Uncertainty Part 4: Load correlations for surfaceThermoPt111 library and adsorption tree by sevyharris · Pull Request #2934 · ReactionMechanismGenerator/RMG-Py

sevyharris · 2026-04-24T02:18:01Z

Dependencies:

Uncertainty Part 1: Basic surface extension #2924
Uncertainty Part 1.5: Adding in quadrature #2933
Uncertainty Part 3: Export Covariance Matrices #2932
add BEEF uncertainty covariance RMG-database#715 <--- we should merge this first

Not dependent but will need to rerun the covariance calculation script after these get merged:

Updates and additions to Pt(111) adsorption correction tree RMG-database#717
Update Pt(111) surface thermo library with NOx chemistry and consistent DFT references RMG-database#716

Motivation or Problem

The uncertainty tool currently assumes all entries within a library are uncorrelated with other entries in that same library, but in some cases, such as BEEF-vdW DFT, we have correlation information.

This PR allows the uncertainty tool to load the library's covariance matrix and use those values in its analysis. It now supports:

library-library correlations for surfaceThermoPt111
group-group correlations for the adsorptionPt111 adsorption correction tree
group-library correlations for the adsorption correction tree and surfaceThermoPt111 library

Description of Changes

This adds the other_covariances dictionary to the ThermoParameterUncertainty class. The idea is that you populate this dictionary with all relevant covariances and then look them up later.
This adds the load_thermo_covariances_from_libraries function, which loads a covariance matrix and species dictionary in matching order for a given library, then picks out all the covariances relevant to the mechanism and adds them to the thermo_covariances_dict (which gets copied to other_covariances)
This also adds the load_thermo_covariances_from_groups function, which loads a covariance matrix and species dictionary in matching order for a given library, then picks out all the covariances relevant to the mechanism and adds them to the thermo_covariances_dict (which gets copied to other_covariances)

Testing

Here's a demo notebook showing how BEEF info adds a lot more off-diagonal elements to the covariance matrix.
I spot checked some specific covariance values to make sure they match what's calculated in the corresponding RMG-database notebook
I ran a whole local uncertainty analysis with the BEEF correlations turned on, and it's able to compute the overall variance in a reasonable timeframe. The covariance lookups aren't too expensive (the sensitivity is still the bottleneck by far).

Reviewer Tips

You'll need database ReactionMechanismGenerator/RMG-database#715 checked out to be able to load the stored covariance matrices and run the examples.

The implementation is kind of ugly and I'd recommend starting with the demo notebook to see this in action.

github-actions · 2026-04-24T04:38:00Z

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): 00:00:00:54
Current: Execution time (DD:HH:MM:SS): 00:00:00:53
Reference: Memory used: 810.75 MB
Current: Memory used: 810.01 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: [CH]1C2C=CC13C=CC23
tested: [CH]1C2C=CC13C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
172.50	80.61	27.59	35.91	43.44	49.89	59.09	64.21	71.65
174.31	74.05	26.66	34.03	40.90	47.10	57.16	64.03	72.57

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-49.69	-33.15	-23.24	-16.65	-8.43	-3.52	2.99	6.21
k(T):	-50.88	-34.04	-23.95	-17.24	-8.88	-3.88	2.75	6.03

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(91.423,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(93.051,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2C=CC3=CC2C13(80) origin: Intra_R_Add_Endocyclic
tested:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2C=CC3=CC2C13(80) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-59.93	-40.64	-29.08	-21.38	-11.79	-6.05	1.56	5.34
k(T):	-56.49	-38.05	-27.01	-19.66	-10.50	-5.02	2.25	5.85

kinetics: Arrhenius(A=(6.50724e+19,'s^-1'), n=-0.859, Ea=(106.547,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 6.0""")
kinetics: Arrhenius(A=(6.50724e+19,'s^-1'), n=-0.859, Ea=(101.822,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 6.0""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.
Multiplied by reaction path degeneracy 6.0

Details

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): 00:00:01:54
Current: Execution time (DD:HH:MM:SS): 00:00:01:54
Reference: Memory used: 892.42 MB
Current: Memory used: 893.11 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 239 reactions.
Test model has 239 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1591 reactions.
Test model has 1591 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(31) <=> CCC[C](C)OO(78) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(33) <=> [OH](22) + CCCC(C)=O(30) origin: intra_H_migration

Details

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): 00:00:01:00
Current: Execution time (DD:HH:MM:SS): 00:00:01:00
Reference: Memory used: 891.60 MB
Current: Memory used: 896.78 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species.
Test model has 41 species. ✅
Original model has 359 reactions.
Test model has 359 reactions. ✅

nitrogen Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 981 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 in family Intra_R_Add_Endocyclic.""")
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 in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.

Details

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): 00:00:01:40
Current: Execution time (DD:HH:MM:SS): 00:00:01:40
Reference: Memory used: 772.76 MB
Current: Memory used: 772.58 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 1524 reactions.
Test model has 1524 reactions. ✅

Details

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 ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:40
Current: Execution time (DD:HH:MM:SS): 00:00:00:40
Reference: Memory used: 893.42 MB
Current: Memory used: 894.37 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

Details

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): 00:00:00:24
Current: Execution time (DD:HH:MM:SS): 00:00:00:25
Reference: Memory used: 947.45 MB
Current: Memory used: 952.28 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): 00:00:02:54
Current: Execution time (DD:HH:MM:SS): 00:00:02:08
Reference: Memory used: 2432.32 MB
Current: Memory used: 2406.95 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. ✅

