Date: Sun Apr 30 18:25:46 2023 -0400 add an abort to test_sdc if some integrations fail (#1177) also abort for CPU or GPU, since the abort is outside of the GPU kernel unit_test/test_react/main.cpp unit_test/test_sdc/main.cpp commit cb0a9fc3ff1a316381080fe92b86572629cc0e30 Author: Michael Zingale Date: Sat Apr 29 14:33:51 2023 -0400 add codespell CI (#1176) .codespell-ignore-words .codespellrc .github/workflows/codespell.yml CHANGES.md EOS/helmholtz/actual_eos.H integration/VODE/actual_integrator.H integration/VODE/vode_type.H integration/integrator_rhs_strang.H integration/nse_update_strang.H interfaces/burn_type.H networks/aprox19/README.md networks/general_null/breakout.net networks/general_null/gammalaw_aux.net networks/general_null/network_param_file.py networks/rprox/README.md neutrinos/sneut5.H nse_solver/nse_check.H screening/screen.H sphinx_docs/source/integrators.rst unit_test/burn_cell_primordial_chem/README.md unit_test/burn_cell_sdc/parse_integration_failure.py unit_test/test_ase/make_table/README.md unit_test/test_conductivity/main.cpp unit_test/test_eos/main.cpp unit_test/test_jac/main.cpp unit_test/test_react/main.cpp unit_test/test_react/test_network_combinations.py unit_test/test_rhs/main.cpp unit_test/test_screening/main.cpp unit_test/test_sdc/main.cpp util/build_scripts/write_probin.py util/esum.H util/esum_cxx.py util/skynet/README.md commit 5cd303adca91cf1a4410b6be9a4b42a7e6304d94 Author: Michael Zingale Date: Sat Apr 29 13:40:57 2023 -0400 spellcheck the codes with codespell (#1175) sphinx_docs/source/basics.rst sphinx_docs/source/data_structures.rst sphinx_docs/source/eos.rst sphinx_docs/source/integrators.rst sphinx_docs/source/networks.rst sphinx_docs/source/nse.rst sphinx_docs/source/preface.rst sphinx_docs/source/rp_intro.rst sphinx_docs/source/sdc.rst sphinx_docs/source/templated_networks.rst sphinx_docs/source/unit_tests.rst commit fc4258c6707a12d2bca0785a59ee276506f9f9c5 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Wed Apr 26 23:15:26 2023 +0200 Simplified PrimordialChem RHS network file (#1172) This PR simplifies the RHS file for primordial chemistry by a significant amount, by using sympy's CSE (common subexpression elimination) process to simplify expressions for all the jacobians and d Temperature /dt. The file size has reduced from 9.8 MB to 241 kB (6k lines of code compared to 30k earlier), with a factor of 11 speed-up in compilation. This change is proving pivotal to compiling Quokka on GPUs without memory exhaustion errors. Tests run successfully as before. PR ready for review. networks/primordial_chem/actual_rhs.H commit 55ce5a0f38ae586a34b3f741d337f6a51c83d465 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Mon Apr 24 14:07:21 2023 +0200 Added WORKING_DIRECTORY for CMake execute_process scripts (#1171) This PR specifies the WORKING_DIRECTORY for execute_process commands invoked in root CMakeLists.txt. It is not necessarily the case that current directory = CMAKE_BINARY_DIR, so explicitly specifying the working directory is important. CMakeLists.txt commit abda4ae34158799773cc909deca8f8f25fd97563 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Apr 11 01:51:28 2023 +0200 Optimized CMakeLists (#1170) Optimized CMakeLists and made them simpler. This optimization was also necessary to correctly define the scope of microphysics variables and compiler definitions when being used as an external submodule. CMakeLists.txt unit_test/CMakeLists.txt commit dc41ef4e8b40987fd273b4b385c080d56ea27986 Author: Michael Zingale Date: Tue Apr 4 14:34:30 2023 -0400 use our .clang-tidy when building with AMReX (#1161) .clang-tidy EOS/helmholtz/actual_eos.H Make.Microphysics interfaces/ArrayUtilities.H interfaces/burn_type.H neutrinos/sneut5.H unit_test/burn_cell/burn_cell.H unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_sdc/burn_cell.H commit 1e757a57ab323af11fd328a06eb9977b99e92074 Author: Michael Zingale Date: Tue Apr 4 13:14:35 2023 -0400 ubuntu-18.04 is deprecated and the build fails (#1168) update to ubuntu-latest .github/workflows/gh-pages.yml commit 334c126ff23e64b34860f00eb7858e842dcdad09 Author: Michael Zingale Date: Tue Apr 4 08:10:09 2023 -0400 add linkcheck to the docs action (#1167) .github/workflows/docs-test.yml sphinx_docs/source/conf.py sphinx_docs/source/refs.bib commit 9c2b98d50301822457c32ef17a1c58648828dc3e Author: Michael Zingale Date: Sat Apr 1 09:28:11 2023 -0400 update changes CHANGES.md commit a453d3a5c1733880c5b594ca9ef2095846c4bfa7 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Fri Mar 31 16:35:58 2023 +0200 CMake - clubbing all include directories into one variable (#1166) this CMake PR adds a cosmetic change to CMakeLists that is necessary when including Microphysics as a submodule in an external code. I clubbed all the include directories into one variable and defined it in the parent scope. CMakeLists.txt unit_test/CMakeLists.txt commit 6e65f17aa6d3ad437bc30142893d5490ce2da58e Author: Eric T. Johnson Date: Thu Mar 30 23:47:03 2023 -0400 Make sure generated code is identical between make runs and fix CI failure (#1165) This fixes cache misses when using ccache and a race condition that was causing intermittent CI failures Make.Microphysics util/build_scripts/write_probin.py commit 27bca0437d07db2d424033fed06279871bbcd6c6 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Mar 28 15:07:04 2023 +0200 Added flags and updated file paths for building primordial chem test with cmake (#1164) This PR is related to the cmake functionality for the primordial chem test in Microphysics. It updates the path to Microphysics files in CMakeLists such that they can be found when Microphysics is used as a submodule in another code. It also adds a couple of flags in CMakeLists that the user can specify if they want to build the primordial chem test with amrex. CMakeLists.txt unit_test/CMakeLists.txt unit_test/burn_cell_primordial_chem/CMakeLists.txt commit 7c3de88f47373d25fe667cbd95a4aaced81ee1ae Author: Michael Zingale Date: Mon Mar 27 19:18:21 2023 -0400 abort if we fail to open the NSE table (#1162) networks/aprox19/nse_table.H commit fc700fa2a1b08f90c0d186456a0340d4a8c20304 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Fri Mar 24 16:32:48 2023 +0100 Attempting to add cmake functionality to microphysics (#1151) adds three CMakeLists.txt files - one in root, one in root/unit_test, and another one in root/unit_test/burn_cell_primordial_chem. CMakeLists.txt unit_test/CMakeLists.txt unit_test/burn_cell_primordial_chem/CMakeLists.txt commit 47547e7e222d03886edae3d73659fba0b9e51535 Author: Michael Zingale Date: Tue Mar 21 12:25:32 2023 -0400 add code of conduct (#1152) code_of_conduct.md commit d6c98ffe2af4c0315a2800d3c0f9427d6b876e2d Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Mar 20 16:03:09 2023 -0400 add sphinx_rtd_theme to extensions (#1160) sphinx_docs/source/conf.py commit 87518821d7d11bd6190564ac8dc13051a366ff31 Author: Michael Zingale Date: Fri Mar 17 19:50:07 2023 -0400 allow us to optionally skip interpolating X from the NSE table (#1158) this can be expensive and unnecessary when we are iterating networks/aprox19/nse_table.H commit 49f8ea1ee3b17f54f6e9313ed382b3d26afe5021 Author: Michael Zingale Date: Thu Mar 16 18:12:42 2023 -0400 pass tf_t as const reference to aprox rates (#1156) rates/aprox_rates.H commit a063c7c97d832c5ec9e83de7842f23570e0e4c61 Author: Michael Zingale Date: Thu Mar 16 18:10:51 2023 -0400 address some more compiler issues (#1153) this also changes the job_info test to test on an empty string with string.empty() integration/VODE/vode_dvode.H integration/VODE/vode_dvstep.H nse_solver/nse_index.H util/build_scripts/runtime_parameters.py util/microphysics_math.H commit f8fb1850a7ec93def935d2576fd6e9fec1c90784 Author: Michael Zingale Date: Thu Mar 16 12:41:21 2023 -0400 split nse_update.H into Strang and Simplified-SDC versions (#1155) this makes it more readable integration/Make.package integration/nse_update_simplified_sdc.H integration/nse_update_strang.H interfaces/burner.H commit 541aa4c718c6c4a7afd7e9516e89a314ae2b2931 Author: Michael Zingale Date: Thu Mar 16 07:43:54 2023 -0400 table_type.H is no longer a pynucastro file (#1154) networks/ECSN/table_type.H networks/ignition_reaclib/C-burn-simple/table_type.H networks/ignition_reaclib/URCA-simple/table_type.H networks/nova/table_type.H networks/nova2/table_type.H networks/sn160/table_type.H networks/subch_approx/table_type.H networks/subch_full/table_type.H networks/subch_simple/table_type.H commit a480b6a9d68d06de405d4019aad2ef80de7bfacf Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Mar 14 09:29:07 2023 -0400 nse_table compatibility (#1147) make burn_t nse status for NSE in general. interfaces/burn_type.H networks/aprox19/nse_table_check.H commit 1f07dde0ed5a47c196bcb984d13e983900e5cd4b Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Mar 8 18:02:42 2023 -0500 store chemical potentials to nse_state (#1149) also store chemical potentials so get_nse_state() returns all information needed for nse calculations. nse_solver/nse_solver.H commit 3e4cd8658d3528cf632ec8ec2fb351c3de7d5001 Merge: 7cc2e5f3 d6f3ab67 Author: Michael Zingale Date: Wed Mar 8 09:30:26 2023 -0500 Merge branch 'main' into development commit 7cc2e5f3c47337965f602a5d16ea3082b851f502 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Mar 7 12:50:57 2023 -0500 add another option to completely skip molar fraction nse check after integration fails (#1146) here I add an option to completely skip the molar fraction check for self-consistent NSE only after the integration failed. With the previously added option, nse_molar_independent, we directly use the NSE mass fractions for comparing forward and reverse rates. This way, we allow the system to burn for some time, and break out to NSE if it is having a hard time. Also changed the input state for functions in nse_check.H to use burn_t only. interfaces/burner.H nse_solver/_parameters nse_solver/nse_check.H nse_solver/nse_solver.H sphinx_docs/source/nse.rst commit 9b7b620fe51ecae956a09ec9b8cafae63338871c Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Mar 6 20:30:52 2023 -0500 add a boolean in burn_t to indicate nse status (#1144) add a boolean in burn_t to indicate NSE status, for diagnostic purposes. interfaces/burn_type.H nse_solver/nse_check.H commit d6f3ab67cd54bd6881ca8b4a024c1a4cd28bc386 Author: Simon Guichandut <40605210+simonguichandut@users.noreply.github.com> Date: Mon Mar 6 19:42:11 2023 -0500 add cno extras network (#1145) Network for hot CNO hydrogen burning plus helium burning. For burning in mixed H/He Type I X-ray bursts. Contains the same isotopes as MESA's cno_extras.net, minus he3 since we do not really care about pp. networks/CNO_extras/.DS_Store networks/CNO_extras/CNO_extras.py networks/CNO_extras/Make.package networks/CNO_extras/NETWORK_PROPERTIES networks/CNO_extras/_parameters networks/CNO_extras/actual_network.H networks/CNO_extras/actual_network_data.cpp networks/CNO_extras/actual_rhs.H networks/CNO_extras/cno_extras.png networks/CNO_extras/cno_extras_hide_alpha.png networks/CNO_extras/inputs.burn_cell.VODE networks/CNO_extras/partition_functions.H networks/CNO_extras/pynucastro.net networks/CNO_extras/reaclib_rates.H networks/CNO_extras/table_rates.H networks/CNO_extras/table_rates_data.cpp networks/CNO_extras/tfactors.H commit 751f2f5f59228a06267ad40f16f76afa529722b8 Author: Michael Zingale Date: Fri Mar 3 17:24:47 2023 -0500 remove some unused code + change inits to quiet clang-tidy (#1143) neutrinos/sneut5.H commit 8ed98e1772757f0139bb07be925bd9e57e3bf252 Author: Michael Zingale Date: Fri Mar 3 13:56:50 2023 -0500 start of some clang-tidy fixes (#1141) mostly updates header guards to conform to our standards and not conflict with reserved patterns EOS/breakout/actual_eos.H EOS/eos_composition.H EOS/gamma_law/actual_eos.H EOS/helmholtz/actual_eos.H EOS/multigamma/actual_eos.H EOS/multigamma/eos_composition.H EOS/polytrope/actual_eos.H EOS/primordial_chem/actual_eos.H EOS/primordial_chem/eos_composition.H EOS/rad_power_law/actual_eos.H EOS/tillotson/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 constants/fundamental_constants.H integration/BackwardEuler/be_type.H 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_type.H integration/integrator.H integration/integrator_rhs_strang.H interfaces/ArrayUtilities.H interfaces/burn_type.H interfaces/burner.H interfaces/conductivity.H interfaces/eos.H interfaces/eos_data.H interfaces/eos_override.H interfaces/eos_type.H interfaces/network.H interfaces/tfactors.H networks/aprox13/actual_network.H networks/general_null/network_header.template networks/iso7/actual_network.H networks/powerlaw/actual_network.H networks/powerlaw/actual_rhs.H networks/rate_type.H neutrinos/sneut5.H rates/aprox_rates.H rates/aprox_rates_data.H screening/screen.H unit_test/test_aprox_rates/variables.H unit_test/test_conductivity/variables.H unit_test/test_eos/variables.H unit_test/test_jac/jac_zones.H unit_test/test_jac/variables.H unit_test/test_react/react_zones.H unit_test/test_react/variables.H unit_test/test_rhs/rhs_zones.H unit_test/test_rhs/variables.H unit_test/test_screening/variables.H unit_test/test_sdc/react_zones.H unit_test/test_sdc/variables.H unit_test/write_job_info.cpp util/build_scripts/write_probin.py util/esum.H util/esum_cxx.py commit 802bdcc16b659a723805d8529ac0d663d20bc5c8 Author: Michael Zingale Date: Fri Mar 3 11:46:53 2023 -0500 don't test on header guard presence (#1142) use NET_NETWORK_IMPLEMENTATION instead nse_solver/nse_solver.H commit 9d7ccb661298f725c1b99cfabc43ce78aadcb293 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Mar 3 08:37:22 2023 -0500 add another option to use nse mass fractions for NSE_NET check (#1139) Since forward and reverse rates depend on the mass fractions, to do a more cruel estimation, we can use nse mass fractions instead. This way, the thermodynamic condition becomes the only deciding factor. Note here we still need to make sure the current mass fractions are not terribly away from the nse mass fractions, so only allow it after the first check, which checks on whether the current mass fractions are close to the nse mass fractions. nse_solver/_parameters nse_solver/nse_check.H sphinx_docs/source/nse.rst commit 91458774f92444eb2a6fe37dc0bd4f0253437ead Author: Eric T. Johnson Date: Fri Mar 3 08:36:43 2023 -0500 Default-initialize all members in eos_t & friends (#1140) Fixes issue #1130 interfaces/eos_type.H commit 99d11bec591f003ac9ac60420cbe0520a61e10a3 Author: Michael Zingale Date: Thu Mar 2 19:32:39 2023 -0500 add the clang-tidy CI check (#1137) .clang-tidy .github/workflows/c-linter.yml commit 7334569bcb62665c9bac61a18148a4f3daa52e18 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Mar 2 14:29:22 2023 -0500 add an option to ignore checking the timescale of the rate for NSE_NET (#1138) add an option to ignore the check where we want the time scale of the rates to be smaller than the sound crossing time scale. nse_solver/_parameters nse_solver/nse_check.H sphinx_docs/source/nse.rst commit e4144f853324ec3db480c32b235ac00c368a8b4b Author: Michael Zingale Date: Wed Mar 1 08:06:08 2023 -0500 update changes CHANGES.md commit 3e0cd9935c22ea457a424caa2667340f2d3d5b7a Author: Eric T. Johnson Date: Tue Feb 21 16:28:31 2023 -0500 Fix some more compiler/linter warnings (#1135) Make.Microphysics_extern integration/VODE/vode_dvjac.H networks/rhs.H screening/screen.H commit 70ba11ce21b751cf344b77fce643347cd94769cb Author: Michael Zingale Date: Mon Feb 20 19:00:01 2023 -0500 update to latest pynucastro (#1136) networks/ase/actual_rhs.H networks/ase/partition_functions.H networks/ase/reaclib_rates.H networks/ase/subch_simple.png networks/ase/subch_simple.py networks/ase/table_rates.H commit df3f57709aa3b710f678084d072b4c9e63706cd8 Author: Michael Zingale Date: Thu Feb 16 14:55:20 2023 -0500 update the pynucastro nets to the latest pynucastro (#1134) this will quiet compiler warnings networks/ECSN/actual_rhs.H networks/ECSN/partition_functions.H networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H networks/ignition_reaclib/C-burn-simple/Make.package networks/ignition_reaclib/C-burn-simple/actual_network.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/C-burn-simple/partition_functions.H networks/ignition_reaclib/C-burn-simple/reaclib_rates.H networks/ignition_reaclib/C-burn-simple/table_rates.H networks/ignition_reaclib/C-burn-simple/tfactors.H networks/ignition_reaclib/URCA-simple/Make.package networks/ignition_reaclib/URCA-simple/actual_network.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/partition_functions.H networks/ignition_reaclib/URCA-simple/reaclib_rates.H networks/ignition_reaclib/URCA-simple/table_rates.H networks/ignition_reaclib/URCA-simple/tfactors.H networks/nova/Make.package networks/nova/actual_network.H networks/nova/actual_rhs.H networks/nova/nova.png networks/nova/partition_functions.H networks/nova/reaclib_rates.H networks/nova/table_rates.H networks/nova/tfactors.H networks/nova2/Make.package networks/nova2/actual_network.H networks/nova2/actual_rhs.H networks/nova2/nova.png networks/nova2/partition_functions.H networks/nova2/reaclib_rates.H networks/nova2/table_rates.H networks/nova2/tfactors.H networks/partition_test/actual_rhs.H networks/partition_test/partition_functions.H networks/partition_test/reaclib_rates.H networks/partition_test/table_rates.H networks/subch_approx/actual_rhs.H networks/subch_approx/partition_functions.H networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.png networks/subch_approx/table_rates.H networks/subch_full/actual_rhs.H networks/subch_full/partition_functions.H networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.png networks/subch_full/table_rates.H commit 3d4214483f2f6ba9272560be20c7c140e5dc1328 Author: Michael Zingale Date: Wed Feb 15 14:08:16 2023 -0500 modernize the subch_simple network script (#1133) this also adds a hook for using partition functions to get reverse rates networks/subch_simple/Make.package networks/subch_simple/actual_network.H networks/subch_simple/actual_rhs.H networks/subch_simple/partition_functions.H networks/subch_simple/pynucastro.net networks/subch_simple/reaclib_rates.H networks/subch_simple/subch_simple.png networks/subch_simple/subch_simple.py networks/subch_simple/table_rates.H networks/subch_simple/tfactors.H commit 44953037a3e9e596c466987298b063a9590e3445 Author: Michael Zingale Date: Mon Feb 13 20:46:50 2023 -0500 address some issues from the linters (#1131) networks/general_null/actual_rhs.H networks/ignition_chamulak/actual_rhs.H unit_test/test_aprox_rates/aprox_rates_util.cpp unit_test/test_aprox_rates/test_aprox_rates.H unit_test/test_aprox_rates/variables.H unit_test/test_aprox_rates/variables.cpp unit_test/test_conductivity/conductivity_util.cpp unit_test/test_conductivity/test_cond.H unit_test/test_conductivity/variables.H unit_test/test_conductivity/variables.cpp unit_test/test_eos/eos_util.cpp unit_test/test_eos/test_eos.H unit_test/test_eos/variables.H unit_test/test_eos/variables.cpp unit_test/test_jac/jac_zones.H unit_test/test_jac/variables.H unit_test/test_jac/variables.cpp unit_test/test_react/react_zones.H unit_test/test_react/variables.H unit_test/test_react/variables.cpp unit_test/test_rhs/rhs_zones.H unit_test/test_rhs/variables.H unit_test/test_rhs/variables.cpp unit_test/test_screening/screening_util.cpp unit_test/test_screening/test_screen.H unit_test/test_screening/variables.H unit_test/test_screening/variables.cpp unit_test/test_sdc/react_zones.H unit_test/test_sdc/variables.H unit_test/test_sdc/variables.cpp commit b803fe648af0a75ab3ea62d9c81579a1f97e08b9 Author: Michael Zingale Date: Mon Feb 13 20:23:05 2023 -0500 implement tricubic interpolation for tabular NSE (#1114) networks/aprox19/_parameters networks/aprox19/nse_table.H unit_test/test_nse_interp/GNUmakefile unit_test/test_nse_interp/Make.package unit_test/test_nse_interp/README.md unit_test/test_nse_interp/_parameters unit_test/test_nse_interp/main.cpp unit_test/test_nse_interp/nse_cell.H commit edefe06d1ee4909cac187903b302dbfffdd853a3 Author: Brendan Boyd <42776109+biboyd@users.noreply.github.com> Date: Mon Feb 13 15:27:17 2023 -0500 Update ECSN network and benchmark test (#1132) Update the ECSN network and bench mark test based on changes in pynucastro/pynucastro#502 networks/ECSN/Make.package networks/ECSN/actual_network.H networks/ECSN/actual_rhs.H networks/ECSN/partition_functions.H networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H networks/ECSN/table_rates_data.cpp networks/ECSN/tfactors.H unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out commit febab1f7acb56eb681f18acaa69350dc228d725b Author: Michael Zingale Date: Fri Feb 10 18:33:50 2023 -0500 silence some more compiler warnings (#1129) integration/integrator_rhs_simplified_sdc.H integration/integrator_type_simplified_sdc.H commit 0bee1f65047f27b6d5e4f8d6a42b78310064a085 Author: Eric T. Johnson Date: Fri Feb 10 08:34:27 2023 -0500 Fixes to screening routines (#1128) My testing with autodiff found a couple mistakes in the analytic derivatives for the chabrier1998 screening. Also fixed some compiler warnings in chugunov2007 and chugunov2009. screening/screen.H commit a6476d0551dd33ea71788160d73968d3f6de5b40 Author: Michael Zingale Date: Fri Feb 10 07:53:17 2023 -0500 silence compiler warnings for rprox (#1126) integration/integrator_rhs_strang.H networks/rprox/actual_rhs.H networks/rprox/rprox_rates.H commit b79fe5f73a2291e96b937718418335852155eaa1 Author: Eric T. Johnson Date: Wed Feb 8 17:53:23 2023 -0500 Clean up rate tabulation in aprox19, aprox21, and iso7 (#1127) As discussed in #1124 networks/aprox19/actual_network.H networks/aprox21/actual_network.H networks/iso7/actual_network.H commit cc58fec0c014bc8024def8917be3a53b78ab73ae Author: Eric T. Johnson Date: Tue Feb 7 09:06:39 2023 -0500 Explicitly initialize rates to 0 in tabulate_rates (#1123) Fixes uninitialized memory errors introduced by #1054. networks/rhs.H commit 379d922f11b8abe27de5de4e464a203dcdb5b1ed Author: Michael Zingale Date: Mon Feb 6 18:38:34 2023 -0500 add the check-ifdefs action (#1118) .github/workflows/check-ifdefs.yml .github/workflows/check_ifdefs.py .github/workflows/good_defines.txt commit c5171631e43171cbda765042e3a4fee68400847a Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Feb 6 10:58:04 2023 -0500 hybrj and NSE routine fix. (#1122) Fixed some bugs in the NSE routine. Fixed uninitialized variable issues caused by minpack hybrid solver. Fixed erroneous arithmetic operations during hybrid solver due to NaN, INF and division by zero. nse_solver/nse_check.H nse_solver/nse_solver.H util/hybrj/hybrj.H util/hybrj/hybrj_dogleg.H util/hybrj/hybrj_enorm.H util/hybrj/hybrj_r1mpyq.H commit 0c85d6aceae44a718e29f0e15fd515e9ac132609 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Feb 2 11:51:39 2023 -0500 fix unitialized variable (#1119) nse_solver/nse_check.H commit 816070c20be50401b6ca8bee7765c1c48e90ed1c Author: Michael Zingale Date: Wed Feb 1 12:50:15 2023 -0500 some cleaning for the NSE table (#1113) there is now a table_idx() function that can be used to get the correct index into the 1-d table. this makes new constexpr for the table deltas eliminates arrays to store T, rho, ye at the table points, since those are easily computed networks/aprox19/actual_network.H networks/aprox19/actual_network_data.cpp networks/aprox19/nse_table.H networks/aprox21/actual_network.H sphinx_docs/source/nse.rst commit c750b283ab868f319a92bf8d7b4da82dfc89644b Author: Michael Zingale Date: Wed Feb 1 07:50:54 2023 -0500 update changes for 23.02 CHANGES.md commit 0858a6ed39a893391443372da77233804fe3415a Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Tue Jan 31 11:36:35 2023 -0500 in_nse() input change (#1110) we now only operate on a burn_t networks/aprox19/nse_table_check.H nse_solver/nse_check.H commit a3ac00ba522f2f10a36ab9111bcec51a35caf5b8 Author: Michael Zingale Date: Mon Jan 30 19:07:15 2023 -0500 remove eta from tabular NSE (#1117) we were not using this feature, and I don't think it's the correct approach integration/nse_update.H networks/aprox19/_parameters nse_solver/_parameters commit 83211c03392be894bd1b836ceb411b56e52df4d2 Author: Eric T. Johnson Date: Mon Jan 30 19:06:47 2023 -0500 Fix uninitialized variable in chabrier1998 screening (#1116) screening/screen.H commit 5e1d020cd6cc438319b5b9085e95e8ffc2ec253b Author: Michael Zingale Date: Sun Jan 29 11:51:33 2023 -0500 initial h1_index mass fraction in nse_solver (#1115) the state was undefined and causing valgrind errors nse_solver/nse_solver.H commit 7f50db767e259d0d77f503e866ad5e932967d829 Author: Michael Zingale Date: Thu Jan 26 14:26:41 2023 -0500 fix a bug/typo in the NSE+SDC EOS call (#1112) integration/nse_update.H commit 4a082ffcbd0ead23bb3f2e6635beef6439de7b14 Author: Michael Zingale Date: Wed Jan 25 15:49:48 2023 -0500 swtich Strang over to use T_fixed + update SDC + NSE (#1111) we were not being consistent with how we handled T_fixed, which is set if we are doing drive_initial_convection (Castro Strang update coming soon). The idea is that the zone's internal energy should not be computed off of T_fixed, but all of the reaction rates should be. This update fixes some issues with NSE and Strang burning where were we computing e with T_fixed, thus changing the amount of internal energy in a zone. integration/integrator_type_strang.H integration/nse_update.H interfaces/burn_type.H nse_solver/nse_solver.H unit_test/burn_cell/burn_cell.H unit_test/test_react/react_zones.H commit d64aa25b2577d89c2efc9dde87f49092225d57f6 Author: Michael Zingale Date: Mon Jan 16 09:26:53 2023 -0500 for Strang + NSE, we need to call EOS (#1098) after integrating, we call the EOS to get T in case we complete the burn with NSE, but we were not setting the aux data to be consistent with the mass fractions, so we got the thermodynamics wrong. The reason is that with Castro AMReX-Astro/Castro#2310 we no longer subtract off the initial energy. This means that when we exit NSE, we need to have the valid full energy. However, since the burn_t comes in without the energy initialized, we need to call the EOS with the input rho, T, aux to get an initial valid e. integration/VODE/actual_integrator.H integration/nse_update.H unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out commit 1e475055cd64b5150a5bdab4b7f7f811fb16d932 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jan 11 21:07:13 2023 -0500 change preprocessors (#1108) we renamed USE_NSE to USE_NSE_TABLE .github/workflows/nse_table.yml Make.Microphysics_extern integration/Make.package networks/Make.package networks/aprox19/Make.package sphinx_docs/source/nse.rst commit 6e17c0d6fbc8c5904b486e3e0368dbb459e3cef8 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed Jan 11 19:12:41 2023 -0500 nse compilation fixes (#1109) fix compilation errors after including NSE preprocessor for self-consistent nse. integration/nse_update.H interfaces/burner.H nse_solver/_parameters nse_solver/nse_check.H nse_solver/nse_solver.H unit_test/test_nse/nse_example.H commit b0e5e0cc7667785cf62e23edef8e8d345553fefe Author: Michael Zingale Date: Tue Jan 10 17:13:13 2023 -0500 update action versions to suppress warnings + skip primordial_chem (#1104) in particular checkoutv3 is needed now also, primordial_chem times out in the compilation test .github/workflows/compile_action.yml .github/workflows/create_release.yml .github/workflows/find_changed_files.py .github/workflows/gh-pages.yml commit 380d048eea6580799f0458cf38fe53ffd86de1e8 Author: Michael Zingale Date: Thu Jan 5 13:00:32 2023 -0500 update for 23.01 CHANGES.md commit dc4a7e216c061efdbaced041a495f5b2d7e6dd2d Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Thu Dec 22 01:15:05 2022 +1100 Added burn_cell test for primordial chem (#1064) This PR will add the burn_cell test for primordial chemistry. The test is identical to the one used in other astrochem codes. It basically sets up a one-zone model of a collapsing primordial molecular cloud. We initialize the abundances of each chemical specie (H, H+, H2, D, HD, etc.) at some initial density. We then increase the density in steps of 0.1*freefall_time, and the output at each step is the number densities of all chemical species and the gas temperature. The model stops when the densities are > 3e-6 g/cm^3 or the number of steps > 1000, or the maximum time exceeds the given value. unit_test/burn_cell_primordial_chem/GNUmakefile unit_test/burn_cell_primordial_chem/Make.package unit_test/burn_cell_primordial_chem/README.md unit_test/burn_cell_primordial_chem/_parameters unit_test/burn_cell_primordial_chem/burn_cell.H unit_test/burn_cell_primordial_chem/inputs_primordial_chem unit_test/burn_cell_primordial_chem/main.cpp unit_test/burn_cell_primordial_chem/state_over_time.txt commit 5bade97f0c44743b9e5703ffc03ff74d691b9b4b Author: Michael Zingale Date: Tue Dec 20 15:22:35 2022 -0500 some more NSE compilation fixes (#1102) nse_solver/nse_check.H nse_solver/nse_solver.H util/microphysics_sort.H commit afd2315ac9aa6ff954c91e973a7c969c58d097d8 Author: Michael Zingale Date: Tue Dec 20 13:57:31 2022 -0500 move init_nse_net into network_init() (#1101) interfaces/network_initialization.cpp nse_solver/make_table/main.cpp unit_test/test_ase/main.cpp unit_test/test_ase/make_table/main.cpp unit_test/test_nse/main.cpp commit 66791039c0145000b514a10a7384816bb8efc4e3 Author: Michael Zingale Date: Tue Dec 20 13:46:46 2022 -0500 hook the self-consistent NSE into network integration (#1099) this adds an "NSE_NET" branch to nse_update.H in the integrator integration/nse_update.H interfaces/burner.H commit 736eae49cc9162621355fb45cff2e9428ffa3f90 Author: Michael Zingale Date: Tue Dec 20 13:30:14 2022 -0500 fix self-consistent NSE compilation (#1100) we need to inline the functions so the compiler doesn't complain about multiple versions. Also add a check that we are not trying to do both kinds of NSE. Make.Microphysics_extern nse_solver/nse_solver.H commit acd17b4d6eefc6bedc365a5dcefa7b4c3941fdbd Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Dec 16 14:27:30 2022 -0500 add comments to screen5 routine (#1063) screening/screen.H sphinx_docs/source/refs.bib sphinx_docs/source/screening.rst commit 8abdcd8cbc2e3c0f180b7d5319a5229aabc9b351 Author: Michael Zingale Date: Fri Dec 16 14:15:29 2022 -0500 start cleaning up the different NSE headers (#1096) this is part of the way towards letting the approaches coexist integration/VODE/vode_dvode.H integration/nse_update.H networks/aprox19/Make.package networks/aprox19/actual_network_data.cpp networks/aprox19/nse_table.H networks/aprox19/nse_table_check.H nse_solver/Make.package nse_solver/README.md nse_solver/nse_check.H nse_solver/nse_solver.H commit 1206caea6cdf400fdab53829a36c8a0d60b304af Author: Michael Zingale Date: Fri Dec 16 13:12:18 2022 -0500 some updates to burn_cell_sdc (#1094) this now deals with the aux data when we build with NSE and also fixes the run with multiple steps unit_test/burn_cell_sdc/_parameters unit_test/burn_cell_sdc/burn_cell.H unit_test/burn_cell_sdc/ci-benchmarks/aprox19_BE_state_over_time.txt unit_test/burn_cell_sdc/ci-benchmarks/aprox19_state_over_time.txt unit_test/burn_cell_sdc/parse_integration_failure.py commit 4e8f60856b7102d7b8888c75a87391aa1dcfc735 Author: Michael Zingale Date: Fri Dec 16 13:11:49 2022 -0500 put nse_relax_factor on He+Fe as well (#1082) interfaces/burner.H networks/aprox19/nse.H unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out commit 0d4e0eca0fb90831ae330b795b36af763eabf46a Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Dec 15 18:02:47 2022 -0500 hide nse_state from in_nse() interface (#1097) nse_solver/nse_solver.H sphinx_docs/source/nse.rst unit_test/test_ase/GNUmakefile unit_test/test_ase/burn_cell.H unit_test/test_ase/make_table/GNUmakefile unit_test/test_ase/make_table/burn_cell.H commit 5a17b740d2be235d29726ddc847d935f19d87044 Author: Michael Zingale Date: Thu Dec 15 18:02:14 2022 -0500 renormalize X after interpolating from NSE table (#1095) integration/nse_update.H commit 6848bad439aa9035940301d736e7c60a2858df59 Author: Michael Zingale Date: Wed Dec 14 15:23:50 2022 -0500 add aux in SDC to burn_type ostream (#1093) interfaces/burn_type.H commit 3e8f3c2297ea2128a6c23bd63ae914a5ce847d96 Author: Michael Zingale Date: Sat Dec 10 09:12:12 2022 -0500 add aux to burn_cell so it works with aprox19 + NSE (#1087) Also add a unit test (CI) that tests this out. .github/workflows/nse_table.yml unit_test/burn_cell/burn_cell.H unit_test/burn_cell/ci-benchmarks/aprox19_nse_unit_test.out unit_test/burn_cell/inputs_aprox19.nse unit_test/burn_cell_sdc/burn_cell.H commit 827bf090b64b1967f4155f9f0e2e0a95725ae965 Author: Michael Zingale