RMG-database Halogen training reactions

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 https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2135

Jul 28 '21 17:07 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])

Aug 02 '21 21:08 davidfarinajr

Cross validation for R_Addition_MultipleBond tree

R_add_tree_cross_val.pdf

Oct 15 '21 15:10 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?

Oct 21 '21 20:10 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.

Nov 05 '21 16:11 davidfarinajr

I'm thinking about dropping this commit https://github.com/ReactionMechanismGenerator/RMG-database/pull/515/commits/4a17fe7641079756a44a84e045ab14cb25badfcc 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.

Nov 07 '21 16:11 davidfarinajr

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.

Nov 07 '21 18:11 rwest

The new intra_halogen_migration family is here https://github.com/ReactionMechanismGenerator/RMG-database/pull/546. I dropped the commit changing the groups for the intra_H_migration family for this PR

Nov 07 '21 21:11 davidfarinajr

Cross validation for H Abstraction tree

tree_cross_val.pdf tree_cross_val.csv

Nov 16 '21 15:11 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

Nov 16 '21 15:11 davidfarinajr

R Recom tree tree_cross_val.csv tree_cross_val.pdf

Nov 16 '21 15:11 davidfarinajr

Discussed this PR with @mjohnson541 at developer hours. I didn't realize the kinetics rank is used to weight the sample in fitting the Arr BM rules 😅 . I'm going to go back and change the ranks based on the guidelines here http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/kinetics.html#priority-of-kinetic-databases. I think rank 10 makes sense for imported literature rates since we don't know where they are coming from in most cases, and rank 7 makes sense for AutoTST DFT calculations (although these calculations do not include rotor scans)

Dec 07 '21 17:12 davidfarinajr

These are all of the reactions in regression tests where the rate at 1000K changes by ~3 orders of magnitude or more

Non-identical kinetics!
505
original:
506
rxn: [c]1ccccc1(3) + C=Cc1ccccc1(16) <=> benzene(1) + [CH]=Cc1ccccc1(12)		origin: H_Abstraction
507
tested:
508
rxn: [c]1ccccc1(3) + C=Cc1ccccc1(16) <=> benzene(1) + [CH]=Cc1ccccc1(12)		origin: H_Abstraction
509
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
510

511
k(T):  |  -0.51|   0.90|   1.85|   2.54|   3.52|   4.21|   5.33|   6.05
512
k(T):  |   4.02|   5.03|   5.70|   6.20|   6.90|   7.38|   8.18|   8.69
513

514
Kinetics: Arrhenius(A=(0.01102,'cm^3/(mol*s)'), n=4.401, Ea=(4.745,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 174 used for Cd/H2/NonDeC;Cb_rad
515
Kinetics: Arrhenius(A=(63200,'cm^3/(mol*s)'), n=3.11, Ea=(3.413,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_Ext-3C-R_N- Sp-4R!H-3C_N-1BrCClHINOPSSi->Cl_Ext-4R!H-R_N-5R!H-u1_Ext-5R!H-R_Ext-6R!H-R_Ext-6R!H-R_Ext-7R!H-R_Ext-7R!H-R_N-Sp-7R!H-6R!H_1CH->C_Ext-1C-R_N- Sp-8R!H-1C_Ext-8R!H-R_Ext-9R!H-R
516
kinetics: From training reaction 174 used for Cd/H2/NonDeC;Cb_rad
517
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_Ext-3C-R_N- Sp-4R!H-3C_N-1BrCClHINOPSSi->Cl_Ext-4R!H-R_N-5R!H-u1_Ext-5R!H-R_Ext-6R!H-R_Ext-6R!H-R_Ext-7R!H-R_Ext-7R!H-R_N-Sp-7R!H-6R!H_1CH->C_Ext-1C-R_N- Sp-8R!H-1C_Ext-8R!H-R_Ext-9R!H-R

