Changing default to exclude recombination terms in neutrino cooling #1793

khanakbhargava · 2025-05-23T20:03:20Z

No description provided.

zingale · 2025-05-23T20:39:18Z

you'll need to regenerate the benchmarks. You can see how they are created and where they are stored by looking at the files in Microphysics/.github/workflows/

khanakbhargava · 2025-05-26T02:57:23Z

Benchmarks regenerated

zingale · 2025-05-26T16:00:30Z

test suite:
http://groot.astro.sunysb.edu/Microphysics/test-suite/gfortran/

zingale · 2025-05-26T16:03:48Z

diffs are small for all tests except for the nova:
http://groot.astro.sunysb.edu/Microphysics/test-suite/gfortran/2025-05-26-001/test_react_C-nova-VODE.html

Merge branch 'recomb_change' of github.com:khanakbhargava/Microphysics into recomb_change

khanakbhargava · 2025-06-12T20:26:35Z

This is what I get if I decrease `atol_spec` to 1e-9, this is what I get -
variable name absolute error relative error
(||A - B||) (||A - B||/||A||)

level = 0
density 0 temperature 0 Xnew_hydrogen-1 0.0003234254081 Xnew_hydrogen-2 2.187376969e-07 Xnew_helium-3 3.234794476e-07 Xnew_helium-4 6.166231632e-05 Xnew_beryllium-7 2.084076017e-06 Xnew_boron-8 1.284328151e-05 Xnew_carbon-12 3.434749464e-05 Xnew_carbon-13 5.981044115e-07 Xnew_nitrogen-13 8.498445155e-05 Xnew_nitrogen-14 9.580186795e-07 Xnew_nitrogen-15 6.11827947e-06 Xnew_oxygen-14 0.00036067797 Xnew_oxygen-15 6.354772133e-05 Xnew_oxygen-16 1.141692746e-05 Xnew_oxygen-17 9.116305634e-08 Xnew_fluorine-17 1.183814367e-05 Xnew_fluorine-18 3.418844033e-07 Xold_hydrogen-1 0 Xold_hydrogen-2 0 Xold_helium-3 0 Xold_helium-4 0 Xold_beryllium-7 0 Xold_boron-8 0 Xold_carbon-12 0 Xold_carbon-13 0 Xold_nitrogen-13 0 Xold_nitrogen-14 0 Xold_nitrogen-15 0 Xold_oxygen-14 0 Xold_oxygen-15 0 Xold_oxygen-16 0 Xold_oxygen-17 0 Xold_fluorine-17 0 Xold_fluorine-18 0 wdot_hydrogen-1 3.234254081 wdot_hydrogen-2 0.002187376969 wdot_helium-3 0.003234794476 wdot_helium-4 0.6166231632 wdot_beryllium-7 0.02084076017 wdot_boron-8 0.1284328151 wdot_carbon-12 0.3434749464 wdot_carbon-13 0.005981044115 wdot_nitrogen-13 0.8498445155 wdot_nitrogen-14 0.009580186795 wdot_nitrogen-15 0.0611827947 wdot_oxygen-14 3.6067797 wdot_oxygen-15 0.6354772133 wdot_oxygen-16 0.1141692746 wdot_oxygen-17 0.0009116305634 wdot_fluorine-17 0.1183814367 wdot_fluorine-18 0.003418844033 rho_Hnuc 2.762322344e+22 0
0
0.000403189225
4.687248835e-06
6.928813174e-06
7.514224861e-05
4.465877179e-05
0.000275084997
0.0004091504917
1.281652162e-05
0.001130776265
8.640752866e-06
0.0001311059142
0.001852726065
0.0002756014688
0.0002441092047
1.953491965e-06
0.0001702587684
7.326094357e-06
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.01782814026
4.687236362e-06
6.93178038e-06
0.0004068784622
4.465877426e-05
0.004033838659
0.0007360177422
1.28165231e-05
0.00182109539
1.492113945e-05
0.0001311059886
0.002436889222
0.0003455339729
0.000676479143
1.953494065e-06
0.0005177717027
7.326094357e-06
0.0004787366732