Date: Sat Dec 10 09:11:37 2022 -0500 update test_sdc_vode_rhs (#1089) switch to the analytic Jacobian also remove some copies between burn_t and eos_t unit_test/test_sdc_vode_rhs/inputs_aprox19 unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit 47ff1f74be9e2c53684a2995a849afdd35a25623 Author: Michael Zingale Date: Fri Dec 9 18:36:50 2022 -0500 mass fraction runtime parameter cleaning (#1086) Lots of tests had the same code to interpret mass fraction runtime parameters. This consolidates them all. unit_test/_parameters unit_test/burn_cell/GNUmakefile unit_test/burn_cell/_parameters unit_test/burn_cell/burn_cell.H unit_test/burn_cell_sdc/GNUmakefile unit_test/burn_cell_sdc/_parameters unit_test/burn_cell_sdc/burn_cell.H unit_test/eos_cell/GNUmakefile unit_test/eos_cell/_parameters unit_test/eos_cell/eos_cell.H unit_test/react_util.H unit_test/test_jac/_parameters unit_test/test_nse/GNUmakefile unit_test/test_nse/_parameters unit_test/test_nse/nse_example.H unit_test/test_react/_parameters unit_test/test_rhs/_parameters unit_test/test_sdc/_parameters unit_test/test_sdc_vode_rhs/GNUmakefile unit_test/test_sdc_vode_rhs/_parameters unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit d6c629ef2e5bba9523d2f6fe02160ac7f2374e4a Author: Michael Zingale Date: Fri Dec 9 14:21:07 2022 -0500 split the nse_update functions out of aprox19 (#1084) this will allow us to use them for both types of NSE we support integration/Make.package integration/nse_update.H interfaces/burner.H networks/aprox19/nse.H commit a8b220bdfb7569df47fa447d9d79768b57fd7c8f Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Dec 8 14:47:40 2022 -0500 add Chabrier&Potekhin1998 screening (#1085) It adds the Chabrier&Potekhin1998 screening as Alex did for pynucastro. I also added the quantum correction from the strong screening section of screen5 to it, which is suggested in the appendix of Calder2007. I tested it with NSE and it works as expected. Make.Microphysics_extern screening/screen.H sphinx_docs/source/refs.bib sphinx_docs/source/screening.rst unit_test/test_ase/make_table/GNUmakefile commit e920a81591e6471201086d81a1ff6260f3153c0d Author: Michael Zingale Date: Tue Dec 6 17:29:33 2022 -0500 fix a bibtex ref (#1083) things got scrambled in a merge commit sphinx_docs/source/refs.bib commit 85f387df376a1af817bda4dff90091dab0bc31bc Author: Michael Zingale Date: Sun Dec 4 13:31:49 2022 -0500 update the SDC docs to reflect lots of recent changes (#1075) sphinx_docs/source/refs.bib sphinx_docs/source/sdc.rst commit 6934966f57a6c971627c757b6f165c33a7e824d6 Author: Michael Zingale Date: Sun Dec 4 13:30:41 2022 -0500 update the subch_full and subch_approx nets (#1072) also simplify the script based on recent pynucastro changes networks/subch_approx/Make.package networks/subch_approx/actual_network.H networks/subch_approx/actual_rhs.H networks/subch_approx/partition_functions.H networks/subch_approx/pynucastro.net networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.py networks/subch_approx/tfactors.H networks/subch_full/Make.package networks/subch_full/actual_network.H networks/subch_full/actual_rhs.H networks/subch_full/partition_functions.H networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.py networks/subch_full/tfactors.H commit 89718bb7b45dd28f08a84ea6ef0f3b9abc2768ea Author: Michael Zingale Date: Sun Dec 4 13:30:20 2022 -0500 update the Strang docs based on recent PRs (#1076) sphinx_docs/source/integrators.rst commit 195b33dade6a5e9850ccd51e147f7e83f84a7369 Author: Michael Zingale Date: Sun Dec 4 13:30:03 2022 -0500 add a BackwardEuler SDC CI test (#1077) .github/workflows/burn_cell_sdc.yml unit_test/burn_cell_sdc/ci-benchmarks/aprox19_BE_state_over_time.txt commit 5fa060c4d984b759e2b9546370f89c9fa5e83309 Author: Michael Zingale Date: Sun Dec 4 13:29:43 2022 -0500 have test_react output the burn state that took the longest (#967) this creates a file called zone_state.out with the burn_t unit_test/test_react/main.cpp unit_test/test_react/react_zones.H commit 55e2ed7425693645d95173f46aec1997174529eb Author: Max Katz Date: Sun Dec 4 11:54:58 2022 -0500 Use rate containers in rhs_term and jac_term (#1081) networks/rhs.H commit 78f753a6a60f81d186e36d25d4d5b545d84af7a4 Author: Max Katz Date: Sun Dec 4 11:09:19 2022 -0500 Add a safeguard to jac_term (#1079) This simply ensures that for d(f(Y_1)) / dY_2, Y_1 is actually present in a given RHS term. This is a redundant check for now which can give us some freedom later. networks/rhs.H commit c967c4ac489f45efdf1d16a6c69b8acab0959b48 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Dec 2 19:15:18 2022 -0500 add docs for dynamic nse (#1073) sphinx_docs/source/nse.rst sphinx_docs/source/refs.bib commit bff7636ac061d28f3915cd46afde179ff67f47f7 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Dec 2 19:14:31 2022 -0500 Adaptive Statistical Equilibrium (#983) This is an implementation of the adaptive NSE from Kushnir and Katz. At the moment it only works with a pynucastro network. networks/ase/Make.package networks/ase/NETWORK_PROPERTIES networks/ase/_parameters networks/ase/actual_network.H networks/ase/actual_network_data.cpp networks/ase/actual_rhs.H networks/ase/inputs.burn_cell.VODE networks/ase/partition_functions.H networks/ase/pynucastro.net networks/ase/reaclib_rates.H networks/ase/subch_simple.png networks/ase/subch_simple.py networks/ase/table_rates.H networks/ase/table_rates_data.cpp networks/ase/tfactors.H nse_solver/_parameters nse_solver/nse_index.H nse_solver/nse_index.cpp nse_solver/nse_solver.H unit_test/test_ase/GNUmakefile unit_test/test_ase/Make.package unit_test/test_ase/README.md unit_test/test_ase/_parameters unit_test/test_ase/burn_cell.H unit_test/test_ase/inputs_ase unit_test/test_ase/main.cpp unit_test/test_ase/make_table/GNUmakefile unit_test/test_ase/make_table/Make.package unit_test/test_ase/make_table/README.md unit_test/test_ase/make_table/_parameters unit_test/test_ase/make_table/burn_cell.H unit_test/test_ase/make_table/main.cpp commit c97ee4a6e3c2e2b7269843313af46dfb4c721ad2 Author: Michael Zingale Date: Fri Dec 2 13:42:55 2022 -0500 add dx back into the burn_t (#1074) we can use this to estimate the time to equilibriation for reactions interfaces/burn_type.H commit 2b1e3c7ec470df8de161aeab698afbbd4c945340 Author: Michael Zingale Date: Thu Dec 1 10:00:33 2022 -0500 update CHANGES CHANGES.md commit e6ec0450993e73ee3afc9412ff90da1c06af86ba Author: Michael Zingale Date: Wed Nov 30 21:05:15 2022 -0500 get the BackwardEuler solver working with simplified-SDC (#1042) integration/BackwardEuler/Make.package integration/BackwardEuler/actual_integrator_simplified_sdc.H integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/Make.package integration/VODE/_parameters integration/_parameters integration/integrator_rhs_simplified_sdc.H integration/integrator_type_simplified_sdc.H commit 1539b0186ab25c51c4cf20e5363129165d3e2ac2 Author: Michael Zingale Date: Mon Nov 28 19:39:24 2022 -0500 remove jacobian = 3 option (#1069) this did parts of the Jacobian numerically and the conversion to energy analytically. But it never seems to have been a big win, and maintaining this code path is not worth it. integration/VODE/vode_dvjac.H integration/integrator_rhs_simplified_sdc.H commit ca6d25613a12dc8c7741ec58e770b49242aabf69 Author: Max Katz Date: Sun Nov 27 17:18:01 2022 -0500 Construct some containers for data in rhs.H (#1054) Containers for state data and rate data are constructed. These significantly clean up interfaces (and therefore make them more extensible in the future) and also help quiet unused variable warnings. interfaces/Make.package interfaces/rhs_type.H interfaces/tfactors.H networks/aprox13/actual_network.H networks/aprox19/actual_network.H networks/aprox21/actual_network.H networks/iso7/actual_network.H networks/rhs.H rates/Make.package commit bee474f20869eeea3fa2f824c8bbc51a1a663bb2 Author: Michael Zingale Date: Sun Nov 27 17:01:46 2022 -0500 some simplified-SDC cleaning (#1066) rename fill_unevolved_variables to update_density_in_time -- this more accurately describes what it does. also output the initial rhoe on failure integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvode.H integration/integrator_rhs_simplified_sdc.H integration/integrator_type_simplified_sdc.H commit 3a515a6b8c519fb76cc85f863072aaa555b8bea3 Author: Michael Zingale Date: Sun Nov 27 14:53:31 2022 -0500 generalize the SDC helper routines (#1065) this let's them be used by other integrators also fix some includes integration/BackwardEuler/be_integrator.H integration/Make.package integration/VODE/Make.package integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvhin.H integration/VODE/vode_dvjac.H integration/VODE/vode_dvode.H integration/VODE/vode_rhs.H integration/VODE/vode_type.H integration/integrator_rhs_simplified_sdc.H integration/integrator_rhs_strang.H integration/integrator_type_simplified_sdc.H commit b292e272a425b881e72910f2cba8f2610fcfa19e Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Sat Nov 26 01:28:17 2022 +1100 Defined internal energy given density and temperature for primordial chem EOS (#1061) EOS/primordial_chem/actual_eos.H commit 034716692bbf719964b47151cba1365b4766458d Author: Max Katz Date: Fri Nov 25 09:07:13 2022 -0500 Mark some screening variables maybe_unused (#1062) screening/screen.H commit 63248ba93603cf6c3d479d3987d73737cd9e0e6a Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Wed Nov 23 09:03:10 2022 +1100 Added declarations of two parameters for EOS/primordial_chem (#1057) This PR declares two parameters that I use in the EOS for primordial chemistry that were somehow left out of the earlier PRs. EOS/primordial_chem/actual_eos.H commit 84d75f1d039798ada16c1d688b79af0104b846ef Author: Michael Zingale Date: Tue Nov 22 17:01:16 2022 -0500 template the VODE rhs/jac stuff (#1060) this also lets BackwardEuler use these same functions integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/BackwardEuler/be_type_strang.H integration/Make.package integration/integrator_data.H integration/integrator_rhs_strang.H unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out commit a751d605bb9b20c641f29f143ca1c8fbf21dfbe4 Author: Michael Zingale Date: Mon Nov 21 21:05:13 2022 -0500 more BackwardEuler refactoring (#1045) this moves y and jac to the be_t integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/BackwardEuler/be_type_strang.H unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out commit 1595553911c564f8b695f3d9f69c3c59af8db134 Author: Michael Zingale Date: Sun Nov 20 16:05:52 2022 -0500 Some refactoring of the BackwardEuler solver (#1041) This sets us up for doing the simplified-SDC implementation integration/BackwardEuler/Make.package integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/be_integrator.H integration/BackwardEuler/be_type.H integration/BackwardEuler/be_type_strang.H unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out commit 2baf46b61db7bcd42b49e85f3971bafd075e465b Author: Michael Zingale Date: Sun Nov 20 15:23:23 2022 -0500 eliminate an eos_t temporary in the SDC code path with energy (#1050) integration/VODE/vode_type_simplified_sdc.H commit d4c2160040a1df15df621585f6ca19bd5d5f6878 Author: Michael Zingale Date: Sun Nov 20 14:42:45 2022 -0500 add subtract_internal_energy to BackwardEuler (#1051) integration/BackwardEuler/actual_integrator.H integration/VODE/_parameters integration/_parameters commit 07ea35070f949b6fd3e98a94c7db86ab17bac7c1 Author: Michael Zingale Date: Sun Nov 20 14:41:51 2022 -0500 fix true SDC compilation with VODE (#1052) this is a temporary fix until we actually refactor true SDC to only evolve (rho X, rho e) integration/VODE/vode_dvhin.H integration/VODE/vode_dvode.H integration/VODE/vode_type.H commit 6c0ac775f9ec27dd1ec250a524902b8d5293b80f Author: Michael Zingale Date: Sun Nov 20 14:39:42 2022 -0500 fix compilation with aprox19 + NSE (#1053) interfaces/burn_type.H commit 306cb5f9cffd266596b615dbab38844df45e9f12 Author: Michael Zingale Date: Sat Nov 19 14:52:17 2022 -0500 we don't need the first EOS call in the SDC burn (#1044) it is overwritten when we do our first vode_to_burn integration/VODE/actual_integrator_simplified_sdc.H commit 692257a1849056c85dd56c4e6ce6f534c33ec316 Author: Michael Zingale Date: Sat Nov 19 13:34:21 2022 -0500 fix an FPE in burn_cell (#1049) we need to call the EOS before calling actual_rhs unit_test/burn_cell/burn_cell.H unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out commit f38204ac404e3a2658ba44b6877d107ab27c3d22 Author: Michael Zingale Date: Sat Nov 19 13:33:55 2022 -0500 template some VODE funcs to be used by other integrators (#1046) integration/Make.package integration/VODE/Make.package integration/VODE/_parameters integration/VODE/actual_integrator.H integration/VODE/vode_rhs.H integration/VODE/vode_type.H integration/_parameters integration/integrator_type_strang.H commit e222dd70bc5ac956616ad8b01280e18434e4030e Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Sat Nov 19 04:32:23 2022 +1100 Changes to integration/VODE for primordial ISM chemistry (#999) This PR deals with changes I have made in VODE for primordial chemistry. All the changes basically reflect that since we use number densities for primordial chem, we want to disable some of the sanity checks in VODE that are appropriate for mass fractions. We also do not want to subtract the initial internal energy as is appropriate for nuclear astrochemistry. To disable the checks related to these, I have created two new flags in VODE/_parameters. The default values of these flags is such that users who do not use primordial chem will not need to worry about them, and the code should work just like before. Please let me know what you think. integration/VODE/_parameters integration/VODE/actual_integrator.H integration/VODE/vode_dvstep.H integration/VODE/vode_rhs.H integration/VODE/vode_type_strang.H commit 4ce4d428449eb06ca869c744e3de5cd67467c203 Author: Michael Zingale Date: Thu Nov 17 18:42:27 2022 -0500 move some general SDC routines out of VODE (#1043) this allows other integrators to use them integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_type_simplified_sdc.H interfaces/burn_type.H commit aaa0dacb17e90628d494810d18d2e5e8cec6994a Author: Michael Zingale Date: Thu Nov 17 14:03:14 2022 -0500 remove INTEGRATOR_HAS_FORTRAN_IMPLEMENTATION (#1047) integration/VODE/Make.package commit e810d1bd54c5eba3c7e6249db490f78aefdc6d76 Author: Michael Zingale Date: Thu Nov 17 09:28:18 2022 -0500 make VODE species tolerances scalars instead of arrays (#1039) we always use the same tol for all species integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvhin.H integration/VODE/vode_dvode.H integration/VODE/vode_type.H commit a4b77ad153041c4ad1f66f6f92802b17dcb20e8a Author: Michael Zingale Date: Thu Nov 17 09:27:53 2022 -0500 add CI for QSS (#1035) .github/workflows/burn_cell.yml unit_test/burn_cell/ci-benchmarks/aprox13_QSS_unit_test.out commit 6265d51ce22a3972883829a7a0ee3acdd08676ff Author: Michael Zingale Date: Thu Nov 17 09:27:35 2022 -0500 remove the python bindings (#1036) these are not supported anymore and pynucastro largely replicates what they did python_library/.f2py_f2cmap python_library/.f90wrap_kind_map python_library/GNUmakefile python_library/Make.package python_library/README.md python_library/StarKiller Notebook Test.ipynb python_library/StarKiller/README.md 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/call_integrator.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 python_library/StarKiller/setup.py python_library/_parameters python_library/dof2py.sh python_library/dowrap.sh python_library/probin.ignition python_library/starkiller_initialization.f90 sphinx_docs/source/basics.rst unit_test/burn_cell_python/Burn Cell.ipynb unit_test/burn_cell_python/Burn-Subch.ipynb unit_test/burn_cell_python/Burn-Test-ECSN.ipynb unit_test/burn_cell_python/BurnUtils.py unit_test/burn_cell_python/README.md unit_test/burn_cell_python/Test-Aprox13.ipynb unit_test/burn_cell_python/probin_aprox13 unit_test/burn_cell_python/probin_burn_subch unit_test/burn_cell_python/probin_ecsn commit 8ab4fc98504898bf4aea54f8e927162c467fe91d Author: Michael Zingale Date: Wed Nov 16 14:04:09 2022 -0500 sync up some code between Strang and SDC drivers (#1038) this makes the diff cleaner integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H commit 5b6556fec56df303dce07cded7ed9abab52b196e Author: Michael Zingale Date: Wed Nov 16 13:19:21 2022 -0500 fix uninitialized variable in burn_cell_sdc (#1040) unit_test/burn_cell_sdc/burn_cell.H commit b5f646988dc0e1dc61504e1f5bdd2ddf8a784adc Author: Michael Zingale Date: Tue Nov 15 11:38:13 2022 -0500 remove the Strang self_heat parameter (#1037) it is never used integration/BackwardEuler/actual_integrator.H integration/ForwardEuler/actual_integrator.H integration/QSS/actual_integrator.H integration/VODE/actual_integrator.H interfaces/burn_type.H unit_test/test_jac/jac_zones.H unit_test/test_rhs/rhs_zones.H commit 6bc0ff4065e479e40546ac4cb8b52b05e406553c Author: Max Katz Date: Mon Nov 14 08:17:05 2022 -0500 Subtract off initial energy at end of QSS integration (#1034) This synchronizes QSS with the other integrators and the applications. integration/QSS/actual_integrator.H commit c7cbb5631a29b177ff9a195f525c03e248fc41ce Author: Max Katz Date: Mon Nov 14 08:16:38 2022 -0500 Harden QSS integrator (#1032) These changes mostly prevent trace species from controlling the update. integration/QSS/actual_integrator.H commit 02b0020fb79fd56e6b7a69ea837ff49fbc24eae2 Author: Max Katz Date: Sun Nov 13 11:01:08 2022 -0500 Minor QSS cleanup (#1031) integration/QSS/actual_integrator.H commit 5f67725313e2b22a108734ee8cb2b451a3228849 Author: Michael Zingale Date: Sun Nov 13 11:00:22 2022 -0500 add BackwardEuler test to the burn_cell CI (#1030) also move the benchmark files into the ci-benchmarks directory also add the number of steps taken in BackwardEuler to the burn_t .github/workflows/burn_cell.yml integration/BackwardEuler/actual_integrator.H unit_test/burn_cell/ci-benchmarks/ecsn_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_BE_unit_test.out unit_test/burn_cell/ci-benchmarks/subch_approx_unit_test.out commit bddba4aa40058bd5a6f56d8df8f6d9da180231cc Author: Max Katz Date: Sun Nov 13 09:40:39 2022 -0500 Sync QSS integrator with new RHS scheme (#1026) This requires some minor changes to rhs.H so that the RHS infrastructure can separately return the forward and reverse terms, but it is worth it because we can remove most of the code duplication in this integrator. VODE should be unchanged. integration/QSS/actual_integrator.H networks/rhs.H unit_test/burn_cell_sdc/ci-benchmarks/aprox19_state_over_time.txt commit a79174a85d2085036c02dfeff91b5edb3f5ce480 Author: Max Katz Date: Sun Nov 13 07:50:49 2022 -0500 Document QSS integrator (#1029) sphinx_docs/source/integrators.rst sphinx_docs/source/refs.bib commit b0bbf7b2587c7fb02ee27f69b145b01b2e858809 Author: Michael Zingale Date: Sat Nov 12 20:25:14 2022 -0500 add BackwardEuler to the integration docs (#1028) sphinx_docs/source/integrators.rst commit 304d6e61473eebd2dfb0bcfc38c4d5e2e6ce1fec Author: Michael Zingale Date: Sat Nov 12 19:58:58 2022 -0500 implement a simple C++ backward Euler integrator (#504) Make.Microphysics_extern integration/BackwardEuler/Make.package integration/BackwardEuler/README.md integration/BackwardEuler/_parameters integration/BackwardEuler/actual_integrator.H integration/BackwardEuler/be_type.H integration/utils/numerical_jacobian.H commit f0eef8c71b3e83a538d8dc6e9998e489ea095cd9 Author: Max Katz Date: Sat Nov 12 08:57:23 2022 -0500 Fix compilation for ForwardEuler integrator (#1027) integration/ForwardEuler/_parameters integration/ForwardEuler/actual_integrator.H commit c073a11e1167bf6de45d3d026c82ec6d64f1f09c Author: Michael Zingale Date: Fri Nov 11 09:50:44 2022 -0500 StarKillerCxxNetwork -> AmrexAstroCxxNetwork (#1025) networks/ECSN/ecsn_network_generation.py networks/ignition_reaclib/C-burn-simple/c.py networks/ignition_reaclib/URCA-simple/urca.py networks/nova/nova.py networks/nova2/nova2.py networks/partition_test/part_test.py networks/sn160/sn160.py networks/subch_approx/subch_approx.py networks/subch_full/subch_full.py networks/subch_simple/subch_simple.py commit 10f30b1c3679d2c9c41c40b46bdfe5291cc7215a Author: Michael Zingale Date: Fri Nov 11 09:50:32 2022 -0500 remove EOS_GAMMA_LAW_GENERAL define (#1018) it is never used as far as I can tell Make.Microphysics_extern commit ad7da3c3a5e2934e4222578c8e88aedf23351357 Author: Michael Zingale Date: Fri Nov 11 09:50:15 2022 -0500 remove the USE_GPU_PRAGMA and our own CUDA settings (#1017) this is from before AMReX had CUDA support Make.Microphysics commit ee8b96611b94ceeb4eb27dd1b380125eea586b48 Author: Michael Zingale Date: Fri Nov 11 09:50:04 2022 -0500 clean up some of the python scripts (#1009) this removes the Fortran bits and addresses flake8 networks/Make.package 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/update_headers.py commit 0d57093f0aaa0300c07c17fcd5330e29a12a2dc4 Author: Michael Zingale Date: Mon Nov 7 11:57:11 2022 -0500 add a HIP action to the CI (#1022) .github/workflows/dependencies_hip.sh .github/workflows/hip.yml commit f4c824ffc018a136ad9b474e40e44a53c45a01e2 Author: Michael Zingale Date: Mon Nov 7 11:50:45 2022 -0500 add CUDA action (#1023) .github/workflows/cuda.yml .github/workflows/dependencies_nvcc11.sh commit 3ded4a6dbed67a4b82af89729a4b8102d3913ed0 Author: Michael Zingale Date: Mon Nov 7 11:17:31 2022 -0500 add an SDC github action (#1024) .github/workflows/burn_cell_sdc.yml unit_test/burn_cell_sdc/ci-benchmarks/aprox19_state_over_time.txt unit_test/burn_cell_sdc/inputs_aprox19.ci commit 154a83d87810a03334faa9183154881750dee054 Author: Michael Zingale Date: Mon Nov 7 08:34:52 2022 -0500 read the helmtable into local memory, bcast, and then copy to managed (#1020) this gets around some MPI issues with GPUs EOS/helmholtz/actual_eos.H commit cfe7aa2463945a216fa57d5dbe14e87054db2469 Author: Michael Zingale Date: Tue Nov 1 16:23:44 2022 -0400 update the NSE docs (#1004) we now have 2 different solvers, so this attempts to explain their differences sphinx_docs/source/eos.rst sphinx_docs/source/nse.rst sphinx_docs/source/refs.bib commit 17de5791c77e804e0d99dfba4cb96cf1c818229e Author: Michael Zingale Date: Tue Nov 1 13:10:14 2022 -0400 remove USE_CXX_REACTIONS (#1015) this is no longer needed -- everything is C++ Make.Microphysics_extern interfaces/Make.package networks/aprox13/Make.package networks/aprox19/Make.package networks/aprox21/Make.package networks/general_null/Make.package networks/ignition_chamulak/Make.package networks/ignition_simple/Make.package networks/iso7/Make.package networks/rprox/Make.package networks/triple_alpha_plus_cago/Make.package networks/vode_example/Make.package nse_solver/make_table/GNUmakefile unit_test/burn_cell/GNUmakefile unit_test/burn_cell_sdc/GNUmakefile unit_test/eos_cell/GNUmakefile unit_test/test_conductivity/GNUmakefile unit_test/test_jac/GNUmakefile unit_test/test_nse/GNUmakefile unit_test/test_part_func/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 util/hybrj/test/GNUmakefile commit dd631fbd8368fbba5b79fa079061de934dce57b1 Author: Michael Zingale Date: Tue Nov 1 12:21:59 2022 -0400 add a documentation build CI (#1013) .github/workflows/docs-test.yml commit e23f58a6122f67bd68e301073e046b5f519fa1bd Author: Michael Zingale Date: Tue Nov 1 12:21:40 2022 -0400 add an eos_cell CI (#1014) .github/workflows/eos_cell.yml interfaces/eos_type.H unit_test/eos_cell/ci-benchmarks/eos_gamma_law.out unit_test/eos_cell/ci-benchmarks/eos_helmholtz.out commit da09fcd3a915038e5c9aea00a0c6f6a0691cab41 Author: Michael Zingale Date: Tue Nov 1 09:27:19 2022 -0400 update changes CHANGES.md commit 0c372871f188f0974c1fe3b4a6c4bb2e0b51a42a Author: Michael Zingale Date: Mon Oct 31 22:41:08 2022 -0400 rename actual_nse -> nse_net (#1005) This is part of the clean up of the 2 different NSE approaches we have. Make.Microphysics_extern interfaces/burn_type.H interfaces/eos_type.H nse/Make.package nse_solver/Make.package nse_solver/_parameters nse_solver/make_table/GNUmakefile nse_solver/make_table/Make.package nse_solver/make_table/README.md nse_solver/make_table/_parameters nse_solver/make_table/burn_cell.H nse_solver/make_table/main.cpp nse_solver/nse_index.H nse_solver/nse_index.cpp nse_solver/nse_solver.H unit_test/test_nse/GNUmakefile unit_test/test_nse/main.cpp unit_test/test_nse/nse_example.H util/hybrj/test/GNUmakefile commit 85e77071cbca0665f775125339ae570480421fc6 Author: Michael Zingale Date: Mon Oct 31 14:32:38 2022 -0400 fix indexing in aux check (#1012) networks/general_null/network_param_file.py commit 8da376f9cee91edd6c813b0756c43f8d58d970ab Author: Michael Zingale Date: Mon Oct 31 11:56:15 2022 -0400 add an NSE CI test (#1011) .github/workflows/burn_cell.yml .github/workflows/nse_test.yml unit_test/test_nse/ci-benchmarks/aprox21_ci.out commit 2c84b843ca822452bc244cbc6ae8ff58516fd992 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Mon Oct 31 08:38:22 2022 -0400 swap h1 and p index for nse. (#1010) let p_index be the photoionization proton index for both aprox and non-aprox network. nse/actual_nse.H unit_test/test_nse/inputs_subch_full commit ced9a15b04e0e2550ae2e1299a7f086dfee9db6d Author: Michael Zingale Date: Sun Oct 30 20:27:54 2022 -0400 aprox21 does not work with the NSE table (#1006) networks/aprox21/actual_network_data.cpp commit 9f181b6d90075d2e8d7a96fd964069ca742dc2d6 Author: Michael Zingale Date: Sun Oct 30 20:17:47 2022 -0400 rename NSE_THERMO -> AUX_THERMO (#1003) there is nothing about NSE in using the auxiliary state to define the composition, and our choice of the aux composition is sufficiently general enough that it should work for non-NSE applications. This also renames set_nse_aux_from_X to set_aux_comp_from_X and puts it into eos_composition.H Finally, we still define NSE_THERMO for backwards compatibility, but it will be removed once application codes are ported. EOS/eos_composition.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvode.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/utils/numerical_jacobian.H interfaces/burner.H networks/Make.package networks/aprox19/aprox19.net networks/aprox19/nse.H networks/general_null/network_param_file.py networks/general_null/write_network.py networks/get_naux.py sphinx_docs/source/eos.rst sphinx_docs/source/nse.rst unit_test/burn_cell_sdc/burn_cell.H unit_test/test_react/main.cpp unit_test/test_sdc/main.cpp unit_test/test_sdc/react_zones.H unit_test/test_sdc_vode_rhs/vode_rhs_test.H commit 820f45d58bb8992ee76cbaed4c27050d9ea67cbf Author: Michael Zingale Date: Wed Oct 26 07:58:44 2022 -0400 we no longer need HSE_CXX_IMPLEMEMENTATION (#1000) all nets are C++ interfaces/network_initialization.cpp networks/ECSN/Make.package networks/Make.package networks/aprox13/Make.package networks/aprox19/Make.package networks/aprox21/Make.package networks/general_null/Make.package networks/ignition_chamulak/Make.package networks/ignition_reaclib/C-burn-simple/Make.package networks/ignition_reaclib/URCA-simple/Make.package networks/ignition_simple/Make.package networks/iso7/Make.package networks/nova/Make.package networks/nova2/Make.package networks/partition_test/Make.package networks/powerlaw/Make.package networks/primordial_chem/Make.package networks/rprox/Make.package networks/sn160/Make.package networks/subch_approx/Make.package networks/subch_full/Make.package networks/subch_simple/Make.package networks/triple_alpha_plus_cago/Make.package networks/vode_example/Make.package commit 1dbcf8c236d3db93c8ac40afb4969247f3995a90 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Oct 11 03:08:53 2022 +1100 added primordial chem networks (#997) Add the primordial chemistry network. This has 14 species + T evolution. Co-authored-by: Piyush Sharda networks/primordial_chem/Make.package networks/primordial_chem/NETWORK_PROPERTIES networks/primordial_chem/_parameters networks/primordial_chem/actual_network.H networks/primordial_chem/actual_network_data.cpp networks/primordial_chem/actual_rhs.H networks/primordial_chem/pynucastro.net commit 1831c7ca57f658e3f8a87d20ea3d2d789b89e99c Author: Michael Zingale Date: Mon Oct 10 11:55:11 2022 -0400 add BL_NO_FORT = TRUE to the remaining unit tests (#998) none of Microphysics needs Fortran unit_test/burn_cell/GNUmakefile unit_test/eos_cell/GNUmakefile unit_test/test_nse/GNUmakefile unit_test/test_part_func/GNUmakefile unit_test/test_screening/GNUmakefile unit_test/test_sdc_vode_rhs/GNUmakefile commit baa4f033098cbb76b6fe8106e49b6ac0f00fc4b3 Author: Michael Zingale Date: Mon Oct 3 19:16:11 2022 -0400 increase precision of output from burn_cell (#993) unit_test/burn_cell/burn_cell.H commit 7ef288cf57fed88b55ca85307eb1c729dbe5e22a Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Tue Oct 4 02:26:00 2022 +1100 Added more functionality to primordial chem EOS (#985) properly implement a multigamma-type EOS for primordial chemistry given dens/temp or dens/eint as inputs (with number densities of all species). This concludes all the changes that were required in the EOS for primordial_chem. EOS/README.md EOS/primordial_chem/_parameters EOS/primordial_chem/actual_eos.H EOS/primordial_chem/actual_eos_data.H EOS/primordial_chem/actual_eos_data.cpp commit fa0153099c2cb29d113b4c7d247e42e2da076ed2 Author: Michael Zingale Date: Sat Oct 1 09:01:48 2022 -0400 update changes CHANGES.md commit 76782c81e2b7d86fa2216c192a26b2e228649165 Author: Michael Zingale Date: Fri Sep 30 15:22:59 2022 -0400 add names to .zenodo.json (#995) .zenodo.json commit 9bf53bb5ba65f2195199f47478dee79748cde42c Author: Eric Johnson Date: Tue Sep 27 17:45:37 2022 -0400 Add a null screening routine (#992) Selected by `SCREEN_METHOD=null` closes #984 CHANGES.md Make.Microphysics_extern screening/screen.H sphinx_docs/source/screening.rst commit afd81bf854207095ec64349d2b1b8569fd852a9d Author: Michael Zingale Date: Tue Sep 27 14:47:46 2022 -0400 some fixes to burn_cell to allow for pynucastro python comparison (#991) this fixes the no-energy evolution, outputs some more detail and has an inputs file that correctly sets up the burn to match python unit_test/burn_cell/_parameters unit_test/burn_cell/burn_cell.H unit_test/burn_cell/ecsn_unit_test.out unit_test/burn_cell/inputs_subch_compare unit_test/burn_cell/subch_approx_unit_test.out commit b685b7d3b5e62066d9c3a5eb52c0826824764219 Author: Michael Zingale Date: Mon Sep 26 18:19:48 2022 -0400 update burn_cell with more info (#987) we now output the t=0 RHS and the number of steps taken unit_test/burn_cell/burn_cell.H unit_test/burn_cell/ecsn_unit_test.out unit_test/burn_cell/subch_approx_unit_test.out commit 5ab473fe101e8f2be53c3c7dda280125e7b063d8 Author: Michael Zingale Date: Mon Sep 26 15:20:30 2022 -0400 add the option to disable clipping species (#989) currently for both Strang and simplfiied-SDC integration, we clip the species in clean_state to lie in [0, 1]. But we already have step rejection logic that enforces this, and some testing shows that this clipping makes VODE work a lot harder. integration/VODE/_parameters integration/VODE/vode_type_simplified_sdc.H integration/VODE/vode_type_strang.H commit 1c7ce889539f09e24c2ff605a32333984eeb2889 Merge: 9058965d 02c97fe6 Author: Michael Zingale Date: Sun Sep 25 13:08:17 2022 -0400 Merge branch 'main' into development commit 9058965d9ec0f1294f1336e7d6b39240e31bca5b Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Sep 23 15:52:17 2022 -0400 improve and clean up nse solver (#982) Added convergence check for hybrj, and switched back to mode 1 Transplant the fine-tuning of initial guess procedure in pynucastro for scipy.fsolve to hybrj solver, making it more robust at solving nse. change criteria for making the table of solving initial guesses. With fine-tuning, it is easier to solve them. modify NR procedure to use constraint equations for hybrj (although it is almost never a case we should use nr over hybrj, especially with the fine-tuning procedure added) Add partition function and spin state to complete it. nse/_parameters nse/actual_nse.H nse/make_table/burn_cell.H unit_test/test_nse/_parameters unit_test/test_nse/inputs_aprox13 unit_test/test_nse/inputs_aprox19 unit_test/test_nse/inputs_aprox21 unit_test/test_nse/inputs_iso7 unit_test/test_nse/inputs_subch2 unit_test/test_nse/nse_example.H commit 5ca9c57c10a2c12e12b03ee750969ad884b7b506 Author: Michael Zingale Date: Thu Sep 22 13:46:49 2022 -0400 add a unit test for partition functions (#980) this relies on the partition_functions.H written out by a pynucastro net networks/partition_test/Make.package networks/partition_test/NETWORK_PROPERTIES networks/partition_test/_parameters