Non-identical kinetics!
730
original:
731
rxn: benzene(1) + [CH]1C=CC=CC1(6) <=> [c]1ccccc1(3) + C1=CCCC=C1(58)		origin: H_Abstraction
732
tested:
733
rxn: [c]1ccccc1(3) + C1=CCCC=C1(73) <=> benzene(1) + [CH]1C=CC=CC1(6)		origin: H_Abstraction
734
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
735

736
k(T):  | -23.31| -15.90| -11.36|  -8.27|  -4.29|  -1.81|   1.70|   3.62
737
k(T):  |   3.75|   4.22|   4.58|   4.87|   5.34|   5.70|   6.36|   6.82
738

739
Kinetics: Arrhenius(A=(0.258,'cm^3/(mol*s)'), n=4.34, Ea=(37.716,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1694 used for Cb_H;C_rad/H/CdCs
740
Kinetics: Arrhenius(A=(3.38027,'cm^3/(mol*s)'), n=3.724, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_Ext-3C-R_N- Sp-4R!H-3C_N-1BrCClHINOPSSi->Cl_Ext-4R!H-R_N-5R!H-u1_Ext-5R!H-R_Ext-6R!H-R_Ext-6R!H-R_Ext-7R!H-R_Ext-7R!H-R_N- Sp-7R!H-6R!H_1CH->C_Ext-1C-R_Ext-1C-R_Ext-8R!H-R_N-9R!H->S_Sp-10R!H-8R!H_1C-inRing_Ext-10R!H-R_Ext-11R!H-R
741
kinetics: From training reaction 1694 used for Cb_H;C_rad/H/CdCs
742
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_Ext-3C-R_N- Sp-4R!H-3C_N-1BrCClHINOPSSi->Cl_Ext-4R!H-R_N-5R!H-u1_Ext-5R!H-R_Ext-6R!H-R_Ext-6R!H-R_Ext-7R!H-R_Ext-7R!H-R_N- Sp-7R!H-6R!H_1CH->C_Ext-1C-R_Ext-1C-R_Ext-8R!H-R_N-9R!H->S_Sp-10R!H-8R!H_1C-inRing_Ext-10R!H-R_Ext-11R!H-R

Non-identical kinetics!
1022
original:
1023
rxn: HO2(9) + CH2NH2(59) <=> O2(2) + NC(1)		origin: H_Abstraction
1024
tested:
1025
rxn: HO2(9) + CH2NH2(59) <=> O2(2) + NC(1)		origin: H_Abstraction
1026
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
1027

1028
k(T):  |  -9.06|  -5.62|  -3.48|  -2.00|  -0.05|   1.20|   3.04|   4.10
1029
k(T):  |   6.34|   6.46|   6.55|   6.61|   6.71|   6.77|   6.89|   6.96
1030

1031
Kinetics: Arrhenius(A=(0.444344,'cm^3/(mol*s)'), n=3.706, Ea=(16.317,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [X_H;C_pri_rad] for rate rule [Orad_O_H;C_rad/H2/N]
1032
Kinetics: Arrhenius(A=(2.28791e+11,'cm^3/(mol*s)'), n=0.497, Ea=(0.347,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N-Sp-4R!H#3C_N-Sp-4R!H=3C_N-4R!H->F_N-1BrCClHINOPSSi->Br_N-1CClHI NO->Cl_N-1CHINO->H_N-1CINO->I_N-1CNO->N_1CO-u0_N-1CO->C_N-4BrCClNOS->O_N-4BrCClNS->C_N-4BrClN->Br_4ClN->N""")
1033
kinetics: Estimated using template [X_H;C_pri_rad] for rate rule [Orad_O_H;C_rad/H2/N]
1034
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N-Sp-4R!H#3C_N-Sp-4R!H=3C_N-4R!H->F_N-1BrCClHINOPSSi->Br_N-1CClHI NO->Cl_N-1CHINO->H_N-1CINO->I_N-1CNO->N_1CO-u0_N-1CO->C_N-4BrCClNOS->O_N-4BrCClNS->C_N-4BrClN->Br_4ClN->N

