Update bidentate #646

bjkreitz · 2024-03-27T01:27:49Z

Updates
I updated the BEP rate rules and training reactions for the following bidentate reaction families Surface_Dissociation, Surface_Bidentate_Dissociation, Surface_Dissociation_to_Bidentate, Surface_vdW_to_Bidentate based on new data that we published in our latest paper DOI: 10.1039/d3dd00184a. The original data compiled by Katrin was in the modified Arrhenius format, but a regular Arrhenius format has a sufficient accuracy and makes the manual evaluation of the microkinetics easier. Accordingly, I changed the training reaction format.
I also added comments to the training reactions and rate rules to point to the publication.

Review
Generate a mechanism and check if these family works as expected. These updates shouldn't have a major impact on the microkinetic models.

github-actions · 2024-03-27T03:13:37Z

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): 00:00:01:06
Current: Execution time (DD:HH:MM:SS): 00:00:01:05
Reference: Memory used: 2784.02 MB
Current: Memory used: 2778.73 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): 00:00:02:17
Current: Execution time (DD:HH:MM:SS): 00:00:02:08
Reference: Memory used: 2906.26 MB
Current: Memory used: 2913.37 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](30) <=> [OH](22) + CC=O(69) origin: intra_H_migration

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1618 reactions.
Test model has 1613 reactions. ❌
The original model has 6 reactions that the tested model does not have. ❌
rxn: CCO[O](30) <=> [OH](22) + CC=O(69) origin: intra_H_migration
rxn: [CH2]CCOO(80) + CCCCCOO(105) <=> CCCOO(36) + CC[CH]CCOO(108) origin: H_Abstraction
rxn: [CH2]CCOO(80) + CCCCCOO(105) <=> CCCOO(36) + CCC[CH]COO(107) origin: H_Abstraction
rxn: [CH2]CCOO(80) + CCCCCOO(105) <=> CCCOO(36) + C[CH]CCCOO(109) origin: H_Abstraction
rxn: [CH2]CCOO(80) + CCCCCOO(105) <=> CCCOO(36) + CCCC[CH]OO(138) origin: H_Abstraction
rxn: CCCOO(36) + [CH2]CCCCOO(110) <=> [CH2]CCOO(80) + CCCCCOO(105) origin: H_Abstraction
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](30) <=> C[CH]OO(70) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCCCO[O](104) + CC(CC(C)OO)O[O](103) <=> 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): 00:00:01:23
Current: Execution time (DD:HH:MM:SS): 00:00:01:22
Reference: Memory used: 2902.57 MB
Current: Memory used: 2900.38 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. ❌

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)
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

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): 00:00:02:22
Current: Execution time (DD:HH:MM:SS): 00:00:02:22
Reference: Memory used: 2758.12 MB
Current: Memory used: 2767.81 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): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:53
Reference: Memory used: 2877.62 MB
Current: Memory used: 2875.93 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: 2947.58 MB
Current: Memory used: 2979.51 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): 00:00:02:24
Current: Execution time (DD:HH:MM:SS): 00:00:02:25
Reference: Memory used: 3435.49 MB
Current: Memory used: 3447.67 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): 00:00:06:14
Current: Execution time (DD:HH:MM:SS): 00:00:06:05
Reference: Memory used: 3372.04 MB
Current: Memory used: 3390.90 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 233 reactions.
Test model has 232 reactions. ❌
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCO[O](35) <=> [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](35) <=> [OH](21) + CC=O(61) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](36) <=> C[CH]OO(62) 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 ✅

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github-actions · 2024-04-09T16:41:33Z

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): 00:00:01:06
Current: Execution time (DD:HH:MM:SS): 00:00:01:06
Reference: Memory used: 2760.75 MB
Current: Memory used: 2774.97 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	82.78	35.48	45.14	53.78	61.40	73.58	82.20	95.08
83.22	84.16	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): 00:00:02:10
Current: Execution time (DD:HH:MM:SS): 00:00:02:09
Reference: Memory used: 2892.80 MB
Current: Memory used: 2906.71 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 216 reactions.
Test model has 216 reactions. ✅

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](128) 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 1613 reactions.
Test model has 1610 reactions. ❌
The original model has 4 reactions that the tested model does not have. ❌
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 1 reactions that the original model does not have. ❌
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](128) 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

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: 2893.32 MB
Current: Memory used: 2907.62 MB

nitrogen Failed Core Comparison ❌

Original model has 41 species.
Test model has 41 species. ✅
Original model has 360 reactions.
Test model has 359 reactions. ❌
The original model has 1 reactions that the tested 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 997 reactions.
Test model has 995 reactions. ❌
The original model has 2 reactions that the tested 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): 00:00:02:24
Current: Execution time (DD:HH:MM:SS): 00:00:02:20
Reference: Memory used: 2753.90 MB
Current: Memory used: 2762.03 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): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:56
Reference: Memory used: 2864.21 MB
Current: Memory used: 2873.63 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: 2961.26 MB
Current: Memory used: 2961.49 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): 00:00:02:28
Reference: Memory used: 3446.99 MB
Current: Memory used: 3449.18 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): 00:00:06:13
Current: Execution time (DD:HH:MM:SS): 00:00:06:11
Reference: Memory used: 3363.59 MB
Current: Memory used: 3377.26 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](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 1 reactions that the tested model does not have. ❌
rxn: CCO[O](35) <=> C[CH]OO(63) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](34) <=> [OH](22) + CC=O(62) 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 🤖

kirkbadger18 · 2024-04-09T22:01:27Z

input/kinetics/families/Surface_Bidentate_Dissociation/rules.py

@@ -12,14 +12,18 @@
        A = (1.187E12, '1/s'),


cm^2/(mol*s)

The unit 1/s is correct

kirkbadger18

I looked through the new values and they all seem to match up with what is in the paper. The only changes I am requesting are unit conversions/giving the same unit name to all reactions/rules.