Details

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): 00:00:14:26
Current: Execution time (DD:HH:MM:SS): 00:00:24:16
Reference: Memory used: 2620.17 MB
Current: Memory used: 3387.95 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 128 reactions.
Test model has 134 reactions. ❌
The original model has 7 species that the tested model does not have. ❌
spc: CCH2
spc: C=CC(18)
spc: CC[CH]C(C)OO(32)
spc: [CH2]C(CCC)OO(33)
spc: C[CH]C(CC)OO(37)
spc: CC[CH]CCOO(64)
spc: [CH2]CCCCOO(66)
The tested model has 7 species that the original model does not have. ❌
spc: CCCCCO
spc: CC=O(87)
spc: CCCC=O(88)
spc: [CH2]CCC(C)O(93)
spc: CC1CC(C)O1(96)
spc: CC=CC(C)OO(97)
spc: CC(CC(C)OO)OO
The original model has 35 reactions that the tested model does not have. ❌
rxn: C[CH]C(CC)OO(37) <=> CCC(CC)O[O](21) origin: intra_H_migration
rxn: [O]O(13) + C[CH]C(CC)OO(37) <=> oxygen(1) + CCC(CC)OO(25) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + pentane(2) <=> C[CH]CCC(11) + CCC(CC)OO(25) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + pentane(2) <=> CC[CH]CC(7) + CCC(CC)OO(25) origin: H_Abstraction
rxn: OO(23) + C[CH]C(CC)OO(37) <=> [O]O(13) + CCC(CC)OO(25) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCC(CC)OO(25) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCC(CC)OO(25) <=> CCC(CC)O[O](21) + CCC(CC)OO(25) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC(CC)OO(25) <=> C[CH]C(CC)OO(37) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]C(CC)OO(37) <=> C=CCCC(17) + CCC(CC)OO(25) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]C(CC)OO(37) <=> C=CCCC(17) + CCC(CC)OO(25) origin: Disproportionation
rxn: CC[CH]C(C)OO(32) <=> CCCC(C)O[O](20) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]C(C)OO(32) <=> oxygen(1) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(24) origin: H_Abstraction
rxn: OO(23) + CC[CH]C(C)OO(32) <=> [O]O(13) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCC(CC)OO(25) <=> CCC(CC)O[O](21) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)OO(24) <=> CC[CH]C(C)OO(32) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]C(C)OO(32) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]C(C)OO(32) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
rxn: CCCCCO[O](61) <=> [CH2]CCCCOO(66) origin: intra_H_migration
rxn: CC[CH]CCOO(64) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2) origin: R_Recombination
rxn: C[CH]CCC(11) <=> C[CH2](6) + C=CC(18) origin: R_Addition_MultipleBond
rxn: CCCC(C)O[O](20) <=> [CH2]C(CCC)OO(33) origin: intra_H_migration
rxn: [O]O(13) + [CH2]C(CCC)OO(33) <=> oxygen(1) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(24) origin: H_Abstraction
rxn: OO(23) + [CH2]C(CCC)OO(33) <=> [O]O(13) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCC(CC)OO(25) <=> CCC(CC)O[O](21) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [O]O(13) + C=CCCC(17) <=> [CH2]C(CCC)OO(33) origin: R_Addition_MultipleBond
rxn: [CH2]CCCC(12) + [CH2]C(CCC)OO(33) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]C(CCC)OO(33) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
The tested model has 41 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](26) + [OH](26) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: CC=O(87) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCC(CC)OO(24) <=> O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](26) + O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [OH](26) + O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [O]O(13) + O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](26) + O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(93) origin: intra_H_migration
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(97) origin: Disproportionation
rxn: [CH3](10) + CCCC=O(88) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [OH](26) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + C[CH]CCCOO(75) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(75) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + C[CH]CCCOO(75) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: C[CH]CC(C)OO(37) <=> [OH](26) + CC1CC(C)O1(96) origin: Cyclic_Ether_Formation

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 77 species.
Test model has 100 species. ❌
Original model has 254 reactions.
Test model has 385 reactions. ❌
The tested model has 23 species that the original model does not have. ❌
spc: CCCCCOOOO
spc: CCCCCO
spc: [CH2]COO(80)
spc: [CH2]CCOO(81)
spc: [CH2]OO(82)
spc: [CH2]CCCOO(83)
spc: CCCC[CH]OO(84)
spc: CCCCO
spc: CCC(C)O
spc: CC=O(87)
spc: CCCC=O(88)
spc: CCCCO(89)
spc: CC[CH]C(C)O(90)
spc: [CH2]C(O)CCC(91)
spc: C[CH]CC(C)O(92)
spc: [CH2]CCC(C)O(93)
spc: C[CH]CCOO(94)
spc: [CH2]C(C)C(C)OO(95)
spc: CC1CC(C)O1(96)
spc: CC=CC(C)OO(97)
spc: C=CCC(C)OO(98)
spc: CC([O])CC(C)O(99)
spc: CC(CC(C)OO)OO
The tested model has 131 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](26) + [OH](26) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: CC=O(87) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCC(CC)OO(24) <=> O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](26) + O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [OH](26) + O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [O]O(13) + O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](26) + O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(93) origin: intra_H_migration
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(97) origin: Disproportionation
rxn: [CH3](10) + CCCC=O(88) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [OH](26) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + C[CH]CCCOO(75) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(75) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + C[CH]CCCOO(75) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: C[CH]CC(C)OO(37) <=> [OH](26) + CC1CC(C)O1(96) origin: Cyclic_Ether_Formation
rxn: oxygen(1) + CCCCCO[O](61) <=> CCCCCOOO[O](77) origin: R_Recombination
rxn: CC[C](CC)OO(52) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CCC[C](C)OO(58) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2](3) + CCCCOO(55) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCCCOO(55) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCCCO[O](61) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]COO(80) + [CH2]CC(5) <=> CCCCCOO(78) origin: R_Recombination
rxn: C[CH2](6) + [CH2]CCOO(81) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CC[CH]CCOO(74) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]OO(82) + [CH2]CCC(9) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CCC[CH]COO(73) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH3](10) + [CH2]CCCOO(83) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + C[CH]CCCOO(75) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CCCC[CH]OO(84) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + [CH2]CCCCOO(76) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + [O]O(13) <=> OO(23) origin: R_Recombination
rxn: [CH2](3) + CCCC[O](85) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCC(C)[O](86) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCC(C)[O](86) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCC(C)=O(34) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](44) <=> CCC[C](C)O(89) origin: intra_H_migration
rxn: CC[CH]C(C)O(90) <=> CCCC(C)[O](44) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> [CH2]C(O)CCC(91) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> C[CH]CC(C)O(92) origin: intra_H_migration
rxn: [CH2](3) + C[CH]CCOO(94) <=> C[CH]CC(C)OO(37) origin: 1,2_Insertion_carbene
rxn: [CH2]C(C)C(C)OO(95) <=> C[CH]CC(C)OO(37) origin: 1,2_shiftC
rxn: [H](8) + CC=CC(C)OO(97) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: [H](8) + C=CCC(C)OO(98) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: C[CH]OO(56) + C=CC(19) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: CC[CH]C(C)OO(35) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: [CH2]CCC(C)OO(38) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CCC[C](C)OO(58) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> [CH2]C(CCC)OO(36) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CC([O])CC(C)O(99) origin: intra_OH_migration
rxn: [O]O(13) + CC[CH]CCOO(74) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCC[CH]COO(73) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC[CH]OO(84) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCCOO(76) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: oxygen(1) + CCCC(C)[O](44) <=> [O]O(13) + CCCC(C)=O(34) origin: Disproportionation
rxn: oxygen(1) + CCCC(C)[O](44) <=> CCCC(C)OO[O](49) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + C=CCC(C)OO(98) origin: Disproportionation
rxn: CCCC(C)[O](44) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)O(47) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(74) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCC[CH]COO(73) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCOO(78) <=> OO(23) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(76) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> O(42) + CC[C](CC)OO(52) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> O(42) + C[CH]C(CC)OO(31) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> CC[C](CC)OO(52) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> C[CH]C(CC)OO(31) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> [CH2]CC(CC)OO(32) + CCCC(C)O(47) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + CCC[C](C)OO(58) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + CC[CH]C(C)OO(35) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + [CH2]C(CCC)OO(36) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> O(42) + [CH2]CCC(C)OO(38) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(25) <=> CCC[C](C)OO(58) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(25) <=> CC[CH]C(C)OO(35) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(25) <=> [CH2]C(CCC)OO(36) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(25) <=> [CH2]CCC(C)OO(38) + CCCC(C)O(47) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CC[CH]CCOO(74) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCC[CH]COO(73) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + [CH2]CCCCOO(76) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(74) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCC[CH]COO(73) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(76) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(74) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC[CH]COO(73) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(76) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CC[CH]CCOO(74) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCC[CH]COO(73) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> C[CH]CCCOO(75) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCCC[CH]OO(84) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> [CH2]CCCCOO(76) + CCCC(C)O(47) origin: H_Abstraction