Non-identical kinetics!
1187
original:
1188
rxn: HCNH(58) + NC(1) <=> H2CNH(61) + CH2NH2(59)		origin: H_Abstraction
1189
tested:
1190
rxn: HCNH(58) + NC(1) <=> H2CNH(61) + CH2NH2(59)		origin: H_Abstraction
1191
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
1192

1193
k(T):  |   2.23|   3.40|   4.14|   4.66|   5.36|   5.82|   6.51|   6.93
1194
k(T):  |  -8.87|  -5.11|  -2.81|  -1.24|   0.77|   2.02|   3.80|   4.76
1195

1196
Kinetics: Arrhenius(A=(2.87777e+07,'cm^3/(mol*s)'), n=1.828, Ea=(5.153,'kcal/mol'), T0=(1,'K'), comment="""Estimated using an average for rate rule [Cs/H3/NonDeN;Y_rad]
1197
Kinetics: Arrhenius(A=(750147,'cm^3/(mol*s)'), n=2.115, Ea=(19.198,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_N-4R!H->C_N-4BrClFNOS->S_N-1BrCClHINOPSSi->Cl_1BrCHNO->C_1C-u0_4NO->N
1198
kinetics: Estimated using an average for rate rule [Cs/H3/NonDeN;Y_rad]
1199
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_N-4R!H->C_N-4BrClFNOS->S_N-1BrCClHINOPSSi->Cl_1BrCHNO->C_1C-u0_4NO->N

Non-identical kinetics!
1532
original:
1533
rxn: HO2(9) + NH(T)(45) <=> O2(2) + NH2(41)		origin: H_Abstraction
1534
tested:
1535
rxn: HO2(9) + NH(T)(45) <=> O2(2) + NH2(41)		origin: H_Abstraction
1536
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
1537

1538
k(T):  |   1.35|   2.52|   3.23|   3.72|   4.34|   4.73|   5.29|   5.59
1539
k(T):  |   5.77|   6.44|   6.77|   6.95|   7.08|   7.09|   6.95|   6.76
1540

1541
Kinetics: Arrhenius(A=(9.06257e+09,'cm^3/(mol*s)'), n=0.69, Ea=(5.925,'kcal/mol'), T0=(1,'K'), comment="""Estimated using average of templates [X_H;NH_triplet] + [Orad_O_H;Y_rad_birad_trirad_quadrad] for rate rule [Orad_O_H;NH_triplet]
1542
Kinetics: Arrhenius(A=(1.27507e+24,'cm^3/(mol*s)'), n=-3.242, Ea=(5.905,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_N-3BrCClHINOS->C_Ext-1R-R_Sp-4R!H-1R_N-3BrClHINOS->Cl_N-1R->S_N-4R!H->Cl_N-3BrHINOS->S_N-3BrHINO->I_4BrCFNOS->O_N-4O-u0_N-3BrHNO->O""")
1543
kinetics: Estimated using average of templates [X_H;NH_triplet] + [Orad_O_H;Y_rad_birad_trirad_quadrad] for rate rule [Orad_O_H;NH_triplet]
1544
kinetics: Estimated from node Root_N-3R->F_N-3BrCClHINOS->C_Ext-1R-R_Sp-4R!H-1R_N-3BrClHINOS->Cl_N-1R->S_N-4R!H->Cl_N-3BrHINOS->S_N-3BrHINO->I_4BrCFNOS->O_N-4O-u0_N-3BrHNO->O

Non-identical kinetics!
1667
original:
1668
rxn: NH(T)(45) + H2CNH(61) <=> NH2(41) + H2CN(56)		origin: H_Abstraction
1669
tested:
1670
rxn: NH(T)(45) + H2CNH(61) <=> NH2(41) + H2CN(56)		origin: H_Abstraction
1671
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
1672

1673
k(T):  |  -1.41|   0.57|   1.80|   2.64|   3.74|   4.44|   5.45|   6.02
1674
k(T):  |   2.63|   5.03|   6.50|   7.52|   8.83|   9.65|  10.84|  11.50
1675

