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Published 20 hours ago • verified publisher icon ReactionMechanismGenerator

update Pt111 library

Open bjkreitz opened this issue 1 year ago • 11 comments

Update of the thermo library The previous surfaceThermoPt111.py database was a mixture of VASP and QE calculations. The usage of different electronic structure codes with slightly different settings resulted in constant offsets between the enthalpies of formation of the adsorbates. I created a new database that has a consistent set of QE values for all adsorbates that do not contain N. We are working on the nitrogen containing species and we will add the commits to this PR.

Additionally, I added another 42 adsorbates with more heavy atoms to the database based on calculations performed in this paper https://doi.org/10.1002/anie.202306514.

I also changed the notation of the adsorbate labels in the database. The current labels are rather confusing. I adopted a notation that we have used in the last couple of papers, which is more similar to the SMILES notation.

X indicates a bond to the surface. It is always on the left hand site of an atom that is bonded to the surface e.g. XCCH2 it means that C is bonded to the surface. If the X is on the right hand side and at the end of a label, it means that this species is physisorbed e.g. H2OX.

bjkreitz avatar Mar 07 '24 15:03 bjkreitz

I generated a new CPOX model on Pt with this database. The new model ended up with 10 more species and 67 more reactions. The structures of the new species looks good to me, except that some labels used SMILES directly, for examples XCH2OH was named as OC#[Pt](249) and XCCH3 was named as CC#[Pt](259), this is an issue in RMG-Py 2627. The library looks good to me.

12Chao avatar Mar 07 '24 17:03 12Chao

Regression Testing Results

⚠️ One or more regression tests failed. Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:05 Current: Execution time (DD:HH:MM:SS): 00:00:01:05 Reference: Memory used: 2765.03 MB Current: Memory used: 2783.06 MB

aromatics Passed Core Comparison ✅

Original model has 15 species. Test model has 15 species. ✅ Original model has 11 reactions. Test model has 11 reactions. ✅

aromatics Failed Edge Comparison ❌

Original model has 106 species. Test model has 106 species. ✅ Original model has 358 reactions. Test model has 358 reactions. ✅

Non-identical thermo! ❌ original: C1=CC2C=CC=1C=C2 tested: C1=CC2C=CC=1C=C2

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
164.90 80.93 22.21 28.97 35.25 40.69 48.70 53.97 64.36
129.39 79.85 22.98 30.09 36.61 42.21 50.22 55.39 65.95

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(124cyclohexatriene) thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(1,4-Cyclohexadiene)

Non-identical kinetics! ❌ original: rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -3.00 -0.74 0.70 1.71 3.07 3.97 5.33 6.15
k(T): 4.24 4.69 5.05 5.33 5.79 6.14 6.78 7.23

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(9.943,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -7.44 -4.08 -2.05 -0.69 1.02 2.06 3.46 4.18
k(T): 5.77 5.83 5.88 5.92 5.97 6.02 6.10 6.16

kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(18.137,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0 Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0 Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -7.17 -3.66 -1.56 -0.16 1.60 2.65 4.05 4.75
k(T): 4.06 4.76 5.18 5.46 5.81 6.02 6.30 6.44

kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(19.262,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS Multiplied by reaction path degeneracy 3.0""") kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(3.841,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS Multiplied by reaction path degeneracy 3.0""") Identical kinetics comments: kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.48 -21.35 -15.79 -12.03 -7.23 -4.28 -0.16 2.03
k(T): -4.55 -1.90 -0.23 0.94 2.49 3.50 5.02 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.063,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -31.23 -21.91 -16.23 -12.40 -7.51 -4.50 -0.31 1.91
k(T): -5.30 -2.46 -0.68 0.57 2.21 3.28 4.87 5.80

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(48.686,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(13.089,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 53.5 to 54.8 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 53.5 to 54.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -27.24 -18.91 -13.84 -10.40 -6.02 -3.30 0.48 2.51
k(T): -1.38 0.48 1.67 2.52 3.68 4.45 5.66 6.39

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(43.208,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(7.718,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -11.95 -7.61 -5.01 -3.27 -1.10 0.20 1.93 2.80
k(T): -0.49 0.99 1.87 2.46 3.19 3.64 4.23 4.52

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(23.821,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(8.084,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") Identical kinetics comments: kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -12.28 -7.86 -5.21 -3.44 -1.23 0.10 1.87 2.75
k(T): -0.66 0.85 1.76 2.37 3.13 3.58 4.19 4.49