networks/partition_test/actual_network.H networks/partition_test/actual_network_data.cpp networks/partition_test/actual_rhs.H networks/partition_test/inputs.burn_cell.VODE networks/partition_test/part_test.py networks/partition_test/partition_functions.H networks/partition_test/pynucastro.net networks/partition_test/reaclib_rates.H networks/partition_test/table_rates.H networks/partition_test/table_rates_data.cpp networks/partition_test/tfactors.H unit_test/test_part_func/GNUmakefile unit_test/test_part_func/Make.package unit_test/test_part_func/_parameters unit_test/test_part_func/main.cpp unit_test/test_part_func/pf_cell.H commit 02c97fe60ef95a860b1513a5271d3cf1d9d9d9d1 Author: Piyush Sharda <34922596+psharda@users.noreply.github.com> Date: Fri Sep 23 01:58:11 2022 +1000 added a new EOS folder for primordial chem (#981) Co-authored-by: Piyush Sharda EOS/primordial_chem/Make.package EOS/primordial_chem/_parameters EOS/primordial_chem/actual_eos.H EOS/primordial_chem/actual_eos_data.H EOS/primordial_chem/actual_eos_data.cpp EOS/primordial_chem/eos_composition.H commit e34b20a4023ee709f903bccda523491097f1f563 Author: Michael Zingale Date: Wed Sep 21 10:21:09 2022 -0400 add the number of steps taken to the burn_t (#970) integration/ForwardEuler/actual_integrator.H integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H interfaces/burn_type.H unit_test/test_react/main.cpp unit_test/test_react/react_zones.H commit 1adf1bdb9d7654215c985d2c27b0645520dabde8 Author: Michael Zingale Date: Tue Sep 13 15:27:18 2022 -0400 add a C++ version of Powell's hybrid method (#976) this is a conversion of the Fortran MINPACK hybrj to C++ as a templated header-only library. The main functional change is that we assume square matrices now. Make.Microphysics_extern nse/_parameters nse/actual_nse.H nse/make_table/burn_cell.H util/hybrj/Make.package util/hybrj/README.md util/hybrj/hybrj.H util/hybrj/hybrj.H.hack util/hybrj/hybrj_dogleg.H util/hybrj/hybrj_enorm.H util/hybrj/hybrj_qform.H util/hybrj/hybrj_qrfac.H util/hybrj/hybrj_r1mpyq.H util/hybrj/hybrj_r1updt.H util/hybrj/hybrj_type.H util/hybrj/test/GNUmakefile util/hybrj/test/Make.package util/hybrj/test/main.cpp commit 91211ba4578f0d8756fcb118cda16f1c3b0b935e Author: Michael Zingale Date: Wed Sep 7 10:45:42 2022 -0400 fix screening of pynucastro approx nets (#978) networks/subch_approx/actual_rhs.H networks/subch_approx/reaclib_rates.H networks/subch_simple/actual_rhs.H networks/subch_simple/reaclib_rates.H unit_test/burn_cell/subch_approx_unit_test.out commit b803a42d8ccc36334a6ad517411d9bd73ad3b3da Author: Michael Zingale Date: Wed Sep 7 09:22:57 2022 -0400 correct the species derivatives in the analytic SDC Jacobian (#956) This addresses #729 for simplified SDC. It captures the (small) effect that the df/dX |_e means that if we hold e constant and change species, then T needs to change (this is all with rho not changing) integration/VODE/vode_rhs_simplified_sdc.H commit 6562231332d3346b43ce15c84998d076e3d1b5ac Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Sat Sep 3 08:06:43 2022 -0400 add default index so p_index is not initialized to 0, which causes issues (#979) To fix the issue where nse indices are initialized to 0, which causes an issue when the network does not have photoionization proton. All indices are now initialized to -1 to prevent this issue. nse/nse_index.cpp commit 6506e1ea2406ac62b21e7dc970237e68dc295492 Author: Michael Zingale Date: Fri Sep 2 16:31:36 2022 -0400 add a simple driver to make an NSE table (#974) this can be built simply by typing make in nse/make_table/ nse/actual_nse.H nse/make_table/GNUmakefile nse/make_table/Make.package nse/make_table/README.md nse/make_table/_parameters nse/make_table/burn_cell.H nse/make_table/main.cpp commit 41703270a91d089136af926c7d64b0f26a672596 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Fri Sep 2 11:50:34 2022 -0400 Nse init (#977) This pr attempts to address issue #972 . Also gives a check on whether the input electron fraction is within the valid range. If not, the solver gets electron fraction by using the actual electron fraction. Also renamed files and edited README since we are not doing any integration anymore, no more burning. nse/Make.package nse/actual_nse.H nse/nse_index.H nse/nse_index.cpp unit_test/test_nse/Make.package unit_test/test_nse/README.md unit_test/test_nse/main.cpp unit_test/test_nse/nse_example.H commit 8163803658d0a2942608200062620f44d9d308d5 Merge: 9e8b9932 8d22e048 Author: Michael Zingale Date: Thu Sep 1 09:56:20 2022 -0400 Merge branch 'development' commit 8d22e048ab9da37e5f120032267c5745852ddad6 Author: Michael Zingale Date: Thu Sep 1 09:56:04 2022 -0400 update changes CHANGES.md commit e3a6cb1103b1b6053fc71fd22de791c3d6ee96c8 Author: Michael Zingale Date: Fri Aug 26 21:30:12 2022 -0400 some more NSE cleaning (#973) this allows us to come in with a y_e and not rederive it from the mass fractions. In this manner, we can just use rho, T, and y_e as inputs. It also marks state as const in a few places. nse/_parameters nse/actual_nse.H unit_test/Make.unit_test commit 60470c30bf3490510d88af54e60c48e643d36193 Author: Michael Zingale Date: Fri Aug 26 18:41:51 2022 -0400 simplify the NSE driver (#971) there is no sense of time in an NSE state, so eliminate the loop over time unit_test/test_nse/_parameters unit_test/test_nse/burn_cell.H unit_test/test_nse/inputs_aprox13 unit_test/test_nse/inputs_aprox19 unit_test/test_nse/inputs_aprox21 unit_test/test_nse/inputs_iso7 unit_test/test_nse/inputs_subch2 commit b9a0f9aa1037802df18cb108af38b2d3de76fda6 Author: Michael Zingale Date: Mon Aug 22 13:13:41 2022 -0400 an even simpler subch net (#964) This is a further approximation of the subch_full network. In addition to removing the same 6 nuclei as subch_approx (by doing an (a,p)(p,g) approximation), it also removes * The reverse of C12+C12, C12+O16, and O16+O16 -- these reverse rates are not in aprox13 * The C12+Ne20 rates and their reverses * (a,g) links between Na23 and Al27 and between Al27 and P31 -- these are not in aprox13 networks/subch_simple/Make.package networks/subch_simple/NETWORK_PROPERTIES networks/subch_simple/README.md networks/subch_simple/_parameters networks/subch_simple/actual_network.H networks/subch_simple/actual_network_data.cpp networks/subch_simple/actual_rhs.H networks/subch_simple/inputs.burn_cell.VODE networks/subch_simple/pynucastro.net networks/subch_simple/python_net_approx.ipynb networks/subch_simple/reaclib_rates.H networks/subch_simple/subch_simple.png networks/subch_simple/subch_simple.py networks/subch_simple/table_rates.H networks/subch_simple/table_rates_data.cpp networks/subch_simple/table_type.H commit fe93b5a193082b91fc0e73e4c87536b7fbcaa095 Author: Michael Zingale Date: Tue Aug 16 10:41:28 2022 -0400 start templating pynucastro nets (#950) this updates the subch_approx and subch_full nets with the latest pynucastro C++ output in particular, it now templates the rate evals, resulting in a speed-up w/o changing answers networks/subch_approx/actual_rhs.H networks/subch_approx/reaclib_rates.H networks/subch_full/actual_rhs.H networks/subch_full/reaclib_rates.H commit d7421d4a9219c82966cbda41a7e837d90614bac5 Author: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu Aug 11 12:17:07 2022 -0400 NSE solver (#963) This adds the ability to solve for the NSE state of a network, following the formulation in Calder et al. 2007. To be solvable, this requires at least 1 nuclei with Z != N (due to the structure of the Jacobian). This is a first step in allowing nets to automatically transition to NSE. Make.Microphysics_extern constants/fundamental_constants.H interfaces/burn_type.H interfaces/eos_type.H nse/Make.package nse/actual_nse.H unit_test/test_nse/GNUmakefile unit_test/test_nse/Make.package unit_test/test_nse/README.md unit_test/test_nse/_parameters unit_test/test_nse/burn_cell.H unit_test/test_nse/inputs_aprox13 unit_test/test_nse/inputs_aprox19 unit_test/test_nse/inputs_aprox21 unit_test/test_nse/inputs_iso7 unit_test/test_nse/inputs_subch2 unit_test/test_nse/main.cpp commit ffefdd6216b438f1418d61c7cc40192c7495c1cb Author: Michael Zingale Date: Thu Aug 4 16:20:21 2022 -0400 fix the screening of derived ReacLib rates (#957) in some cases, the forward rates were derived from the reverse rates via detailed balance in ReacLib, but we were screening symmetrically based on the reverse rate (because ReacLib calls all derived rates "reverse", even if they are exothermic) networks/subch_approx/actual_rhs.H networks/subch_approx/table_rates.H networks/subch_full/actual_rhs.H networks/subch_full/reaclib_rates.H networks/subch_full/table_rates.H unit_test/burn_cell/subch_approx_unit_test.out commit 9e8b9932065142da4873bf45235d21f5d79edec2 Author: Brendan Boyd <42776109+biboyd@users.noreply.github.com> Date: Tue Aug 2 14:24:58 2022 -0400 update urca network (#958) updates URCA-simple network using latest pynucastro release. This update addresses issue #952 networks/ignition_reaclib/URCA-simple/reaclib_rate_metadata.dat networks/ignition_reaclib/URCA-simple/reaclib_rates.H networks/ignition_reaclib/URCA-simple/table_rates.H networks/ignition_reaclib/URCA-simple/table_rates_data.cpp commit 593f02b0d0c17838ba1dbc0d780a42c185e8d9c2 Author: Michael Zingale Date: Sun Jul 31 14:07:56 2022 -0400 Simple sdc analytic jac memory (#955) this is similar to the change we did for the jacobian = 3 version in #917 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 commit a4952214a8d74d391a1e600d8b5e7d7a835ac5cb Author: Michael Zingale Date: Wed Jul 20 17:38:16 2022 -0400 only output stats from I/O processor (#953) unit_test/test_react/main.cpp commit 7acbea131aea94c0bf50cfd8911cb3fdfb9d6f38 Author: Michael Zingale Date: Tue Jul 19 17:08:00 2022 -0400 update burn_cell CI tests (#951) add an ECSN unit test switch subch_full to subch_approx .github/workflows/burn_cell.yml unit_test/burn_cell/README.md unit_test/burn_cell/ecsn_unit_test.out unit_test/burn_cell/inputs_subch_approx unit_test/burn_cell/subch2_unit_test.out unit_test/burn_cell/subch_approx_unit_test.out commit 29a6e0f13434da9ece6f4e740a3f06f4e1a62060 Author: Eric Johnson Date: Sat Jul 16 10:49:50 2022 -0400 Template out T derivatives from screening methods (#949) also remove the commented-out density derivatives in screen5 screening/screen.H commit da28cc0d917e9763c38e67c386bf85b64992540b Author: Max Katz Date: Thu Jul 14 13:14:12 2022 -0400 Require test_screening factors to be evaluated at compile time (#948) This is the fix to the issue observed in #946, which was a GPU stack overflow caused by the recursion in gcem that does the std::exp evaluation. unit_test/test_screening/screening_util.cpp commit fbfb1e359e5b2f69b2a32fdc06c6e4bbe4c1378f Author: Michael Zingale Date: Thu Jul 14 13:01:54 2022 -0400 rename subch -> subch_approx and subch2 -> subch_full (#947) .github/workflows/burn_cell.yml CHANGES.md networks/subch networks/subch/README.md networks/subch2 networks/subch_approx/Make.package networks/subch_approx/NETWORK_PROPERTIES networks/subch_approx/README.md networks/subch_approx/_parameters networks/subch_approx/actual_network.H networks/subch_approx/actual_network_data.cpp networks/subch_approx/actual_rhs.H networks/subch_approx/inputs.burn_cell.VODE networks/subch_approx/pynucastro.net networks/subch_approx/python_net_approx.ipynb networks/subch_approx/reaclib_rates.H networks/subch_approx/subch_approx.png networks/subch_approx/subch_approx.py networks/subch_approx/table_rates.H networks/subch_approx/table_rates_data.cpp networks/subch_approx/table_type.H networks/subch_full/Make.package networks/subch_full/NETWORK_PROPERTIES networks/subch_full/README.md networks/subch_full/_parameters networks/subch_full/actual_network.H networks/subch_full/actual_network_data.cpp networks/subch_full/actual_rhs.H networks/subch_full/inputs.burn_cell.VODE networks/subch_full/network_plot.py networks/subch_full/pynucastro.net networks/subch_full/reaclib_rates.H networks/subch_full/subch_full.png networks/subch_full/subch_full.py networks/subch_full/subch_network_explore.ipynb networks/subch_full/subch_plotting.ipynb networks/subch_full/table_rates.H networks/subch_full/table_rates_data.cpp networks/subch_full/table_type.H sphinx_docs/source/networks.rst sphinx_docs/source/subch_approx.png sphinx_docs/source/subch_full.png commit 6c6c6fcd6e2c33fd37dba5a40724198d39f78e9f Author: Michael Zingale Date: Wed Jul 13 15:17:02 2022 -0400 subch net is now an approx version of subch2 (#942) This removes 6 nuclei from subch2 by doing an (a,p)(p,g) approximation. networks/subch/NETWORK_PROPERTIES networks/subch/_parameters networks/subch/actual_network.H networks/subch/actual_network_data.cpp networks/subch/actual_rhs.H networks/subch/inputs.burn_cell.VODE networks/subch/network_plot.py networks/subch/pynucastro.net networks/subch/python_net_approx.ipynb networks/subch/reaclib_rates.H networks/subch/subch.png networks/subch/subch.py networks/subch2/subch2.py sphinx_docs/source/networks.rst sphinx_docs/source/subch.png sphinx_docs/source/subch2.png unit_test/burn_cell/Mass_Fractions_C++.ipynb unit_test/burn_cell/compare_networks.ipynb unit_test/burn_cell/inputs_subch_compare commit eab79fe28dfd23c806a6ef5a69294d41d36eab19 Author: Michael Zingale Date: Wed Jul 13 15:16:35 2022 -0400 make the Jacobian type part of dvode_type (#944) also switch some ints to short to save memory integration/VODE/actual_integrator.H integration/VODE/actual_integrator_simplified_sdc.H integration/VODE/vode_dvjac.H integration/VODE/vode_rhs_simplified_sdc.H integration/VODE/vode_type.H util/linpack.H commit 51acf48d187293c06068bb9c569f4938001e4d00 Author: Eric Johnson Date: Thu Jul 7 10:51:22 2022 -0400 Start templating out T derivatives from screening (#941) This just adds template parameters to the individual methods and wrappers that disable the T derivatives if we're doing a numerical Jacobian. screening/screen.H commit 5b1496269820067db9fd396ed3b9eed3b34e69bf Author: Michael Zingale Date: Thu Jul 7 10:23:04 2022 -0400 hardcode the reaclib rates in the networks (#934) this updates all of the pynucastro nets we no longer need the reaclib_rates_metadata.dat file .github/workflows/burn_cell.yml Make.Microphysics_extern networks/ECSN/actual_network.H networks/ECSN/actual_network_data.cpp networks/ECSN/actual_rhs.H networks/ECSN/reaclib_rate_metadata.dat networks/ECSN/reaclib_rates.H 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.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_network.H networks/ignition_reaclib/URCA-simple/actual_network_data.cpp 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/actual_network.H networks/nova/actual_network_data.cpp networks/nova/actual_rhs.H networks/nova/nova.png networks/nova/reaclib_rate_metadata.dat networks/nova/reaclib_rates.H networks/nova2/actual_network.H networks/nova2/actual_network_data.cpp networks/nova2/actual_rhs.H networks/nova2/nova.png networks/nova2/reaclib_rate_metadata.dat networks/nova2/reaclib_rates.H networks/sn160/actual_network.H networks/sn160/actual_network_data.cpp networks/sn160/actual_rhs.H networks/sn160/reaclib_rate_metadata.dat networks/sn160/reaclib_rates.H networks/subch/actual_network.H networks/subch/actual_network_data.cpp networks/subch/actual_rhs.H networks/subch/reaclib_rate_metadata.dat networks/subch/reaclib_rates.H networks/subch2/actual_network.H networks/subch2/actual_network_data.cpp networks/subch2/actual_rhs.H networks/subch2/reaclib_rate_metadata.dat networks/subch2/reaclib_rates.H unit_test/burn_cell/subch2_unit_test.out commit 94202288bd6ba64819a65015291a06c2c001c682 Author: Max Katz Date: Tue Jul 5 09:31:09 2022 -0400 Use new screening interface in test_screening (#940) unit_test/test_screening/screening_util.cpp commit cfab8d9afe94ef71c50107e7e66e3d7eaae6a201 Author: Michael Zingale Date: Mon Jul 4 17:38:46 2022 -0400 add the name of the screening method to screen.H (#939) screening/screen.H unit_test/test_screening/main.cpp commit 6d32ebec9c4fbe49e98bd662c7ab50d4a52a80df Author: Eric Johnson Date: Mon Jul 4 15:49:24 2022 -0400 Fix typo in chugunov2007 screening (#937) screening/screen.H commit 89311f02e39e0805595a5e4a2dd32fe9def28a65 Author: Michael Zingale Date: Mon Jul 4 09:24:15 2022 -0400 powerlaw overrides the default jacobian to 2 -- reset it here (#936) for test_rhs, we need the analytic Jacobian, even though it does nothing here. unit_test/test_rhs/inputs_powerlaw commit f9115a922540b47bffe58e1e7c1be7da425a32be Author: Michael Zingale Date: Sun Jul 3 21:09:23 2022 -0400 use std::cbrt() where applicable (#932) rates/aprox_rates.H rates/tfactors.H screening/screen.H commit 995cdf54f93eb000651fba9e9d6b58c78744b4ed Author: Michael Zingale Date: Sun Jul 3 21:09:05 2022 -0400 test_rhs only makes sense with jacobian = 1 (#935) the idea of this test is to directly call the network's RHS functions, so we only want to test the Jacobian that the network implements unit_test/test_rhs/main.cpp commit 7bd18afcfbccf15310d0a7b1fa19cec25ffc43b8 Author: Michael Zingale Date: Fri Jul 1 09:10:05 2022 -0400 update changes CHANGES.md commit a6a757145e74e0eb794d2ee9b68aaefc6320be8c Author: Michael Zingale Date: Tue Jun 28 20:23:00 2022 -0400 add screening docs (#933) sphinx_docs/source/index.rst sphinx_docs/source/refs.bib sphinx_docs/source/screening.rst commit 5146750acbb84805464695b145a4ee63506ec940 Author: Eric Johnson Date: Thu Jun 23 15:49:17 2022 -0400 Add new reaction rate screening routines (#887) This adds 2 new screening formulations based on Chugunov, DeWitt, and Yakovlev 2007 and Chugunov and DeWitt 2009 as discussed in #146. Make.Microphysics_extern screening/screen.H screening/screen_data.H unit_test/test_screening/GNUmakefile commit 42f480267136932d4c7ff839767ba06a9402c08c Author: Eric Johnson Date: Wed Jun 22 17:55:48 2022 -0400 Rename main screening routine from screen5 to screen (#931) In preparation for #887 networks/ECSN/actual_rhs.H networks/ignition_chamulak/actual_rhs.H networks/ignition_reaclib/C-burn-simple/actual_rhs.H networks/ignition_reaclib/URCA-simple/actual_rhs.H networks/ignition_simple/actual_rhs.H networks/nova/actual_rhs.H networks/nova2/actual_rhs.H networks/rhs.H networks/rprox/actual_rhs.H networks/sn160/actual_rhs.H networks/subch/actual_rhs.H networks/subch2/actual_rhs.H networks/triple_alpha_plus_cago/actual_rhs.H screening/screen.H unit_test/test_screening/screening_util.cpp commit ef2eb86c6809bb9b5c03abe52334a55b3bc8bab6 Author: Max Katz Date: Thu Jun 16 17:20:43 2022 -0400 Update pynucastro nets (#930) networks/ECSN/20f-20o_electroncapture.dat networks/ECSN/20ne-20f_electroncapture.dat networks/ECSN/_parameters networks/ECSN/actual_network.H networks/ECSN/actual_rhs.H networks/ECSN/reaclib_rate_metadata.dat networks/ECSN/reaclib_rates.H networks/ECSN/table_rates.H networks/ignition_reaclib/C-burn-simple/_parameters networks/ignition_reaclib/C-burn-simple/actual_network.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/C-burn-simple/table_rates.H networks/ignition_reaclib/URCA-simple/_parameters networks/ignition_reaclib/URCA-simple/actual_network.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/ignition_reaclib/URCA-simple/table_rates.H networks/nova/_parameters networks/nova/actual_network.H networks/nova/actual_rhs.H networks/nova/reaclib_rate_metadata.dat networks/nova/reaclib_rates.H networks/nova/table_rates.H networks/nova2/_parameters networks/nova2/actual_network.H networks/nova2/actual_rhs.H networks/nova2/reaclib_rate_metadata.dat networks/nova2/reaclib_rates.H networks/nova2/table_rates.H networks/sn160/_parameters networks/sn160/actual_network.H networks/sn160/actual_rhs.H networks/sn160/reaclib_rate_metadata.dat networks/sn160/reaclib_rates.H networks/sn160/table_rates.H networks/subch/_parameters networks/subch/actual_network.H networks/subch/actual_rhs.H networks/subch/reaclib_rate_metadata.dat networks/subch/reaclib_rates.H networks/subch/table_rates.H networks/subch2/actual_rhs.H networks/subch2/reaclib_rate_metadata.dat networks/subch2/reaclib_rates.H networks/subch2/table_rates.H commit 0a8fd568769e9d288c85bc70cfaa60b90e89840c Author: Jean M. Sexton Date: Thu Jun 16 13:34:33 2022 -0700 Change aion, aion_inv, and zion to have constexpr for ROCm (#929) This seems to work for Castro/Exec/hydro_tests/Sod with rocm 5.1.0 .github/workflows/find_changed_files.py networks/general_null/network_header.template commit 35a553f4b8590adafc4b0d8d69ec5c1dc972ddd8 Author: Max Katz Date: Tue Jun 14 11:15:50 2022 -0400 Add some more [[maybe_unused]] to Helmholtz (#928) EOS/helmholtz/actual_eos.H commit b8e427c1f7974b86b2cf3551b8cb918294976a11 Author: Michael Zingale Date: Mon Jun 6 10:21:21 2022 -0400 add comment noting that these are CF88 rates (#927) rates/aprox_rates.H commit d740207cd6b53f1853a88d51cd1e02b3455beed5 Author: Michael Zingale Date: Wed Jun 1 08:06:33 2022 -0400 update for release CHANGES.md commit 52173caf781630bc5c2d1dd3bf654c5d37cd6c69 Author: Michael Zingale Date: Sun May 29 18:13:06 2022 -0400 add a new action that runs burn_cell (#924) this will be able to tell us if we broke the execution this uses a pynucastro net, and we can leverage this with pynucastro CI to autogenerate the network there as well. .github/workflows/burn_cell.yml unit_test/burn_cell/README.md unit_test/burn_cell/inputs_subch2 unit_test/burn_cell/subch2_unit_test.out commit 39742967595553fdb8151f17253257dcf8709770 Author: Michael Zingale Date: Sun May 22 11:12:34 2022 -0400 add runtime parameters to disable some subch2 rates (#921) networks/subch2/_parameters networks/subch2/actual_network.H networks/subch2/actual_rhs.H networks/subch2/reaclib_rate_metadata.dat networks/subch2/reaclib_rates.H networks/subch2/subch2.py sphinx_docs/source/networks.rst sphinx_docs/source/subch2.png commit 75a69f607310824e8bd4cc55ee28787378f6aa69 Author: Michael Zingale Date: Sun May 1 09:06:12 2022 -0400 add subch2 note CHANGES.md commit 61c46f9e74a69fb70cc2de90f3bc4dfd2f854a2d Author: Max Katz 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 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 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 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 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 Date: Fri Apr 1 11:38:41 2022 -0400 update changes CHANGES.md commit 4f1304edcb92dd3e6711496b5437a1e07dc86591 Author: Michael Zingale 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 Date: Fri Mar 25 13:16:10 2022 -0400 add pivoting note (#904) sphinx_docs/source/templated_networks.rst commit b2f7b602c0cf7efd5d5a392a2982558e8771f597 Author: Michael Zingale 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 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 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 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 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 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 Date: Sat Mar 12 17:29:40 2022 -0500 document the EOS modes (#903) sphinx_docs/source/eos.rst commit b7734485e3bfc658dcf225d9785e49cde6821275 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Feb 27 17:46:08 2022 -0500 fix some array sizes in sneut (#880) neutrinos/sneut5.H commit 260ac6168eaf3a2d8efebc4faa42fdd0f10f720d Author: Eric Johnson 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 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 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 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 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 Date: Tue Feb 1 08:19:59 2022 -0500 update changes CHANGES.md commit 0edf069b80564b042f6011b32d1ddc71f18c782b Author: Michael Zingale 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 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 Date: Sat Jan 15 16:55:51 2022 -0800 Initialize VODE type data (#876) integration/VODE/vode_dvode.H commit d89cb25ceb7e59d4dd78e2b7b0e19ad838c2cf4b Author: Michael Zingale 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 Date: Fri Jan 14 20:21:36 2022 -0500 fix shadowing in 3-alpha (#874) rates/aprox_rates.H commit 6cc2eeccd7ad2d5ca9e8b5abba54df21abcea0f7 Author: Michael Zingale Date: Fri Jan 14 18:45:15 2022 -0500 silence some unused var warnings (#875) screening/screen.H commit c498d2e8c9897ddd9b239a0f452115ae3896d94a Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Jan 2 16:16:46 2022 -0500 fix make typo (#858) integration/Make.package commit a2979b235c9b4933293e4341633da1bea848f87d Author: Michael Zingale 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 Date: Sat Jan 1 11:33:31 2022 -0500 update changes CHANGES.md commit 8080dc192beacbb6afb9018a65131efa1cfde40c Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Dec 1 09:30:29 2021 -0500 update changes CHANGES.md commit c45dec4e4b84c22034bd674f2f66666cf431f16d Author: Michael Zingale 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 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 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 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 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 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 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 Date: Sat Nov 6 14:00:41 2021 -0400 Merge branch 'main' into development commit 323535bbdccb8b3137ce0dda369723de604bcdfd Author: Michael Zingale 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 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 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 Date: Mon Nov 1 09:32:25 2021 -0400 update for 21.11 CHANGES.md commit 02a8f1ef0250df29d26cf06b6ec77033b88d0b97 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Sep 1 08:15:16 2021 -0400 update changes for 21.09 CHANGES.md commit b079ee86ca830cc2622d192fb9e7f21b80bcfc9e Author: Michael Zingale 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 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 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 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 Date: Mon Aug 30 09:32:54 2021 -0400 fix compilation with Strang + NSE (#752) interfaces/burner.H commit 71ae6bfac1cef1902bb94c7e4177df90559bbb8a Author: Michael Zingale Date: Fri Aug 27 11:36:53 2021 -0400 fix mathjax rendering (#750) sphinx_docs/source/conf.py commit d5a72a5d3ec2f831c2bf327c39d16ff8e4472c3c Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 Date: Sun Aug 1 20:43:43 2021 -0400 update changes CHANGES.md commit edc950da91a7c94e2870d6c71b13838d833f36e4 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 Date: Wed Jul 28 21:24:00 2021 -0700 Merge commit 'b904ef8bedaa64a980aff33dce4f2a1ae9d9dd68' as 'util/gcem' commit b904ef8bedaa64a980aff33dce4f2a1ae9d9dd68 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Jul 1 09:15:53 2021 -0400 Merge branch 'development' commit 7f332d214b11445a92674187974ba496d8b05a7f Author: Michael Zingale Date: Thu Jul 1 09:15:42 2021 -0400 21.07 changes CHANGES.md commit f2da8cec7b2037a224811bc580a706ed63d48829 Author: Michael Zingale Date: Tue Jun 29 10:22:12 2021 -0400 add amrex:: prefix to Real (#704) interfaces/microphysics_F.H commit 0f336e49b71110f3dadd35f29347a0ae7bc8c3e5 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Tue Jun 1 10:14:41 2021 -0400 highlight major changes CHANGES.md commit 243e667582683658c23f6995befe1c4a27dea516 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun May 2 09:55:34 2021 -0400 update changes CHANGES.md commit 89320520a8e4d44e4926fc346f83d7c15a93d877 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Apr 1 09:32:34 2021 -0400 update changes CHANGES.md commit e12a253e23a20f783aa92619545342954ec4a3e0 Author: Max Katz 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 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 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 integration/VODE/actual_integrator.H interfaces/burner.H commit 7c7d1caa87625a5ea6160c4ef5f1583ebc99870b Author: Max Katz 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 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 Date: Mon Mar 22 18:15:28 2021 -0400 add include (#630) unit_test/write_job_info.cpp commit 08faa5782ae6d778b07646b09cf449edd42bb5a1 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Feb 28 12:05:55 2021 -0500 revert a debugging hack (#608) unit_test/react_util.H commit 46fcc130da061a1e4875e164acca6696e08797f5 Author: Michael Zingale Date: Sat Feb 27 17:59:53 2021 -0500 fix forward Euler integration (#606) integration/ForwardEuler/actual_integrator.H commit d1bf7bc64ff8741fb4ad3cb3eecabb649b15311d Author: Max Katz 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 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 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 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 Date: Mon Feb 22 19:50:23 2021 -0500 fix true SDC compilation (#596) interfaces/burn_type.H commit c915a578477228a17b0bd5987849de4b62cf2bc5 Author: Michael Zingale Date: Mon Feb 22 12:23:31 2021 -0500 add discussions (#595) README.md commit 606836398c107213b7ad817203ebdce336e6729e Author: Max Katz 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 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 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 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 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 Date: Thu Feb 18 09:23:32 2021 -0800 Remove for_jacobian_tderiv (#580) networks/aprox13/actual_rhs.H commit dacd8ef0ce03b590c014eab61637831cc1527171 Author: Max Katz 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 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 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 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 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 Date: Wed Feb 17 18:18:07 2021 -0800 Remove deriva (#579) networks/aprox13/actual_rhs.H commit 590861dad0800c5e9003b6269e218d00a4983ca6 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Feb 3 20:30:46 2021 -0500 fix an asset on the GPU (#557) screening/screen.H commit 57238ba6b075d670213014f319a3294aa148e314 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Jan 17 10:59:54 2021 -0500 update doc pointer (#537) README.md commit 1dafd2e6849935987c117b9835f2cec6f6007973 Author: Michael Zingale 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 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&>(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 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 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 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 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 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 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 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 Date: Sun Jan 10 06:02:42 2021 -0800 jacobian override needs correct namespace (#528) networks/powerlaw/_parameters commit 6279aacf181aea76fae527335531dd47a7161190 Author: Michael Zingale 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 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 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 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 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 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 Date: Wed Jan 6 11:01:37 2021 -0500 fix breakout EOS compilation (#521) EOS/breakout/actual_eos.H commit 20c2e2711b2587a0f7d79c635971557fdb5bb57d Author: Michael Zingale 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 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 Date: Tue Jan 5 14:09:30 2021 -0500 fix CUDA compilation (#520) unit_test/write_job_info.cpp commit 305901c0376fcd03ad35d44e0e35af8707c3c28e Author: Michael Zingale 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 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 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 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 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 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 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 Date: Mon Jan 4 06:49:37 2021 -0800 Some updates to the README (#517) README.md commit e6a784c6f0dc2b41c3cde4ca3ee8a1d58ca3388e Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Dec 24 07:20:43 2020 -0800 Fix iso7 Fortran finalization (#484) networks/iso7/actual_network.F90 commit 6f97814076988c00a3cba5cdc9c5d2bcef5c599f Author: Max Katz 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::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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Dec 17 22:20:58 2020 -0500 fix doc builds (#463) sphinx_docs/source/conf.py commit 0bbd91c02f5cd6770baa8200cac7179441763d43 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Dec 3 12:45:33 2020 -0500 fix more github-linguist stuff (#451) .gitattributes commit 76599f9f6d44d25729a7cc26f6061140b964a3e9 Author: Michael Zingale 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 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 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 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 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 Date: Sun Nov 29 18:50:54 2020 -0500 ignore Jupyter and TeX in language stats (#444) .gitattributes commit ac5ed9a09b49065bab82d993c1b14d4e9eaece3d Author: Max Katz Date: Sun Nov 22 05:24:01 2020 -0800 Add include (#440) EOS/helmholtz/actual_eos.H commit bf864ef7fd5cb31bf74445298de538e73cbfb40a Author: Michael Zingale 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 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 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 Date: Wed Nov 18 12:53:51 2020 -0800 Fix capitalization (#432) opacity/breakout/actual_opacity.H commit 3069e855717602fa11b66220767e978a36a43c55 Author: Max Katz 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 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 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 Date: Wed Nov 18 05:29:16 2020 -0800 Add includes (#429) constants/fundamental_constants.H commit 7d6a60abdec3cfbc60064207aabd442349619c9b Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Tue Oct 27 12:43:47 2020 -0400 fix #if -> #ifdef (#406) integration/VODE/vode_type.F90 commit 789ba2f010fab83664eae92af3e9045f99a87576 Author: Michael Zingale 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 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 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 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 Date: Thu Oct 1 07:48:07 2020 -0400 update changes CHANGES.md commit ee0b99f301693ad98ed7183faa08cff3f32de452 Author: Michael Zingale Date: Fri Sep 25 12:37:40 2020 -0400 update changes CHANGES.md commit 08b5d9de0e57166ace2328afb25342ed5d67cf8c Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Sun Sep 6 12:56:01 2020 -0400 fix compilation interfaces/microphysics.F90 commit acf72fade7b0722d9c31fa0068ae51c9059adb29 Author: Michael Zingale 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 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 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 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 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 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 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 Date: Tue Sep 1 10:04:04 2020 -0400 update changes CHANGES.md commit 4b73a5293031916a5301cbb2d7689f8a008d9f42 Author: Michael Zingale 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 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 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 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 Date: Fri Aug 28 19:53:24 2020 -0400 update changes CHANGES.md commit e6ed3f2f6259d2d67b70c97f4839015f3945d42b Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Jul 31 11:00:34 2020 -0400 update the changelog CHANGES.md commit ca01493910f41cc7efe89cb40af5f86fca2a2471 Author: Michael Zingale 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 Date: Sun Jul 26 17:29:26 2020 -0400 fix NAUX for this network (#360) networks/breakout/NETWORK_PROPERTIES commit 5bc24e1fb43b3f540c46e995a34fca3795d76c53 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Jul 15 21:07:57 2020 -0400 eliminate some divides (#342) EOS/composition.F90 commit 710ddb8f8b101283e188c27be07ab184199395a8 Author: Michael Zingale 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 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 Date: Wed Jul 8 11:01:38 2020 -0400 Merge branch 'main' into development commit ea9007c7ea75b7d522ea742e4cb66ba870cb2114 Author: Max Katz 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 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 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 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 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 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 Date: Wed Jul 1 08:52:08 2020 -0400 update changes CHANGES.md commit 8cadd69dd4fc7f9201dc28d7cf80b5341b1ae72c Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri May 1 08:48:31 2020 -0400 Merge branch 'development' commit 6acbe6fbb86a72df9fec9796f0898a3ea315688a Author: Michael Zingale Date: Fri May 1 08:47:19 2020 -0400 some updates CHANGES.md commit 55ce324ed87f5a3feabd834294acc868f7e9710f Author: Michael Zingale 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 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 Date: Fri Apr 24 02:44:47 2020 -0700 Remove unused variables neutrinos/sneut5.H rates/aprox_rates.H commit 5d868e82a6752981dced341685896859dbbf6d24 Author: Max Katz Date: Sun Apr 19 22:23:26 2020 -0700 Only include RHS if using reactions interfaces/network_initialization.cpp commit 30689493db963614860f61bbc39f729a7e73578f Author: Donald Willcox 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 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 Date: Thu Apr 16 11:26:50 2020 -0400 remove .fortran unit_test/test_react/main.cpp commit 428cc54a0ffdba19c97e0248354a03fa399189c3 Author: Donald Willcox 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 Date: Thu Apr 16 10:48:31 2020 -0400 fix compilation EOS/breakout/actual_eos.H commit 6deceb4f129a9190f56e409e7b9ac6372a16a811 Author: Michael Zingale 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 Date: Thu Apr 16 09:39:11 2020 -0400 fix constants namespace EOS/gamma_law/actual_eos.H commit 2e98bde19674024dafaae5e7c93a73124587d970 Author: Max Katz Date: Wed Apr 15 12:28:13 2020 -0700 Opt in to new network interface interfaces/Make.package commit 76bbd7f5ff4e3198a5801a57f899663bf8c42593 Author: Max Katz Date: Wed Apr 15 12:07:23 2020 -0700 Fix namespace issues in conductivity conductivity/stellar/actual_conductivity.H commit 34b3a2fc4210cd17151b40916f76e64ee0b2932b Author: Michael Zingale Date: Wed Apr 15 14:53:04 2020 -0400 update changes CHANGES.md commit 2686629e2b5cc35a1bc219ebf1eaf46c05dd59d9 Author: Donald Willcox 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 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 Date: Tue Apr 14 15:45:46 2020 -0700 Inline some constants screening/screen.H commit d0acf80b97b022c35598ae470ef9a1ffae6fdb2e Author: Michael Zingale Date: Tue Apr 14 08:31:15 2020 -0400 update changes CHANGES.md commit 5b020c3af34809444f438e7e362cecdc40813528 Author: Michael Zingale 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 Date: Mon Apr 13 21:35:54 2020 -0400 add a comment integration/VODE/vode_dvjust.H commit 0de426bf7be9052ea2120d3815b7c91c4d4f95ab Author: Max Katz 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 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 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 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 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 Date: Fri Apr 3 10:19:44 2020 -0400 add init networks/ECSN/actual_network.F90 commit 12baac070e908a97a91fcc56cd4fe2c31c91096b Author: Michael Zingale 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 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 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 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 Date: Wed Apr 1 08:59:31 2020 -0400 update changes CHANGES.md commit 3f4981ed051656d64730519a58efc6c8f6cf2392 Author: Michael Zingale 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 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 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 Date: Sat Mar 28 10:46:29 2020 -0400 fix my min hack screening/screen.H commit d774034ab96e5702e755241060362880a21883d3 Merge: 3acf4d34 7ae76f15 Author: Michael Zingale 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 Date: Sat Mar 28 10:26:00 2020 -0400 update changes CHANGES.md commit 7ae76f15cd3e36e5cbb1ce8824961e3d08beeda0 Author: Michael Zingale 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 Date: Fri Mar 27 19:19:00 2020 -0400 hack around a min screening/screen.H commit eb8fe42e0e10ba2f54ba9e9d48708958bad9dfc4 Author: Michael Zingale Date: Fri Mar 27 16:17:03 2020 -0400 fix output name unit_test/test_screening/main.cpp commit 09187840b109ccebc98237b4e82f36d0a02b2322 Author: Michael Zingale 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 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 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 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 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 Date: Fri Mar 27 12:14:27 2020 -0400 fallback to pynucastro.net networks/update_headers.py commit f2df1cf5cd2a7af60e19999a318ad19e731f6538 Author: Michael Zingale Date: Fri Mar 27 10:56:08 2020 -0400 add a debugging target networks/Make.package commit d16b4286e6e0bfd912210d3b1a7686e89b1e514b Author: Michael Zingale Date: Fri Mar 27 08:33:02 2020 -0400 fix compilation EOS/rad_power_law/rad_power_law.F90 commit 3ec6f18bff4e752bbd8b89056bbe526757b26c5d Author: Michael Zingale Date: Thu Mar 26 18:50:09 2020 -0400 update changes CHANGES.md commit d8ffa66a03d14593eb0b9f35b9debb7e68708058 Merge: b60c87dc 5b48458e Author: Donald Willcox 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 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 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 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 Date: Thu Mar 26 12:34:17 2020 -0700 delete build output file unit_test/test_screening_C/out commit ed568937d07a954169a4a47ee56cf3c91a69da6a Author: Donald Willcox 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 Date: Thu Mar 26 12:32:23 2020 -0700 add newline for readability unit_test/test_screening/variables.F90 commit 46994197d508c3c74b7795e12733d56beb1feb97 Author: Donald Willcox 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 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 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 Date: Thu Mar 26 13:16:26 2020 -0400 hide the automatically generated files Make.Microphysics commit 88bd23735766e7facccbbe6eb5ee1aa922efaf79 Merge: 64c41450 01abe059 Author: Donald Willcox 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 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 Date: Thu Mar 26 13:04:20 2020 -0400 remove stray .format networks/update_headers.py commit abf7e5f9b33a782779872e6571c75e4680bdf393 Author: Michael Zingale Date: Thu Mar 26 12:33:13 2020 -0400 commit the new interface screening/screen_data.H commit c773b9680db04cd2b1d750e79851f8e2a18381a7 Author: Michael Zingale Date: Thu Mar 26 12:19:40 2020 -0400 add asserts unit_test/test_screening_C/main.cpp commit 12db438d93829a6bf6abad2228ed6c20b766cbe6 Author: Michael Zingale 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 Date: Thu Mar 26 10:38:18 2020 -0400 add a << method screening/screen.H commit 5ea83a63d9089d778421dc2bf4109c85c94e9fab Merge: 16b8cc0f ca525a05 Author: Michael Zingale Date: Thu Mar 26 10:12:56 2020 -0400 Merge branch 'development' into cxx-screening commit ca525a05a27e46d0d5f513bcab9f75e402077e56 Author: Michael Zingale 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 Date: Thu Mar 26 09:17:44 2020 -0400 remove unused var screening/screen.F90 screening/screening.cpp commit 65c7fdaa46ae76249cc610b1ae6c54a541f764c9 Author: Michael Zingale 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 Date: Wed Mar 25 21:33:39 2020 -0400 add missing file screening/Make.package screening/screening.H commit 91fb03a26d75b23a9dadf07cbfad044eebfd137c Author: Michael Zingale Date: Wed Mar 25 21:33:13 2020 -0400 remove unused vars screening/screen.F90 commit f514510c627f1b66cfc842fff1ede8c95369979a Author: Michael Zingale Date: Wed Mar 25 21:31:28 2020 -0400 make pass by ref screening/screen.H commit b22cb987d713d52ed73bf905b198700053cdb91a Author: Michael Zingale 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 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 Date: Wed Mar 25 18:50:18 2020 -0400 Merge branch 'development' into cxx-screening commit 02a6986befb6ca545ba79d6ddbf30dadd56e5a7c Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Wed Mar 25 13:55:08 2020 -0400 first pass screening/Make.package screening/screen.H commit 433e79afd5f30d0e7c85a90cba779b5b728fc890 Author: Michael Zingale 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 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 Date: Wed Mar 25 09:48:35 2020 -0400 Merge branch 'development' into cxx-screening commit e7b5cceb3f879e61d894f851ce8976d3abe1d27d Author: Alice Harpole 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 Date: Wed Mar 25 09:19:51 2020 -0400 add screening header screening/screen.H commit 064f0f5d83a77f81ae458a71f8130c3a822a683b Author: Donald Willcox 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 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 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 Date: Tue Mar 24 16:38:49 2020 -0400 M_PI -> M_PI*M_PI rates/aprox_rates.H commit de276c592285e4f0fa6c34164d92e63910efc8cf Author: Alice Harpole Date: Tue Mar 24 16:34:52 2020 -0400 fix iron 56 rate rates/aprox_rates.H commit 315b347579e2c0f229d1f7ada272fe80f57a6e87 Author: Alice Harpole 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 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 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 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 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 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 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 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 Date: Mon Mar 23 13:54:14 2020 -0400 add semicolons rates/aprox_rates.H commit 786cdc5a76e1f2c29075139ec9aef97ed6af5935 Author: Alice Harpole 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 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 Date: Fri Mar 20 11:10:37 2020 -0700 Fix compile bug integration/VODE/vode_type.F90 commit cd6d035e4ac7e2285c5cd505cf6923fbe94ba40f Author: Max Katz 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 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 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 Date: Fri Mar 20 08:51:35 2020 -0700 Fix typo integration/VODE/cuVODE/source/cuvode_dvnlsd.F90 commit 5f8665020f53d63d39275349810bf733a39879d4 Author: Max Katz 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 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 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 Date: Thu Mar 19 00:24:25 2020 -0700 Linpack cleanup integration/VODE/cuVODE/source/linpack_module.F90 commit c2e238f0a94b2208ca7bfc92a75462808e43d0a6 Author: Max Katz 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 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 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 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 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 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 Date: Wed Mar 18 23:09:28 2020 -0700 K = 0 always integration/VODE/cuVODE/source/cuvode_dvindy.F90 commit a97e103bd58ce95870ed672cbd3cd0538b04fa54 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Mar 18 21:37:10 2020 -0400 update changes CHANGES.md commit 5e8a0553927763cf90c5a03b60b907a6b599dddd Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Wed Mar 18 09:12:23 2020 -0400 update changes CHANGES.md commit f87c1b3ff0d9ca8a6b511bbe7817bcf5474bac67 Author: Michael Zingale 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 Date: Wed Mar 18 00:53:09 2020 -0400 more goto extermination (#280) integration/VODE/cuVODE/source/cuvode.F90 commit 8147834516c4a1c4c649593bd3e404e16237db2e Author: Max Katz 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 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 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 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 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 Date: Tue Mar 17 10:08:08 2020 -0700 Simplify output code integration/VODE/cuVODE/source/cuvode_output.F90 commit 0b4bfbb3001276aa2c5bbb542254c8f211705116 Author: Michael Zingale 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 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 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 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 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 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 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 EOS/helmholtz/actual_eos.H EOS/helmholtz/actual_eos_data.H EOS/helmholtz/actual_eos_data.cpp commit 4d25f2ef9ab0e87ff1023f62e6725c68f0cd8122 Author: Max Katz 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 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 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 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 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 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 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 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 Date: Sun Mar 1 14:16:33 2020 -0500 update changes CHANGES.md commit 7ec6ea8d9c7dd1986331b90a7f52ef210cd91b08 Author: Max Katz 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 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 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 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 Date: Sat Feb 29 15:25:04 2020 -0500 update changes CHANGES.md commit e6aa0b4f2d261136731fe988ff093a76207c513b Merge: f35c2031 8f24ecc4 Author: Donald Willcox Date: Fri Feb 28 18:15:56 2020 -0800 Merge pull request #267 from starkiller-astro/license License commit f35c2031ae48f027001b53586eb08f5f44bbd792 Author: Michael Zingale 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 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 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 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 Date: Tue Feb 25 08:51:57 2020 -0500 update changes CHANGES.md commit 26958c1cb5bbfbcc7834eef23c1b57dc83102051 Author: Max Katz 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 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 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 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 Date: Mon Feb 24 21:33:02 2020 -0500 Merge branch 'development' into license commit f1c3b03efc8366f3abd46b8c3b412248a450ca38 Merge: c4b88825 68b72b21 Author: Michael Zingale 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 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 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 Date: Mon Feb 24 10:46:27 2020 -0500 Merge branch 'development' into license commit b433808ec07df0c942bc15382dce321ca4580b06 Author: Max Katz 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 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 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 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 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 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 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 Date: Sun Feb 23 10:57:28 2020 -0800 Add const for safety EOS/eos_composition.H commit bc1e828ab2189e60e50811e4dd7a226d422d8ba5 Author: Max Katz 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 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 Date: Sat Feb 22 12:04:45 2020 -0500 fix header include Make.Microphysics commit c38e9b98d810232219405326028c241dffb4b42b Author: Max Katz 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 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 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 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 Date: Fri Feb 21 20:26:16 2020 -0800 Real -> amrex::Real interfaces/eos_type.H commit b1d2ccfcbcae1fd3c9e41932e210ce45c789dfe3 Author: Michael Zingale Date: Fri Feb 21 10:54:52 2020 -0500 update changes CHANGES.md commit 659a6caaf9980b8315ff54547a9bad08dd1c09a1 Author: Michael Zingale 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 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 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 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 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 Date: Tue Feb 18 18:25:26 2020 -0500 fix dependencies networks/general_null/Make.package commit 4e6e736a28770d406d0bbeab1e6987ef59a43e73 Author: Michael Zingale Date: Mon Feb 17 08:47:38 2020 -0500 remove unused tfactors (#259) rates/tfactors.F90 commit b8930d5f12638c8c07194730df4af9a70cf95901 Author: Michael Zingale 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 Date: Sun Feb 16 18:16:09 2020 -0500 remove the C++ parameter autogenerated stuff with clean Make.Microphysics commit 598408c6644942eafb0bf7c157657a7971537bc9 Author: Michael Zingale 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 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 Date: Sat Feb 15 08:53:49 2020 -0800 Update .gitignore .gitignore commit 25a276627f7f9f1be3b0162ff03bdfd72be38afc Author: Michael Zingale 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 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 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 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 Date: Tue Feb 11 14:02:49 2020 -0500 revert change networks/breakout/network_properties.H commit 5a224ce352a157a77006aa5f672875b953e9687d Author: Michael Zingale 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 Date: Tue Feb 11 11:45:38 2020 -0500 add network_name networks/powerlaw/actual_network.f90 commit d193a6103f8a2680ef1afd494f83a5160bd28668 Author: Michael Zingale 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 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 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 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 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 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 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 Date: Sun Feb 9 11:47:27 2020 -0500 remove stray character networks/powerlaw/actual_network.f90 commit 744d74576b067be5393d407687a0cd56877c2fb0 Author: Michael Zingale 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 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 Date: Sat Feb 8 20:01:11 2020 -0500 update changes CHANGES.md commit 8a347c77072e5db7947d3569abc06c766b526ca7 Author: Michael Zingale 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 Date: Sat Feb 8 19:51:20 2020 -0500 update changes CHANGES.md commit f5927924ee13b9d72cf412735723f74783d14007 Author: Michael Zingale 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 Date: Sat Feb 8 19:48:34 2020 -0500 update changes CHANGES.md commit 20ee38aee80a602285f3a8b9de84cd24a61dc02d Author: Michael Zingale 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 Date: Wed Feb 5 12:19:51 2020 -0500 update F90 build system EOS/GPackage.mak commit 369624664df738552b0e736046b7a76617755512 Author: Michael Zingale 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 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 Date: Mon Feb 3 15:31:34 2020 -0500 fix plotfile variable name unit_test/test_eos/variables.F90 commit 9b1bc259ffe5c16f75978584ea191118391aa642 Author: Michael Zingale Date: Sat Feb 1 13:08:17 2020 -0500 update changes CHANGES.md commit a5bb8d24982c62fa1e70c43669ff25fb3c3a9f02 Author: Michael Zingale Date: Mon Jan 27 20:00:01 2020 -0500 fix some compilation problems EOS/helmholtz/actual_eos.F90 commit f8b89ad13bd7d76ee4b33849b8feb3c435b83193 Author: Michael Zingale Date: Mon Jan 27 19:13:52 2020 -0500 more warnings EOS/composition.F90 commit e5d5b14c8360a530c4c86efd51b98a152589e1ea Author: Michael Zingale Date: Mon Jan 27 19:11:20 2020 -0500 address some compiler warnings EOS/helmholtz/actual_eos.F90 commit 4774a8bd4c672163048b468e84de344e4a438e4b Author: Michael Zingale 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 Date: Mon Jan 20 18:32:26 2020 -0800 Add acc routine markings EOS/helmholtz/actual_eos.F90 commit 207dfc21498da6cc5cf7e04fb6c3a8bae026fa14 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Wed Jan 1 13:45:48 2020 -0500 update changes1 CHANGES.md commit 930626c34b4f657c785c766ef4ba257af4cf0ec7 Author: Michael Zingale Date: Tue Dec 31 20:00:56 2019 -0500 update CHANGES CHANGES.md commit 59e53f9b9703a059d7acd45e7a7d7eceb6e691f5 Author: Donald Willcox 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 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 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 Date: Tue Dec 17 13:52:58 2019 -0500 revert rates file rates/aprox_rates.F90 commit 1f5f373545283b441f41cb91d11d2db19e3cec59 Author: Alice Harpole 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 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 Date: Tue Dec 17 13:06:53 2019 -0500 git couldn't merge the rates properly commit d44e805232ba50c2b32fe54dfa20754c01b4b5e2 Author: Michael Zingale 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 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 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 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 Date: Mon Dec 16 16:15:06 2019 -0500 add alice .zenodo.json commit a69b4cb7c9078c0f054bc13ef816c7e13d7137fa Merge: bcaba170 44a9b4ad Author: Alice Harpole 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 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 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 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 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 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 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 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 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 Date: Wed Dec 11 07:57:50 2019 -0800 Merge pull request #230 from starkiller-astro/python Thanks! commit 16888ed4a4aaadb01cb005a1d2f856febadbaa33 Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Mon Dec 9 15:54:08 2019 -0500 redo rates rates/aprox_rates.F90 commit 2cbf12b6ab9bd311ab8e6db89bc5defb065248aa Author: Michael Zingale Date: Mon Dec 9 10:01:17 2019 -0500 sync up with the MAESTROeX version interfaces/sdc_type.F90 commit fc1ca7741863d58cd7a28e48fc7cc561db0c2256 Author: Michael Zingale 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 Date: Mon Dec 9 08:27:51 2019 -0500 update changes CHANGES.md unit_test/test_sdc/probin.aprox13 commit d0705d2933d221dd15c6653411168acfd9623d87 Author: Michael Zingale 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 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 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 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 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 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 Date: Wed Dec 4 13:00:54 2019 -0800 Merge branch 'development' into bye_bye_vode commit 8d66767eff781c023847c997421f05f071ee37d8 Author: Donald Willcox 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 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 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 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 Date: Wed Dec 4 11:28:41 2019 -0800 Fix path for VODE90-VODE. integration/VODE/GPackage.mak commit 476987df2379a5db8a0deeadaccdc295c58599e6 Author: Donald Willcox 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 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 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 Date: Tue Dec 3 17:03:18 2019 -0500 nspec -> nspec_evolve integration/utils/nonaka_plot.f90 commit 0c421083b8e058bd96845207ecc4c94bd4af708b Author: Michael Zingale Date: Tue Dec 3 14:34:21 2019 -0500 update changes CHANGES.md commit 4eaf4bc8bfe44472fcbb84e56583e94bf984fc0e Merge: 78bd70d6 f91d5580 Author: Michael Zingale Date: Tue Dec 3 14:14:36 2019 -0500 Merge branch 'development' into bye_bye_vode commit f91d55800a6eab160bfb845a1c8c67fd0fab66b7 Author: Michael Zingale Date: Mon Dec 2 09:27:14 2019 -0500 update release CHANGES.md commit 62bb9169b64249a5536a5565e825245f74803683 Author: Max Katz 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 Date: Sat Nov 30 13:45:18 2019 -0500 update integrator numbers integration/integrator.F90 integration/integrator_sdc.F90 commit fcf372adf2c00667ba03ac432d4e0aefefd944f5 Author: Michael Zingale Date: Sat Nov 30 13:14:02 2019 -0500 need make overrides integration/Make.package networks/Make.package commit 75df97d76d5d44af42eb373f3cbe3b08da93c303 Author: Michael Zingale 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 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 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 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 Date: Thu Nov 21 10:56:44 2019 -0500 add comment integration/utils/temperature_integration.F90 commit b7bd98dc9d071364ae7d23a7b8a62f977c56b9f4 Author: Donald Willcox 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 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 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 Date: Mon Nov 18 17:01:13 2019 -0500 fix compilation integration/VODE90/vode_integrator_true_sdc.F90 commit 1f49333061c8197611ae4cefdb7b90adef6cba03 Author: Michael Zingale Date: Mon Nov 18 14:07:22 2019 -0500 fix latexism sphinx_docs/source/basics.rst commit bf072bd95a3d727fc995c2707ba2828ecc1fb1b5 Author: Max Katz 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 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 Date: Sun Nov 17 17:49:45 2019 -0500 Merge branch 'burn_cell_cbuild' into development commit 9230ef8a31ff84e6c54238a0a004315dfff64c08 Author: Michael Zingale Date: Sun Nov 17 17:46:26 2019 -0500 store the final time integration/VODE90/actual_integrator.F90 commit 792ffdc18f921601f6a3b23e0edbbc41ddf3f9b8 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Nov 10 18:31:29 2019 -0500 define mu EOS/helmholtz/actual_eos.F90 commit 9c42057e9a6a38f680d8c6f52f602ba6ea27ae7a Author: Michael Zingale Date: Sun Nov 10 18:29:55 2019 -0500 update changes CHANGES.md commit 0ae03a6e60eac08d3e0a5cb2c199d31dbb37dac4 Author: Max Katz 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 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 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 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 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 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 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 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 Date: Wed Nov 6 08:07:42 2019 -0500 fix compilation integration/VBDF/bdf_type.f90 commit 5acbdda444fbb2f8d5c49b6b2c95247b2eb734ca Author: Michael Zingale Date: Wed Nov 6 08:04:14 2019 -0500 initialize mu EOS/helmholtz/actual_eos.F90 commit 6e295c49e4ecbee8d62a0755ec183fb6656dbdfa Author: Michael Zingale 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 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 Date: Mon Nov 4 16:40:00 2019 -0500 update changes CHANGES.md commit 3d8bfee78d7c290bb4a81ebfc2d652b4c9f7a99e Author: Michael Zingale 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 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 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 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 Date: Sun Nov 3 07:51:11 2019 -0500 update changes CHANGES.md commit 096d3d1b5ca513fe3a23d72c28ff889cee46d85d Author: Michael Zingale Date: Sat Nov 2 18:29:52 2019 -0400 remove a space unit_test/test_eos/variables.F90 commit 85728a00d574f8747ef8dfb4bc46458a7a5864ed Author: Michael Zingale 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 Date: Sat Nov 2 14:21:43 2019 -0400 turn on retry_burn unit_test/test_react/probin.3alpha commit 3e6ce0f286bcbb63511ef926c1dca579b47d9351 Author: Michael Zingale Date: Fri Nov 1 07:42:34 2019 -0400 changes for 19.11 CHANGES.md commit f25dc42e3065ad4f6817ac5dd89b67e3220c43b4 Author: Michael Zingale Date: Thu Oct 31 15:45:31 2019 -0400 update changes with rprox CHANGES.md commit a34abc888078badcf8e1191c8656372245066dcf Author: Michael Zingale 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 Date: Tue