zingale · 2025-06-12T21:05:12Z

but rtol will still dominate. Try:

integrator.atol_spec=1.e-12 integrator.rtol_spec=1.e-9 integrator.rtol_enuc=1.e-8

khanakbhargava · 2025-06-12T22:59:35Z

With those numbers this is what we get -

```

variable name absolute error relative error
(||A - B||) (||A - B||/||A||)

level = 0
density 0 0
temperature 0 0
Xnew_hydrogen-1 0.001416709338 0.001766101011
Xnew_hydrogen-2 0.002834663803 0.06074295743
Xnew_helium-3 0.004247647361 0.09098307545
Xnew_helium-4 0.005672472646 0.006912525757
Xnew_beryllium-7 8.465868522e-05 0.001814114683
Xnew_boron-8 1.029737496e-05 0.0002205552652
Xnew_carbon-12 0.0006622651288 0.007888962672
Xnew_carbon-13 0.000537969196 0.01152791001
Xnew_nitrogen-13 0.001005873834 0.01338383947
Xnew_nitrogen-14 0.001003678605 0.009052577963
Xnew_nitrogen-15 0.0004047647637 0.008673525723
Xnew_oxygen-14 0.001854017611 0.009523694371
Xnew_oxygen-15 0.0010916356 0.004734337731
Xnew_oxygen-16 1.08695612e-05 0.0002324057808
Xnew_oxygen-17 7.827734275e-05 0.001677369828
Xnew_fluorine-17 1.236297895e-05 0.0001778070639
Xnew_fluorine-18 0.0001465121853 0.003139546827
Xold_hydrogen-1 0 0
Xold_hydrogen-2 0 0
Xold_helium-3 0 0
Xold_helium-4 0 0
Xold_beryllium-7 0 0
Xold_boron-8 0 0
Xold_carbon-12 0 0
Xold_carbon-13 0 0
Xold_nitrogen-13 0 0
Xold_nitrogen-14 0 0
Xold_nitrogen-15 0 0
Xold_oxygen-14 0 0
Xold_oxygen-15 0 0
Xold_oxygen-16 0 0
Xold_oxygen-17 0 0
Xold_fluorine-17 0 0
Xold_fluorine-18 0 0
wdot_hydrogen-1 14.16709338 0.0780931002
wdot_hydrogen-2 28.34663803 0.06074279578
wdot_helium-3 42.47647361 0.09102203819
wdot_helium-4 56.72472646 0.03742978021
wdot_beryllium-7 0.8465868522 0.001814114783
wdot_boron-8 0.1029737496 0.003234216207
wdot_carbon-12 6.622651288 0.01419139562
wdot_carbon-13 5.37969196 0.01152791134
wdot_nitrogen-13 10.05873834 0.0215544393
wdot_nitrogen-14 10.03678605 0.01563229272
wdot_nitrogen-15 4.047647637 0.008673530651
wdot_oxygen-14 18.54017611 0.01252650816
wdot_oxygen-15 10.916356 0.005935652422
wdot_oxygen-16 0.108695612 0.0006440464365
wdot_oxygen-17 0.7827734275 0.001677371631
wdot_fluorine-17 0.1236297895 0.0005407267252
wdot_fluorine-18 1.465121853 0.003139546827
rho_Hnuc 1.23019428e+23 0.002132043417

khanakbhargava · 2025-06-12T23:05:46Z

This is what I get if I decrease atol_spec to 1e-9, this is what I get -

variable name absolute error relative error
(||A - B||) (||A - B||/||A||)
level = 0 density 0 0 temperature 0 0 Xnew_hydrogen-1 0.0003234254081 0.000403189225 Xnew_hydrogen-2 2.187376969e-07 4.687248835e-06 Xnew_helium-3 3.234794476e-07 6.928813174e-06 Xnew_helium-4 6.166231632e-05 7.514224861e-05 Xnew_beryllium-7 2.084076017e-06 4.465877179e-05 Xnew_boron-8 1.284328151e-05 0.000275084997 Xnew_carbon-12 3.434749464e-05 0.0004091504917 Xnew_carbon-13 5.981044115e-07 1.281652162e-05 Xnew_nitrogen-13 8.498445155e-05 0.001130776265 Xnew_nitrogen-14 9.580186795e-07 8.640752866e-06 Xnew_nitrogen-15 6.11827947e-06 0.0001311059142 Xnew_oxygen-14 0.00036067797 0.001852726065 Xnew_oxygen-15 6.354772133e-05 0.0002756014688 Xnew_oxygen-16 1.141692746e-05 0.0002441092047 Xnew_oxygen-17 9.116305634e-08 1.953491965e-06 Xnew_fluorine-17 1.183814367e-05 0.0001702587684 Xnew_fluorine-18 3.418844033e-07 7.326094357e-06 Xold_hydrogen-1 0 0 Xold_hydrogen-2 0 0 Xold_helium-3 0 0 Xold_helium-4 0 0 Xold_beryllium-7 0 0 Xold_boron-8 0 0 Xold_carbon-12 0 0 Xold_carbon-13 0 0 Xold_nitrogen-13 0 0 Xold_nitrogen-14 0 0 Xold_nitrogen-15 0 0 Xold_oxygen-14 0 0 Xold_oxygen-15 0 0 Xold_oxygen-16 0 0 Xold_oxygen-17 0 0 Xold_fluorine-17 0 0 Xold_fluorine-18 0 0 wdot_hydrogen-1 3.234254081 0.01782814026 wdot_hydrogen-2 0.002187376969 4.687236362e-06 wdot_helium-3 0.003234794476 6.93178038e-06 wdot_helium-4 0.6166231632 0.0004068784622 wdot_beryllium-7 0.02084076017 4.465877426e-05 