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(24.273,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(8.328,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") Identical kinetics comments: kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.44 -21.32 -15.76 -12.01 -7.22 -4.26 -0.16 2.03
k(T): -4.51 -1.87 -0.20 0.96 2.51 3.52 5.03 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.606,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.01,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.5 to 50.2 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.5 to 50.2 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -32.11 -22.57 -16.76 -12.84 -7.84 -4.76 -0.49 1.78
k(T): -6.18 -3.12 -1.20 0.13 1.88 3.01 4.70 5.67

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(49.895,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(14.299,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 56.6 to 59.8 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 56.6 to 59.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -33.97 -23.97 -17.88 -13.77 -8.54 -5.32 -0.86 1.50
k(T): -8.04 -4.52 -2.32 -0.81 1.18 2.46 4.32 5.39

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(52.457,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(16.86,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.48 -21.35 -15.79 -12.03 -7.23 -4.28 -0.16 2.03
k(T): -4.55 -1.90 -0.23 0.94 2.49 3.50 5.02 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.063,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -19.49 -12.98 -9.00 -6.29 -2.81 -0.64 2.42 4.08
k(T): 3.96 4.60 5.07 5.43 5.98 6.39 7.11 7.60

kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(33.226,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0 Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(1.036,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0 Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:09 Current: Execution time (DD:HH:MM:SS): 00:00:02:09 Reference: Memory used: 2914.72 MB Current: Memory used: 2914.24 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species. Test model has 37 species. ✅ Original model has 216 reactions. Test model has 215 reactions. ❌ The original model has 1 reactions that the tested model does not have. ❌ rxn: CCO[O](31) <=> [OH](22) + CC=O(72) origin: intra_H_migration

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species. Test model has 202 species. ✅ Original model has 1613 reactions. Test model has 1613 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: CCO[O](31) <=> [OH](22) + CC=O(72) origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: CCO[O](29) <=> C[CH]OO(70) origin: intra_H_migration

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:24 Current: Execution time (DD:HH:MM:SS): 00:00:01:23 Reference: Memory used: 2896.53 MB Current: Memory used: 2915.18 MB

nitrogen Failed Core Comparison ❌

Original model has 41 species. Test model has 41 species. ✅ Original model has 359 reactions. Test model has 360 reactions. ❌ The tested model has 1 reactions that the original model does not have. ❌ rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction

nitrogen Failed Edge Comparison ❌

Original model has 132 species. Test model has 132 species. ✅ Original model has 995 reactions. Test model has 997 reactions. ❌ The tested model has 2 reactions that the original model does not have. ❌ rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction rxn: HON(T)(83) + HCO(13) <=> NO(38) + CH2O(18) origin: Disproportionation

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:22 Current: Execution time (DD:HH:MM:SS): 00:00:02:22 Reference: Memory used: 2760.39 MB Current: Memory used: 2773.20 MB

oxidation Passed Core Comparison ✅

Original model has 59 species. Test model has 59 species. ✅ Original model has 694 reactions. Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species. Test model has 230 species. ✅ Original model has 1526 reactions. Test model has 1526 reactions. ✅

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:54 Current: Execution time (DD:HH:MM:SS): 00:00:00:54 Reference: Memory used: 2864.21 MB Current: Memory used: 2879.26 MB

sulfur Passed Core Comparison ✅

Original model has 27 species. Test model has 27 species. ✅ Original model has 74 reactions. Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species. Test model has 89 species. ✅ Original model has 227 reactions. Test model has 227 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary The tested model has 1 reactions that the original model does not have. ❌ rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:35 Current: Execution time (DD:HH:MM:SS): 00:00:00:35 Reference: Memory used: 2985.10 MB Current: Memory used: 2957.16 MB

superminimal Passed Core Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 21 reactions. Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species. Test model has 18 species. ✅ Original model has 28 reactions. Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:26 Current: Execution time (DD:HH:MM:SS): 00:00:02:24 Reference: Memory used: 3443.41 MB Current: Memory used: 3437.14 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:06:07 Current: Execution time (DD:HH:MM:SS): 00:00:06:05 Reference: Memory used: 3371.37 MB Current: Memory used: 3372.49 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 37 species. Test model has 37 species. ✅ Original model has 232 reactions. Test model has 233 reactions. ❌ The tested model has 1 reactions that the original model does not have. ❌ rxn: CCO[O](34) <=> [OH](21) + CC=O(61) origin: intra_H_migration