Oct 29 17:21:08 2019 -0400 fix some sizes integration/VODE90/cuvode_parameters.F90 commit 464dc7ffeec074a65da58fd18512b3d31b6cdf45 Author: Michael Zingale 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 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 Date: Tue Oct 29 07:35:07 2019 -0700 Remove extra line EOS/helmholtz/Make.package commit b47be203e6b64a07f98113f8f2742b55c9d16521 Author: Max Katz 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 Date: Sun Oct 27 19:05:02 2019 -0700 Disable CUDA verbosity by default Make.Microphysics commit cde1cbb2a55c1b582fdb043eb07fcf8d18fc46a3 Author: Max Katz 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 Date: Sun Oct 27 08:06:10 2019 -0400 fix markdown formatting CHANGES.md commit 1a587899ece1034ae5c4e13173d38436c556ca08 Author: Michael Zingale Date: Sun Oct 27 08:04:39 2019 -0400 rename to get markdown update changes CHANGES CHANGES.md commit 9d347b77ab51f438aff4ba1b2c60c8345829c275 Author: Michael Zingale 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 Date: Wed Oct 16 14:56:30 2019 -0400 fix compilation conductivity/stellar/stellar_conductivity.F90 commit 05c2e8b4786ce8739f43e83091ddd8de190492c0 Author: Michael Zingale Date: Wed Oct 16 14:55:58 2019 -0400 add cond_name conductivity/stellar/stellar_conductivity.F90 commit 41f6f06c4b391853360043cb44faa3e3d8b7da3f Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Tue Oct 1 14:59:25 2019 -0400 remove unused variables integration/VODE90/vode_rhs.F90 commit 6804966172a1189d82c40a829cd22356b83569a3 Author: Michael Zingale Date: Tue Oct 1 09:38:52 2019 -0400 update release CHANGES commit 125c9e5640e7b500e489fb36c6d9403a32c095e2 Author: Michael Zingale Date: Sun Sep 29 11:10:20 2019 -0400 update changes CHANGES commit 234ec378076400ab5434126080b5b5aaa1eb3981 Author: Michael Zingale 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 Date: Sat Sep 28 15:10:07 2019 -0400 another fix sphinx_docs/source/networks.rst commit c49c727d15a062410a602c5242a7fb8b947669f1 Author: Michael Zingale Date: Sat Sep 28 14:53:14 2019 -0400 fix an indent sphinx_docs/source/networks.rst commit 7a673b5f84006fcff98ca5074152401ee4cdec7a Author: Michael Zingale 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 Date: Sat Sep 28 13:17:56 2019 -0400 fix some indents sphinx_docs/source/basics.rst commit 94b4fdd9536f74fa2433215c78235edb51a41e90 Author: Michael Zingale Date: Sat Sep 28 09:29:03 2019 -0400 don't store runtime_parameters.rst .gitignore commit 376859991e839a30524e29e4308e0a634c9efa83 Author: Michael Zingale Date: Sat Sep 28 09:26:23 2019 -0400 get rid of the copy sphinx_docs/Makefile commit e457feb77abe3f61a71c44ef67d317410047e998 Author: Michael Zingale 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 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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/theme_overrides.css docs/_static/underscore-1.3.1.js docs/_static/underscore.js docs/_static/up-pressed.png 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/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 commit 13cb2a9cd906c8e90f8e829ead00d6a9951a7328 Author: Michael Zingale 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 Date: Sat Sep 28 09:21:15 2019 -0400 more fixes sphinx_docs/rp.py commit 7b37f127188e7eb25851d47b3862420c51ef3aa6 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Aug 30 14:39:30 2019 -0700 Initialize Nonaka plot module. integration/integrator.F90 commit 0c4c5651ccc38a5079a1d33d8bbad2679ab3cb85 Author: Donald Willcox 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 Date: Thu Aug 1 10:00:00 2019 -0400 update changes CHANGES commit 279c1ea497f7106b0d82e934c217693a92787d21 Merge: 4520e856 dcb60ede Author: Michael Zingale Date: Thu Aug 1 09:59:46 2019 -0400 Merge branch 'development' commit dcb60edeb4423c39f33e0013eb5aedf1449811c1 Author: Michael Zingale Date: Wed Jul 31 19:52:29 2019 -0400 update changes CHANGES commit 291e30a406c7b785ea372e4f3a14257a2806d0bd Author: Michael Zingale 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 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 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 Date: Mon Jun 3 10:37:26 2019 -0400 Merge branch 'development' commit 4295c85048ba1e24f1c41fd4978fc04d73e5f618 Author: Abigail Bishop 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 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 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 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 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 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 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 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 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 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 Date: Mon May 6 20:20:35 2019 -0700 Fix code formatting. sphinx_docs/source/gpu.rst commit 00d326e147d50dbc55194ab01afef57c077a7568 Author: Donald Willcox Date: Mon May 6 20:09:48 2019 -0700 OpenACC page -> GPU page. sphinx_docs/source/index.rst commit 65d73c357177404aed46d934343d1e5437bfd327 Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed May 1 08:51:45 2019 -0400 Merge branch 'development' commit 06bfa2c0a7ce48a9f47bf334b9e551596e09107f Author: Michael Zingale Date: Wed May 1 08:51:30 2019 -0400 update changes CHANGES commit be0af567fe7875a109db159c7f14ef95c3e1844c Author: Michael Zingale Date: Tue Apr 30 22:07:43 2019 -0400 add note util/DNSQE/TODO commit 79d87353c3262e7bacdd32e530e37c6c85b88797 Author: Michael Zingale Date: Tue Apr 30 21:58:40 2019 -0400 add Make.package util/DNSQE/Make.package commit a57d1611f7e7173cdb2b00b5b25352ce464d30dc Merge: 1de421e5 88a4a5aa Author: Michael Zingale 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 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 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 Date: Mon Apr 29 19:47:02 2019 -0400 update changes CHANGES commit a6f227ff62a9b19e21f4452fe6ac69c705bbe11b Merge: 5fa2c911 e16e4dcd Author: Donald Willcox 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 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 Date: Mon Apr 29 16:05:18 2019 -0400 add integrator file to dowrap.sh python_library/dowrap.sh commit 0d7a06d18f9a30a5c1bd0a981fe141ee34c77d41 Author: Donald Willcox 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 Date: Sat Apr 27 20:11:50 2019 -0400 fix compilation integration/numerical_jacobian.F90 commit 533e909053415e537899a2636062feb8bbb0d720 Author: Michael Zingale Date: Sat Apr 27 09:26:41 2019 -0400 compare Jacobians in terms of X integration/numerical_jacobian.F90 commit 8fd8eb8c5989c08e624e69159a0bdff43b5112fc Author: Michael Zingale 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 Date: Sat Apr 27 09:14:56 2019 -0400 Merge branch 'development' into numerical_jac commit 71beec502e849e9a7c831a327f693f5c83be5a1e Merge: ecbfec43 a9b1b7e9 Author: Michael Zingale 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 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 Date: Fri Apr 26 18:39:17 2019 -0700 Merge remote-tracking branch 'origin/development' into numerical_jac commit a9b1b7e991f515eb50ee91b7d9a10acd97252e8f Author: Donald Willcox Date: Fri Apr 26 18:36:22 2019 -0700 Wrap the numerical jacobian module. python_library/dowrap.sh commit 8b9fd8003149756de416bc812fa6eb049bf86240 Author: Donald Willcox 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 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 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 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 Date: Thu Apr 25 21:58:28 2019 -0400 Merge branch 'development' into numerical_jac commit 6eb345efb0b04b5f1a8ff09448ecb8cc6d0c2aef Author: Michael Zingale 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 Date: Thu Apr 25 20:07:59 2019 -0400 add the travis badge README.md commit c3c3e954adfd164829d4262357b1371b74b56872 Author: Michael Zingale Date: Thu Apr 25 20:07:59 2019 -0400 add the travis badge README.md commit a012e1dc65c94ff411285a29e853621f8a640947 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 Date: Tue Apr 9 19:21:59 2019 -0700 remove commented prints networks/ECSN/actual_rhs.F90 commit a5ad1186bddd321946c462e45e40aa137bed61d9 Author: Donald Willcox Date: Tue Apr 9 19:21:29 2019 -0700 remove prints networks/ECSN/actual_network.F90 commit 70c66ed412822a6b595cbfa41cade7fcb2b64d26 Merge: 2b66a8d2 4f16a454 Author: Max Katz 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 Date: Wed Apr 10 00:38:24 2019 -0400 Update CHANGES CHANGES commit f218f8c23e57ac9856cecb39f56cd292fede74cb Author: Donald Willcox 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 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 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 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 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 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 Date: Tue Apr 9 08:57:10 2019 -0400 fix dfdy(ihe4,ini56) (#175) networks/aprox21/actual_rhs.F90 commit 37bef3e3ebe47a693ec53151a86e8aff65c54d9f Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Apr 3 16:54:55 2019 -0700 Update readme text python_library/StarKiller/README.md commit 76f563b1dc4e255d5c270b93f9c931d68e86545b Author: Donald Willcox Date: Wed Apr 3 16:50:03 2019 -0700 Add examples to package_data. python_library/StarKiller/setup.py commit 1e2511d98bccbd322032831b2aa30db60eadf996 Author: Donald Willcox 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 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 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 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 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 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 Date: Mon Apr 1 15:37:17 2019 -0400 add DOI badge README.md commit 78c608a4b7552be32190859153f0a0dab549ccd7 Merge: eb2ada4e 4c44a8eb Author: Michael Zingale Date: Mon Apr 1 13:12:34 2019 -0400 Merge branch 'development' commit ecbfec4306ceabefb3db247c6ffd025aad72ce7b Merge: 25d0977d 4c44a8eb Author: Michael Zingale 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 Date: Wed Mar 27 13:42:18 2019 -0400 add Adam .zenodo.json commit b25ee328704cd80fcf395d1a97e4cd2354ddb4ef Author: Michael Zingale Date: Tue Mar 26 15:03:36 2019 -0400 add abby .zenodo.json commit 6b9e99fa66de19df9d52b240ab080782c9eabb2f Author: Donald Willcox 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 Date: Mon Mar 25 10:17:46 2019 -0400 add Chris .zenodo.json commit 347666995ff84fad7f3ab3c05d3c0c5c7682efa0 Author: Max Katz Date: Mon Mar 25 03:40:56 2019 -0400 go away integration/BS/_parameters commit 218104dac011c53e7117ebf4f4dd6a21b91ba280 Author: Max Katz 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 Date: Sun Mar 24 12:34:49 2019 -0400 add Xinlong .zenodo.json commit 0d59a1226420df85536683c87948987357b78db0 Author: Michael Zingale Date: Sat Mar 23 16:11:20 2019 -0400 add Frank .zenodo.json commit 23fe45126eb78c7b5f0a4bce6e5a534917c1662f Author: Michael Zingale Date: Sat Mar 23 15:24:13 2019 -0400 add Carl .zenodo.json commit 3774ed7b8b4a50ff9a5c27a2901b42a9534fd3a9 Author: Michael Zingale Date: Sat Mar 23 13:15:04 2019 -0400 start of a .zenodo.json .zenodo.json commit 5081d91b4eec28140f1036defd1e2d871f66ae52 Merge: d19c043b 5b405509 Author: Michael Zingale 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 Date: Fri Mar 22 15:31:16 2019 -0400 add xinlong to mailmap .mailmap commit 5b405509687654ce89f8495acf1b42f8b4b10d0b Author: Donald Willcox 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 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 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 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 Date: Fri Mar 15 12:47:46 2019 -0700 Revert "space" This reverts commit 9fa1f2752b80ac03b8957ea6d548fb8cc7c6e6b5. README.md commit 9fa1f2752b80ac03b8957ea6d548fb8cc7c6e6b5 Author: Donald Willcox Date: Fri Mar 15 12:46:13 2019 -0700 space README.md commit 66111af543eef48efcaf981ec1c166cfad3ec3ee Author: Donald Willcox 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 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 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 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 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 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 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 Date: Thu Mar 14 17:53:29 2019 -0400 Merge branch 'master' of https://github.com/sailoridy/Microphysics commit 12ed33af982f917d03abcee834563d89c8a6cfcb Author: Xinlong Li 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 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 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 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 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 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 Date: Thu Mar 14 17:17:43 2019 -0400 Merge branch 'master' of https://github.com/sailoridy/Microphysics commit f7d14a9bab619d6e246f94b9fceeb863b0db7aef Author: Xinlong Li Date: Thu Mar 14 17:17:31 2019 -0400 ECSN unit_test/burn_cell/main.f90 commit fbc4c0fbabf9806e6beb250e26350bd19857bea2 Author: Donald Willcox 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 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 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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 Date: Thu Mar 14 16:00:06 2019 -0400 Delete main.f90 unit_test/burn_cell/main.f90 commit ba44b7b595eb41961cd87ac904cc86c8634683ce Author: Xinlong Li 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 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 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 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 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 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 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 Date: Mon Mar 11 07:53:44 2019 -0400 Define CUDA Make.Microphysics commit a67a3b468a874bfe4fc57be4bd0faa6942bcd14c Author: Xinlong Li 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 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2019 -0500 acc routine information for screening screening/screen.F90 commit 02b93b277c200983773358b17049c20e6a6933d9 Author: Max Katz 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 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 Date: Mon Feb 25 11:00:00 2019 -0500 ECSN commit dcd3b760494f74d3c694e6038bdc2efd99e5aaa7 Author: Xinlong Li 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 Date: Mon Feb 25 10:33:12 2019 -0500 Delete main.f90 unit_test/burn_cell/main.f90 commit 2765dcaf097f517d46814e9a2e765053a200fb9b Author: Xinlong Li 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 Date: Mon Feb 25 10:27:41 2019 -0500 Merge branch 'master' of https://github.com/sailoridy/Microphysics commit a48dc7348ed51bd8d5d7fd742c230ab1fa9e2b8d Author: Xinlong Li 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 Date: Mon Feb 25 03:27:08 2019 -0500 Create symlink to URCA-simple rate metadata file Make.Microphysics commit 059b76ed01b91fa5f7e4b37ae1ce4eb4cbe56e9b Author: Max Katz Date: Mon Feb 25 03:10:42 2019 -0500 Fix VODE90 compilation integration/VODE90/actual_integrator.F90 commit 5b293a9d0d9966b5c25155ac6e874097a61deb3f Author: Max Katz 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 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 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 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 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 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 Date: Fri Feb 1 09:27:03 2019 -0500 update changes CHANGES commit da53ec663bcbaafbc19e602d1834d3124cf6a89c Author: Michael Zingale Date: Thu Jan 31 13:29:46 2019 -0500 ECSN composition networks/general_null/ECSN.net commit a37a226f701fbf19788a745b7e7aed755ff77072 Author: Michael Zingale Date: Wed Jan 2 11:52:46 2019 -0500 make this GPUable EOS/multigamma/actual_eos.F90 commit 59f62c24aa5611b32e7435176ba842cf49db666f Author: Michael Zingale Date: Wed Jan 2 09:48:18 2019 -0500 update changes CHANGES commit e0cda1172837fd7c44a7661ca1e7943c60df8f6f Author: Donald Willcox 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 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 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 Date: Wed Dec 19 19:23:21 2018 -0800 testing -- Preface sphinx_docs/source/preface.rst commit c0e5e28c10af2265c29692767048e2e9cfa46d95 Author: Donald Willcox Date: Wed Dec 19 19:19:04 2018 -0800 Add jupyter and ipywidgets to requirements. requirements.txt commit 8ef98593320246c721f273e80f265894fc59ef4c Author: Donald Willcox 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 Date: Wed Dec 19 18:41:45 2018 -0800 Use Python 3.5 for building docs. .travis.yml commit 18da27c91d3d2f6acd4cdc92956c751682701524 Author: Donald Willcox Date: Wed Dec 19 18:17:13 2018 -0800 Use 1 space after periods. README.md commit a2942c03c31e6c6edbed3962ea1cb0e65c5a3b74 Author: Donald Willcox 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 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 Date: Mon Dec 10 17:15:50 2018 -0800 Remove redundant lines. GMicrophysics.mak commit 50bdc55c20ec7771af5656dc950e68c05c855f97 Author: Donald Willcox Date: Mon Dec 10 17:08:38 2018 -0800 Fix conductivity compilation bug when building with FBoxLib. GMicrophysics.mak commit da3850067abf957847fe52ae657587cfb7b2d547 Author: Donald Willcox 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 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 Date: Mon Dec 3 10:34:09 2018 -0500 add the .nojekyll docs/.nojekyll commit 5ca9c52a5ef62fe07384485fce802f3bf69fca1c Author: Michael Zingale 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 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 Date: Mon Dec 3 10:25:05 2018 -0500 update changes CHANGES commit bfb58eec9390d1bfc1257994c9d7e1ee43a96cdb Merge: 5c6caed2 8529022a Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Mon Nov 12 13:50:32 2018 -0500 add doxy_files .gitignore commit 33cc4432172f712c85a1465cc56ffda7fe28756c Author: Michael Zingale Date: Mon Nov 12 13:49:59 2018 -0500 add doxygen file sphinx_docs/Doxyfile commit eeaa2cf6614f66cd6fb2cd8d4a337caf7d22b7fb Author: Michael Zingale 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 docs/_static/fonts/Lato/lato-bold.woff2 docs/_static/fonts/Lato/lato-bolditalic.eot docs/_static/fonts/Lato/lato-bolditalic.ttf docs/_static/fonts/Lato/lato-bolditalic.woff docs/_static/fonts/Lato/lato-bolditalic.woff2 docs/_static/fonts/Lato/lato-italic.eot docs/_static/fonts/Lato/lato-italic.ttf docs/_static/fonts/Lato/lato-italic.woff docs/_static/fonts/Lato/lato-italic.woff2 docs/_static/fonts/Lato/lato-regular.eot docs/_static/fonts/Lato/lato-regular.ttf docs/_static/fonts/Lato/lato-regular.woff docs/_static/fonts/Lato/lato-regular.woff2 docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 docs/_static/fonts/fontawesome-webfont.woff2 commit 6882070dac040f510b3f58dc411b8946b5d37229 Author: Michael Zingale 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 docs/_static/fonts/fontawesome-webfont.svg 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 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 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 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 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 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 Date: Thu Nov 1 10:15:07 2018 -0400 update changes CHANGES commit 380c1d074060497bcb11e6916d2e989eaacbb1a1 Author: Michael Zingale 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 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 Date: Thu Nov 1 10:13:28 2018 -0400 update sphinx_docs/source/runtime_parameters.rst commit d27d694ddced1178d81295a7d9490302316523c7 Author: Donald Willcox 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 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 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 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 Date: Mon Oct 29 10:46:37 2018 -0400 fix density networks/ECSN/network_plot.py commit 94f2a69613886e77dd9ed8e5aa86f758fb701069 Author: Donald Willcox 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 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 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 Date: Sat Oct 27 21:51:36 2018 -0400 add a note sphinx_docs/notes.txt commit bc4af6182e8f10ad61fb53f27d6b46a8bc582407 Author: Michael Zingale 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 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 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 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 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 Date: Sat Oct 27 12:15:34 2018 -0400 add a network plot networks/subch/network_plot.py commit 0656f9862802f83ae565a00cabe394938e4a131c Author: Donald Willcox 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 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 Date: Fri Oct 26 18:17:38 2018 -0700 Wrap extern with f2py. python_library/dowrap.sh commit 1cef25e36f3b6026255cc8eace0dd4408bcabd3d Author: Michael Zingale 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 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 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 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 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 Date: Fri Oct 26 19:09:16 2018 -0400 some notes on tables sphinx_docs/notes.txt commit 51823a4a449723fc91a032985963a2f469929326 Author: Michael Zingale 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 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 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 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 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 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 Date: Fri Oct 26 15:10:58 2018 -0400 add .nojekyll docs/.nojekyll commit b9cddc0b3ab3bf8a2de6ca4ecf329084a06b8899 Author: Michael Zingale 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 docs/_static/up-pressed.png 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 Date: Fri Oct 26 14:56:44 2018 -0400 add build/ .gitignore commit ac683ad23bd035117be1cb1920a4b431a9d28afa Author: Michael Zingale 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 Date: Fri Oct 26 14:48:29 2018 -0400 unneeded docs_new/source/_temp.rst commit 3e22db16cfa9a8699eda2d7c149be30c1504e0a4 Author: Michael Zingale 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 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 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 Date: Thu Oct 25 19:13:29 2018 -0400 add a plot networks/ECSN/network_plot.py commit 5a20b3eed492214f7224a316e8ae9e0df5955358 Author: Michael Zingale Date: Thu Oct 25 19:00:07 2018 -0400 enable reverse rates networks/ECSN/ecsn.py commit da52422bec0a1dfc3eca5248258c6213b5059ff8 Merge: 94214961 a1cf4b6c Author: Michael Zingale 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 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 Date: Thu Oct 25 14:21:42 2018 -0400 Added solar radius to constants unit_test/constants_cgs.f90 commit 205ec965b71b2004b989056dafc06ea1fe01b26e Author: Donald Willcox 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 Date: Tue Oct 23 13:02:44 2018 -0400 add an aprox21 networks/general_null/aprox21.net commit 85984c07c38bbf8b785687c72295d1ef339afc96 Author: Michael Zingale Date: Tue Oct 23 12:32:13 2018 -0400 update changes CHANGES commit fd438e5ea43f399d74a8a4f8b7bca239bb2488be Merge: e6e1e331 21e0dbbe Author: Michael Zingale Date: Tue Oct 23 12:31:34 2018 -0400 Merge branch 'master' into development commit e6e1e331b2950efdd6428dcd66d7cbb418ecb24b Author: Michael Zingale Date: Tue Oct 23 12:30:55 2018 -0400 fix some symbols Docs/maestrosymbols.tex commit 497cf00640f5b1a9a80922f3dfc4c475beee98e8 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sat Oct 13 09:45:42 2018 -0400 longer integration time unit_test/test_react/probin.nova commit 3d4ec3d085394a77252f6a889c348fc0e1c0f0c6 Author: Michael Zingale Date: Sat Oct 13 09:44:18 2018 -0400 this nova inputs works unit_test/test_react/probin.nova commit 0b99f22b61db1244940e0aa01cfc09fb122e6109 Author: Michael Zingale 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 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 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 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 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 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 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 Date: Thu Oct 11 22:03:05 2018 -0400 Remove unused variable. integration/VODE90/vode_type.F90 commit 7a42b381927ebefbd3b8e568f8f48bc19c04aa6c Author: Donald Willcox 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 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 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 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 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 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 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 Date: Tue Oct 9 09:05:39 2018 -0400 add integrator_scaling.F90 integration/GPackage.mak commit a49be99acd498f6572e05614e4da5d7e0a316509 Author: Donald Willcox 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 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 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 Date: Thu Oct 4 10:21:31 2018 -0400 move USE_CUDA block Make.Microphysics commit abb3c1a34813beb7539c2c15c93836b88f27014b Author: Michael Zingale Date: Tue Oct 2 16:07:44 2018 -0400 remove old commented out F90 build stuff Make.Microphysics commit a58ad3b5ba0f1555c8fc4ef6e55e401788af35c6 Author: Michael Zingale Date: Tue Oct 2 15:55:44 2018 -0400 remove space Make.Microphysics commit 21e0dbbe8cb6a66b1b9d03fd8f3b5e38522b2c11 Author: Michael Zingale Date: Tue Oct 2 15:55:44 2018 -0400 remove space Make.Microphysics commit 8bdbe4578af3254d5063ae82859b1fc9bf720c89 Author: Michael Zingale Date: Tue Oct 2 15:48:13 2018 -0400 add USE_GPU_PRAGMA Make.Microphysics commit 29177c8053832f67cafd2d52014e0a90b8ce4c49 Merge: 7e5f9182 dc4db807 Author: Michael Zingale 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 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 Date: Tue Oct 2 13:16:19 2018 -0400 Update defines EOS/gamma_law_general/actual_eos.F90 commit e33020a2c8e63e7499243d16495ba2e970b3f824 Author: Michael Zingale Date: Mon Oct 1 12:52:29 2018 -0400 update changes CHANGES commit 8fd850f2a5281723104a569d4306b538fbd8fda3 Author: Michael Zingale 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 Date: Sun Sep 30 19:43:01 2018 -0400 add a mailmap .mailmap commit 0d65d1d572aff7b56104d94f6a5abc7fa87e43ce Author: Donald Willcox 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 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 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 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 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 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 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 Date: Wed Sep 26 19:17:53 2018 -0700 Moved notes to docs. integration/VODE90/cuVODE/docs/NOTES.md commit 1dda19cbb199bcbcbb3cf8c4d92a2e868f318fa7 Author: Donald Willcox 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 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 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 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 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 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 Date: Sun Sep 23 19:23:07 2018 -0400 fix the fix networks/subch/Make.package commit 6f1170f483e677f4fc73702d21c02ae8d1555e66 Merge: 95e3eab0 6d9c27ff Author: Michael Zingale 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 Date: Sun Sep 23 19:09:15 2018 -0400 update files networks/subch/Make.package commit 6d9c27ff6b35c59970e94a3aa40e67b6890338f5 Author: Max Katz 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 Date: Tue Sep 18 19:36:46 2018 +0000 Make functions return results. neutrinos/sneut5.F90 commit 5e6775bd88d6be6276db724f80a308e861d60020 Merge: c3b37415 455528d4 Author: Donald Willcox 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 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 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 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 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 Date: Mon Sep 17 14:22:44 2018 -0400 WIP Getting c++ test_react to run on GPUs. commit 90189c69bf792048e5577580b53796c57af898af Author: Donald Willcox 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 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 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 Date: Sun Sep 9 20:31:41 2018 -0400 sync up with Castro interfaces/eos_type.F90 commit 7ea83e5422fe425651f4f0231d8e9f1a8c85e6bd Author: Michael Zingale Date: Sun Sep 9 20:06:40 2018 -0400 VODE90 doesn't need BLAS or linpack networks/Make.package commit 84a52c56ca73d7c44bdfaae17a977e7b6f65d6c4 Author: Michael Zingale 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 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 Date: Sun Sep 9 15:15:29 2018 -0400 remove AMREX_ARLIM_ARG unit_test/test_react/main.cpp commit 1d0fa9e30efa7862973458ccf6eacc5c09eb8c3d Author: Michael Zingale 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 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 Date: Fri Sep 7 14:42:58 2018 -0400 remove comment networks/nova/nova.py commit 2d9b2f21f01e59249e28255edb4b686e7548aa3a Author: Michael Zingale 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 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 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 Date: Thu Sep 6 20:03:02 2018 -0400 update changes CHANGES commit 78beecbbc4c911fe77cf0e1fcecd54b639e76ec8 Author: Michael Zingale 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 Date: Thu Sep 6 13:39:19 2018 -0400 fix compilation networks/general_null/actual_burner.f90 commit 9d42ce2e9d7932257c542216c92c50ed96cb7046 Author: Michael Zingale Date: Thu Sep 6 13:31:13 2018 -0400 .f90 -> .F90 networks/general_null/GPackage.mak commit a0352d73b76a03f01fb3b21b9431ba9a4c525b5e Author: Michael Zingale Date: Thu Sep 6 13:22:48 2018 -0400 fix FBoxLib compilation networks/general_null/GPackage.mak commit d213ff756a232c635ffb5a4a86f8e4d13b7def9d Author: Michael Zingale Date: Mon Sep 3 12:40:45 2018 -0400 update changes CHANGES commit 12f57a5a9dfd8bc1b3bcd9559aef6d15ae5cecdf Author: Michael Zingale 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 Date: Mon Aug 20 10:56:53 2018 -0400 Add option for disabling esum loop unrolling util/esum.py commit bcb98986ced32efb84b378b66f385c14fee898cf Author: Max Katz 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 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 Date: Mon Aug 20 05:42:55 2018 -0400 Add Kahan summation util/esum.py util/esum_module.F90 commit cb3bdab34dbe249e87c214cce4e20fb44981cd83 Author: Max Katz 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 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 Date: Mon Aug 20 03:04:00 2018 -0400 Fix typo util/esum.py util/esum_module.F90 commit 0d9c362d65e041621af1e863e2a8adf4b0f90e97 Author: Max Katz 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 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 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 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 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 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 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 Date: Mon Aug 13 18:28:38 2018 -0400 Fix accidentally edited file util/microphysics_math.F90 commit 5f7a3a0d78d34ea2e3d87f70c44678cc3aee8022 Author: Max Katz 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 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 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 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 Date: Mon Aug 13 03:49:01 2018 -0400 Update CHANGES CHANGES commit 5d451cc5c0b3be973c5ec1dec6d0670b7c6ff44d Author: Max Katz 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 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 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 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 Date: Sun Aug 12 04:07:13 2018 -0400 Add tabulation for iso7 networks/iso7/actual_rhs.f90 commit 749f9c9e84dbb4c24e793e0f0d84ef38037fe1cd Author: Michael Zingale 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 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 Date: Wed Aug 1 08:40:04 2018 -0400 update CHANGES CHANGES commit 0203d68fa2e838133a528197aa399e693193f55c Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Tue Jul 10 18:52:48 2018 -0400 fix arrows Docs/networks/networks.tex commit 39e3ce8e774996a981b644c56264867a24efda49 Author: Michael Zingale 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 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 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 Date: Sun Jul 8 19:18:57 2018 -0400 update changes CHANGES commit 37a3bfcaab14d840e0aaec9bedd9fea4c60a2fa6 Author: Michael Zingale 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 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 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 Date: Thu Jul 5 15:45:41 2018 -0400 no longer need xin unit_test/test_eos/_parameters commit abcee83992bc15f1abc1c1c581aba03079e181ad Author: Michael Zingale 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 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 Date: Mon Jul 2 09:46:23 2018 -0400 update changes CHANGES commit 6bd3d789284cc96e964bf056f679fc53bb264efb Author: Max Katz Date: Tue Jun 26 03:03:06 2018 -0700 Mark up Helmholtz with !