wdot_boron-8 0.1284328151 0.004033838659 wdot_carbon-12 0.3434749464 0.0007360177422 wdot_carbon-13 0.005981044115 1.28165231e-05 wdot_nitrogen-13 0.8498445155 0.00182109539 wdot_nitrogen-14 0.009580186795 1.492113945e-05 wdot_nitrogen-15 0.0611827947 0.0001311059886 wdot_oxygen-14 3.6067797 0.002436889222 wdot_oxygen-15 0.6354772133 0.0003455339729 wdot_oxygen-16 0.1141692746 0.000676479143 wdot_oxygen-17 0.0009116305634 1.953494065e-06 wdot_fluorine-17 0.1183814367 0.0005177717027 wdot_fluorine-18 0.003418844033 7.326094357e-06 rho_Hnuc 2.762322344e+22 0.0004787366732

In this case first I had changed both atol and rtol which increased the errors. So I tried changing on atol and kept rtol same.

zingale · 2025-06-12T23:11:43Z

I'm confused. Building test_react with NETWORK_DIR=nova and running with the default inputs_nova, with and without neutrino_cooling.include_recomb=0, I get:

            variable name            absolute error            relative error
                                        (||A - B||)         (||A - B||/||A||)
 ----------------------------------------------------------------------------
 level = 0
 density                                          0                         0
 temperature                                      0                         0
 Xnew_hydrogen-1                     0.002900523754            0.003615856646
 Xnew_hydrogen-2                    3.405119581e-09           7.296704234e-08
 Xnew_helium-3                      3.184265904e-08           6.820582793e-07
 Xnew_helium-4                      0.0003260954393            0.000397384862
 Xnew_beryllium-7                    6.89112015e-06           0.0001476668603
 Xnew_boron-8                       0.0001033543836            0.002213706378
 Xnew_carbon-12                      0.000313750046            0.003737419204
 Xnew_carbon-13                     5.383900647e-07           1.153692862e-05
 Xnew_nitrogen-13                   0.0004792861154            0.006377212609
 Xnew_nitrogen-14                   5.821435557e-06            5.25060548e-05
 Xnew_nitrogen-15                   4.988225887e-09            1.06890494e-07
 Xnew_oxygen-14                      0.003323361289             0.01704102841
 Xnew_oxygen-15                     0.0005099571427            0.002211731292
 Xnew_oxygen-16                     0.0001148089399            0.002454781471
 Xnew_oxygen-17                     1.159735315e-07           2.485144432e-06
 Xnew_fluorine-17                   0.0001169055276            0.001681501883
 Xnew_fluorine-18                   2.235094891e-09           4.789489052e-08
 Xold_hydrogen-1                                  0                         0
 Xold_hydrogen-2                                  0                         0
 Xold_helium-3                                    0                         0
 Xold_helium-4                                    0                         0
 Xold_beryllium-7                                 0                         0
 Xold_boron-8                                     0                         0
 Xold_carbon-12                                   0                         0
 Xold_carbon-13                                   0                         0
 Xold_nitrogen-13                                 0                         0
 Xold_nitrogen-14                                 0                         0
 Xold_nitrogen-15                                 0                         0
 Xold_oxygen-14                                   0                         0
 Xold_oxygen-15                                   0                         0
 Xold_oxygen-16                                   0                         0
 Xold_oxygen-17                                   0                         0