Additionally I ran a mechanism with both the main branch and this branch for the dehydrogenation reaction that was outlined in the paper. I used 5% CH3CH3, and 95% N2, and ran until a conversion of 0.1 was reached. Both core models were very similar, only differing by one species, and their thermo values stayed the same as expected. When looking at the reactions, both models had at least one reaction from each of these 6 reaction families. The new model generated 22 reactions that were within these 6 families, and the old model generated 24 reactions within these families. The reactions found were identical except for the old model having 2 extra. As expected the heats of reaction did not change. Also the rates of reaction changed by very little; when looking at log10, the differences were under 0.5.

input/kinetics/families/Surface_Bidentate_Dissociation/training/reactions.py

kirkbadger18 · 2024-04-09T22:04:58Z

input/kinetics/families/Surface_Dissociation/rules.py

@@ -30,10 +30,10 @@
    index = 2,
    label = "C-H_Bidentate;VacantSite",
    kinetics = SurfaceArrheniusBEP(
-        A = (7.250e16, 'm^2/(mol*s)'), 
+        A = (1.36e18, 'm^2/(mol*s)'),


Convert units to be consistent --> cm^2/(mol*s)

After looking through the reaction families again, I saw that everything is actually in m instead of cm. I changed the units of the family Surface_Dissociation_to_Bidentate to be consistent with the rest.

input/kinetics/families/Surface_Dissociation/training/reactions.py

input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py

input/kinetics/families/Surface_Dissociation_to_Bidentate/training/reactions.py

rwest

Not a very in-depth review - I looked through the diff (looks ok - helpful longDesc strings, numbers and units look reasonable) and the PR description and the discussion with Kirk (thanks for the review Kirk!). All looks ok to me.

Is it good to go?

bjkreitz · 2024-04-11T13:38:36Z

Yes, this should be good to go. I changed the units from the family Surface_Dissociation_to_Bidentate from cm^4 to m^4 to be consistent with the rest of the families. I re-requested the review from Kirk. @ChrisBNEU can you take a quick look, too?

github-actions · 2024-04-11T15:20:52Z

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: 2765.77 MB
Current: Memory used: 2769.51 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	82.78	35.48	45.14	53.78	61.40	73.58	82.20	95.08
83.22	84.16	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)

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): 00:00:02:07
Current: Execution time (DD:HH:MM:SS): 00:00:02:08
Reference: Memory used: 2905.84 MB
Current: Memory used: 2911.19 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(69) 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(69) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](31) <=> 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): 00:00:01:21
Current: Execution time (DD:HH:MM:SS): 00:00:01:21
Reference: Memory used: 2902.66 MB
Current: Memory used: 2899.67 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): 00:00:02:22
Reference: Memory used: 2766.61 MB
Current: Memory used: 2769.13 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: 2873.88 MB
Current: Memory used: 2878.32 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: 2987.69 MB
Current: Memory used: 2955.40 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): 00:00:02:24
Current: Execution time (DD:HH:MM:SS): 00:00:02:25
Reference: Memory used: 3462.42 MB
Current: Memory used: 3425.24 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): 00:00:06:09
Current: Execution time (DD:HH:MM:SS): 00:00:06:07
Reference: Memory used: 3374.21 MB
Current: Memory used: 3372.86 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](21) + 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 1 reactions that the tested model does not have. ❌
rxn: CCO[O](34) <=> C[CH]OO(63) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](35) <=> [OH](21) + CC=O(62) 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 ✅

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ChrisBNEU

This looks good. I ran the attached example, using the compare tool it looks like the changes aren't huge. Where they are different, the bidentate-forming reactions are generally a little slower (which is a good thing, I think the general feeling was they were too fast before).
2024_04_11_pr646_rate_recalc.zip

bjkreitz added Complexity: Low Topic: Catalysis labels Mar 27, 2024

bjkreitz requested review from rwest, 12Chao, ChrisBNEU and kirkbadger18 March 27, 2024 01:27

bjkreitz self-assigned this Mar 27, 2024

bjkreitz added 2 commits April 8, 2024 10:18

update bidentate dissociation

2e16eca

update remaining families

ec3ce5d

bjkreitz force-pushed the update_bidentate branch from dd3500a to ec3ce5d Compare April 8, 2024 14:18

kirkbadger18 reviewed Apr 9, 2024

View reviewed changes

rwest approved these changes Apr 11, 2024

View reviewed changes

dissociation to bidentate units

2db340e

bjkreitz requested a review from kirkbadger18 April 11, 2024 13:38

kirkbadger18 approved these changes Apr 11, 2024

View reviewed changes

ChrisBNEU approved these changes Apr 12, 2024

View reviewed changes

rwest merged commit 8825a0c into main Apr 12, 2024
3 checks passed

rwest deleted the update_bidentate branch April 12, 2024 19:17

Update bidentate #646

Update bidentate #646

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bjkreitz commented Mar 27, 2024

github-actions bot commented Mar 27, 2024

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

github-actions bot commented Apr 9, 2024

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

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bjkreitz commented Apr 11, 2024

github-actions bot commented Apr 11, 2024

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

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