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species. Test model has 206 species. ✅ Original model has 1508 reactions. Test model has 1508 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: CCO[O](34) <=> C[CH]OO(62) origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: CCO[O](34) <=> [OH](21) + CC=O(61) origin: intra_H_migration

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

beep boop this comment was written by a bot :robot:

github-actions[bot] avatar Mar 28 '24 21:03 github-actions[bot]

I recalculated and updated the Nasa polynomials for the N containing adsorbates in this database using QE with settings that match what Bjarne has used on the rest of the species in this database. Upon reoptimizing these species I found that XNHXNH and NHNHX had the same energies and both looked like bidentate species, so I commented out NHNHX for now. Also when looking at the XNXO optimized structure, it is really just XN next to XO, so I commented out this species also. Additionally I added 7 new nitrogen containing species with 3 or more heavy atoms.

After adding these values in I ran a test where I oxidized NH3 to a conversion of 0.1 in the presence of reactive CO and O2, and saw that both core models looked almost identical; the model with the old data had 23 species, and the model with the new data had 24, and this set of species was mostly identical. In the edge, the model with the old data found 72 species and the new model found 174 species. The extra species are mainly multidentate adsorbates containing mixes of multiple heavy atoms.

kirkbadger18 avatar Mar 29 '24 20:03 kirkbadger18

Does RMG try to propose (via any reaction families) the species that you found, via DFT, to be unstable or non-existent? Rather than just "comment them out" of a thermo library, I feel we should teach RMG that they're not real, and what to do with them instead?

(edit to add: it's ok that this pull request doesn't do all that I just mentioned - this one is about updating the Pt thermo library, and it's OK to just do that. But it was more of a general question, and now seems a good time to discuss, as you have just done the DFT.)

rwest avatar Mar 29 '24 20:03 rwest

I will have to look on Monday, I am pretty sure that it forms XNXN, and I was unable to find a stable version of this via dft. I am not sure if it finds NHNHX or XNXO, but certainly nothing is systematically preventing these species from forming. I think the best way now is to provide a prohibited species list, but maybe we can find a better way to go about this?

Also, this is really just a first pass at these species; it may be possible to find a distinct NHNHX or an XNXO, but I have only tried a couple starting positions and have not found these yet, but certainly going forward there will be a list of species that we won’t be able to get dft to find. I can already think of a handful that I tried 3-4 ways to make and it didn’t form: XOXONNXOXO, XNNO, XOXONNXO. Beyond finding species that don’t bind, there may also be a list of ways that a larger adsorbate could bind, and we may only find one or two of these binding configurations(vdw, bidentate, tridenfate). Definitely something to discuss.

kirkbadger18 avatar Mar 29 '24 23:03 kirkbadger18

Regression Testing Results

⚠️ One or more regression tests failed. Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:05 Current: Execution time (DD:HH:MM:SS): 00:00:01:09 Reference: Memory used: 2772.61 MB Current: Memory used: 2776.84 MB

aromatics Passed Core Comparison ✅

Original model has 15 species. Test model has 15 species. ✅ Original model has 11 reactions. Test model has 11 reactions. ✅

aromatics Failed Edge Comparison ❌

Original model has 106 species. Test model has 106 species. ✅ Original model has 358 reactions. Test model has 358 reactions. ✅

Non-identical thermo! ❌ original: C1=CC2C=CC=1C=C2 tested: C1=CC2C=CC=1C=C2

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
164.90 80.93 22.21 28.97 35.25 40.69 48.70 53.97 64.36
129.39 79.85 22.98 30.09 36.61 42.21 50.22 55.39 65.95

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(124cyclohexatriene) thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(1,4-Cyclohexadiene)

Non-identical kinetics! ❌ original: rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -3.00 -0.74 0.70 1.71 3.07 3.97 5.33 6.15
k(T): 4.24 4.69 5.05 5.33 5.79 6.14 6.78 7.23