$gpu EOS/helmholtz/actual_eos.F90 commit 4b06c0337accccb72f776789355810322a81e868 Author: Max Katz Date: Mon Jun 25 23:24:57 2018 -0700 Add !$gpu EOS/gamma_law_general/actual_eos.F90 commit 023729c5114d8fe145a662dfda7ada0d25bfed46 Author: Max Katz 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 Date: Mon Jun 25 00:24:11 2018 -0700 vector -> array integration/BS/stiff_ode.F90 commit df1fa863b1554198d9424e801472c19e89536801 Author: Max Katz 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 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 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 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 Date: Wed Jun 20 12:36:49 2018 -0400 update changes CHANGES commit 076f276b9d09de283d3d7545a027cfa05c8e54c5 Author: Donald Willcox 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 Date: Tue Jun 19 23:13:08 2018 -0400 Use CUDA-enabled probin template. unit_test/dummy.probin.template commit 9fc45dc278db388149ceaaeb4fa652b6a490458d Author: Donald Willcox 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 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 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 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 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 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 Date: Tue Jun 19 11:50:38 2018 -0400 fix file name EOS/breakout/Make.package commit 7daf820d44ffdbda7745ca2b4f8be7f39a9a556e Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 Date: Sat Jun 16 23:18:00 2018 -0700 Capital F GMicrophysics.mak commit 449ccaed9ef75f99c45fe2bc66e8dfb186dcdb0e Author: Max Katz Date: Sat Jun 16 23:09:29 2018 -0700 probin.f90 -> probin.F90 GMicrophysics.mak commit 3df01617f7575f6eb98833379014097bd6765744 Author: Max Katz Date: Sat Jun 16 22:49:41 2018 -0700 Define AMREX_DEVICE for CUDA GMicrophysics.mak commit 38588d5a0672a05206c706f6409bda5fbd74c19a Author: Donald Willcox 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 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 Date: Sat Jun 16 22:53:44 2018 -0700 dp_t -> rt integration/BS/test/test.f90 commit 1f218f4ff4e8a2752e067873b9ac70a8410e71dc Author: Max Katz Date: Sat Jun 16 22:52:55 2018 -0700 Helmholtz cleanup EOS/helmholtz/actual_eos.F90 commit 53d4289efd699c3a71354529e7ff1940a9bc3344 Author: Max Katz Date: Sat Jun 16 22:26:58 2018 -0700 vector -> vektor neutrinos/sneut5.f90 commit 8c7547e2ba790694e78df9453681259228dcff83 Author: Michael Zingale Date: Thu Jun 14 21:07:55 2018 -0400 odule -> module networks/ignition_simple_SDC/actual_network.f90 commit d3f47c35d0177e3a90120ee5986231917536801c Author: Michael Zingale Date: Wed Jun 13 10:19:55 2018 -0400 BOXLIB_HOME -> FBOXLIB_HOME unit_test/test_sdc/GNUmakefile commit 3523ac0ee2bc077d8b2c4ac1ba6799fdda021800 Author: Michael Zingale 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 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 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 Date: Mon Jun 11 18:23:28 2018 -0400 ignore AMREX_DEVICE GMicrophysics.mak commit e82452b891c4bc629b979b5927ad923dced6ed70 Author: Michael Zingale Date: Mon Jun 11 17:54:32 2018 -0400 update for FBoxLib util/regression_testing/Microphysics-tests.ini commit f500aa3fd148b5bf4563258ef4bfee17c95383bd Author: Michael Zingale Date: Mon Jun 11 17:52:06 2018 -0400 update SDC dp_t integration/VODE/vode_type_sdc.f90 commit 605664719d532a36bd6d8d6d164048b58ef1ed94 Author: Michael Zingale 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 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 Date: Mon Jun 11 17:38:56 2018 -0400 update the probin template unit_test/dummy.probin.template commit cd096f72909515407f60306c65667a49569eedc7 Author: Michael Zingale 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 Date: Mon Jun 11 17:24:00 2018 -0400 more rt fixes networks/xrb_simple/actual_rhs.f90 commit c0dda7c6f254e631c476115a8eb39fe1a3520ac7 Author: Michael Zingale 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 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 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 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 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 Date: Mon Jun 11 14:40:51 2018 -0400 fix compilation EOS/multigamma/actual_eos.F90 commit 2e61d9a8501cbef6527832ace76a1dd6c2d845fd Author: Max Katz 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 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 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 Date: Sun Jun 10 22:16:37 2018 -0400 Merge branch 'burn_retry_fix' into development commit 980b9e1a7a2f9ee3cdfe7c4b0d8a41c241d49487 Author: Max Katz 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 Date: Mon Jun 4 15:06:51 2018 -0400 Merge branch 'master' into development commit e23a50b003acc4398b4a095beb81ab09d9d562ff Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 Date: Tue May 1 12:57:44 2018 -0400 update CHANGES CHANGES commit b46fb1c3ffb0d70a7eb60baeeacab6c71a02b9a7 Merge: 60070f5b f17c5464 Author: Michael Zingale Date: Mon Apr 30 19:00:16 2018 -0400 Merge branch 'master' into development commit 60070f5b5d9e3a5d63b7688e09b2f0f58c2997d2 Author: Abigail Bishop 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 Date: Fri Apr 13 15:58:53 2018 -0400 update runtime parameters Docs/runtime_parameters/runtime_parameters.tex commit 9c62803475babcc5e12d485d16255a451af93a41 Author: Michael Zingale 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 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 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 Date: Thu Apr 12 00:25:02 2018 -0400 Fix comment integration/BS/bs_rhs.F90 commit f17c5464507fe83ec36e76fe7f1b034369ba2755 Merge: 23fa9b17 ce462ad0 Author: Michael Zingale Date: Mon Apr 9 19:34:16 2018 -0400 Merge branch 'master' of ssh://github.com/starkiller-astro/Microphysics commit 23fa9b17ea8c47dc142241b5af551bce557e0765 Author: Michael Zingale 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 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 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 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 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 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 Date: Sun Apr 8 21:59:27 2018 -0400 update README util/cj_detonation/README.md commit 0cd265c46c6e2d95e3607d964ddab74323708c1c Author: Michael Zingale Date: Fri Apr 6 21:58:07 2018 -0400 add CJ note CHANGES commit 49daae3f6322d4383f4b6bb912e46c79bfaf2916 Author: Michael Zingale 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 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 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 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 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 Date: Fri Apr 6 12:53:48 2018 -0400 make it util/cj_detonation/GPackage.mak commit 8df2c62a7c13b5db5b2b1330900b1fbfe173e081 Author: Michael Zingale 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 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 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 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 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 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 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 Date: Mon Apr 2 12:12:25 2018 -0400 update changes CHANGES commit 11a46077e38d88bfdb0ec641d0128c9e5a0cb91b Author: Michael Zingale Date: Sun Apr 1 12:51:22 2018 -0400 update changes CHANGES commit 3be68f5f0c67bf47eb6ff19dd359b6f64e1416ff Merge: e633d35f 71c69867 Author: Michael Zingale 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 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 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 Date: Thu Mar 29 21:57:31 2018 -0400 update params Docs/runtime_parameters/runtime_parameters.tex commit 1a70814e19ef5ab455d0be4fbd77f10a87e78b2a Author: Donald Willcox 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 Date: Wed Feb 28 20:15:01 2018 -0500 update the README networks/subch/README.md commit 27b290bdfa503494a726b3966f93f8f7a33405e8 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 Date: Sun Dec 17 23:30:18 2017 -0500 Print more data when retrying a burn integration/integrator.F90 commit 2aebdeb62aa5b87ad347eca7b4e7566b6db0fd90 Author: Michael Zingale 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 Date: Sat Dec 2 14:48:49 2017 -0500 Merge branch 'master' into development commit 8b7c4336374bea99c1c399bba5c711981cabcc0a Merge: f483bce6 1c0075bf Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Nov 3 09:31:00 2017 -0400 add development and contribution notes README.md commit 7c51872bfc1bcb43b040e37568cc7aac8bf2c1e4 Author: Michael Zingale Date: Thu Nov 2 16:26:47 2017 -0400 VODE is the default now unit_test/burn_cell/GNUmakefile commit 5b32b0824cb2086444b883d786cc7b782fc7f2a1 Author: Michael Zingale Date: Wed Nov 1 14:42:40 2017 -0400 update CHANGES CHANGES commit a7db0384a229b129bc60487552b06499aa1da23a Author: Max Katz Date: Mon Oct 30 23:19:05 2017 -0400 Make actual_eos_finalize public EOS/helmholtz/actual_eos.F90 commit 19d56b4bf72139c050c249fb88ef2771bc2b8089 Author: Max Katz 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 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 Date: Sun Oct 29 19:56:00 2017 -0400 Update Helmholtz for CUDA EOS/helmholtz/actual_eos.F90 commit 05130972130ad35b80873961228013b4b5668cad Author: Michael Zingale Date: Sat Oct 28 21:39:37 2017 -0400 VODE is now default unit_test/test_react/GNUmakefile commit 9918f222d4df55c0132330668040209773dc2f3b Author: Michael Zingale Date: Sat Oct 28 21:19:07 2017 -0400 fix num util/esum.py commit 05809aacf685ccda7f41dd7b5d76117fc688c8da Author: Michael Zingale Date: Sat Oct 28 21:08:45 2017 -0400 fix function end and args util/esum.py commit 166bd045cdebc13ee5109eb54ae269dc936d1083 Author: Michael Zingale 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 Date: Fri Oct 27 13:10:45 2017 -0400 update changes CHANGES commit 471ed7b962b6f13080deaaeedb5d99e66c5511cc Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Sun Oct 22 15:40:07 2017 -0400 Merge branch 'boost' into development. closes #64 commit 1d3bd73970e50f14223ea6ce9e9f71ba073dd49e Merge: 15f05dba 3c6aa72c Author: Donald Willcox 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 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 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 Date: Sun Oct 22 11:12:28 2017 -0400 a notebook to explore boosting Docs/tests/ode_scaling.ipynb commit e9fcf9d2e7a16da6ea699765bf60910d842d0bf8 Author: Michael Zingale 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 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 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 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 Date: Fri Oct 20 22:29:07 2017 -0400 a test of 3 numbers util/test/test_esum.f90 commit b8841dc455ab455fd9041deeb9d25f7159eaddac Author: Michael Zingale Date: Fri Oct 20 22:18:05 2017 -0400 rename util/test/GNUmakefile util/test/test_esum.f90 commit c7a18415fd0adb83f75beea5e2effc068aa862dc Author: Michael Zingale Date: Fri Oct 20 22:15:25 2017 -0400 this works util/test/GNUmakefile util/test/test_enum.f90 commit ef7768757d951ccecee561de557d613af7aa53be Author: Michael Zingale 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 Date: Thu Oct 19 15:44:52 2017 -0400 fix compilation integration/VODE/vode_rhs.f90 commit 0ae04e27e263b74730bc1b8c19aab7232562f149 Author: Michael Zingale 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 Date: Wed Oct 18 16:23:43 2017 -0400 fix OMP unit_test/test_sdc/main.f90 commit 36e87980fa89157af910125daa4f8650fb17aa6b Author: Donald Willcox 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 Date: Wed Oct 18 12:38:26 2017 -0400 Merge branch 'master' into development commit d3c22c2ad2182b9963df1eefefb7eb7a70f419f5 Merge: 6dab20dd b58cdde4 Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Mon Oct 9 20:42:44 2017 -0400 some compilation fixes integration/BS/bs_type_sdc.F90 commit 6dab20ddac88166c1d4b45dd7566be1ff4c31ac1 Author: Michael Zingale Date: Mon Oct 2 12:59:26 2017 -0400 update changes CHANGES commit 82f66f0f21539df943667aa229ee2bba6d718c1d Author: Michael Zingale 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 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 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 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 Date: Mon Sep 25 09:36:39 2017 -0400 update runtime parameters Docs/runtime_parameters/runtime_parameters.tex commit 39928f78e658711a96b568ff69c88af11f48aff9 Author: Mu-Hung Chang 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Sep 7 16:44:07 2017 -0400 Fixed compilation. unit_test/burn_cell/GNUmakefile commit 502a05141f86984932d30376be5f05fc48cb65d9 Merge: 13bf2bf5 25bd5b68 Author: Michael Zingale 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 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 Date: Fri Sep 1 10:12:09 2017 -0400 update changes CHANGES commit 7d4b11f9c33aeba9ab9f301df72850e314851bc2 Merge: 16ef070f 665d4714 Author: Michael Zingale 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 Date: Thu Aug 31 20:10:37 2017 -0400 update changes CHANGES commit 665d4714782725f9bda97fa97af26be738fc4048 Merge: 9d3ddb13 240fa0cd Author: Michael Zingale 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 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 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 Date: Fri Aug 25 01:08:29 2017 -0400 use d instead of e rates/aprox_rates.f90 commit 3d52c45f37ce3ea80ee3377343be0f58c8161beb Author: Carl E. Fields 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 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 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 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 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 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 Date: Fri Aug 25 00:32:24 2017 -0400 update t9 array rates/aprox_rates.f90 commit b261056c586c97d1b1edc8909148c9da0afc2940 Author: Carl E. Fields 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 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 Date: Mon Aug 14 21:02:39 2017 -0400 add note about retry CHANGES commit d8426eb990203c3c400ff71d859d896658e288dd Merge: 247ac1dc 0041b71a Author: Michael Zingale 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 Date: Sun Aug 13 03:52:03 2017 -0400 Reverse VODE/BS compilation order integration/Make.package commit ba5094d56520de041c0c9718196f0c5c03f351bf Author: Max Katz Date: Sun Aug 13 02:09:17 2017 -0400 Update the INTEGRATOR definitions for SDC integration/integrator_sdc.F90 commit 86abbd7ddb6946e2144d94a4ab7885757a2d0e03 Author: Max Katz 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 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 Date: Sat Aug 12 11:54:58 2017 -0400 Merge branch 'development' into multi-integrator commit 247ac1dc380748eb289d880e7cb850d7e340cc52 Merge: 6d8f1128 3a8b401f Author: Michael Zingale 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 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 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 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 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 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 Date: Mon Aug 7 23:20:30 2017 -0400 Call integrator_init wrapper unit_test/test_sdc/main.f90 commit 9d8202640d9805dd942ccb08cff0699b9cf00c38 Author: Max Katz 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 Date: Tue Aug 1 09:09:17 2017 -0400 update headings CHANGES commit 9ff4a33c090ce153b5f16c43262e3818f5207579 Merge: 236502a4 657eae3b Author: Michael Zingale Date: Thu Jul 27 20:38:13 2017 -0400 Merge branch 'development' into new_helm_table commit 657eae3b60e3a592166150d89bc31f414daa2720 Author: Michael Zingale 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 Date: Tue Jul 25 15:29:05 2017 -0400 some documentation CHANGES Docs/MicrophysicsUsersGuide.tex Docs/transport/transport.tex commit 98eedd0a3850952a6be6c165564c5439050dda15 Author: Michael Zingale 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 Date: Tue Jul 25 13:39:58 2017 -0400 for unit tests of conductivity unit_test/conductivity.F90 commit 236502a4474d962164a7669830d91d95e8fa0299 Author: Michael Zingale Date: Tue Jul 25 09:49:26 2017 -0400 add to changelog CHANGES commit 21458e11efae73c86d01017267d41420f6fa84f6 Merge: 1e9fab55 6af76779 Author: Michael Zingale Date: Tue Jul 25 09:47:54 2017 -0400 Merge branch 'development' into new_helm_table commit 1e9fab5563de739f44521e62591520af0c248680 Author: Maria Barrios Sazo 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 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 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 Date: Tue Jul 18 13:18:42 2017 -0400 add a cleanup TODO util/DNSQE/TODO commit c1003393c58e68e1adc5a2cad8858f473ae0c52d Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Mon Jul 3 12:59:22 2017 -0400 add aprox21 fix CHANGES commit efb0e52e0cda64203dc5aedb32202e9b9ae578b8 Merge: 5185e85a 1d1ab783 Author: Michael Zingale 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 Date: Mon Jul 3 12:35:06 2017 -0400 Merge branch 'master' into development commit e87977c452837866b81e403ae31274fc70061f84 Merge: 6d511d97 5185e85a Author: Michael Zingale 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 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 Date: Wed Jun 14 01:25:29 2017 -0400 BoxLib -> AMReX unit_test/test_eos/GNUmakefile commit caf4baf96976e9243661ae6fdc706d2a9cf30bf5 Author: Adam M. Jacobs 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 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 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 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 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 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 Date: Mon Jun 5 17:23:05 2017 -0400 fix compilation integration/VODE/vode_type_sdc.f90 commit 117abb933bf2d273c9b41b2b9cd3d9650386324b Author: Michael Zingale Date: Thu Jun 1 12:46:11 2017 -0400 update for 17.06 CHANGES commit 79c141af108bfa58c5d7f7a0f136398f9c657a6a Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu May 25 12:35:47 2017 -0400 update to reflect aim for generality README.md commit de6adbb02849f327e7d98944cdd481a463bf0281 Author: Donald Willcox 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 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 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 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 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 Date: Wed May 17 18:52:13 2017 -0400 Removed diagnostic write statements. integration/VODE90/vode_source/dvode.f90 commit b14d1ff4cadceb358234acac12e0cb4eeaf9be23 Author: Donald Willcox 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 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 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 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 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 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 Date: Mon May 15 19:07:17 2017 -0400 Reformatted VODE Readme. integration/VODE90/vode_source/README commit f320be64ac22582c20504259c07f144fdd06c2cf Author: Donald Willcox 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 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 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 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 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 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 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 Date: Sat May 13 03:58:45 2017 -0400 Removed deck... integration/VODE90/vode_source/dvnlsd.f commit 7abb46bc0c32d1bc0105a9468c5e650d89202786 Author: Donald Willcox 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 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 Date: Mon Apr 3 10:23:34 2017 -0400 styling CHANGES commit 88ba21f470b2121802e7c01829f77d6abab8553e Author: Donald Willcox Date: Thu Mar 23 17:26:12 2017 -0400 Remove latex. unit_test/burn_cell/burn_cell_nl.py commit 5aec6b953ded82c9ac2e91da205047651202349f Author: Donald Willcox 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 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 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 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 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 Date: Tue Jan 3 10:12:31 2017 -0500 update for merge CHANGES commit 2043246e810d521eba7c8d40fcb8055ed63569d1 Author: Michael Zingale 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 Date: Wed Dec 28 19:38:08 2016 -0500 add updates CHANGES commit 048e6f902bd128b0367788b48ec6f3a4249042aa Merge: 0ed9e816 d8d8a93d Author: Michael Zingale 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 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 Date: Wed Dec 28 14:02:49 2016 -0500 add a comment integration/VODE/vode_type_sdc.f90 commit 8985fda1cc7677bea693be4236d5febf6ed34261 Author: Michael Zingale 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 Date: Wed Dec 28 12:10:55 2016 -0500 Merge branch 'development' into nomolar commit 0ed9e816b2fee9238a0131cd0aeca63602cc86f0 Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Dec 1 09:29:08 2016 -0500 update changes CHANGES commit c66e8ace35e3934450059299c0ab073b314884ec Author: Michael Zingale Date: Wed Nov 30 09:14:27 2016 -0500 changes from the past month CHANGES commit 2f29e6dd17d3ebd519244dd433c67b8af1d7332b Author: Michael Zingale Date: Wed Nov 30 09:04:13 2016 -0500 fix compilation networks/xrb_simple/actual_rhs.f90 commit be323d40d9a863b676be3840b9fbbd270aefd888 Author: Michael Zingale 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 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 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 Date: Mon Nov 28 14:49:05 2016 -0500 add aion_inv unit_test/network.f90 commit 037b1ce6f8f1ad9926cc3a87abce7f951f6ea7a5 Author: Michael Zingale Date: Tue Nov 22 10:10:19 2016 -0500 clarify indices integration/VODE/rpar.F90 commit 476ec0b1ece95e7c65f101e38566dfa7012fc311 Author: Michael Zingale 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 Date: Mon Nov 21 20:34:07 2016 -0500 update for SDC integration/VODE/Make.package commit 76eac69dc9ab352f27a06ee2958292365cd66bcd Author: Michael Zingale Date: Mon Nov 21 20:28:38 2016 -0500 fix compilation integration/BS/actual_integrator_sdc.F90 commit 069c0c50dfe6cc14eb84e668dd5283c3591229a4 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Sun Nov 20 22:14:36 2016 -0500 fix some indexing integration/VODE/rpar.F90 commit 3b8f3da7a96effa9d857ef51bcdea6ca75a080ec Author: Michael Zingale Date: Sun Nov 20 22:07:13 2016 -0500 also need T_from_eden integration/VODE/rpar.F90 commit 9c1437b89f07bd40a4ea0c0b410b0f5bf46550f9 Author: Michael Zingale Date: Sun Nov 20 21:44:31 2016 -0500 need the advective terms too integration/VODE/rpar.F90 commit c1ded479e4b041f3fedab5b169428cdd0b1369df Author: Michael Zingale Date: Sun Nov 20 19:07:18 2016 -0500 SDC vs. non-SDC rpar integration/VODE/rpar.F90 commit 0e79e90353cd2c3f4ec55286d3f913cdfa5772e5 Author: Michael Zingale Date: Sun Nov 20 18:44:20 2016 -0500 a little more on VODE Docs/networks/networks.tex commit 8b6671ae008828e2382fdc0f99f5d565114779d9 Author: Michael Zingale 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 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 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 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 Date: Sat Nov 19 11:58:45 2016 -0500 Merge branch 'development' into vode-sdc commit 936a09c05702f8de8b9e8f2f812ee9e9cd488d02 Merge: a8cef279 148a9d5f Author: Michael Zingale Date: Sat Nov 19 11:04:03 2016 -0500 Merge branch 'development' into nomolar commit 148a9d5f530df13f48039b4c35c7f2807720ec5b Author: Michael Zingale Date: Fri Nov 18 14:15:15 2016 -0500 typo Docs/sdc/sdc.tex commit b3816eb7e950dac35ece177b92a565248dd46175 Author: Michael Zingale Date: Fri Nov 18 14:01:20 2016 -0500 update the SDC Docs/sdc/sdc.tex commit e627df582f73811c1eb729fb40d3f8914f8fabcc Author: Michael Zingale Date: Fri Nov 18 10:10:45 2016 -0500 make signs consistent with code Docs/sdc/sdc.tex commit 5caaa6feca7ce09a69d30e1374e276f3fbd6dc11 Author: Michael Zingale 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 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 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 Date: Tue Nov 15 14:00:24 2016 -0500 Merge branch 'development' into nomolar commit 98c2cad7781e57f4eaafa6aa905eabf6fb89efc4 Author: Michael Zingale Date: Tue Nov 15 14:00:06 2016 -0500 add rprox unit_test/test_react/test_network_combinations.py commit 32a63135a41291af057072ffbfe2c477be55b1ba Author: Michael Zingale Date: Mon Nov 14 18:00:56 2016 -0500 some cleaning Docs/networks/networks.tex commit 7c669e1171e841d096061ffbb05a1493603192a9 Merge: f606f53e 9516d433 Author: Michael Zingale Date: Mon Nov 14 17:50:02 2016 -0500 Merge branch 'development' into nomolar commit 9516d43360738a36ede8e73adc671897b6c512fa Author: Michael Zingale 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 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 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 Date: Wed Nov 9 18:24:50 2016 -0500 Merge branch 'development' into nomolar commit f3ce1d3bd9b761c69b93b19e9bb1ce7d82f4d571 Author: Michael Zingale 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 Date: Wed Nov 9 14:32:23 2016 -0500 OMP on by default unit_test/test_react/GNUmakefile commit ad6fb586d7dd633a89a0378b83b851b1b8a2024c Author: Michael Zingale Date: Wed Nov 9 14:32:03 2016 -0500 more options unit_test/test_react/test_network_combinations.py commit 9213c43a0732d39eb35c9469a52fdfa400d2aa19 Author: Michael Zingale 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 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 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 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 Date: Wed Nov 9 10:43:25 2016 -0500 add a return code unit_test/test_react/main.f90 commit 10413865e023c945822740b43dc29d894d9f0c01 Author: Michael Zingale 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 Date: Wed Nov 9 09:14:52 2016 -0500 Merge branch 'development' into nomolar commit 2d5c49b736f55f7b52548eb4d74bbf40f7911b41 Author: Michael Zingale 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 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 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 Date: Tue Nov 8 15:25:42 2016 -0500 Merge branch 'development' into nomolar commit 8907cac2b17196d5d1818227e145109ba248034e Author: Michael Zingale Date: Tue Nov 8 14:28:41 2016 -0500 add new test CHANGES commit 0792cd06a7a332b8af2340c5bd0172fa92051ab7 Author: Michael Zingale 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 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 Date: Tue Nov 8 12:58:36 2016 -0500 Merge branch 'development' into nomolar commit 3f76b93cceaf7bfb2beb5450b7f86ac778093e71 Author: Michael Zingale 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 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 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 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 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 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 Date: Sat Nov 5 22:07:18 2016 -0400 fix SDC unit_test/microphysics.F90 commit e8dd7cf2fbfd454fbfd96946ea900fbd25ff60ce Author: Michael Zingale 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 Date: Sat Nov 5 21:47:09 2016 -0400 add the SDC defines GMicrophysics.mak commit 1f6b8222832988c8c71a58908408ee5305260663 Author: Michael Zingale 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 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 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 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 Date: Sat Nov 5 20:54:29 2016 -0400 add SDC hooks integration/BS/GPackage.mak commit ecfcd6485fa3e06e9df156066e9b92ba19e1c4db Author: Max Katz Date: Sat Nov 5 10:59:54 2016 -0400 Add a timer unit_test/test_react/main.f90 commit 621aa9deff88dd0aa840b749533961c837b99ef8 Author: Max Katz 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 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 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 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 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 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 Date: Thu Nov 3 21:43:30 2016 -0400 use the timestep estimator by default integration/BS/_parameters commit 8d5ee5c863e43a9802918a7726721409f91c4bc3 Author: Michael Zingale 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 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 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 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 Date: Tue Nov 1 09:52:35 2016 -0400 Merge branch 'development' commit 209c975cc9f819645159a04c7b0e808aeda41aa9 Author: Max Katz 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 Date: Fri Oct 28 10:10:15 2016 -0400 add another net unit_test/test_react/README.md commit 4eb14bac0072406dd3a5e5decef5ab1dd9d3bbf3 Author: Max Katz 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 Date: Thu Oct 27 22:13:07 2016 -0400 updates unit_test/test_react/README.md commit e5bf0694593b1fdf6d81d3faeef127c458cdfa68 Author: Michael Zingale Date: Thu Oct 27 21:48:27 2016 -0400 update table unit_test/test_react/README.md commit b6805ca5b074709f9e85d7880640aa30cccda92f Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Mon Oct 3 10:57:15 2016 -0400 no 16.10 changes? CHANGES commit 875bbde96d2bf340213f7d741d5a69c46779d886 Merge: 74a5ec52 2f6740bc Author: Michael Zingale 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 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 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 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 Date: Thu Sep 15 15:48:50 2016 -0400 don't init MPI twice unit_test/microphysics.f90 commit 6bcd117d595c2050a036199119870020657a7fc7 Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Sep 8 22:10:34 2016 -0400 Fix typo EOS/helmholtz/actual_eos.F90 commit af8279cc0acea22afd9d3cb800cf3e0e3ac9becb Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Sep 1 13:19:09 2016 -0400 new tag CHANGES commit 5104de85aa3f0b8e94c49a24df41e79a234fd8ed Merge: 8d68c187 a5ec24e8 Author: Donald Willcox 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 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 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 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 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 Date: Sat Aug 27 21:50:00 2016 -0400 remove the scaling stuff Docs/networks/networks.tex commit