1676
Kinetics: Arrhenius(A=(2.0199e+07,'cm^3/(mol*s)'), n=1.75, Ea=(9.676,'kcal/mol'), T0=(1,'K'), comment="""Estimated using average of templates [N3d/H/NonDe;NH_triplet] + [N3d/H/NonDeC;Y_1centerbirad] for rate rule [N3d/H/NonDeC;NH_triplet]
1677
Kinetics: Arrhenius(A=(6.26e+12,'cm^3/(mol*s)'), n=1.82, Ea=(11.906,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_N-3BrCClHINOS->C_Ext-1R-R_N-Sp-4R!H-1R_N- Sp-4R!H#1R_N-4R!H->O_N-3BrClHINOS->H_N-3BrClINOS->Cl_3BrINOS->N_N-3N-u1_N-4CNS->N""")
1678
kinetics: Estimated using average of templates [N3d/H/NonDe;NH_triplet] + [N3d/H/NonDeC;Y_1centerbirad] for rate rule [N3d/H/NonDeC;NH_triplet]
1679
kinetics: Estimated from node Root_N-3R->F_N-3BrCClHINOS->C_Ext-1R-R_N-Sp-4R!H-1R_N- Sp-4R!H#1R_N-4R!H->O_N-3BrClHINOS->H_N-3BrClINOS->Cl_3BrINOS->N_N-3N-u1_N-4CNS->N

Non-identical kinetics!
2067
original:
2068
rxn: O=S(44) + HO2(10) <=> SO2(15) + OH(5)		origin: R_Addition_MultipleBond
2069
tested:
2070
rxn: O=S(44) + HO2(10) <=> SO2(15) + OH(5)		origin: R_Addition_MultipleBond
2071
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
2072

2073
k(T):  |  -5.05|  -2.66|  -1.16|  -0.12|   1.24|   2.12|   3.41|   4.16
2074
k(T):  |   7.81|   7.69|   7.60|   7.52|   7.40|   7.31|   7.14|   7.02
2075

2076
Kinetics: Arrhenius(A=(452.858,'cm^3/(mol*s)'), n=2.649, Ea=(11.356,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [R_R;OJ-O2s] for rate rule [Sd_R;OJ-O2s]
2077
Kinetics: Arrhenius(A=(1.49945e+16,'cm^3/(mol*s)'), n=-0.955, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R-inRing_Ext-3R-R_N-Sp-4R!H=3R_N-3R->C""")
2078
kinetics: Estimated using template [R_R;OJ-O2s] for rate rule [Sd_R;OJ-O2s]
2079
kinetics: Estimated from node Root_N-3R-inRing_Ext-3R-R_N-Sp-4R!H=3R_N-3R->C

Non-identical kinetics!
2569
original:
2570
rxn: O=S(44) + HO2(10) <=> SO2(15) + OH(5)		origin: R_Addition_MultipleBond
2571
tested:
2572
rxn: O=S(44) + HO2(10) <=> SO2(15) + OH(5)		origin: R_Addition_MultipleBond
2573
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
2574

2575
k(T):  |  -5.05|  -2.66|  -1.16|  -0.12|   1.24|   2.12|   3.41|   4.16
2576
k(T):  |   7.81|   7.69|   7.60|   7.52|   7.40|   7.31|   7.14|   7.02
2577

2578
Kinetics: Arrhenius(A=(452.858,'cm^3/(mol*s)'), n=2.649, Ea=(11.356,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [R_R;OJ-O2s] for rate rule [Sd_R;OJ-O2s]
2579
Kinetics: Arrhenius(A=(1.49945e+16,'cm^3/(mol*s)'), n=-0.955, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R-inRing_Ext-3R-R_N-Sp-4R!H=3R_N-3R->C""")
2580
kinetics: Estimated using template [R_R;OJ-O2s] for rate rule [Sd_R;OJ-O2s]
2581
kinetics: Estimated from node Root_N-3R-inRing_Ext-3R-R_N-Sp-4R!H=3R_N-3R->C