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(9.943,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -7.44 -4.08 -2.05 -0.69 1.02 2.06 3.46 4.18
k(T): 5.77 5.83 5.88 5.92 5.97 6.02 6.10 6.16

kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(18.137,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0 Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0 Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -7.17 -3.66 -1.56 -0.16 1.60 2.65 4.05 4.75
k(T): 4.06 4.76 5.18 5.46 5.81 6.02 6.30 6.44

kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(19.262,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS Multiplied by reaction path degeneracy 3.0""") kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(3.841,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS Multiplied by reaction path degeneracy 3.0""") Identical kinetics comments: kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.48 -21.35 -15.79 -12.03 -7.23 -4.28 -0.16 2.03
k(T): -4.55 -1.90 -0.23 0.94 2.49 3.50 5.02 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.063,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -31.23 -21.91 -16.23 -12.40 -7.51 -4.50 -0.31 1.91
k(T): -5.30 -2.46 -0.68 0.57 2.21 3.28 4.87 5.80

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(48.686,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(13.089,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 53.5 to 54.8 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 53.5 to 54.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -27.24 -18.91 -13.84 -10.40 -6.02 -3.30 0.48 2.51
k(T): -1.38 0.48 1.67 2.52 3.68 4.45 5.66 6.39

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(43.208,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(7.718,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation tested: rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -11.95 -7.61 -5.01 -3.27 -1.10 0.20 1.93 2.80
k(T): -0.49 0.99 1.87 2.46 3.19 3.64 4.23 4.52

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(23.821,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(8.084,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") Identical kinetics comments: kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -12.28 -7.86 -5.21 -3.44 -1.23 0.10 1.87 2.75
k(T): -0.66 0.85 1.76 2.37 3.13 3.58 4.19 4.49

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(24.273,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(8.328,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0""") Identical kinetics comments: kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.44 -21.32 -15.76 -12.01 -7.22 -4.26 -0.16 2.03
k(T): -4.51 -1.87 -0.20 0.96 2.51 3.52 5.03 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.606,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.01,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.5 to 50.2 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.5 to 50.2 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -32.11 -22.57 -16.76 -12.84 -7.84 -4.76 -0.49 1.78
k(T): -6.18 -3.12 -1.20 0.13 1.88 3.01 4.70 5.67

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(49.895,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(14.299,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 56.6 to 59.8 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 56.6 to 59.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -33.97 -23.97 -17.88 -13.77 -8.54 -5.32 -0.86 1.50
k(T): -8.04 -4.52 -2.32 -0.81 1.18 2.46 4.32 5.39

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(52.457,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(16.86,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.48 -21.35 -15.79 -12.03 -7.23 -4.28 -0.16 2.03
k(T): -4.55 -1.90 -0.23 0.94 2.49 3.50 5.02 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.063,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌ original: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83) origin: Disproportionation tested: rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83) origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -19.49 -12.98 -9.00 -6.29 -2.81 -0.64 2.42 4.08
k(T): 3.96 4.60 5.07 5.43 5.98 6.39 7.11 7.60

kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(33.226,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0 Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(1.036,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0""") kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0 Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R Multiplied by reaction path degeneracy 9.0

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:09 Current: Execution time (DD:HH:MM:SS): 00:00:02:14 Reference: Memory used: 2897.89 MB Current: Memory used: 2901.83 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species. Test model has 37 species. ✅ Original model has 215 reactions. Test model has 216 reactions. ❌ The tested model has 1 reactions that the original model does not have. ❌ rxn: CCO[O](31) <=> [OH](22) + CC=O(72) origin: intra_H_migration

Non-identical kinetics! ❌ original: rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](127) origin: Peroxyl_Disproportionation tested: rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128) origin: Peroxyl_Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 7.83 7.49 7.23 7.02 6.68 6.42 5.95 5.61
k(T): 3.77 4.45 4.86 5.14 5.48 5.68 5.96 6.09