Details

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 ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:33
Current: Execution time (DD:HH:MM:SS): 00:00:00:33
Reference: Memory used: 737.27 MB
Current: Memory used: 737.98 MB

fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

Observables Test Case: fragment Comparison

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

fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:03:21
Current: Execution time (DD:HH:MM:SS): 00:00:02:34
Reference: Memory used: 2453.85 MB
Current: Memory used: 2558.14 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

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

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:32
Current: Execution time (DD:HH:MM:SS): 00:00:00:30
Reference: Memory used: 894.53 MB
Current: Memory used: 893.26 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Details

Observables Test Case: minimal_surface Comparison

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

minimal_surface Passed Observable Testing ✅

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github-actions · 2026-04-29T01:39:28Z

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): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:56
Reference: Memory used: 809.35 MB
Current: Memory used: 809.57 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: [CH]1C2C=CC13C=CC23
tested: [CH]1C2C=CC13C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
174.31	74.05	26.66	34.03	40.90	47.10	57.16	64.03	72.57
172.50	80.61	27.59	35.91	43.44	49.89	59.09	64.21	71.65

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)

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(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentadiene) + ring(1,3-Cyclohexadiene)

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-50.88	-34.04	-23.95	-17.24	-8.88	-3.88	2.75	6.03
k(T):	-49.69	-33.15	-23.24	-16.65	-8.43	-3.52	2.99	6.21

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(93.051,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(91.423,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Details

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): 00:00:02:01
Current: Execution time (DD:HH:MM:SS): 00:00:01:59
Reference: Memory used: 892.84 MB
Current: Memory used: 892.07 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 239 reactions.
Test model has 239 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1591 reactions.
Test model has 1591 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(CCC=O)OO(116) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(=O)CCCOO(112) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CC(C[CH]COO)OO(118) <=> CC(CC[CH]OO)OO(133) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> C[C](CCCOO)OO(132) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCC(CC)O[O](36) + CCCCCO[O](37) <=> oxygen(1) + CCC([O])CC(67) + CCCCC[O](69) origin: Peroxyl_Disproportionation
tested:
rxn: CCC(CC)O[O](35) + CCCCCO[O](36) <=> oxygen(1) + CCC([O])CC(69) + CCCCC[O](67) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	3.54	4.28	4.73	5.02	5.39	5.62	5.91	6.06
k(T):	8.02	7.64	7.35	7.11	6.75	6.48	5.99	5.64

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.064,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R in family Peroxyl_Disproportionation.""")
kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(-0.265,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing in family Peroxyl_Disproportionation.""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R in family Peroxyl_Disproportionation.
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing in family Peroxyl_Disproportionation.

Details

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): 00:00:01:04
Current: Execution time (DD:HH:MM:SS): 00:00:01:05
Reference: Memory used: 897.61 MB
Current: Memory used: 897.32 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species.
Test model has 41 species. ✅
Original model has 359 reactions.
Test model has 359 reactions. ✅

nitrogen Passed Edge Comparison ✅

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 981 reactions. ✅

Details

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): 00:00:01:47
Current: Execution time (DD:HH:MM:SS): 00:00:01:46
Reference: Memory used: 772.74 MB
Current: Memory used: 771.79 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 1524 reactions.
Test model has 1524 reactions. ✅

Details

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 ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:42
Current: Execution time (DD:HH:MM:SS): 00:00:00:41
Reference: Memory used: 892.52 MB
Current: Memory used: 892.49 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

Details

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): 00:00:00:26
Current: Execution time (DD:HH:MM:SS): 00:00:00:26
Reference: Memory used: 974.00 MB
Current: Memory used: 970.29 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): 00:00:02:19
Current: Execution time (DD:HH:MM:SS): 00:00:02:59
Reference: Memory used: 2292.97 MB
Current: Memory used: 2445.72 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. ✅

Details

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): 00:00:22:24
Current: Execution time (DD:HH:MM:SS): 00:00:15:05
Reference: Memory used: 2596.12 MB
Current: Memory used: 2727.58 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 138 reactions.
Test model has 124 reactions. ❌
The original model has 6 species that the tested model does not have. ❌
spc: CCCCCO
spc: CC=CC(C)OO(88)
spc: CC=O(93)
spc: CCCC=O(94)
spc: [CH2]CCC(C)O(99)
spc: CC(CC(C)OO)OO
The tested model has 6 species that the original model does not have. ❌
spc: CCH2
spc: [CH2]CCC(9)
spc: C=CC(19)
spc: C[CH]C(CC)OO(31)
spc: CC[CH]C(C)OO(35)
spc: CC[CH]CCOO(64)
The original model has 42 reactions that the tested model does not have. ❌
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](26) + [OH](26) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(17) origin: Disproportionation
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + CCCC(C)O[O](20) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [OH](26) + O(42) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [O]O(13) + O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCC(CC)OO(25) <=> O(42) + CCC(CC)O[O](21) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(25) <=> [OH](26) + O(42) + CCC(CC)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](26) + O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: [CH3](10) + CCCC=O(94) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCC(CC)OO(25) <=> O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(88) origin: Disproportionation
rxn: [OH](26) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(25) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(25) + CCCCCOO(78) <=> O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(25) <=> [O]O(13) + O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
The tested model has 28 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) <=> CCC(CC)O[O](20) origin: intra_H_migration
rxn: [O]O(13) + C[CH]C(CC)OO(31) <=> oxygen(1) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + pentane(2) <=> CC[CH]CC(7) + CCC(CC)OO(24) origin: H_Abstraction
rxn: OO(23) + C[CH]C(CC)OO(31) <=> [O]O(13) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + pentane(2) <=> C[CH]CCC(11) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC(CC)OO(24) <=> C[CH]C(CC)OO(31) + pentane(2) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]C(CC)OO(31) <=> C=CCCC(18) + CCC(CC)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]C(CC)OO(31) <=> C=CCCC(18) + CCC(CC)OO(24) origin: Disproportionation
rxn: CC[CH]C(C)OO(35) <=> CCCC(C)O[O](22) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]C(C)OO(35) <=> oxygen(1) + CCCC(C)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(27) origin: H_Abstraction
rxn: OO(23) + CC[CH]C(C)OO(35) <=> [O]O(13) + CCCC(C)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCC(C)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)OO(27) <=> CC[CH]C(C)OO(35) + pentane(2) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]C(C)OO(35) <=> C=CCCC(18) + CCCC(C)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]C(C)OO(35) <=> C=CCCC(18) + CCCC(C)OO(27) origin: Disproportionation
rxn: CC[CH]CCOO(64) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2) origin: R_Recombination
rxn: C[CH]CCC(11) <=> C[CH2](6) + C=CC(19) origin: R_Addition_MultipleBond
rxn: [CH3](10) + [CH2]CCC(9) <=> pentane(2) origin: R_Recombination