Non-identical kinetics!
3872
original:
3873
rxn: HO2(10) + HCCO(32) <=> O2(2) + CH2CO(25)		origin: H_Abstraction
3874
tested:
3875
rxn: HO2(10) + HCCO(32) <=> O2(2) + CH2CO(25)		origin: H_Abstraction
3876
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
3877

3878
k(T):  | -11.53|  -7.40|  -4.83|  -3.05|  -0.72|   0.78|   2.97|   4.22
3879
k(T):  |   4.93|   4.95|   4.96|   4.97|   4.99|   5.01|   5.03|   5.05
3880

3881
Kinetics: Arrhenius(A=(0.0205168,'cm^3/(mol*s)'), n=4.261, Ea=(19.764,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [X_H;Cd_Cdd_rad/H] for rate rule [Orad_O_H;Cd_Cdd_rad/H]
3882
Kinetics: Arrhenius(A=(3.75613e+10,'cm^3/(mol*s)'), n=0.144, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_4R!H->C_1BrCClHINOPSSi->O_Ext-1O-R_N-5R!H->C_N-5BrClFINOPSSi-u0_Ext-4C-R_N-6R!H->F""")
3883
kinetics: Estimated using template [X_H;Cd_Cdd_rad/H] for rate rule [Orad_O_H;Cd_Cdd_rad/H]
3884
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_4R!H->C_1BrCClHINOPSSi->O_Ext-1O-R_N-5R!H->C_N-5BrClFINOPSSi-u0_Ext-4C-R_N-6R!H->F

Non-identical kinetics!
3902
original:
3903
rxn: HCO(14) + CC(C)OO(50) <=> CH2O(18) + CC(C)O[O](56)		origin: H_Abstraction
3904
tested:
3905
rxn: HCO(14) + CC(C)OO(50) <=> CH2O(18) + CC(C)O[O](56)		origin: H_Abstraction
3906
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
3907

3908
k(T):  | -28.84| -20.57| -15.52| -12.08|  -7.67|  -4.92|  -1.05|   1.04
3909
k(T):  |  -8.00|  -5.04|  -3.21|  -1.96|  -0.33|   0.69|   2.17|   2.99
3910

3911
Kinetics: Arrhenius(A=(0.0009569,'cm^3/(mol*s)'), n=4.45, Ea=(42.343,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [ROOH_sec;CO_rad] for rate rule [ROOH_sec;CO_pri_rad]
3912
Kinetics: Arrhenius(A=(903.801,'cm^3/(mol*s)'), n=2.314, Ea=(14.671,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_N-4R!H->C_N-4BrClFNOS->S_N-1BrCClHINOPSSi->Cl_N-1BrCHNO->C_N-1BrHNO->Br_Ext-1HNO-R_5R!H-u0_Ext-5R!H-R""")
3913
kinetics: Estimated using template [ROOH_sec;CO_rad] for rate rule [ROOH_sec;CO_pri_rad]
3914
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_N-4R!H->C_N-4BrClFNOS->S_N-1BrCClHINOPSSi->Cl_N-1BrCHNO->C_N-1BrHNO->Br_Ext-1HNO-R_5R!H-u0_Ext-5R!H-R

Non-identical kinetics!
4994
original:
4995
rxn: [CH2](2) + C(3) <=> ethane(1)		origin: 1,2_Insertion_carbene
4996
tested:
4997
rxn: [CH2](2) + C(3) <=> ethane(1)		origin: 1,2_Insertion_carbene
4998
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
4999

5000
k(T):  |   6.97|   6.93|   6.91|   6.90|   6.89|   6.89|   6.89|   6.90
5001
k(T):  |  -2.83|  -1.72|  -0.85|  -0.14|   0.97|   1.84|   3.41|   4.53
5002