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""") kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""") kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species. Test model has 202 species. ✅ Original model has 1618 reactions. Test model has 1610 reactions. ❌ The original model has 10 reactions that the tested model does not have. ❌ rxn: CCO[O](31) <=> C[CH]OO(70) origin: intra_H_migration rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(35) + CC[CH]CCOO(108) origin: H_Abstraction rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(35) + CCC[CH]COO(107) origin: H_Abstraction rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(35) + C[CH]CCCOO(109) origin: H_Abstraction rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(35) + CCCC[CH]OO(135) origin: H_Abstraction rxn: CCCOO(35) + [CH2]CCCCOO(110) <=> [CH2]CCOO(77) + CCCCCOO(105) origin: H_Abstraction rxn: C[CH]CCCO(157) + CCCCCO[O](103) <=> CC=CCCO(183) + CCCCCOO(105) origin: Disproportionation rxn: C[CH]CCCO(157) + CCCCCO[O](103) <=> C=CCCCO(184) + CCCCCOO(105) origin: Disproportionation rxn: C[CH]CCCO(157) + C[CH]CCCO(157) <=> CC=CCCO(183) + CCCCCO(130) origin: Disproportionation rxn: C[CH]CCCO(157) + C[CH]CCCO(157) <=> C=CCCCO(184) + CCCCCO(130) origin: Disproportionation The tested model has 2 reactions that the original model does not have. ❌ rxn: CCO[O](31) <=> [OH](22) + CC=O(72) origin: intra_H_migration rxn: CCCCCO[O](103) + CCCCCO[O](103) <=> oxygen(1) + CCCCC=O(120) + CCCCCO(130) origin: Peroxyl_Termination

Non-identical kinetics! ❌ original: rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](127) origin: Peroxyl_Disproportionation tested: rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128) origin: Peroxyl_Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 7.83 7.49 7.23 7.02 6.68 6.42 5.95 5.61
k(T): 3.77 4.45 4.86 5.14 5.48 5.68 5.96 6.09

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""") kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""") kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

Non-identical kinetics! ❌ original: rxn: CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129) origin: Peroxyl_Disproportionation tested: rxn: CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](128) + CC([O])CC(C)OO(127) origin: Peroxyl_Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 7.79 7.46 7.21 7.00 6.67 6.41 5.94 5.60
k(T): 3.52 4.27 4.71 5.01 5.39 5.61 5.91 6.06

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0.053,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.""") kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.096,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""") kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:22 Current: Execution time (DD:HH:MM:SS): 00:00:01:24 Reference: Memory used: 2901.44 MB Current: Memory used: 2894.68 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species. Test model has 41 species. ✅ Original model has 360 reactions. Test model has 360 reactions. ✅

nitrogen Failed Edge Comparison ❌

Original model has 132 species. Test model has 132 species. ✅ Original model has 997 reactions. Test model has 997 reactions. ✅

Non-identical thermo! ❌ original: O1[C]=N1 tested: O1[C]=N1

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
116.46 53.90 11.62 12.71 13.49 13.96 14.14 13.85 13.58
141.64 58.66 12.26 12.27 12.09 11.96 12.26 12.72 12.15

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO) thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)

Non-identical kinetics! ❌ original: rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic tested: rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -49.54 -33.65 -24.16 -17.85 -10.01 -5.35 0.80 3.82
k(T): -66.25 -46.19 -34.19 -26.21 -16.28 -10.36 -2.54 1.31

kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""") kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""") Identical kinetics comments: kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:19 Current: Execution time (DD:HH:MM:SS): 00:00:02:25 Reference: Memory used: 2767.96 MB Current: Memory used: 2769.38 MB

oxidation Passed Core Comparison ✅

Original model has 59 species. Test model has 59 species. ✅ Original model has 694 reactions. Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species. Test model has 230 species. ✅ Original model has 1526 reactions. Test model has 1526 reactions. ✅

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:53 Current: Execution time (DD:HH:MM:SS): 00:00:00:55 Reference: Memory used: 2877.94 MB Current: Memory used: 2870.53 MB

sulfur Passed Core Comparison ✅

Original model has 27 species. Test model has 27 species. ✅ Original model has 74 reactions. Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species. Test model has 89 species. ✅ Original model has 227 reactions. Test model has 227 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary The tested model has 1 reactions that the original model does not have. ❌ rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:35 Current: Execution time (DD:HH:MM:SS): 00:00:00:35 Reference: Memory used: 2963.45 MB Current: Memory used: 2979.88 MB

superminimal Passed Core Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 21 reactions. Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species. Test model has 18 species. ✅ Original model has 28 reactions. Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:25 Current: Execution time (DD:HH:MM:SS): 00:00:02:25 Reference: Memory used: 3454.52 MB Current: Memory used: 3438.71 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:06:12 Current: Execution time (DD:HH:MM:SS): 00:00:06:04 Reference: Memory used: 3399.35 MB Current: Memory used: 3388.20 MB

RMS_CSTR_liquid_oxidation Passed Core Comparison ✅

Original model has 37 species. Test model has 37 species. ✅ Original model has 233 reactions. Test model has 233 reactions. ✅