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 99 species.
Test model has 77 species. ❌
Original model has 380 reactions.
Test model has 264 reactions. ❌
The original model has 22 species that the tested model does not have. ❌
spc: CCCCCO
spc: [CH2]COO(80)
spc: [CH2]CCOO(81)
spc: [CH2]OO(82)
spc: [CH2]CCCOO(83)
spc: CCCC[CH]OO(84)
spc: C[CH]CCOO(85)
spc: [CH2]C(C)C(C)OO(86)
spc: CC1CC(C)O1(87)
spc: CC=CC(C)OO(88)
spc: C=CCC(C)OO(89)
spc: CC([O])CC(C)O(90)
spc: CCCCO
spc: CCC(C)O
spc: CC=O(93)
spc: CCCC=O(94)
spc: CCCCO(95)
spc: CC[CH]C(C)O(96)
spc: [CH2]C(O)CCC(97)
spc: C[CH]CC(C)O(98)
spc: [CH2]CCC(C)O(99)
spc: CC(CC(C)OO)OO
The original model has 120 reactions that the tested model does not have. ❌
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](26) + [OH](26) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(17) origin: Disproportionation
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + CCCC(C)O[O](20) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [OH](26) + O(42) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [O]O(13) + O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCC(CC)OO(25) <=> O(42) + CCC(CC)O[O](21) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(25) <=> [OH](26) + O(42) + CCC(CC)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](26) + O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: [CH3](10) + CCCC=O(94) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCC(CC)OO(25) <=> O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(88) origin: Disproportionation
rxn: [OH](26) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(25) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(25) + CCCCCOO(78) <=> O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(25) <=> [O]O(13) + O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2](3) + CCCCOO(50) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCCCOO(50) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCCCO[O](61) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]COO(80) + [CH2]CC(5) <=> CCCCCOO(78) origin: R_Recombination
rxn: C[CH2](6) + [CH2]CCOO(81) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CC[CH]CCOO(64) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]OO(82) + [CH2]CCC(9) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CCC[CH]COO(63) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH3](10) + [CH2]CCCOO(83) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + C[CH]CCCOO(65) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CCCC[CH]OO(84) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + [CH2]CCCCOO(66) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + [O]O(13) <=> OO(23) origin: R_Recombination
rxn: [CH2](3) + C[CH]CCOO(85) <=> C[CH]CC(C)OO(37) origin: 1,2_Insertion_carbene
rxn: [CH2]C(C)C(C)OO(86) <=> C[CH]CC(C)OO(37) origin: 1,2_shiftC
rxn: C[CH]CC(C)OO(37) <=> [OH](26) + CC1CC(C)O1(87) origin: Cyclic_Ether_Formation
rxn: [H](8) + CC=CC(C)OO(88) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: [H](8) + C=CCC(C)OO(89) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: C[CH]OO(52) + C=CC(18) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: CC[CH]C(C)OO(35) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: [CH2]CCC(C)OO(38) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CCC[C](C)OO(54) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> [CH2]C(CCC)OO(36) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CC([O])CC(C)O(90) origin: intra_OH_migration
rxn: [CH2](3) + CCCC[O](91) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCC(C)[O](92) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCC(C)[O](92) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCC(C)=O(34) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](44) <=> CCC[C](C)O(95) origin: intra_H_migration
rxn: CC[CH]C(C)O(96) <=> CCCC(C)[O](44) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> [CH2]C(O)CCC(97) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> C[CH]CC(C)O(98) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCC[CH]COO(63) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC[CH]OO(84) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + C=CCC(C)OO(89) origin: Disproportionation
rxn: oxygen(1) + CCCC(C)[O](44) <=> [O]O(13) + CCCC(C)=O(34) origin: Disproportionation
rxn: oxygen(1) + CCCC(C)[O](44) <=> CCCC(C)OO[O](49) origin: R_Recombination
rxn: CCCC(C)[O](44) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)O(47) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCC[CH]COO(63) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCOO(78) <=> OO(23) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + CCC[C](C)OO(54) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + CC[CH]C(C)OO(35) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + [CH2]C(CCC)OO(36) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> O(42) + [CH2]CCC(C)OO(38) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(24) <=> CCC[C](C)OO(54) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(24) <=> CC[CH]C(C)OO(35) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(24) <=> C[CH]CC(C)OO(37) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(24) <=> [CH2]C(CCC)OO(36) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(24) <=> [CH2]CCC(C)OO(38) + CCCC(C)O(47) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(25) <=> O(42) + CC[C](CC)OO(58) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(25) <=> O(42) + C[CH]C(CC)OO(31) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(25) <=> CCC(CC)O[O](21) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(25) <=> CC[C](CC)OO(58) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(25) <=> C[CH]C(CC)OO(31) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(25) <=> [CH2]CC(CC)OO(32) + CCCC(C)O(47) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CC[CH]CCOO(64) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCC[CH]COO(63) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> O(42) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCC[CH]COO(63) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC[CH]OO(84) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC[CH]COO(63) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC[CH]OO(84) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CC[CH]CCOO(64) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCC[CH]COO(63) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> C[CH]CCCOO(65) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCCC[CH]OO(84) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> [CH2]CCCCOO(66) + CCCC(C)O(47) origin: H_Abstraction
The tested model has 4 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CC[C](CC)OO(59) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction

Details

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 ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:34
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 737.51 MB
Current: Memory used: 737.46 MB

fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

Observables Test Case: fragment Comparison

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

fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:46
Current: Execution time (DD:HH:MM:SS): 00:00:03:32
Reference: Memory used: 2474.09 MB
Current: Memory used: 2515.16 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

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

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:33
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 891.51 MB
Current: Memory used: 893.86 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Details

Observables Test Case: minimal_surface Comparison

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

minimal_surface Passed Observable Testing ✅

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github-actions · 2026-05-10T19:21:07Z

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): 00:00:00:54
Current: Execution time (DD:HH:MM:SS): 00:00:00:55
Reference: Memory used: 810.75 MB
Current: Memory used: 810.44 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: [CH]1C2=CC3C1C=CC23
tested: [CH]1C2=CC3C1C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
167.21	73.60	28.78	36.79	44.00	50.25	59.65	65.52	74.04
169.15	73.17	31.27	38.45	44.76	50.28	59.14	65.47	72.92

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s2_5_5_diene_1_5) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentene) + radical(cyclopentene-allyl)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s3_5_5_ene_1) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentane) + radical(cyclopentene-allyl)

Non-identical thermo! ❌
original: [CH]1C2C=CC3C(=C2)C13
tested: [CH]1C2C=CC3C(=C2)C13

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
125.44	71.45	27.43	34.15	40.42	46.18	56.01	63.43	71.86
144.84	79.03	29.08	35.37	40.95	45.86	53.89	59.79	67.35

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_ene_1) + polycyclic(s3_5_6_diene_1_5) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-4)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,4-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4)