 Xold_fluorine-17                                 0                         0
 Xold_fluorine-18                                 0                         0
 wdot_hydrogen-1                        29.00523754               0.154353026
 wdot_hydrogen-2                    3.405119577e-05           7.296684808e-08
 wdot_helium-3                      0.0003184265904           6.823503488e-07
 wdot_helium-4                          3.260954393             0.00215174343
 wdot_beryllium-7                      0.0689112015           0.0001476668685
 wdot_boron-8                           1.033543836             0.03256168126
 wdot_carbon-12                          3.13750046            0.006723215271
 wdot_carbon-13                      0.005383900647           1.153692996e-05
 wdot_nitrogen-13                       4.792861154             0.01027041676
 wdot_nitrogen-14                     0.05821435557           9.066945772e-05
 wdot_nitrogen-15                   4.988225885e-05           1.068905547e-07
 wdot_oxygen-14                         33.23361289             0.02240148581
 wdot_oxygen-15                         5.099571427            0.002772974892
 wdot_oxygen-16                         1.148089399            0.006774420301
 wdot_oxygen-17                      0.001159735315           2.485147103e-06
 wdot_fluorine-17                       1.169055276            0.005114468992
 wdot_fluorine-18                   2.235094891e-05           4.789489052e-08
 rho_Hnuc                           2.924848519e+23            0.005060005906

if I rerun them with the tolerances I suggest above, I see:

            variable name            absolute error            relative error
                                        (||A - B||)         (||A - B||/||A||)
 ----------------------------------------------------------------------------
 level = 0
 density                                          0                         0
 temperature                                      0                         0
 Xnew_hydrogen-1                    8.971731891e-08           1.118435828e-07
 Xnew_hydrogen-2                    1.350029012e-19           2.892926978e-18
 Xnew_helium-3                      7.337387847e-13           1.571641714e-11
 Xnew_helium-4                      1.819682607e-08            2.21748042e-08
 Xnew_beryllium-7                   1.404178371e-10           3.008953652e-09
 Xnew_boron-8                       5.688766257e-09           1.218453588e-07
 Xnew_carbon-12                      1.74474327e-08           2.078354099e-07
 Xnew_carbon-13                     4.045179526e-11           8.668240837e-10
 Xnew_nitrogen-13                   1.242462192e-08           1.653198051e-07
 Xnew_nitrogen-14                   6.706236694e-11           6.035458646e-10
 Xnew_nitrogen-15                   5.150718745e-13           1.103724818e-11
 Xnew_oxygen-14                     1.060393799e-07           5.447390309e-07
 Xnew_oxygen-15                     2.798004822e-08           1.213472816e-07
 Xnew_oxygen-16                     4.466693803e-09            9.55088169e-08
 Xnew_oxygen-17                     8.564145333e-15           1.835172028e-13
 Xnew_fluorine-17                   6.796461262e-09            9.77449054e-08
 Xnew_fluorine-18                   1.521842486e-17           3.261091042e-16
 Xold_hydrogen-1                                  0                         0
 Xold_hydrogen-2                                  0                         0
 Xold_helium-3                                    0                         0
 Xold_helium-4                                    0                         0
 Xold_beryllium-7                                 0                         0
 Xold_boron-8                                     0                         0
