Halogen training reactions

[davidfarinajr]

added training reactions from halogen kinetic models include NIST HFC and 2-BTP/CF3Br mech and Westmoreland YF mech. Also corrected CH3 in disproportionation training

twin with ReactionMechanismGenerator/RMG-Py#2135

[davidfarinajr]

This is the only test that is failing

1744
FAIL: test that the right number of reactions are in output network
1745
----------------------------------------------------------------------
1746
Traceback (most recent call last):
1747
  File "/home/runner/work/RMG-database/RMG-Py/arkane/explorerTest.py", line 81, in test_reactions
1748
    self.assertEqual(len(self.explorer_job.networks[0].path_reactions), 7)
1749
AssertionError: 6 != 7

This test seems to bounce back and forth between 6 and 7. When we added CO to primaryThermoLib, we changed it from 6 to 7, now it want to be 6 again. Can we change this test to
self.assertIn(len(self.explorer_job.networks[0].path_reactions), [6,7])

[davidfarinajr]

Cross validation for R_Addition_MultipleBond tree

R_add_tree_cross_val.pdf

[davidfarinajr]

looks like the tests dies here
Kinetics family H_Abstraction: groups are not identical? ... make: *** [Makefile:82: test-database] Killed
maybe ~7500 groups is too many to run this test 😂, and if its autogenerated tree, do we need to run this test?

[sevyharris]

This looks good to me. I looked over the files and ran a bunch of examples including 2-BTP, ethane pyrolysis (minimal), cpox (surface), Nitrogen, and Sulfur, and none of them crashed. I picked the Nitrogen regression test as the one to look at for a more thorough review. I was slightly concerned that the halogens version finds fewer species and reactions than the main branch because my lizard brain is convinced that more=better. But most of the "missing" reactions are from Disproportionation, which was regenerated for all those new training reactions, so that makes sense that it would be different. I also ran a few simulations in Cantera for the Nitrogen example to see how the results changed, and you get nearly identical results at high temperatures. The halogens model is marginally slower than the main branch's version, especially at lower temperatures. I don't know much about the chemistry, but it seems reasonable to me.

Well done David! This PR must have taken a lot of work. I'm excited for it to be merged in.

[davidfarinajr]

Thanks for the awesome review @sevyharris, and thanks for getting the rmg regressions tests working! I will also take a look at the regression tests to see if there is anything that catches my eye.

[davidfarinajr]

I'm thinking about dropping this commit 4a17fe7 which makes intra_H_migration intro intra_H/Val7_migration, and instead making a new intra_halogen_migration family. I did not have any halogen migration training reactions at the time, but I am calculating some now. F migration is a lot slower than H (much higher barrier) and we are overestimated rates for these in our models.

[rwest]

Sounds like a reasonable idea. Would leave H migration unperturbed; speed up generation of models with no halogens; and avoid the very different rates from influencing each other.

[davidfarinajr]

The new intra_halogen_migration family is here #546. I dropped the commit changing the groups for the intra_H_migration family for this PR

[davidfarinajr]

Cross validation for H Abstraction tree

tree_cross_val.pdf
tree_cross_val.csv

[davidfarinajr]

Disprop tree

tree_cross_val.pdf
tree_cross_validation.csv

This is outlier

entry(
    index = 69,
    label = "C2H5S-2 + C3H7-2 <=> C2H6S + C3H6-2",
    degeneracy = 2.0,
    kinetics = Arrhenius(A=(6.74e-06,'cm^3/(mol*s)'), n=4.35, Ea=(4.76976,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(1500,'K')),
    rank = 6,
    shortDesc = """CAC calc CBS-QB3 1dhr""",
    longDesc = 
"""
Converted to training reaction from rate rule: C_rad/H/CsS;C/H2/Nd_Csrad
""",
)

ln(kest/ktrain)=10.2