Non-identical thermo! ❌
original: [CH]1C2C=CC13C=CC23
tested: [CH]1C2C=CC13C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
172.50	80.61	27.59	35.91	43.44	49.89	59.09	64.21	71.65
174.31	74.05	26.66	34.03	40.90	47.10	57.16	64.03	72.57

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)

Non-identical thermo! ❌
original: [CH]1C2=CC3C1C3C=C2
tested: [CH]1C2=CC3C1C3C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
100.48	61.70	25.50	33.41	40.70	47.02	56.22	61.78	71.32
98.15	66.21	25.82	33.30	40.19	46.24	55.47	61.34	70.49

thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_ene_1) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(Cyclohexene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-allyl)
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl)

Non-identical thermo! ❌
original: [CH]1C2C=CC3=CC2C13
tested: [CH]1C2C=CC3=CC2C13

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
200.28	76.10	25.91	33.35	40.28	46.48	56.24	62.60	71.29
144.26	70.81	25.26	32.45	39.06	44.87	53.78	59.67	69.60

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_4_4_ene_1) + polycyclic(s3_4_6_diene_1_5) + polycyclic(s3_4_6_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclohexene) + radical(cyclobutane)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_4_4_ene_1) + Estimated bicyclic component: polycyclic(s2_4_6_ane) - ring(Cyclohexane) - ring(Cyclobutane) + ring(Cyclohexene) + ring(Cyclobutene) + polycyclic(s3_4_6_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclohexene) + radical(cyclobutane)

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C=CC23(62) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C=CC23(62) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-46.27	-30.58	-21.19	-14.94	-7.15	-2.49	3.67	6.72
k(T):	-47.51	-31.51	-21.94	-15.56	-7.62	-2.87	3.42	6.54

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(86.724,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(88.43,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC3C(=C2)C13(63) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC3C(=C2)C13(63) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-27.05	-17.33	-11.49	-7.60	-2.72	0.21	4.13	6.10
k(T):	-37.76	-25.37	-17.92	-12.96	-6.74	-3.01	1.98	4.49

kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(53.177,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(67.891,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-49.69	-33.15	-23.24	-16.65	-8.43	-3.52	2.99	6.21
k(T):	-50.88	-34.04	-23.95	-17.24	-8.88	-3.88	2.75	6.03

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(91.423,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(93.051,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-15.17	-8.42	-4.36	-1.66	1.73	3.77	6.50	7.88
k(T):	-14.18	-7.68	-3.77	-1.16	2.10	4.07	6.70	8.03

kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(36.869,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(35.513,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2C=CC3=CC2C13(80) origin: Intra_R_Add_Endocyclic
tested:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2C=CC3=CC2C13(80) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-59.93	-40.64	-29.08	-21.38	-11.79	-6.05	1.56	5.34
k(T):	-25.05	-14.47	-8.15	-3.94	1.29	4.42	8.54	10.57

kinetics: Arrhenius(A=(6.50724e+19,'s^-1'), n=-0.859, Ea=(106.547,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 6.0""")
kinetics: Arrhenius(A=(6.50724e+19,'s^-1'), n=-0.859, Ea=(58.664,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 6.0""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.
Multiplied by reaction path degeneracy 6.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic
tested:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-8.89	-3.16	0.28	2.58	5.46	7.19	9.52	10.69
k(T):	-8.00	-2.50	0.81	3.02	5.79	7.46	9.70	10.83

kinetics: Arrhenius(A=(1.49409e+13,'s^-1'), n=0.283, Ea=(31.249,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(1.49409e+13,'s^-1'), n=0.283, Ea=(30.033,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic.
Multiplied by reaction path degeneracy 3.0

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py aromatics-edge stable_regression_results/aromatics/chemkin/chem_edge_annotated.inp stable_regression_results/aromatics/chemkin/species_edge_dictionary.txt test/regression/aromatics/chemkin/chem_edge_annotated.inp test/regression/aromatics/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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): 00:00:01:53
Current: Execution time (DD:HH:MM:SS): 00:00:01:54
Reference: Memory used: 888.78 MB
Current: Memory used: 888.43 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 239 reactions.
Test model has 239 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1591 reactions.
Test model has 1591 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> CCC[C](C)OO(78) origin: intra_H_migration
rxn: CCCC[CH]OO(96) <=> C[CH]CCCOO(63) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(33) <=> [OH](22) + CCCC(C)=O(30) origin: intra_H_migration
rxn: C[CH]CCCOO(63) <=> [OH](22) + CCCCC=O(60) origin: intra_H_migration

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py liquid_oxidation-edge stable_regression_results/liquid_oxidation/chemkin/chem_edge_annotated.inp stable_regression_results/liquid_oxidation/chemkin/species_edge_dictionary.txt test/regression/liquid_oxidation/chemkin/chem_edge_annotated.inp test/regression/liquid_oxidation/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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): 00:00:00:57
Current: Execution time (DD:HH:MM:SS): 00:00:00:57
Reference: Memory used: 896.82 MB
Current: Memory used: 895.72 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

Errors occurred during core comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-core stable_regression_results/nitrogen/chemkin/chem_annotated.inp stable_regression_results/nitrogen/chemkin/species_dictionary.txt test/regression/nitrogen/chemkin/chem_annotated.inp test/regression/nitrogen/chemkin/species_dictionary.txt` failed. (See above for error)

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

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-edge stable_regression_results/nitrogen/chemkin/chem_edge_annotated.inp stable_regression_results/nitrogen/chemkin/species_edge_dictionary.txt test/regression/nitrogen/chemkin/chem_edge_annotated.inp test/regression/nitrogen/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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): 00:00:01:32
Current: Execution time (DD:HH:MM:SS): 00:00:01:32
Reference: Memory used: 773.62 MB
Current: Memory used: 773.44 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 1524 reactions.
Test model has 1524 reactions. ✅

Details

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 ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:37
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 893.35 MB
Current: Memory used: 892.99 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

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py sulfur-edge stable_regression_results/sulfur/chemkin/chem_edge_annotated.inp stable_regression_results/sulfur/chemkin/species_edge_dictionary.txt test/regression/sulfur/chemkin/chem_edge_annotated.inp test/regression/sulfur/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ❌

Errors occurred during observable testing ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python rmgpy/tools/regression.py test/regression/sulfur/regression_input.py stable_regression_results/sulfur/chemkin test/regression/sulfur/chemkin` failed. (See above for error)

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:23
Current: Execution time (DD:HH:MM:SS): 00:00:00:24
Reference: Memory used: 961.34 MB
Current: Memory used: 956.25 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): 00:00:02:03
Current: Execution time (DD:HH:MM:SS): 00:00:02:17
Reference: Memory used: 2420.87 MB
Current: Memory used: 2403.96 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. ✅

Details

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): 00:00:20:15
Current: Execution time (DD:HH:MM:SS): 00:00:12:04
Reference: Memory used: 2609.38 MB
Current: Memory used: 2484.48 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 176 reactions.
Test model has 145 reactions. ❌
The original model has 1 species that the tested model does not have. ❌
spc: CH3
The tested model has 1 species that the original model does not have. ❌
spc: CC[CH]CCOO(64)
The original model has 38 reactions that the tested model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](24) + [O]O(13) origin: H_Abstraction
rxn: [OH](24) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](24) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: [OH](24) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](24) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
The tested model has 7 reactions that the original model does not have. ❌
rxn: CC[CH]CCOO(64) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](24) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation

Errors occurred during core comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-core stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt` failed. (See above for error)

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 107 species.
Test model has 99 species. ❌
Original model has 545 reactions.
Test model has 380 reactions. ❌
The original model has 8 species that the tested model does not have. ❌
spc: CCCCCOOOO(101)
spc: CCCC(C)OOO(102)
spc: CCCCCO(103)
spc: CCC[CH]CO(104)
spc: CCCCCOOO
spc: OOO(106)
spc: CCC(CC)OOO(107)
spc: CCCCCOOO(108)
The original model has 165 reactions that the tested model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](24) + [O]O(13) origin: H_Abstraction
rxn: [OH](24) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](24) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: [OH](24) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](24) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: H(8) + [OH](24) <=> H2O(42) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + H2O(42) + CCCCC=O(72) origin: Peroxyl_Termination
rxn: [O]O(13) + CCCCCO[O](61) <=> CCCCCOOOO(101) origin: R_Recombination
rxn: [O]O(13) + CCCC(C)[O](44) <=> OO(23) + CCCC(C)=O(34) origin: Disproportionation
rxn: [O]O(13) + CCCC(C)[O](44) <=> oxygen(1) + CCCC(C)O(47) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)[O](44) <=> CCCC(C)OOO(102) origin: R_Recombination
rxn: C=CC[CH]C(64) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=CCCC(17) + C[CH]CCC(11) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> CC=CCC(16) + CCCC(C)O(47) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> C=CCCC(17) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CCCC(17) + CC[CH]CC(7) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(17) + CC[CH]CC(7) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)[O](44) <=> CC=CCC(16) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: C=CCCC(17) + CCC(CC)O[O](22) <=> [CH2]C=CCC(66) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC(=O)CC(30) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCC(O)CC(46) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCC(CC)O[O](22) <=> CCCC(C)=O(34) + CCC(CC)OO(27) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)O[O](21) <=> [CH2]C=CCC(66) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)=O(34) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCC(C)O(47) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)O[O](21) <=> CCCC(C)=O(34) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[C](CC)OO(52) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCC(CC)OO(27) <=> CC[C](CC)OO(52) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCC(C)OO(26) <=> CCC[C](C)OO(57) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C=CCCC(17) + [CH2]CCCC(12) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(17) + [CH2]CCCC(12) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CC[CH]CCOO(74) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCC[CH]COO(73) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> C=CCCC(17) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=CCCC(17) + CCCCCO[O](61) <=> [CH2]C=CCC(66) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + C=CC[CH]C(64) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH2]C=CCC(66) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH2]CCC=C(67) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + C=[C]CCC(68) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH]=CCCC(69) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> [CH2]C(O)CCC(97) origin: R_Addition_MultipleBond
rxn: [OH](24) + C=CCCC(17) <=> CCC[CH]CO(104) origin: R_Addition_MultipleBond
rxn: H2O(42) + C=CCCC(17) <=> CCCCCO(103) origin: 1,3_Insertion_ROR
rxn: H2O(42) + C=CCCC(17) <=> CCCC(C)O(47) origin: 1,3_Insertion_ROR
rxn: C=CC[CH]C(64) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(17) + C[CH]CC(C)OO(37) <=> [CH2]C=CCC(66) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> C=CC[CH]C(64) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> [CH2]C=CCC(66) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> [CH2]CCC=C(67) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)O(47) <=> C=CCCC(17) + CCCC(C)[O](44) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)O(47) <=> C=CCCC(17) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCCCOO(78) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCCCO[O](61) <=> CCCC(C)=O(34) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](24) + CCCC(C)[O](44) <=> H2O(42) + CCCC(C)=O(34) origin: Disproportionation
rxn: [OH](24) + CCCC(C)O(47) <=> H2O(42) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)O(47) <=> OO(23) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CCCC(C)=O(34) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)O[O](21) + CCC(CC)OO[O](48) <=> oxygen(1) + CCCC(C)[O](44) + CCC(CC)O[O](22) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCC(C)OO[O](49) <=> oxygen(1) + CCCC(C)[O](44) + CCCC(C)O[O](21) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCOO[O](105) <=> oxygen(1) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Peroxyl_Disproportionation
rxn: OO(23) + OOO(106) <=> [O]O(13) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCC(CC)OO(27) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OOO(107) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCC(C)OO(26) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OOO(102) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCCCOO(78) <=> [O]O(13) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOOO(108) <=> [O]O(13) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCC(C)OOO(102) <=> H2O(42) + CCC(CC)O[O](22) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCCCOOO(108) <=> H2O(42) + CCC(CC)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](21) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](21) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCCCCOOO(108) <=> H2O(42) + CCCC(C)O[O](21) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOOO(108) <=> H2O(42) + CCCCCO[O](61) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-edge stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_edge_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_edge_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_edge_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:32
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 738.01 MB
Current: Memory used: 738.07 MB

fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

Observables Test Case: fragment Comparison

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

fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:32
Current: Execution time (DD:HH:MM:SS): 00:00:02:46
Reference: Memory used: 2584.82 MB
Current: Memory used: 2606.28 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

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

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:32
Reference: Memory used: 898.96 MB
Current: Memory used: 888.66 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Details

Observables Test Case: minimal_surface Comparison

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

minimal_surface Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/canteramodel.py:550: UserWarning: ReactorSurface::syncState: Behavior changed in Cantera 3.2 for consistency with ReactorBase. To set SurfPhase state from ReactorSurface object, use restoreState(). species_data.append(np.concatenate((cantera_reactor.thermo[species_names_list].X, rsurf.kinetics.coverages)))

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github-actions · 2026-05-11T01:14:30Z

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): 00:00:00:54
Current: Execution time (DD:HH:MM:SS): 00:00:00:56
Reference: Memory used: 810.75 MB
Current: Memory used: 809.49 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: [CH]1C2=CC3C1C=CC23
tested: [CH]1C2=CC3C1C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
167.21	73.60	28.78	36.79	44.00	50.25	59.65	65.52	74.04
169.15	73.17	31.27	38.45	44.76	50.28	59.14	65.47	72.92

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s2_5_5_diene_1_5) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentene) + radical(cyclopentene-allyl)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s3_5_5_ene_1) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentane) + radical(cyclopentene-allyl)

Non-identical thermo! ❌
original: [CH]1C2C=CC3C(=C2)C13
tested: [CH]1C2C=CC3C(=C2)C13

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
125.44	71.45	27.43	34.15	40.42	46.18	56.01	63.43	71.86
144.84	79.03	29.08	35.37	40.95	45.86	53.89	59.79	67.35

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_ene_1) + polycyclic(s3_5_6_diene_1_5) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-4)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,4-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4)