 Xold_carbon-12                                   0                         0
 Xold_carbon-13                                   0                         0
 Xold_nitrogen-13                                 0                         0
 Xold_nitrogen-14                                 0                         0
 Xold_nitrogen-15                                 0                         0
 Xold_oxygen-14                                   0                         0
 Xold_oxygen-15                                   0                         0
 Xold_oxygen-16                                   0                         0
 Xold_oxygen-17                                   0                         0
 Xold_fluorine-17                                 0                         0
 Xold_fluorine-18                                 0                         0
 wdot_hydrogen-1                    0.0008971731891           4.945478386e-06
 wdot_hydrogen-2                                  0                         0
 wdot_helium-3                       7.33740535e-09           1.572318824e-11
 wdot_helium-4                      0.0001819682607            1.20071649e-07
 wdot_beryllium-7                   1.404178363e-06           3.008953798e-09
 wdot_boron-8                       5.688766257e-05           1.786671832e-06
 wdot_carbon-12                      0.000174474327           3.738735578e-07
 wdot_carbon-13                      4.04517948e-07           8.668241743e-10
 wdot_nitrogen-13                   0.0001242462193           2.662418984e-07
 wdot_nitrogen-14                   6.706236633e-07           1.040577035e-09
 wdot_nitrogen-15                   5.150724292e-09           1.103726634e-11
 wdot_oxygen-14                      0.001060393799           7.165103049e-07
 wdot_oxygen-15                     0.0002798004823            1.52138556e-07
 wdot_oxygen-16                     4.466693802e-05           2.646860653e-07
 wdot_oxygen-17                      8.56061888e-11           1.834418332e-13
 wdot_fluorine-17                   6.796461263e-05           2.972303579e-07
 wdot_fluorine-18                   1.705302566e-13           3.654219784e-16
 rho_Hnuc                           9.029586591e+18           1.565108254e-07

so it seems much closer with the tighter tolerances

khanakbhargava · 2025-06-16T16:11:16Z

All checks pass now except for castro, conflicts resolved.

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/chamulak_VODE_unit_test.out

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/ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out

zingale · 2025-06-16T16:35:37Z

yes, please restore the ones that did not fail. that way the git history will reflect what actually needed to be updated for this change.

Fix CI due to AMReX-Astro/Microphysics#1793

turning off recomb terms

1188e37

khanakbhargava changed the base branch from main to development May 23, 2025 20:03

khanakbhargava and others added 4 commits May 25, 2025 18:34

Revised benchmarks for burn cell

2115241

regenerated burn cell benchmarks to correct values

b684597

jac_cell and test_rhs revised benchmarks

2578282

test_rhs plotfile data

7a601eb

yut23 mentioned this pull request May 28, 2025

Adding neutrino cooling parameter to docs #1794

Merged

khanakbhargava and others added 3 commits June 12, 2025 11:56

Merge branch 'AMReX-Astro:main' into recomb_change

31425c7

conflict resolution

392543a

conflict resolution

69fe4c0

Merge branch 'recomb_change' of github.com:khanakbhargava/Microphysics into recomb_change

khanakbhargava and others added 4 commits June 16, 2025 10:23

Merge branch 'development' into recomb_change

885b759

revised ecsn benchmark

17e1254

revised jac_cell benchmark

1de4eb3

test_rhs ecsn.out

8d335e2