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species. Test model has 206 species. ✅ Original model has 1508 reactions. Test model has 1508 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: CCCO[O](34) <=> [OH](21) + CCC=O(50) origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: CCCO[O](36) <=> CC[CH]OO(45) origin: intra_H_migration

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

beep boop this comment was written by a bot :robot:

github-actions[bot] avatar Apr 19 '24 03:04 github-actions[bot]

Regression Testing Results

⚠️ One or more regression tests failed. Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:05 Current: Execution time (DD:HH:MM:SS): 00:00:01:06 Reference: Memory used: 2775.60 MB Current: Memory used: 2763.07 MB

aromatics Passed Core Comparison ✅

Original model has 15 species. Test model has 15 species. ✅ Original model has 11 reactions. Test model has 11 reactions. ✅

aromatics Passed Edge Comparison ✅

Original model has 106 species. Test model has 106 species. ✅ Original model has 358 reactions. Test model has 358 reactions. ✅

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:08 Current: Execution time (DD:HH:MM:SS): 00:00:02:10 Reference: Memory used: 2906.49 MB Current: Memory used: 2915.19 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species. Test model has 37 species. ✅ Original model has 216 reactions. Test model has 215 reactions. ❌ The original model has 1 reactions that the tested model does not have. ❌ rxn: CCO[O](31) <=> [OH](22) + CC=O(72) origin: intra_H_migration

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species. Test model has 202 species. ✅ Original model has 1610 reactions. Test model has 1610 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: CCO[O](31) <=> [OH](22) + CC=O(72) origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: CCO[O](31) <=> C[CH]OO(73) origin: intra_H_migration

Non-identical kinetics! ❌ original: rxn: CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](128) + CC([O])CC(C)OO(127) origin: Peroxyl_Disproportionation tested: rxn: CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129) origin: Peroxyl_Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 3.52 4.27 4.71 5.01 5.39 5.61 5.91 6.06
k(T): 7.79 7.46 7.21 7.00 6.67 6.41 5.94 5.60

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.096,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""") kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0.053,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.""") kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:22 Current: Execution time (DD:HH:MM:SS): 00:00:01:23 Reference: Memory used: 2904.14 MB Current: Memory used: 2897.84 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species. Test model has 41 species. ✅ Original model has 360 reactions. Test model has 360 reactions. ✅

nitrogen Passed Edge Comparison ✅

Original model has 132 species. Test model has 132 species. ✅ Original model has 997 reactions. Test model has 997 reactions. ✅

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:19 Current: Execution time (DD:HH:MM:SS): 00:00:02:24 Reference: Memory used: 2768.42 MB Current: Memory used: 2763.01 MB

oxidation Passed Core Comparison ✅

Original model has 59 species. Test model has 59 species. ✅ Original model has 694 reactions. Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species. Test model has 230 species. ✅ Original model has 1526 reactions. Test model has 1526 reactions. ✅

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:53 Current: Execution time (DD:HH:MM:SS): 00:00:00:54 Reference: Memory used: 2873.28 MB Current: Memory used: 2869.64 MB

sulfur Passed Core Comparison ✅

Original model has 27 species. Test model has 27 species. ✅ Original model has 74 reactions. Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species. Test model has 89 species. ✅ Original model has 227 reactions. Test model has 227 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary The tested model has 1 reactions that the original model does not have. ❌ rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:35 Current: Execution time (DD:HH:MM:SS): 00:00:00:34 Reference: Memory used: 2995.72 MB Current: Memory used: 2961.80 MB

superminimal Passed Core Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 21 reactions. Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species. Test model has 18 species. ✅ Original model has 28 reactions. Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:27 Current: Execution time (DD:HH:MM:SS): 00:00:02:23 Reference: Memory used: 3441.43 MB Current: Memory used: 3454.31 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:06:11 Current: Execution time (DD:HH:MM:SS): 00:00:06:05 Reference: Memory used: 3376.96 MB Current: Memory used: 3371.57 MB

RMS_CSTR_liquid_oxidation Passed Core Comparison ✅

Original model has 37 species. Test model has 37 species. ✅ Original model has 232 reactions. Test model has 232 reactions. ✅

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species. Test model has 206 species. ✅ Original model has 1508 reactions. Test model has 1508 reactions. ✅