Non-identical thermo! ❌
original: [CH]1C2C=CC13C=CC23
tested: [CH]1C2C=CC13C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
172.50	80.61	27.59	35.91	43.44	49.89	59.09	64.21	71.65
174.31	74.05	26.66	34.03	40.90	47.10	57.16	64.03	72.57

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5)

Non-identical thermo! ❌
original: [CH]1C2=CC3C1C3C=C2
tested: [CH]1C2=CC3C1C3C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
100.48	61.70	25.50	33.41	40.70	47.02	56.22	61.78	71.32
98.15	66.21	25.82	33.30	40.19	46.24	55.47	61.34	70.49

thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_ene_1) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(Cyclohexene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-allyl)
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl)

Non-identical thermo! ❌
original: [CH]1C2C=CC3=CC2C13
tested: [CH]1C2C=CC3=CC2C13

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
200.28	76.10	25.91	33.35	40.28	46.48	56.24	62.60	71.29
144.26	70.81	25.26	32.45	39.06	44.87	53.78	59.67	69.60

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_4_4_ene_1) + polycyclic(s3_4_6_diene_1_5) + polycyclic(s3_4_6_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclohexene) + radical(cyclobutane)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_4_4_ene_1) + polycyclic(s3_4_6_ene_1) + Estimated bicyclic component: polycyclic(s2_4_6_ane) - ring(Cyclohexane) - ring(Cyclobutane) + ring(Cyclohexene) + ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclobutene) - ring(Cyclohexene) + radical(cyclobutane)

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C=CC23(62) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C=CC23(62) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-46.27	-30.58	-21.19	-14.94	-7.15	-2.49	3.67	6.72
k(T):	-47.51	-31.51	-21.94	-15.56	-7.62	-2.87	3.42	6.54

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(86.724,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(88.43,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC3C(=C2)C13(63) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC3C(=C2)C13(63) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-27.05	-17.33	-11.49	-7.60	-2.72	0.21	4.13	6.10
k(T):	-37.76	-25.37	-17.92	-12.96	-6.74	-3.01	1.98	4.49

kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(53.177,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(67.891,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC13C=CC23(65) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-49.69	-33.15	-23.24	-16.65	-8.43	-3.52	2.99	6.21
k(T):	-50.88	-34.04	-23.95	-17.24	-8.88	-3.88	2.75	6.03

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(91.423,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(93.051,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-15.17	-8.42	-4.36	-1.66	1.73	3.77	6.50	7.88
k(T):	-14.18	-7.68	-3.77	-1.16	2.10	4.07	6.70	8.03

kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(36.869,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(35.513,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2C=CC3=CC2C13(80) origin: Intra_R_Add_Endocyclic
tested:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2C=CC3=CC2C13(80) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-59.93	-40.64	-29.08	-21.38	-11.79	-6.05	1.56	5.34
k(T):	-25.05	-14.47	-8.15	-3.94	1.29	4.42	8.54	10.57

kinetics: Arrhenius(A=(6.50724e+19,'s^-1'), n=-0.859, Ea=(106.547,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 6.0""")
kinetics: Arrhenius(A=(6.50724e+19,'s^-1'), n=-0.859, Ea=(58.664,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 6.0""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.
Multiplied by reaction path degeneracy 6.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic
tested:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-8.89	-3.16	0.28	2.58	5.46	7.19	9.52	10.69
k(T):	-8.00	-2.50	0.81	3.02	5.79	7.46	9.70	10.83

kinetics: Arrhenius(A=(1.49409e+13,'s^-1'), n=0.283, Ea=(31.249,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(1.49409e+13,'s^-1'), n=0.283, Ea=(30.033,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic.
Multiplied by reaction path degeneracy 3.0

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py aromatics-edge stable_regression_results/aromatics/chemkin/chem_edge_annotated.inp stable_regression_results/aromatics/chemkin/species_edge_dictionary.txt test/regression/aromatics/chemkin/chem_edge_annotated.inp test/regression/aromatics/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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): 00:00:01:53
Current: Execution time (DD:HH:MM:SS): 00:00:01:58
Reference: Memory used: 888.78 MB
Current: Memory used: 894.44 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 239 reactions.
Test model has 239 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1591 reactions.
Test model has 1591 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> CCC[C](C)OO(78) origin: intra_H_migration
rxn: CCCC[CH]OO(96) <=> C[CH]CCCOO(63) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(33) <=> [OH](22) + CCCC(C)=O(30) origin: intra_H_migration
rxn: C[CH]CCCOO(63) <=> [OH](22) + CCCCC=O(60) origin: intra_H_migration

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py liquid_oxidation-edge stable_regression_results/liquid_oxidation/chemkin/chem_edge_annotated.inp stable_regression_results/liquid_oxidation/chemkin/species_edge_dictionary.txt test/regression/liquid_oxidation/chemkin/chem_edge_annotated.inp test/regression/liquid_oxidation/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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): 00:00:00:57
Current: Execution time (DD:HH:MM:SS): 00:00:01:00
Reference: Memory used: 896.82 MB
Current: Memory used: 896.65 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

Errors occurred during core comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-core stable_regression_results/nitrogen/chemkin/chem_annotated.inp stable_regression_results/nitrogen/chemkin/species_dictionary.txt test/regression/nitrogen/chemkin/chem_annotated.inp test/regression/nitrogen/chemkin/species_dictionary.txt` failed. (See above for error)

nitrogen Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 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)
141.64	58.66	12.26	12.27	12.09	11.96	12.26	12.72	12.15
116.46	53.90	11.62	12.71	13.49	13.96	14.14	13.85	13.58

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + 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):	-66.25	-46.19	-34.19	-26.21	-16.28	-10.36	-2.54	1.31
k(T):	-49.54	-33.65	-24.16	-17.85	-10.01	-5.35	0.80	3.82

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 in family Intra_R_Add_Endocyclic.""")
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 in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-edge stable_regression_results/nitrogen/chemkin/chem_edge_annotated.inp stable_regression_results/nitrogen/chemkin/species_edge_dictionary.txt test/regression/nitrogen/chemkin/chem_edge_annotated.inp test/regression/nitrogen/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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): 00:00:01:32
Current: Execution time (DD:HH:MM:SS): 00:00:01:37
Reference: Memory used: 773.62 MB
Current: Memory used: 771.39 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 1524 reactions.
Test model has 1524 reactions. ✅

Details

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 ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:37
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 893.35 MB
Current: Memory used: 885.34 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

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py sulfur-edge stable_regression_results/sulfur/chemkin/chem_edge_annotated.inp stable_regression_results/sulfur/chemkin/species_edge_dictionary.txt test/regression/sulfur/chemkin/chem_edge_annotated.inp test/regression/sulfur/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ❌

Errors occurred during observable testing ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python rmgpy/tools/regression.py test/regression/sulfur/regression_input.py stable_regression_results/sulfur/chemkin test/regression/sulfur/chemkin` failed. (See above for error)

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:23
Current: Execution time (DD:HH:MM:SS): 00:00:00:26
Reference: Memory used: 961.34 MB
Current: Memory used: 955.45 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): 00:00:02:03
Current: Execution time (DD:HH:MM:SS): 00:00:02:19
Reference: Memory used: 2420.87 MB
Current: Memory used: 2304.89 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. ✅