fc1d206dc2618b94b5afedc23b5aa032e4e5d457 Author: Donald Willcox 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 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 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 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 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 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 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 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 Date: Tue Aug 23 16:28:34 2016 -0400 Added URCA tables to gitignore ala helm_table .gitignore commit f85c1baaaa356a453325e33ab1626ec37c8e018b Author: Donald Willcox 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 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 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 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 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 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 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 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 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 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 Date: Sat Aug 13 21:45:47 2016 -0400 fix normt Docs/networks/networks.tex commit 09b4436656e7f6a2a9c6d3c232ac0fc4ad227e9a Author: Michael Zingale Date: Sat Aug 13 21:43:10 2016 -0400 document the VBDF error criteria Docs/networks/networks.tex commit ad273e74da8dfc1c20c70a3cd760b6d92aea4b63 Author: Michael Zingale 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 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 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 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 Date: Fri Aug 12 11:43:33 2016 -0400 remove unused variables integration/VBDF/actual_integrator.F90 commit 0bd389d7ba05e158e8093dee80dd646c43847ac1 Author: Michael Zingale 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 Date: Fri Aug 12 09:57:03 2016 -0400 add VBDF section Docs/runtime_parameters/runtime_parameters.tex commit 966225cbbbc2b0aa02d9838d7f018614bf2093a3 Author: Michael Zingale 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 Date: Fri Aug 12 09:29:16 2016 -0400 update parameter list Docs/runtime_parameters/runtime_parameters.tex commit 64a20da35279618c6029eee68dac14ab7d7ddd25 Author: Michael Zingale 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 Date: Thu Aug 11 19:01:47 2016 -0400 some comments integration/VBDF/NOTES commit 39e106ccbb45a7f2782c8b48334b0aa48f3a5320 Author: Michael Zingale 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 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 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 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 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 Date: Thu Aug 11 13:41:59 2016 -0400 add the VODE timestep estimator integration/VBDF/actual_integrator.F90 commit 28920007f52c35b1b3108268260612e8e30f5a8f Author: Michael Zingale 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 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 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 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 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 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 Date: Wed Aug 10 20:36:06 2016 -0400 some ACC reorg unit_test/test_react/main.f90 commit 6e92f77fc734243af8232470d23c1ab8ffbac500 Author: Michael Zingale Date: Wed Aug 10 19:15:10 2016 -0400 remove ldt unit_test/test_react/main.f90 commit cf2513fa9490acf21a8df82adc69e7b8f7d92e14 Author: Michael Zingale 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 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 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 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 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 Date: Wed Aug 10 13:27:06 2016 -0400 define integer indices Docs/data_structures/data_structures.tex commit 77783f8b35e5436bd9ab0d36dd4f1a01f61f8b99 Author: Michael Zingale 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 Date: Wed Aug 10 10:33:47 2016 -0400 update CHANGES CHANGES commit 7762064895ccf7f820b834efc32d68f8c52358de Merge: 937f2e0e 04117510 Author: Michael Zingale 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 Date: Wed Aug 10 09:33:53 2016 -0400 a little debuggin Docs/openacc/openacc.tex commit 04117510b5d1e7a6bc2ba71a768d229724432830 Author: Max Katz 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 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 Date: Tue Aug 9 13:05:22 2016 -0400 remove some unnecessary acc markup integration/BS/stiff_ode.F90 commit d0cd50359c5632b558f3a91c7736b4bd05c9e59d Author: Michael Zingale Date: Tue Aug 9 13:03:53 2016 -0400 add more OpenACC compilation notes Docs/openacc/openacc.tex commit e292e85b1f7c79903d47f2ece56198ac166c8bea Author: Michael Zingale Date: Tue Aug 9 10:44:25 2016 -0400 fix final update integration/BS/stiff_ode.F90 commit e7a540f8628f9d72d4182803a76c474568e24685 Author: Michael Zingale 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 Date: Tue Aug 9 10:05:30 2016 -0400 some comments integration/BS/stiff_ode.F90 commit 0cd65358fe54410cad258af1c05e21426e4eba93 Author: Michael Zingale 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 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 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 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 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 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 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 Date: Mon Aug 8 12:05:56 2016 -0400 output RHS stats unit_test/test_react/main.f90 commit 03ee21c16e99e6f5227b5e33531b71c2288ff612 Author: Michael Zingale 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 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 Date: Mon Aug 8 09:40:24 2016 -0400 re-remove species derivatives interfaces/burn_type.F90 commit 5b7a63c2132a803c63381b57365a1c94d1fb4318 Author: Michael Zingale 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 Date: Sun Aug 7 00:11:55 2016 -0400 Merge branch 'development' into openacc commit b5730c1c7c4c0413664f5bec48051319b0657008 Author: Max Katz 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 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 Date: Sat Aug 6 19:32:50 2016 -0400 Include module reference networks/general_null/actual_rhs.f90 commit 3f6fa2c64400f207f6572381b855fc74436934e6 Author: Michael Zingale Date: Sat Aug 6 18:17:27 2016 -0400 add note on input validation Docs/EOS/eos.tex commit 50b01686d4867871cfc156d8eb62c72f61ec1c72 Author: Max Katz 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 Date: Mon Aug 1 12:20:44 2016 -0400 remove smallx interfaces/eos_type.f90 commit 5d24194ef13fbece9c188d2902c2bee5d91232de Author: Michael Zingale Date: Mon Aug 1 11:08:15 2016 -0400 fix typo Docs/networks/networks.tex commit 2dcf14463b349b5254b640a872a4684de11d1344 Author: Michael Zingale Date: Mon Aug 1 10:40:58 2016 -0400 some updates CHANGES commit 5552c482e87283139bdd8800c9cf66fbd98823b3 Merge: 9273f858 320e5a02 Author: Michael Zingale Date: Mon Aug 1 10:39:41 2016 -0400 Merge branch 'development' into development-next commit 320e5a023262783648a1b1acdee26d98a9fefdbb Author: Michael Zingale Date: Mon Aug 1 10:39:03 2016 -0400 reset changes since last time CHANGES commit 9273f85863c7b9a3c4135d7e6537ba8fe680e734 Author: Max Katz 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 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 Date: Fri Jul 29 20:42:53 2016 -0400 add num_rate_groups networks/general_null/network.template commit da7660a0e10ad7d8bfeeafc28e2b2cc991b66f9a Author: Michael Zingale Date: Fri Jul 29 20:40:18 2016 -0400 discuss num_rate_types Docs/networks/networks.tex commit ec635c3c1ed135187ae92d060e36d62fe64ae490 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Mon Jul 25 15:13:33 2016 -0400 fix URL README.md commit b204536c89729f43493a24ce5bbc1c69fef79a41 Author: Michael Zingale Date: Mon Jul 25 15:12:34 2016 -0400 add link to user's guide PDF README.md commit 453fcaf93ba2629ad1842d2d54069f63dd2bea55 Author: Michael Zingale Date: Mon Jul 25 14:56:37 2016 -0400 add openacc networks/triple_alpha_plus_cago/actual_network.f90 commit 66a9c2b857337a50cff9bde2c022353b485ed570 Author: Michael Zingale 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 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 Date: Sun Jul 24 20:54:03 2016 -0400 add intent integration/BS/bs_type.f90 commit 727531b8047e28b0f467c7a700c43e806f01a340 Author: Michael Zingale Date: Sun Jul 24 19:26:43 2016 -0400 fix compilation networks/rprox/actual_rhs.f90 commit 0cd806d00f33106f8a8595e790967f1e6f57caaf Author: Michael Zingale 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 Date: Sat Jul 23 20:36:16 2016 -0400 Merge branch 'development' into BS-refactor commit 171b6160b764443aac92d6655bda14e7065ec070 Author: Michael Zingale Date: Sat Jul 23 14:07:34 2016 -0400 more stuff to doc Docs/networks/networks.tex commit d41ee15fd5cf52d7f730c230375d63702a1c2f12 Author: Michael Zingale Date: Sat Jul 23 14:02:34 2016 -0400 remove note about state % rates Docs/networks/networks.tex commit 0e869e8191bdbbf4b84ff76d8d9e64a5c90c8bf4 Author: Michael Zingale 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 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 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 Date: Sat Jul 23 10:45:19 2016 -0400 Merge branch 'development' into BS-refactor commit dc2564e5dfa7851301cb39e8f8540a9a05805c18 Author: Michael Zingale 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 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 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 Date: Fri Jul 22 14:41:40 2016 -0400 Merge branch 'development' into BS-refactor commit 983c18c66f4ca87d5264441096ccb41c2f30b332 Author: Michael Zingale 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 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 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 Date: Fri Jul 22 12:55:27 2016 -0400 new file -- the rate_t networks/rate_type.f90 commit 850574f8426df79a8d937d7f3253d013825a4564 Author: Michael Zingale 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 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 Date: Thu Jul 21 22:22:13 2016 -0400 this works unit_test/test_react/inputs_aprox21 commit 4b55ccc405d8266d14ce170e840bcb6498ba5cc3 Author: Michael Zingale 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 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 Date: Thu Jul 21 20:17:02 2016 -0400 Merge branch 'BS-refactor' into development commit 2b3ad6b86d4cf8a3422bba60810f55b3209ea917 Author: Michael Zingale 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 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 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 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 Date: Thu Jul 21 10:12:40 2016 -0400 Merge branch 'development' into BS-refactor commit 03c56ed6ff33dbe8c9b30c9aca31f9a1eefa7b92 Merge: 3e5e78ea c3c108da Author: Michael Zingale Date: Wed Jul 20 22:15:03 2016 -0400 Merge branch 'development' into BS-refactor commit c3c108da658359f6fa6096da5def2ee606a8dc42 Author: Michael Zingale 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 Date: Wed Jul 20 21:33:46 2016 -0400 Merge branch 'development' into BS-refactor commit a6eb47c7f6026604f17d8f424fde18c4aa7a136e Author: Michael Zingale 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 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 Date: Wed Jul 20 21:15:44 2016 -0400 Merge branch 'development' into BS-refactor commit d94f904b137b9c5458eca0ca373748fc2cde804d Author: Michael Zingale 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 Date: Wed Jul 20 20:54:11 2016 -0400 Merge branch 'development' into BS-refactor commit 1847290d70eb80f975d58830d122b2c832843d9a Author: Michael Zingale Date: Wed Jul 20 20:53:11 2016 -0400 use debug mode networks/aprox13/test/GNUmakefile commit 819102b9dcd2d49b1f04f5147514744c36b4f7c3 Author: Michael Zingale 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 Date: Wed Jul 20 20:35:49 2016 -0400 remove loop networks/aprox13/test/testburn.f90 commit 65160d6965abb88d77204007b08c9357e3c93b70 Author: Michael Zingale 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 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 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 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 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 Date: Wed Jul 20 14:23:02 2016 -0400 Merge branch 'development' into BS-refactor commit 5ead0f38fce5847864e52037454c974b522208e8 Author: Michael Zingale 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 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 Date: Wed Jul 20 09:38:16 2016 -0400 a little more on the usage Docs/basics/basics.tex commit 61b72f91afe4b6a19bb459394a4b30de6eb88364 Author: Michael Zingale Date: Tue Jul 19 22:16:18 2016 -0400 burn_s integration/BS/bs_type.f90 commit 60d1ce9ac171c0182fa48539e93cd2a2e11f90f2 Author: Michael Zingale Date: Tue Jul 19 22:15:33 2016 -0400 remove the species derivatives interfaces/burn_type.F90 commit eee414b88af4d17b99c2b6878f6935014f4103a8 Author: Michael Zingale 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 Date: Tue Jul 19 19:08:07 2016 -0400 Merge branch 'development' into BS-refactor commit 4ef1a3fa44de909f6a3779e908c9e7dc77bf9ed0 Author: Michael Zingale 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 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 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 Date: Tue Jul 19 16:14:06 2016 -0400 document how we call the RHS Docs/networks/networks.tex commit 4fa302b86678efc124f55e46594921e2a7ff87ae Author: Michael Zingale 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 Date: Tue Jul 19 15:34:07 2016 -0400 add a flow chart Docs/networks/networks.tex commit a923f6683904d7b2ae6a0fb86b5e1485408d1e51 Author: Michael Zingale Date: Tue Jul 19 15:08:58 2016 -0400 document BS Docs/networks/networks.tex Docs/refs.bib commit 840e31dd9891aca619c8ba5ad6c17e7512020746 Author: Michael Zingale 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 Date: Tue Jul 19 11:21:42 2016 -0400 finish up to the ODE solvers Docs/networks/networks.tex commit ebfd2b38781834de7008eb904f221181a445ccf7 Author: Michael Zingale Date: Tue Jul 19 10:18:39 2016 -0400 add burning_mode_factor Docs/networks/networks.tex commit e2d105f309116612bdbece3eb5ac9f2ca2b7c6e3 Author: Michael Zingale 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 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 Date: Mon Jul 18 22:08:16 2016 -0400 typo Docs/networks/networks.tex commit 9fef44e0e2a0334409a4599406bfaf55607d72c0 Author: Michael Zingale Date: Mon Jul 18 22:05:11 2016 -0400 add section Docs/networks/networks.tex commit c8b82a93e8cbb2ce18ee0360aec7bf638d0aa2bf Author: Michael Zingale 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 Date: Mon Jul 18 20:57:46 2016 -0400 use update_unevolved_species networks/ignition_simple/actual_rhs.f90 commit 76d6a9343dc175f1fe6e81a2ccf18f314f3dcec8 Author: Michael Zingale 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 Date: Mon Jul 18 19:08:57 2016 -0400 more docing Docs/networks/networks.tex commit 7f9df291b07a75993e2c441d5ef90c544767092f Author: Michael Zingale Date: Mon Jul 18 18:10:30 2016 -0400 document update_unevolved_species Docs/networks/networks.tex commit b07fab135588fb1a6f069009e06a6841d140fdf7 Author: Michael Zingale Date: Mon Jul 18 16:56:20 2016 -0400 more clarity on the internal energy Docs/networks/networks.tex commit 6655d411c062c34f7e3bafbd0f97a8d1fab18a53 Author: Michael Zingale 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 Date: Mon Jul 18 16:09:31 2016 -0400 typo Docs/networks/networks.tex commit 7e4d8512679088b06c651dd6613324e5de40f638 Merge: 92f1023b 69156246 Author: Michael Zingale 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 Date: Mon Jul 18 16:07:02 2016 -0400 some energy stuff Docs/networks/networks.tex commit 69156246a86a14c7d51729f7ab6d377ec5eaf14b Author: Max Katz 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 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 Date: Mon Jul 18 15:52:55 2016 -0400 fix comment integration/_parameters commit 5e3eb6b30bc5a883978109eb1e56ab72774d72ae Author: Michael Zingale 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 Date: Mon Jul 18 14:40:50 2016 -0400 finish T evolution section Docs/networks/networks.tex commit 8eaafda0c768073aa5b9fad2c805931d832644ae Author: Michael Zingale Date: Mon Jul 18 14:32:58 2016 -0400 add a comment integration/BS/bs_type.f90 commit 91ee40b2183646ca205b2ea1d6e8f57c979175b2 Author: Michael Zingale 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 Date: Mon Jul 18 13:24:34 2016 -0400 some T evolution Docs/networks/networks.tex commit 7c6b3b42d3d6d9ac513738dd442a05555724000f Author: Michael Zingale 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 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 Date: Mon Jul 18 10:48:17 2016 -0400 add comment networks/triple_alpha_plus_cago/actual_rhs.f90 commit 212be1ec7462a2e2d58a103b29f5ddb1d979618c Author: Michael Zingale Date: Mon Jul 18 10:01:26 2016 -0400 tweak Docs/networks/networks.tex commit c3d728c3296ca7848cb139b5e5cf5b54554a080a Author: Michael Zingale 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 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 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 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 Date: Sat Jul 16 18:22:32 2016 -0400 remove some redundant code Docs/runtime_parameters/rp.py commit 3138698bc811a2fce4d86138a36ebc085a2ac992 Author: Michael Zingale 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 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 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 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 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 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 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 Date: Fri Jul 15 13:54:57 2016 -0400 remove print networks/ignition_chamulak/actual_rhs.f90 commit c5be7b415482e50d623d5c7c6f96f6bdc4d308e7 Author: Michael Zingale Date: Fri Jul 15 12:50:01 2016 -0400 fix compilation networks/xrb_simple/actual_rhs.f90 commit a157843e511010924264c9137580dac516774222 Author: Michael Zingale 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 Date: Thu Jul 14 22:13:40 2016 -0400 a little more docs Docs/networks/networks.tex commit 5f04b360bab126546449ef628fc5fa9c0ab7d713 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Jul 14 02:26:58 2016 -0400 Remove some unused density derivatives networks/aprox21/actual_rhs.f90 commit 00244a88ad9fa60e5864ca5efc73242440452630 Author: Max Katz Date: Thu Jul 14 00:42:59 2016 -0400 Remove some unused density derivatives networks/aprox19/actual_rhs.f90 commit d2b8fb26b8480bff7b04659cdf0a1e7a7622dee0 Author: Michael Zingale Date: Wed Jul 13 23:07:42 2016 -0400 add spec names to print networks/rprox/test/eval.f90 commit 8d021e444fa5748451adbc25a1b2c1663c463713 Author: Michael Zingale 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 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 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 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 Date: Wed Jul 13 19:20:02 2016 -0400 this atleast works unit_test/test_react/inputs_aprox19 commit 576c4de06d8ac51b68f625a8cba2acb6cc99b70b Author: Michael Zingale Date: Wed Jul 13 15:40:00 2016 -0400 more sections Docs/networks/networks.tex commit 3f3a83effbcf5afbcf23b4aaad1212fcaeb41328 Author: Michael Zingale Date: Wed Jul 13 15:34:23 2016 -0400 update Docs/runtime_parameters/runtime_parameters.tex commit 033ed240cfd77a062d0a2032843794dbc7a730d5 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Wed Jul 13 11:23:24 2016 -0400 update Docs/runtime_parameters/runtime_parameters.tex commit 024f92d822c942d45d3bf89b715e2e6a8b853dfa Author: Michael Zingale Date: Wed Jul 13 11:22:43 2016 -0400 typos Docs/data_structures/data_structures.tex commit 58d9f1239830092c26b01475e2007cc67f8c631a Author: Max Katz 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 Date: Tue Jul 12 20:45:14 2016 -0400 some fixes Docs/EOS/eos.tex commit 3ec4e3e280df3fa78f6036ceb83f900021875ab5 Author: Michael Zingale Date: Tue Jul 12 20:10:20 2016 -0400 more ztwd clarification Docs/EOS/eos.tex commit faa3ca08b85fd0f933941b8bc03bed7a9572ca96 Author: Michael Zingale Date: Tue Jul 12 19:51:48 2016 -0400 fix some ztwd notation Docs/EOS/eos.tex commit 38535ccf30caea0caf18297c0d69c5c91e598bb4 Author: Michael Zingale Date: Tue Jul 12 19:46:44 2016 -0400 document the polytrope EOS Docs/EOS/eos.tex commit 1b1733e5055b431807a1661b61f44e7fc3483b1d Author: Michael Zingale 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 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 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 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 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 Date: Tue Jul 12 13:54:53 2016 -0400 more changes CHANGES commit 01b5f99bb63d1190f429440b42c145bece2e6e32 Author: Michael Zingale Date: Tue Jul 12 13:52:45 2016 -0400 document the unit tests Docs/unit_tests/unit_tests.tex commit 0d30015e6b7f965b1b53e3dd99c0ef5aadc30d89 Author: Michael Zingale 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 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 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 Date: Mon Jul 11 15:42:09 2016 -0400 fix the exclusion rule for helm_table.dat .gitignore commit 7aa4f41599fe6f4179d2455e18bf09527ef5e4c2 Author: Michael Zingale 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 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 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 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 Date: Mon Jul 11 14:15:38 2016 -0400 better philosophizing Docs/basics/basics.tex commit 161d42b0650b8a8e884b729782dc39b85ccf8c45 Author: Michael Zingale 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 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 Date: Mon Jul 11 12:10:01 2016 -0400 C++ macro Docs/maestrosymbols.tex commit 84938fc7ec0bde0c835b608c9d4b7f331cb5963f Author: Michael Zingale 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 Date: Mon Jul 11 11:12:11 2016 -0400 eos -> EOS CHANGES commit b70f280c6f63abcacf53f7b020b486ae9a24866d Author: Michael Zingale Date: Mon Jul 11 11:11:21 2016 -0400 eos -> EOS README.md commit 9f904ee72512c27da106e05fa6642aa281482103 Author: Michael Zingale Date: Mon Jul 11 11:11:11 2016 -0400 eos -> EOS GMicrophysics.mak commit 2aca3f0849ec29369661f3324086e1afe6ae6a91 Author: Michael Zingale 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 Date: Mon Jul 11 10:21:59 2016 -0400 doxygen config util/doxygen/Doxyfile commit 1b4c695d803b838cb7cda40a51eec2d9a5a3519b Author: Michael Zingale Date: Fri Jul 8 22:06:26 2016 -0400 add some notes networks/rprox/test/README commit 37889f65526a410758ee3a87dfb817dad5e073f1 Author: Michael Zingale Date: Fri Jul 8 20:56:58 2016 -0400 update compilation networks/xrb_simple/test/GNUmakefile commit c23cd9606443d177e904126323d245176759b1aa Author: Michael Zingale Date: Fri Jul 8 20:55:28 2016 -0400 get this compiling again networks/ignition_simple/test/GNUmakefile commit 112fb5d56cdcb2a4a462082e8405b2da3d85db07 Author: Michael Zingale Date: Fri Jul 8 20:53:17 2016 -0400 get this compiling again networks/aprox13/test/GNUmakefile commit fd20c6b64e9407b2ffe5ab91d57a7818ad2b63ef Author: Michael Zingale Date: Fri Jul 8 20:50:51 2016 -0400 update GNUmakefile networks/triple_alpha_plus_cago/test/GNUmakefile commit 2038e0555ed90e4f4903208372e9d3b2b402b627 Author: Michael Zingale 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 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 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 Date: Fri Jul 8 15:50:13 2016 -0400 new parameter Docs/runtime_parameters/runtime_parameters.tex commit 62be21f4f56b79cd866eadba595aa44fd4d767b2 Author: Michael Zingale 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 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 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 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 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 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 Date: Fri Jul 8 12:02:49 2016 -0400 new parameters Docs/runtime_parameters/runtime_parameters.tex commit fe7712dedac30af3a7413c31000acaee747e8a54 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Jul 6 19:09:34 2016 -0400 fix attempt at OpenACC unit_test/test_react/main.f90 commit 6f7759174f24b974b61cac56037e6f45ceb6acf0 Author: Max Katz 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 Date: Tue Jul 5 14:33:51 2016 -0400 double precision -> real(dp_t) integration/BS/actual_integrator.F90 commit 58e5b8e5b3e24796802bd069dd477cbef0731eea Author: Michael Zingale Date: Tue Jul 5 12:54:56 2016 -0400 update version number CHANGES commit 05b97420a8f39b6caf2b3f80d39eaa01b053b851 Author: Michael Zingale 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 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 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 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 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 Date: Sat Jul 2 19:56:13 2016 -0400 FIRSTPRIVATE burn_state_in unit_test/test_react/main.f90 commit 0199fec8212e7df420cacb7c8dcfcc72e41baffb Author: Max Katz 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 Date: Sat Jul 2 19:07:40 2016 -0400 Avoid possibility of undefined value unit_test/eos.f90 commit c9ed27016531e58bc2daf4dd17ce0701e00091cf Author: Michael Zingale Date: Sat Jul 2 18:46:56 2016 -0400 remove dynamic scheduling unit_test/test_eos/main.f90 commit e64c7882a4a7a237e52038fdd06f15f215f8d801 Author: Max Katz 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 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 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 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 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 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 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 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 Date: Fri Jul 1 21:31:10 2016 -0400 add OpenMP directives unit_test/test_eos/main.f90 commit 8c1019e4495e2be8535b813d535f8171e79d1834 Author: Michael Zingale Date: Fri Jul 1 21:11:13 2016 -0400 add OpenMP directives unit_test/test_react/main.f90 commit 5ea325ce6758c8606c62ab2d55cb6c3475b446cb Author: Michael Zingale 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 Date: Fri Jul 1 17:54:04 2016 -0400 update docs Docs/runtime_parameters/runtime_parameters.tex commit 61eba03a149ebde8d3cd90e3ea96cb48aa645fe3 Author: Michael Zingale 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 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 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 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 Date: Thu Jun 30 20:00:09 2016 -0400 add a list of changes since the last merge CHANGES commit 5725c927fb0ed9094d3f5d20e614aa19a1d7da97 Author: Max Katz 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 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 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 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 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 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 Date: Sun Jun 26 03:21:49 2016 -0400 Initialize the Pascal matrix integration/VBDF/actual_integrator.F90 commit 32a4f0e9c0767c63a422f043ecdf9a7f52529a7a Author: Max Katz Date: Sun Jun 26 00:33:02 2016 -0400 Simplify esum again util/microphysics_math.F90 commit e1372307395400f61e4bf6196d051dba83d6bda5 Author: Max Katz 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 Date: Fri Jun 24 17:23:46 2016 -0400 remove sdc debug networks/aprox13/actual_rhs.f90 commit faa6fca72ea4f693777eb96840b498698e1468db Author: Michael Zingale 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 Date: Fri Jun 24 17:21:26 2016 -0400 Merge branch 'development' into sdc_diag commit ed9e4464b4e01f0bdbf3ca00798ea9ddf7be4372 Author: Michael Zingale 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 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 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 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 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 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 Date: Thu Jun 23 13:54:35 2016 -0400 fix file openning networks/aprox13/actual_rhs.f90 commit 5b6ddd52a81deaf1bde086de1009d1539ba2349b Author: Michael Zingale 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 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 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 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 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 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 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 Date: Tue Jun 21 19:19:46 2016 -0400 more sanity checks unit_test/test_react/main.f90 commit b7ad8b4d91de969b506735c300d4b3fbf9e341bf Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 Date: Fri Jun 17 00:27:01 2016 -0400 Update device data integration/integrator.f90 commit 2dfdce1407f1a21573433f60787d14ec34b7c8dd Author: Max Katz 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 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 Date: Thu Jun 16 23:33:20 2016 -0400 Some more better indexing integration/BS/bs_convert.f90 commit 08888e7db344dfe29946dc9ffd4fff21dcd01122 Author: Max Katz Date: Thu Jun 16 23:05:01 2016 -0400 Remove a costly array initialization util/microphysics_math.F90 commit d2efc1845ec444b50213111632c47303d5e6a688 Author: Michael Zingale 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 Date: Thu Jun 16 08:20:25 2016 -0400 fix a stray line continuation GMicrophysics.mak commit aad8b2075bda95093c43a75c891dbaee4dd52579 Author: Michael Zingale Date: Tue Jun 14 21:30:29 2016 -0400 add description of test_react and test_eos README.md commit 6759e58dfed789264f73006f64b12951115b9225 Author: Michael Zingale 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 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 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 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 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 Date: Tue Jun 14 13:13:39 2016 -0400 fix a variable name unit_test/test_eos/variables.f90 commit 144f6c65cc9d327902c50c9f3c4abde844b5a0e8 Author: Michael Zingale 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 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 Date: Tue Jun 14 12:17:39 2016 -0400 remove unused parameters unit_test/test_react/_parameters commit 121f5df0293c2a4ef12d98dc745f9b5b44dd007c Author: Michael Zingale 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 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 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 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 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 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 Date: Tue Jun 14 10:04:12 2016 -0400 add comment about eps integration/numerical_jacobian.f90 commit f27a5bf07e6cb8ec7185aa12102eedce9ee78ca1 Author: Michael Zingale Date: Tue Jun 14 08:43:59 2016 -0400 reorder README.md commit 2a8844aeb0b2a95134e7843a5e0b3392fdc957fb Author: Max Katz Date: Tue Jun 14 01:45:58 2016 -0400 Add a missing use statement integration/BS/stiff_ode.F90 commit b4fa2ced5408e98c082efaad3912fda85bd2a0bb Author: Max Katz 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 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 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 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 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 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 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 Date: Mon Jun 13 20:29:13 2016 -0400 make realclean should deal with helm_table.dat GMicrophysics.mak commit a7e4422d3a7c6a264e9212406ce7f73ce5694390 Author: Michael Zingale Date: Mon Jun 13 20:22:42 2016 -0400 update description README.md commit 61572ef1de0579bcfa0266d335ce3ffaeb1848e6 Author: Michael