Non-identical kinetics! ❌ original: rxn: CCCO[O](36) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](96) + CCCC(C)[O](61) origin: Peroxyl_Disproportionation tested: rxn: CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](90) + CCCC(C)[O](61) origin: Peroxyl_Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 3.69 4.39 4.82 5.10 5.45 5.66 5.94 6.08
k(T): 7.83 7.49 7.23 7.02 6.68 6.42 5.95 5.61

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.866,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""") kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""") kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

beep boop this comment was written by a bot :robot:

github-actions[bot] avatar Apr 19 '24 17:04 github-actions[bot]

For CPOX on Pt, CC#[Pt] covers most of the sites and stop the chemistry on the surface at high C/O inlet ratio (> 2), but forbidding CC#[Pt] solved the problem. After CC#[Pt] was left out, CHX became the dominant species on the surface, but the coverage of CHX did not reach to high enough to block the chemistry. The conclusions I can draw from that:

  1. The new database changed the dominant species on the Pt surface, but there is still a way to generate a model that is comparable to the experimental data by forbidding the problematic species.
  2. The C#X bond might be too strong with the data provided in the database

12Chao avatar Apr 27 '24 02:04 12Chao

For CPOX on Pt, CC#[Pt] covers most of the sites and stop the chemistry on the surface at high C/O inlet ratio (> 2), but forbidding CC#[Pt] solved the problem. After CC#[Pt] was left out, CHX became the dominant species on the surface, but the coverage of CHX did not reach to high enough to block the chemistry. The conclusions I can draw from that:

1. The new database changed the dominant species on the Pt surface, but there is still a way to generate a model that is comparable to the experimental data by forbidding the problematic species.

2. The C#X bond might be too strong with the data provided in the database

I did not do an extensive review, but I did construct a mechanism with this from one of the example problems and did not see anything that stood out when I compared it with main. I've attached the mechanisms. pr640.zip

@12chao can you post the chemkin and cantera files for the mechanisms with and without CC#[Pt]? you can put the .inp/.txt/.yaml files into a folder and zip it to attach. I'd like to take a look at that before approving. It may not necessarily be a thermo problem but I'd like to dig into it a little more.

ChrisBNEU avatar Apr 29 '24 11:04 ChrisBNEU

For CPOX on Pt, CC#[Pt] covers most of the sites and stop the chemistry on the surface at high C/O inlet ratio (> 2), but forbidding CC#[Pt] solved the problem. After CC#[Pt] was left out, CHX became the dominant species on the surface, but the coverage of CHX did not reach to high enough to block the chemistry. The conclusions I can draw from that:

1. The new database changed the dominant species on the Pt surface, but there is still a way to generate a model that is comparable to the experimental data by forbidding the problematic species.

2. The C#X bond might be too strong with the data provided in the database

I did not do an extensive review, but I did construct a mechanism with this from one of the example problems and did not see anything that stood out when I compared it with main. I've attached the mechanisms. pr640.zip

@12Chao can you post the chemkin and cantera files for the mechanisms with and without CC#[Pt]? you can put the .inp/.txt/.yaml files into a folder and zip it to attach. I'd like to take a look at that before approving. It may not necessarily be a thermo problem but I'd like to dig into it a little more.

Sure, here are the files. cpox.zip

12Chao avatar Apr 29 '24 20:04 12Chao

I made another model incorporating nitrogen and oxygen, and looked through the model edge. I did this to make sure there were no obvious errors in the species NASA expressions. something more subtle could have been missed, but none of the Cps were changed too dramatically. pr640_with_n2o2.zip

I am leaving a comment here so we can reference this later, if the issue chao addressed comes up again. @bjkreitz, @12Chao and @kirkbadger18 feel free to comment if I have gotten something wrong.

The issue described by chao is likely caused by CC#[Pt] having some coverage dependence that is not accounted for in the cpox model. We know a relationship exists for this species, and that will have to wait for the incorporation of coverage dependence in rmg (which is upcoming). What we should do for cases like this can be tabled for when we can actually incorporate coverage dependence in our models. My simple regression test did not reveal anything else worth noting.

I have reviewed the actual contents of this pr, and did not find any errors. That does not mean there aren't any, especially in the NASA polynomials, but I think both the comparison files I attached do a decent diff of the old and new thermo. I'd say we're good to merge @rwest

ChrisBNEU avatar May 08 '24 16:05 ChrisBNEU