5003
Kinetics: Arrhenius(A=(1.74695e+12,'cm^3/(mol*s)'), n=0.189, Ea=(-0.354,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [carbene;Cs_H] for rate rule [carbene;C_methane]
5004
Kinetics: Arrhenius(A=(1.08927e-19,'cm^3/(mol*s)'), n=8.934, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node CH_N-3Br1sCCl1sF1sHI1s->F1s_N-3Br1sCCl1sH->Cl1s
5005
kinetics: Estimated using template [carbene;Cs_H] for rate rule [carbene;C_methane]
5006
kinetics: Estimated from node CH_N-3Br1sCCl1sF1sHI1s->F1s_N-3Br1sCCl1sH->Cl1s

Non-identical kinetics!
5114
original:
5115
rxn: [CH]C-2(15) <=> C=C(9)		origin: Singlet_Carbene_Intra_Disproportionation
5116
tested:
5117
rxn: [CH]C-2(15) <=> C=C(9)		origin: Singlet_Carbene_Intra_Disproportionation
5118
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
5119

5120
k(T):  |   2.70|   5.04|   6.42|   7.32|   8.42|   9.06|   9.86|  10.22
5121
k(T):  |  11.34|  11.85|  12.11|  12.26|  12.39|  12.43|  12.38|  12.29
5122

5123
Kinetics: Arrhenius(A=(1.84394e+15,'s^-1'), n=-1.078, Ea=(13.587,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [CsJ2-C;singletcarbene;CH] for rate rule [CsJ2-C;CsJ2H;CH3]
5124
Kinetics: Arrhenius(A=(1.38431e+19,'s^-1'), n=-1.939, Ea=(4.11,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node CCH
5125
kinetics: Estimated using template [CsJ2-C;singletcarbene;CH] for rate rule [CsJ2-C;CsJ2H;CH3]
5126
kinetics: Estimated from node CCH

Non-identical kinetics!
5339
original:
5340
rxn: [C]=C(19) + C=C(9) <=> [CH]=C(14) + [CH]=C(14)		origin: H_Abstraction
5341
tested:
5342
rxn: [C]=C(19) + C=C(9) <=> [CH]=C(14) + [CH]=C(14)		origin: H_Abstraction
5343
k(1bar)|300K   |400K   |500K   |600K   |800K   |1000K  |1500K  |2000K  
5344

5345
k(T):  | -14.36|  -9.05|  -5.83|  -3.65|  -0.88|   0.83|   3.19|   4.44
5346
k(T):  |   2.39|   3.22|   3.81|   4.27|   4.96|   5.47|   6.35|   6.96
5347

5348
Kinetics: Arrhenius(A=(1.512e+07,'cm^3/(mol*s)'), n=1.91, Ea=(27.82,'kcal/mol'), T0=(1,'K'), comment="""Estimated using an average for rate rule [Cd/H2/NonDeC;Y_1centerbirad]
5349
Kinetics: Arrhenius(A=(0.0443292,'cm^3/(mol*s)'), n=4.386, Ea=(1.543,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_4R!H->C_N-1BrCClHINOPSSi->O_N-1BrCClHN->Cl_Ext-1BrCHN- R_N-5R!H->S_N-5BrCClFINOPSi->F_N-5BrCClO->Cl_N-5BrCO->O_Sp-5BrBrBrCCCHN=1BrBrBrBrCCCCHHNN
5350
kinetics: Estimated using an average for rate rule [Cd/H2/NonDeC;Y_1centerbirad]
5351
kinetics: Estimated from node Root_N-3R->F_3BrCClHINOS->C_N-1R-u2_N-1R->F_N-3C-inRing_Ext-3C-R_N- Sp-4R!H#3C_Sp-4R!H=3C_4R!H->C_N-1BrCClHINOPSSi->O_N-1BrCClHN->Cl_Ext-1BrCHN- R_N-5R!H->S_N-5BrCClFINOPSi->F_N-5BrCClO->Cl_N-5BrCO->O_Sp-5BrBrBrCCCHN=1BrBrBrBrCCCCHHNN