Zingale Date: Mon Jun 13 15:54:34 2016 -0400 deallocate xn_zone unit_test/test_react/main.f90 commit ec3ef327fddf1c77c1deddee290f4621ee71c4b9 Author: Michael Zingale Date: Mon Jun 13 15:30:46 2016 -0400 hook in the integrator to build_info GMicrophysics.mak commit 9994ffd04722a1a14cb1b50b80f6f82693e8aaba Author: Michael Zingale 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 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 Date: Mon Jun 13 14:39:35 2016 -0400 add a TODO unit_test/test_react/TODO commit d985b26074743ef721e314db1f3573f4948e04a8 Author: Michael Zingale Date: Mon Jun 13 13:30:55 2016 -0400 increased T range unit_test/test_react/inputs_aprox13 commit f47de3cbfa60b9c2755f64b3a4de83fe01b73279 Author: Michael Zingale 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 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 Date: Mon Jun 13 12:59:41 2016 -0400 not used unit_test/test_react/xin.ignition.64 commit 4b58e4ae4a08a51e2af6313a37ab4ba4ce1fb4a0 Author: Michael Zingale 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 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 Date: Mon Jun 13 12:23:51 2016 -0400 rates/ -> aprox_rates/ networks/Make.package commit 5e7068959f5dbc77cba53a7f8f6658b0cbc65c38 Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Mon Jun 13 08:07:25 2016 -0400 a few more ignores .gitignore commit c5971b5d7ef1f15fee7afd131ca375f0d9ab42e8 Author: Michael Zingale 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 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 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 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 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 Date: Sun Jun 12 19:26:30 2016 -0400 remove dupe init_variables unit_test/test_react/varden.f90 commit 1695c97761313c586785bb6a2f9ceb217bb9e2c7 Author: Michael Zingale 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 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 Date: Sun Jun 12 18:34:17 2016 -0400 allow for PROBIN_PARAMETER_DIRS to be appended GMicrophysics.mak commit 123e48d1e3d6ce8d9c8ad688fe5dac8261c65a01 Author: Michael Zingale Date: Sun Jun 12 18:32:45 2016 -0400 add parameters unit_test/test_react/_parameters commit b23a930cbb87014ffcf176310a6d91d7db4ab71c Merge: 456fd2bc 7815a310 Author: Michael Zingale 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 Date: Sun Jun 12 18:29:47 2016 -0400 some compilation fixes unit_test/test_react/varden.f90 commit 7815a3100698c7232dec7fa1faf7d21c1f532f01 Author: Michael Zingale Date: Sun Jun 12 18:22:48 2016 -0400 use the microphysics module networks/aprox13/test/testburn.f90 commit 3a77eeaa954e7ca73982c724bcf4f6f4b20d2e5e Author: Michael Zingale 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 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 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 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 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 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 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 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 Date: Sun Jun 12 12:00:01 2016 -0400 remove unnecessary file networks/triple_alpha_plus_cago/make.out commit 10a4bfdd440023a9112c51b9472800217d0e965d Author: Michael Zingale 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 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 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 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 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 Date: Sat Jun 11 16:37:49 2016 -0400 1.e-30 -> 1.d-30 networks/_parameters commit ac7699414dcba999ca0c4d99c562141bab06b2d5 Author: Michael Zingale 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 Date: Fri Jun 10 15:34:39 2016 -0400 add GPackage.mak interfaces/GPackage.mak commit d43eff5b6cb6198b3671d7180d87c0ac8db975b0 Author: Michael Zingale 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 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 Date: Tue Jun 7 14:52:30 2016 -0400 Merge branch upstream changes into Adam's local changes commit 9f69779cabda791383ed8868674e3fd39dd68349 Author: Adam M. Jacobs 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 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 Date: Tue Jun 7 03:21:43 2016 -0400 Add some parameters for rprox networks/rprox/_parameters commit a5a1debccbc3ffb6a611c48d768c4c49c9989e11 Author: Max Katz Date: Tue Jun 7 03:02:05 2016 -0400 Fix bugs in rprox networks/rprox/actual_rhs.f90 commit 0290118bbc1d874fb109adba58db1d315d92b494 Author: Max Katz 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 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 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 Date: Sun Jun 5 17:42:38 2016 -0400 need the interfaces GMicrophysics.mak commit 6a3d23b2b1c408a87ee6be64597249249eac0928 Author: Michael Zingale 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 Date: Sun Jun 5 17:16:56 2016 -0400 update to reflect recent changes README.md commit e3e20fd3eb37daed55f456b0997a05c3fff87c32 Author: Max Katz 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 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 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 Date: Sun Jun 5 14:45:39 2016 -0400 Hook in a network routine eos/multigamma/multigamma.f90 commit 216a0df303bc2698c7fd1a0fef64134199b15177 Author: Max Katz 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 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 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 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 Date: Sun Jun 5 11:10:31 2016 -0400 we need eos.f90 unit_test/GPackage.mak commit 4d906170b42098c5ddf640cb749b0fe198506661 Author: Michael Zingale Date: Sun Jun 5 11:10:17 2016 -0400 more work getting this all put together GMicrophysics.mak commit 61d88f0ac6c8ce7b730bbafa832d9169fec65315 Author: Michael Zingale Date: Sun Jun 5 11:06:04 2016 -0400 much more ignoring .gitignore commit fcbf03901f5731cb8857cc436951f9c9911ddc76 Merge: 0e64821e 4a36142a Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Sat Jun 4 17:43:27 2016 -0400 Merge branch 'master' into development commit 5fc643ecbb0317e65ba496e23d4bfc2076495b57 Author: Michael Zingale Date: Sat Jun 4 17:40:20 2016 -0400 add a README screening/README commit f8a14dfdf6b2a46551d48d716c9f265475b32159 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 Date: Sat Jun 4 12:53:51 2016 -0400 Avoid data statements in neutrino module neutrinos/sneut5.f90 commit a7769dbf61100e1c09183f10105b98f61107e6a6 Author: Max Katz 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 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 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 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 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 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 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 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 Date: Fri Jun 3 18:03:53 2016 -0400 Fix the call to dgemm integration/VBDF/bdf.f90 commit 83653c072e627e0e71dc0efedddbfa9ac93c913f Author: Max Katz 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 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 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 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 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 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 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 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 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 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 Date: Wed Jun 1 09:41:58 2016 -0400 Update module reference integration/VODE/vode_rpar.f90 commit 359795be95fc9cd0c0ebdef04a561d45109a76eb Author: Max Katz 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 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 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 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 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 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 Date: Tue May 31 15:44:05 2016 -0400 Protect against invalid Jacobian value integration/BS/bs_rhs.f90 commit 348a2e3b2cd65b09f4ff15ae5e38f6ff2e66cb16 Author: Max Katz Date: Tue May 31 15:26:09 2016 -0400 Fix variable dependency networks/aprox13/actual_burner_data.f90 commit 2b999f605e9da5572846e54d14ee769a09c4bb01 Author: Max Katz 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 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 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 Date: Tue May 31 13:17:50 2016 -0400 Default to a numerical Jacobian for powerlaw networks/powerlaw/_parameters commit ba3c89630abf68870bef7822df898e3e46bedce7 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed May 25 15:52:53 2016 -0400 Removed wayward present_or_copyin. integration/BS/bs_rhs.f90 commit 3f6faaafa2900c4d996e18289eed3b73aaad8df9 Author: Max Katz Date: Wed May 25 14:24:58 2016 -0400 Make the Jacobian analytical by default again integration/_parameters commit 13a4aa8fa52c1be1d34b55ff1d204fe69ae11a87 Author: Max Katz 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 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 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 Date: Wed May 25 09:55:58 2016 -0400 Fix missing module include integration/VBDF/vbdf_rhs.f90 commit 437b7ade33b9195d99092a6867a92e83e4834685 Author: Max Katz 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 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 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 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 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 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 Date: Tue May 24 21:55:32 2016 -0400 a few comments networks/iso7/actual_burner.f90 commit ac75e8589613bf7a3c61d9bcba3af5873663469f Author: Max Katz Date: Tue May 24 09:27:53 2016 -0400 Print out an initialization message networks/aprox13/actual_burner.f90 commit fcc537eeef12c882fcf4d16b95ce7a0309122b71 Author: Max Katz 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 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 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 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 Date: Sun May 22 14:27:14 2016 -0400 Fix incorrect variable type util/microphysics_math.F90 commit e7b07afe29cb436b15d78df93f70fdee86686376 Author: Max Katz Date: Sun May 22 04:47:27 2016 -0400 Hack around conflicting parameter definitions eos/helmholtz/helmholtz.f90 commit 1ddef4adfe0ee6bccfc0b79a06cc102fc807dead Author: Max Katz 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 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 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 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 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 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 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 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 Date: Fri May 13 18:12:34 2016 -0400 Merge pull request #2 from dwillcox/development Reaclib commit b2b0177d384ffe83a7014d2686c53fef810552fd Author: Donald Willcox 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 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 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 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 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 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 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 Date: Sat May 7 23:04:45 2016 -0400 Fix recently introduced indexing error integration/BS/stiff_ode.f90 commit 0383494f01bed8fa3c72ec9ff1197a9abc288e90 Author: Max Katz 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 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 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 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 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 Date: Wed May 4 14:40:20 2016 -0400 Remove more obsolete OpenACC stuff eos/helmholtz/helmholtz.f90 commit c8ec9da7ed565cb46a086ce351c149a491d2d5b6 Author: Max Katz Date: Wed May 4 14:39:12 2016 -0400 Remove obsolete OpenACC parameters from Helmholtz eos/helmholtz/_parameters commit 21c3b8911226358759b0debb7d8e4e3abc6261bc Author: Max Katz 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 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 Date: Wed May 4 10:23:54 2016 -0400 Fix typo util/BLAS/Make.package commit 600413fe7aacccc9a9fed9a14b25ca3479309f40 Author: Max Katz 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 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 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 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 Date: Wed May 4 02:57:25 2016 -0400 OpenACCify the numerical Jacobian integration/numerical_jacobian.f90 commit 39eadf5287aa151d02c7a101d14280d71887528f Author: Max Katz Date: Wed May 4 02:52:57 2016 -0400 Remove unintentionally committed temp file util/BLAS/.#GPackage.mak commit 498a1b193c85d6878ef78a7f2c7aee4e3bf8b100 Author: Max Katz 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 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 Date: Wed May 4 02:46:58 2016 -0400 ACC-ify the screening functions screening/screen.f90 commit e663fcea087ed6e10abc4a246b90199f9858559a Author: Max Katz 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 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 Date: Sun May 1 23:57:54 2016 -0400 Add comment explaining BS tolerances integration/BS/actual_integrator.f90 commit 8ad029dcd56f5e9a7260974e0f31c4ad0c8a4e57 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Apr 28 21:20:02 2016 -0400 some cleaning integration/BS/stiff_ode.f90 commit 8f018530a54be113b481a97beda23de9112c0a96 Merge: b03f5095 3c06fc8e Author: Michael Zingale 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 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 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 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 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 Date: Thu Apr 28 08:29:22 2016 -0400 hook in linpack integration/BS/stiff_ode.f90 commit 04b80c4dd2f33565b233fb11d98a90ef8ad74f9a Author: Michael Zingale Date: Thu Apr 28 08:23:29 2016 -0400 hook in Castro's LINPACK integration/BS/test/GNUmakefile commit 8b8793832b4e692306383cd4efa687e74604f5dd Author: Michael Zingale Date: Wed Apr 27 21:36:47 2016 -0400 part of the LU decomposition integration/BS/stiff_ode.f90 commit 02ce7666ab0986473e59616ecb4e3ce4f11ca97e Author: Michael Zingale 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 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 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 Date: Tue Apr 26 22:57:44 2016 -0400 more progress integration/BS/stiff_ode.f90 commit 9e52a70a360b10d54be493536300865f8b34d984 Author: Michael Zingale 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 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 Date: Mon Apr 25 21:00:55 2016 -0400 a numerical Jacobian networks/aprox13/actual_rhs_numjac.f90 commit 2969dad321a9c91cbdbec322a6f0fb7771f21d6f Author: Max Katz 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 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 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 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 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 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 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 Date: Thu Apr 21 23:54:25 2016 -0400 Remove duplicate module reference integration/VODE/vode_rhs.f90 commit c615ef507b23fd67f57eaa3534560f64c9936925 Author: Max Katz Date: Thu Apr 21 23:54:07 2016 -0400 Fix obsolete reference to filename integration/VODE/actual_integrator.f90 commit 85aadeb68c856f49b41f0ba4ba9834c170148a24 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Mon Apr 11 23:50:36 2016 -0400 Limit the Newton iteration changes logarithmically eos/stellarcollapse/stellarcollapse.f90 commit bcf985b9fd9e657b1901062441991d4ae7a84550 Author: Max Katz Date: Mon Apr 11 23:47:58 2016 -0400 Save a conversion factor eos/stellarcollapse/eos_aux_data.f90 commit cadbb9548163eb4b44203a1cee762ebb51ec85da Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Mar 11 12:53:39 2016 -0500 update README eos/README.md commit 6cfc7777daa4a0bf8ddec9c0eb0412bbea2d876a Author: Michael Zingale Date: Fri Mar 11 12:49:09 2016 -0500 update README README.md commit 7c2733089251fda9110da9b9eb770589b34eac58 Author: Michael Zingale 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 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 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 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 Date: Thu Mar 10 11:43:34 2016 -0500 remove trailing whitespace eos/helmholtz/helmholtz.f90 commit fda4de0e346383dfac17c728c4fcfb7f557a7860 Author: Max Katz Date: Sat Feb 13 23:23:09 2016 -0500 Remove unused variables networks/aprox13/actual_rhs.f90 commit f1bba3ff359a8df54dd6e8ef54959ad24f8cb4a4 Author: Max Katz 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 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 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 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 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 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 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 Date: Fri Feb 5 01:55:36 2016 -0500 We do support general_null too! networks/README commit 288e9516e0a8f53e3b43ccc0ee07c21d3de754a8 Author: Max Katz 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 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 Date: Thu Feb 4 14:55:20 2016 -0500 Merge branch 'master' into development commit a737a25ade9cadec544d0859ee4d06dc24de1908 Author: Michael Zingale Date: Thu Feb 4 14:55:01 2016 -0500 update instructions README.md commit 2d722a4d1a9dffdeeca42578290eef4cbaac74c9 Author: Michael Zingale 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 Date: Tue Feb 2 19:23:01 2016 -0500 Restore commented line networks/powerlaw/actual_rhs.f90 commit 37dc4672df2e73e75096b5c713bee06afceedda1 Author: Max Katz 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 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 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 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 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 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 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 Date: Mon Feb 1 16:22:58 2016 -0500 Remove obsolete file networks/THREADSAFE commit f33e67b5f7e9c46eaf670da9c82dc8e04024f38f Author: Max Katz 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 Date: Mon Feb 1 16:12:42 2016 -0500 Add missing use statement networks/powerlaw/actual_burner.f90 commit 50c9db3a87c1e30be096448018de6c5c9e67ab69 Author: Max Katz 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 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 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 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 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 Date: Tue Jan 26 15:29:50 2016 -0500 Fix comment integration/_parameters commit 341e0da4569c377631819e927ca741134764f58b Author: Max Katz Date: Sat Jan 23 20:03:05 2016 -0500 Use msum routine networks/aprox13/actual_rhs.f90 commit b484a25608b317e8b7154306d85bf728f1bc44ef Author: Max Katz 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 Date: Wed Jan 20 11:39:15 2016 -0500 Remove unused variable integration/rhs.f90 commit f7ce25206213c2997637730dbf81e76f948f9389 Author: Max Katz 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 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 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 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 Date: Fri Jan 15 12:33:08 2016 -0500 Add the extra rates needed for aprox19 rates/rates.f90 commit 4eb519ddf78577ddbb4afef36871bbed171e106e Author: Max Katz 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 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 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 Date: Thu Jan 14 10:06:47 2016 -0500 Add save attribute integration/vode_data.f90 commit 931c79406fe40fc556d12b20039465322c5c2b7e Author: Max Katz Date: Thu Jan 14 09:46:27 2016 -0500 Fix module reference networks/aprox13/test-cpp/testjacobian.f90 commit 2a981952b13adf186df4f94da3cb2e7ac18c5be6 Author: Max Katz 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 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 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 Date: Wed Jan 13 17:32:44 2016 -0500 Spacing networks/aprox13/actual_rhs.f90 commit d8775bea56cc5baea80c13af92668fac66eaf07c Author: Max Katz 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 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 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 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 Date: Wed Jan 13 16:08:23 2016 -0500 More tfactors! rates/tfactors.f90 commit abeba63f346d8d4de65c5661d0ffaf4c96ed45ce Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Jan 10 22:43:02 2016 -0500 Various initialization fixes networks/CONe2NSE/CONe2NSE_burner.F90 commit 3b8786d4e04d7f14db8e37fe412c8548f9e1e917 Author: Max Katz 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 Date: Sun Jan 10 22:15:10 2016 -0500 Fix switched indexing networks/CONe2NSE/CONe2NSE_burner.F90 commit 0718d7001d461c22b805167d368f4a975ccc558a Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Tue Jan 5 23:10:10 2016 -0500 Fix analytical Jacobian component indexing networks/aprox13/f_rhs.f90 commit 8b1cf1fd79a5a2ff6a966f3cc0fa1e1a2e86eb37 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Jan 3 01:26:46 2016 -0500 Fix typo networks/CONe2NSE/CONe2NSE_network.F90 commit 6338fd21e14c043a740f60d0947fc656606f6999 Author: Max Katz 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 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 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 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 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 Date: Sat Dec 26 16:37:56 2015 -0500 Wrong filename NSE/NSE_data.F90 commit 82aef309f49087133a933a6768443b7fa710bef1 Author: Max Katz 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 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 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 Date: Sun Dec 20 20:15:54 2015 -0500 Polytrope needed some more thermodynamic derivatives eos/polytrope/polytrope.f90 commit 919ae6f5d53fbd434d5e4c440b2e09f947e59a35 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Oct 30 11:19:34 2015 -0400 Merge branch 'openacc' into development commit e08af1e493e071cba94079f2e810a22aa083cc69 Author: Max Katz 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 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 Date: Wed Oct 21 20:01:38 2015 -0400 more reasonable inert properties networks/powerlaw/powerlaw_network.f90 commit 32b31015493e216d1240b2f228c395680475a673 Author: Chris Malone 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 Date: Wed Oct 21 16:41:51 2015 -0400 forgot some parts networks/ignition_simple/ignition_simple_burner.f90 commit 53a5347a2a25f44174fb8d50ac0695807f4f4793 Author: Chris Malone 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 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 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 Date: Wed Oct 21 14:43:53 2015 -0400 remove vectorized eos networks/aprox13/aprox13_burner.f90 commit 41785e206eb79a080d24d671f041868b91c258a4 Author: Chris Malone Date: Wed Oct 21 14:24:00 2015 -0400 fix typo networks/triple_alpha_plus_cago/Make.package commit 70d7767fb11b74c3725f1b8b2bbe3ee4f71697f3 Author: Chris Malone 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 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 Date: Wed Oct 21 14:11:07 2015 -0400 no longer needed networks/rprox/burner.f90 commit 80d8ac82a7b26992ab4c0df9ea09b11b77ef7e00 Author: Chris Malone 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 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 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 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 Date: Wed Oct 21 11:07:11 2015 -0400 undo all the vectorization changes eos/helmholtz/helmholtz.f90 commit 32b040e00938d6df185296b590eaf8394ce04d4d Author: Chris Malone 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 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 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 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 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 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 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 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 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 Date: Sun Oct 18 21:02:57 2015 -0400 update comments networks/powerlaw/_parameters networks/powerlaw/powerlaw_network.f90 commit 7353970c634a32a8b1a81c286184a4491b0bb896 Author: Michael Zingale Date: Sun Oct 18 20:47:38 2015 -0400 more notation updates networks/powerlaw/_parameters commit b65ba5d1948df0f880323344a8701f42ed8e1b0c Author: Michael Zingale 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 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 Date: Sat Oct 17 18:46:16 2015 -0400 upate networks/powerlaw/_parameters commit 83937730e29b43cfb621d7c1ea66935d6a174e03 Merge: 33398c3a 12017677 Author: Max Katz 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 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 Date: Fri Oct 16 10:56:24 2015 -0700 added some save networks/general_null/network.template commit e13c1883da566933f878b097c18a972f071b46c3 Author: Max Katz 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 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 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 Date: Mon Oct 5 10:32:36 2015 -0400 Merge branch 'master' into development commit 17491e18954e125064da7aa12ef9e7ccd77dbb4f Author: Max Katz 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 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 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 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 Date: Tue Sep 15 17:28:08 2015 -0400 Fix typo networks/aprox13/aprox13_network.f90 commit db303538f2839b3e3a3829aafc0ee072715be2a2 Merge: 8bbeac31 31b30f28 Author: Max Katz Date: Sat Sep 12 23:04:40 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/Microphysics commit 8bbeac31e7f909253ec795bbd0bcf312746dcacf Author: Max Katz 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 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 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 Date: Fri Aug 14 15:37:41 2015 -0400 A .gitignore for the userguide directory. userguide/.gitignore commit 8aded518a2bda404cae296c098a7091e722f4435 Author: Max Katz 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 Date: Fri Aug 14 15:31:10 2015 -0400 Need to change an include statement networks/aprox13/screen5.f90 commit 6d8cd0457037197bc9130eae0f63fe2f19eefa38 Author: Max Katz 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 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 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 Date: Fri Jul 24 15:52:24 2015 -0400 Fix an additional name change networks/aprox13/rhs.f90 commit 638e32d36f199ba1156936b0ac5ae77ff1d40954 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Jul 10 11:53:45 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/Microphysics commit 4a22726f59ff5b0214c610cf7cea13bfb4b87391 Author: Max Katz 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sun Apr 5 18:44:12 2015 -0400 update readme networks/aprox13/README commit 8ca63a97438d70370d2f5cbf0ba871cd134de55c Merge: 1a0b1049 2e87e377 Author: Michael Zingale Date: Sun Apr 5 18:42:17 2015 -0400 Merge /home/zingale/development/AstroDev commit 2e87e377b4b9bd2003d3a35cc7ab23342763ee6d Author: Michael Zingale 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 Date: Sat Apr 4 20:47:51 2015 -0400 adda readme README.md commit 207d4ead457ba065621e6ec121dc1b2112104d2b Author: Michael Zingale Date: Fri Jul 4 15:58:46 2014 -0400 just comment lines f_rhs.f90 commit 68d99a8745763b341580945a27c48e86dbcc25e7 Author: Michael Zingale 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 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 Date: Wed Jul 2 20:52:51 2014 -0400 more steps, if necessary castro_burner.f90 commit ad45645247c73a7c22e43ee5c004dc4ac0a28cf7 Author: Michael Zingale 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 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 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 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 Date: Sun Jul 14 12:53:30 2013 -0400 fix some comments burner.f90 commit 1e01af7a5559ac96b0b907084870360d9cefd325 Author: Michael Zingale 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 Date: Sun Jul 14 12:39:12 2013 -0400 remove unneeded variable test/testburn.f90 commit 7537215f9f666d3565d09aebf2f2c9bd3ace8366 Author: Michael Zingale Date: Fri Jul 12 20:19:41 2013 -0400 comment out the derivatives of the screening factors rhs.f90 commit 79b715e0eff1b3b9d354dff5386f285cc18b3eab Author: Michael Zingale Date: Fri Jul 12 20:11:41 2013 -0400 update README README commit 22dec7a9026a6c15de169a0d4ccb61cc8fc0a1d6 Author: Michael Zingale 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 Date: Fri Jul 12 18:51:20 2013 -0400 require the table test/GNUmakefile commit 5ffada11bc15291aecb70b33f787fb1bd97a6932 Author: lijewski 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 Date: Tue Mar 19 19:54:37 2013 -0400 remove some factors not needed tfactors.f90 commit 83db2a6d0f238d8d001e20fae010dae279ac7266 Author: Michael Zingale Date: Tue Mar 19 16:44:29 2013 -0400 loosen tolerances a little burner.f90 commit 03556072ed640669f4cfb92ad08bdb6def3063dd Author: Michael Zingale 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 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 Date: Tue Mar 19 15:28:19 2013 -0400 needed for MAESTRO NETWORK_REQUIRES commit b219acb3e2c4fd06a0789ae0fc63caed1ed507d6 Author: Michael Zingale 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 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 Date: Tue Mar 19 13:04:16 2013 -0400 more compiling work network.f90 screen5.f90 commit 2ba652423a7fc74c5492e8f0699b913ac1ac1c29 Author: Michael Zingale 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 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 Date: Tue Mar 19 11:44:20 2013 -0400 main burner burner.f90 public_aprox13.f90 commit 793532e34a5e8bcb1253abf7c17a91a3db9b1c77 Author: Michael Zingale 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 Date: Tue Mar 19 10:23:00 2013 -0400 rates now use the tf_t type rates.f90 commit 91282b4e2711a28ced82e931b637fc93e487e920 Author: Michael Zingale 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 Date: Mon Mar 18 20:07:05 2013 -0400 module rhs.f90 commit 1fabee2f48a9880efe9437637b722cfc38ebd851 Merge: a56217b5 f470b0da Author: Michael Zingale 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 Date: Mon Mar 18 20:05:22 2013 -0400 integer indices network_indices.f90 commit f470b0da2d1b52a2e3f5d589b7840755df2e6d56 Author: Michael Zingale Date: Mon Mar 18 20:02:26 2013 -0400 formatting, moduling rhs.f90 commit 5a96064e2caf090874982e1a49250ae445f54014 Merge: 52f32eef d543368d Author: Michael Zingale 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 Date: Mon Mar 18 19:24:34 2013 -0400 initialization stuff network.f90 commit d543368dfa62a15f38ae28ac75dfb8e10e64229b Author: Michael Zingale 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 Date: Mon Mar 18 18:43:08 2013 -0400 more files rhs.f90 sneut5.f90 commit ffb630860eb42f8b348ef2d7b4329da0fbaa8d12 Author: Michael Zingale Date: Mon Mar 18 17:04:24 2013 -0400 more progress README rates.f90 commit 2042149f58537326b626a97cb5c74bb02b6ff904 Author: Michael Zingale Date: Mon Mar 18 15:20:31 2013 -0400 more updates README public_aprox13.f90 tfactors.f90 commit 45b695e78364882f24d5e8e38d590d9144f6fffa Author: Michael Zingale 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