Added PDep rates on the N2H3 PES to the PNL #661

alongd · 2024-08-01T19:59:17Z

Added PDep rate coefficients on the N2H3 PES taken from Keslin et al. 2024 to the primaryNitrogenLibrary

updated indices and some formatting

github-actions · 2024-08-02T07:22:36Z

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): 00:00:01:10
Current: Execution time (DD:HH:MM:SS): 00:00:01:05
Reference: Memory used: 2781.04 MB
Current: Memory used: 2774.64 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): 00:00:02:13
Current: Execution time (DD:HH:MM:SS): 00:00:02:08
Reference: Memory used: 2925.99 MB
Current: Memory used: 2908.34 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](64) + CCCCC[O](128) 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):	3.77	4.45	4.86	5.14	5.48	5.68	5.96	6.09
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=(3.756,'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

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1610 reactions.
Test model has 1618 reactions. ❌
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCCCCO[O](103) + CCCCCO[O](103) <=> oxygen(1) + CCCCC=O(120) + CCCCCO(130) origin: Peroxyl_Termination
The tested model has 9 reactions that the original model does not have. ❌
rxn: [CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(34) + CC[CH]CCOO(108) origin: H_Abstraction
rxn: [CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(34) + CCC[CH]COO(107) origin: H_Abstraction
rxn: [CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(34) + C[CH]CCCOO(109) origin: H_Abstraction
rxn: [CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(34) + CCCC[CH]OO(137) origin: H_Abstraction
rxn: CCCOO(34) + [CH2]CCCCOO(110) <=> [CH2]CCOO(70) + 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

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128) 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):	3.77	4.45	4.86	5.14	5.48	5.68	5.96	6.09
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=(3.756,'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

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](104) + CC(CC(C)OO)O[O](103) <=> 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): 00:00:01:28
Current: Execution time (DD:HH:MM:SS): 00:00:01:24
Reference: Memory used: 2916.92 MB
Current: Memory used: 2913.63 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 133 species.
Test model has 133 species. ✅
Original model has 983 reactions.
Test model has 983 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): 00:00:02:31
Current: Execution time (DD:HH:MM:SS): 00:00:02:28
Reference: Memory used: 2779.41 MB
Current: Memory used: 2771.96 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): 00:00:00:58
Current: Execution time (DD:HH:MM:SS): 00:00:00:54
Reference: Memory used: 2884.28 MB
Current: Memory used: 2883.62 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

The following observables did not match:

❌ Observable species O=S=O varied by more than 0.100 on average between old model SO2(15) and new model SO2(15) in condition 1.

⚠️ The following reaction conditions had some discrepancies:
Condition 1:
Reactor Type: IdealGasReactor
Reaction Time: 0.01 s
T0: 900 K
P0: 30 bar
Initial Mole Fractions: {'S': 0.000756, '[O][O]': 0.00129, 'N#N': 0.997954}

sulfur Failed Observable Testing ❌

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:39
Current: Execution time (DD:HH:MM:SS): 00:00:00:35
Reference: Memory used: 2980.11 MB
Current: Memory used: 2997.18 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): 00:00:02:31
Current: Execution time (DD:HH:MM:SS): 00:00:02:21
Reference: Memory used: 3446.95 MB
Current: Memory used: 3453.89 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): 00:00:06:06
Current: Execution time (DD:HH:MM:SS): 00:00:05:49
Reference: Memory used: 3380.28 MB
Current: Memory used: 3388.82 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](36) <=> [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 2 reactions that the tested model does not have. ❌
rxn: CCO[O](36) <=> [OH](21) + CC=O(62) origin: intra_H_migration
rxn: CCCO[O](35) <=> [OH](21) + CCC=O(44) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CCCO[O](34) <=> CC[CH]OO(45) origin: intra_H_migration
rxn: CCO[O](36) <=> C[CH]OO(62) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCO[O](35) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](95) + CCCC(C)[O](65) origin: Peroxyl_Disproportionation
tested:
rxn: CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](96) + CCCC(C)[O](61) 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):	3.69	4.39	4.82	5.10	5.45	5.66	5.94	6.08

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=(3.866,'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: 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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MichalKesl

Looks good to me

12Chao

Looks good to me.

alongd requested review from 12Chao and MichalKesl August 1, 2024 19:59

alongd force-pushed the n2h3 branch from 4d0786c to 1daea60 Compare August 1, 2024 20:35

alongd added 2 commits August 2, 2024 08:37

Added PDep rates on the N2H3 PES to the PNL

4163d3e

Minor: Style modification to PNL

d6311e2

updated indices and some formatting

alongd force-pushed the n2h3 branch from 1daea60 to d6311e2 Compare August 2, 2024 05:39

MichalKesl approved these changes Aug 4, 2024

View reviewed changes

12Chao approved these changes Aug 4, 2024

View reviewed changes

alongd merged commit 24451a0 into main Aug 4, 2024
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alongd deleted the n2h3 branch August 4, 2024 18:54

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Added PDep rates on the N2H3 PES to the PNL #661

Added PDep rates on the N2H3 PES to the PNL #661

alongd commented Aug 1, 2024

github-actions bot commented Aug 2, 2024

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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Added PDep rates on the N2H3 PES to the PNL #661

Added PDep rates on the N2H3 PES to the PNL #661

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alongd commented Aug 1, 2024

github-actions bot commented Aug 2, 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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