Dec 10 '21 23:12 davidfarinajr

Some of the reactions missing in the test model for oxidation is concerning:

rxn: H(3) + [CH2]CC(38) <=> propane(1)		origin: R_Recombination
3136
rxn: HO2(10) + [CH2]CC(38) <=> O2(2) + propane(1)		origin: H_Abstraction
3137
rxn: C[CH]C(37) <=> [CH2]CC(38)		origin: intra_H_migration
3138
rxn: O(4) + propane(1) <=> OH(5) + [CH2]CC(38)		origin: H_Abstraction
3139
rxn: OH(5) + propane(1) <=> H2O(7) + [CH2]CC(38)		origin: H_Abstraction
3140
rxn: H2O2(11) + [CH2]CC(38) <=> HO2(10) + propane(1)		origin: H_Abstraction
3141
rxn: CH2OH(30) + [CH2]CC(38) <=> CH2O(18) + propane(1)		origin: Disproportionation
3142
rxn: CH3O(24) + [CH2]CC(38) <=> CH2O(18) + propane(1)		origin: Disproportionation
3143
rxn: CH3(19) + propane(1) <=> CH4(28) + [CH2]CC(38)		origin: H_Abstraction
3144
rxn: CH3O(24) + propane(1) <=> CH3OH(31) + [CH2]CC(38)		origin: H_Abstraction
3145
rxn: C2H5(29) + [CH2]CC(38) <=> C2H4(27) + propane(1)		origin: Disproportionation
3146
rxn: C2H6(36) + [CH2]CC(38) <=> C2H5(29) + propane(1)		origin: H_Abstraction
3147
rxn: [CH2]CC(38) + propane(1) <=> C[CH]C(37) + propane(1)		origin: H_Abstraction
3148
rxn: C2H3(26) + [CH2]CC(38) <=> C2H2(21) + propane(1)		origin: Disproportionation
3149
rxn: CH3CO(33) + [CH2]CC(38) <=> CH2CO(25) + propane(1)		origin: Disproportionation
3150
rxn: CH2CHO(34) + [CH2]CC(38) <=> CH2CO(25) + propane(1)		origin: Disproportionation
3151
rxn: [CH2]CC(38) + CC(C)OO(50) <=> CC(C)O[O](56) + propane(1)		origin: H_Abstraction
3152
rxn: COO(61) + [CH2]CC(38) <=> CO[O](53) + propane(1)		origin: H_Abstraction
3153
rxn: CH3(19) + C2H4(27) <=> [CH2]CC(38)		origin: R_Addition_MultipleBond
3154
rxn: CH3CHO(35) + [CH2]CC(38) <=> CH3CO(33) + propane(1)		origin: H_Abstraction
3155
rxn: CH3CHO(35) + [CH2]CC(38) <=> CH2CHO(34) + propane(1)		origin: H_Abstraction
3156
rxn: H(3) + propane(1) <=> H2(6) + [CH2]CC(38)		origin: H_Abstraction

😬 We are missing lots of H Abs from propane in test model, I'll have to take a look at those. Must be much slower. I think we should also compare rates of test branch vs main for reactions in one model but not the other. Perhaps we could add this to regression tests 🤔

Dec 10 '21 23:12 davidfarinajr

For oxidation, [CH2]CC(38) not in test model 🧐

The original model has 12 species that the tested model does not have.
3093
spc: [CH2]CC(38)
3094
spc: [O]C=O(52)
3095
spc: CCO[O](55)
3096
spc: CC[O](73)
3097
spc: COOC(90)
3098
spc: CCCOO(144)
3099
spc: CCC[O](146)
3100
spc: CCCO[O](148)
3101
spc: [CH2]CCOO(150)
3102
spc: [O]OCCCOO(155)
3103
spc: CCOO(168)
3104
spc: O=COO(177)

Dec 10 '21 23:12 davidfarinajr

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Halogen training reactions

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