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Corrected CH2 & CH2* species for reactions in JetSurF2.0 #650

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Corrected CH2 & CH2* species for reactions in JetSurF2.0 #650

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PoojaNem
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This Pull Request is submitted with reference to the email communication with Prof. Alon Grinberg Dana on issue #649 .
The JetSurF2.0 reaction library is corrected for the below reactions:
CH2 + O <=> HCO + H
CH2 + H2 <=> H + CH3
CH3 + OH <=> CH2 + H2O
CH3 + CH2 <=> C2H4 + H
CH4 + CH2 <=> CH3 + CH3
C2H4 + CH2 <=> aC3H5 + H
MultiArrhenius kinetic type is removed from the above reactions as per the JetSurf2.0 mechanism available online (https://web.stanford.edu/group/haiwanglab/JetSurF/JetSurF2.0/Mech_JetSurF2.0.txt)

Furthermore, the following reactions are added to the library based on the web version of the mechanism:
CH3 + OH <=> CH2* + H2O
CH2* + H2 <=> CH3 + H
CH3 + CH2* <=> C2H4 + H
C2H4 + CH2* <=> aC3H5 + H
CH4 + CH2* <=> CH3 + CH3
CH2* + O <=> HCO + H

@alongd Prof. Alon Grinberg Dana, I kindly request you to review the changes and provide your feedback on the same.

@JacksonBurns
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Thank you for the contribution!

@alongd do you have time to look at this?

@JacksonBurns JacksonBurns force-pushed the corrected_triplet_and_singlet_methylene_reactions branch from df9cf23 to b96a10f Compare June 12, 2024 00:34
@JacksonBurns JacksonBurns linked an issue Jun 12, 2024 that may be closed by this pull request
CH2* replaced by CH2 for a reaction in JetSurf2.0 mechanism #649
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@JacksonBurns JacksonBurns force-pushed the corrected_triplet_and_singlet_methylene_reactions branch from b96a10f to ff289cc Compare October 16, 2024 23:31
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Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing.
⚠️ 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): 00:00:01:06
Current: Execution time (DD:HH:MM:SS): 00:00:01:06
Reference: Memory used: 2759.61 MB
Current: Memory used: 2768.84 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: C=CC1C=CC2=CC1C=C2
tested: C=CC1C=CC2=CC1C=C2

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
83.22 84.16 35.48 45.14 53.78 61.40 73.58 82.20 95.08
83.22 82.78 35.48 45.14 53.78 61.40 73.58 82.20 95.08

Identical thermo comments:
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentadiene)

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): 00:00:02:13
Current: Execution time (DD:HH:MM:SS): 00:00:02:10
Reference: Memory used: 2890.75 MB
Current: Memory used: 2892.79 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](29) <=> [OH](22) + CC=O(69) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](127) 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](30) <=> C[CH]OO(70) origin: intra_H_migration
rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(36) + CC[CH]CCOO(108) origin: H_Abstraction
rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(36) + CCC[CH]COO(107) origin: H_Abstraction
rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(36) + C[CH]CCCOO(109) origin: H_Abstraction
rxn: [CH2]CCOO(77) + CCCCCOO(105) <=> CCCOO(36) + CCCC[CH]OO(134) origin: H_Abstraction
rxn: CCCOO(36) + [CH2]CCCCOO(110) <=> [CH2]CCOO(77) + CCCCCOO(105) origin: H_Abstraction
rxn: C[CH]CCCO(157) + CCCCCO[O](104) <=> CC=CCCO(183) + CCCCCOO(105) origin: Disproportionation
rxn: C[CH]CCCO(157) + CCCCCO[O](104) <=> 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](29) <=> [OH](22) + CC=O(69) origin: intra_H_migration
rxn: CCCCCO[O](104) + CCCCCO[O](104) <=> oxygen(1) + CCCCC=O(106) + CCCCCO(130) origin: Peroxyl_Termination

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](127) 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

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): 00:00:01:27
Current: Execution time (DD:HH:MM:SS): 00:00:01:26
Reference: Memory used: 2887.73 MB
Current: Memory used: 2884.48 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 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 983 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): 00:00:02:27
Current: Execution time (DD:HH:MM:SS): 00:00:02:30
Reference: Memory used: 2767.09 MB
Current: Memory used: 2743.50 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): 00:00:00:56
Current: Execution time (DD:HH:MM:SS): 00:00:00:55
Reference: Memory used: 2856.03 MB
Current: Memory used: 2851.97 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): 00:00:00:36
Current: Execution time (DD:HH:MM:SS): 00:00:00:35
Reference: Memory used: 2949.33 MB
Current: Memory used: 2974.04 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): 00:00:02:24
Reference: Memory used: 3429.77 MB
Current: Memory used: 3423.97 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): 00:00:05:57
Current: Execution time (DD:HH:MM:SS): 00:00:06:02
Reference: Memory used: 3368.46 MB
Current: Memory used: 3357.32 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](35) <=> [OH](22) + CC=O(62) 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 2 reactions that the tested model does not have. ❌
rxn: CCCO[O](35) <=> CC[CH]OO(45) origin: intra_H_migration
rxn: CCO[O](36) <=> C[CH]OO(62) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CCO[O](35) <=> [OH](22) + CC=O(62) origin: intra_H_migration
rxn: CCCO[O](34) <=> [OH](22) + CCC=O(44) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCO[O](35) + 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](98) + CCCC(C)[O](65) 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 ✅

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CH2* replaced by CH2 for a reaction in JetSurf2.0 mechanism
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@PoojaNem @JacksonBurns