Details

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): 00:00:20:15
Current: Execution time (DD:HH:MM:SS): 00:00:18:51
Reference: Memory used: 2609.38 MB
Current: Memory used: 2541.68 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 176 reactions.
Test model has 138 reactions. ❌
The original model has 38 reactions that the tested model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](24) + [O]O(13) origin: H_Abstraction
rxn: [OH](24) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](24) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: [OH](24) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](24) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction

Errors occurred during core comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-core stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt` failed. (See above for error)

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 107 species.
Test model has 99 species. ❌
Original model has 545 reactions.
Test model has 380 reactions. ❌
The original model has 8 species that the tested model does not have. ❌
spc: CCCCCOOOO(101)
spc: CCCC(C)OOO(102)
spc: CCCCCO(103)
spc: CCC[CH]CO(104)
spc: CCCCCOOO
spc: OOO(106)
spc: CCC(CC)OOO(107)
spc: CCCCCOOO(108)
The original model has 165 reactions that the tested model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](24) + [O]O(13) origin: H_Abstraction
rxn: [OH](24) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](24) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: [OH](24) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](24) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: H(8) + [OH](24) <=> H2O(42) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + H2O(42) + CCCCC=O(72) origin: Peroxyl_Termination
rxn: [O]O(13) + CCCCCO[O](61) <=> CCCCCOOOO(101) origin: R_Recombination
rxn: [O]O(13) + CCCC(C)[O](44) <=> OO(23) + CCCC(C)=O(34) origin: Disproportionation
rxn: [O]O(13) + CCCC(C)[O](44) <=> oxygen(1) + CCCC(C)O(47) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)[O](44) <=> CCCC(C)OOO(102) origin: R_Recombination
rxn: C=CC[CH]C(64) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=CCCC(17) + C[CH]CCC(11) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> CC=CCC(16) + CCCC(C)O(47) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> C=CCCC(17) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CCCC(17) + CC[CH]CC(7) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(17) + CC[CH]CC(7) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)[O](44) <=> CC=CCC(16) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: C=CCCC(17) + CCC(CC)O[O](22) <=> [CH2]C=CCC(66) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC(=O)CC(30) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCC(O)CC(46) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCC(CC)O[O](22) <=> CCCC(C)=O(34) + CCC(CC)OO(27) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)O[O](21) <=> [CH2]C=CCC(66) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)=O(34) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCC(C)O(47) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)O[O](21) <=> CCCC(C)=O(34) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[C](CC)OO(52) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCC(CC)OO(27) <=> CC[C](CC)OO(52) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCC(C)OO(26) <=> CCC[C](C)OO(57) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C=CCCC(17) + [CH2]CCCC(12) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(17) + [CH2]CCCC(12) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CC[CH]CCOO(74) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCC[CH]COO(73) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> C=CCCC(17) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=CCCC(17) + CCCCCO[O](61) <=> [CH2]C=CCC(66) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + C=CC[CH]C(64) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH2]C=CCC(66) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH2]CCC=C(67) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + C=[C]CCC(68) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH]=CCCC(69) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> [CH2]C(O)CCC(97) origin: R_Addition_MultipleBond
rxn: [OH](24) + C=CCCC(17) <=> CCC[CH]CO(104) origin: R_Addition_MultipleBond
rxn: H2O(42) + C=CCCC(17) <=> CCCCCO(103) origin: 1,3_Insertion_ROR
rxn: H2O(42) + C=CCCC(17) <=> CCCC(C)O(47) origin: 1,3_Insertion_ROR
rxn: C=CC[CH]C(64) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(17) + C[CH]CC(C)OO(37) <=> [CH2]C=CCC(66) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> C=CC[CH]C(64) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> [CH2]C=CCC(66) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> [CH2]CCC=C(67) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)O(47) <=> C=CCCC(17) + CCCC(C)[O](44) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)O(47) <=> C=CCCC(17) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCCCOO(78) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCCCO[O](61) <=> CCCC(C)=O(34) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](24) + CCCC(C)[O](44) <=> H2O(42) + CCCC(C)=O(34) origin: Disproportionation
rxn: [OH](24) + CCCC(C)O(47) <=> H2O(42) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)O(47) <=> OO(23) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CCCC(C)=O(34) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)O[O](21) + CCC(CC)OO[O](48) <=> oxygen(1) + CCCC(C)[O](44) + CCC(CC)O[O](22) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCC(C)OO[O](49) <=> oxygen(1) + CCCC(C)[O](44) + CCCC(C)O[O](21) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCOO[O](105) <=> oxygen(1) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Peroxyl_Disproportionation
rxn: OO(23) + OOO(106) <=> [O]O(13) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCC(CC)OO(27) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OOO(107) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCC(C)OO(26) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OOO(102) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCCCOO(78) <=> [O]O(13) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOOO(108) <=> [O]O(13) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCC(C)OOO(102) <=> H2O(42) + CCC(CC)O[O](22) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCCCOOO(108) <=> H2O(42) + CCC(CC)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](21) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](21) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCCCCOOO(108) <=> H2O(42) + CCCC(C)O[O](21) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOOO(108) <=> H2O(42) + CCCCCO[O](61) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-edge stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_edge_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_edge_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_edge_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:32
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 738.01 MB
Current: Memory used: 737.78 MB

fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

Observables Test Case: fragment Comparison

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

fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:32
Current: Execution time (DD:HH:MM:SS): 00:00:02:47
Reference: Memory used: 2584.82 MB
Current: Memory used: 2445.25 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

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

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:33
Reference: Memory used: 898.96 MB
Current: Memory used: 886.86 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Details

Observables Test Case: minimal_surface Comparison

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

minimal_surface Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/canteramodel.py:550: UserWarning: ReactorSurface::syncState: Behavior changed in Cantera 3.2 for consistency with ReactorBase. To set SurfPhase state from ReactorSurface object, use restoreState(). species_data.append(np.concatenate((cantera_reactor.thermo[species_names_list].X, rsurf.kinetics.coverages)))

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Copilot

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Adds support for loading and applying thermo covariance data (library, group tree, and cross correlations) in the uncertainty tool, enabling correlated uncertainty propagation for surface Pt111 thermo and adsorption corrections.

Changes:

Extend ThermoParameterUncertainty to accept externally provided covariances and consult them when computing variances/covariances.
Add loaders to ingest covariance matrices/species or group trees and populate thermo_covariances_dict.
Wire covariance loading into model source extraction and propagate the dict into uncertainty engines.

When loading covariance matrices, it is possible to have negative correlations. This can lead to a negative contribution to the overall variance, but this will screw up the plotting functions, so for now we set it to zero.

sevyharris · 2026-05-11T22:05:39Z

Hey @JacksonBurns, I think this and ReactionMechanismGenerator/RMG-database#715 are ready to go. I still need to put together a good/official surface uncertainty notebook, but I think you said that doesn't need to hold you back from doing the release. Let me know if you're short on time (this PR ended up ballooning a bit more than intended) and I can send this to someone else for reviewing. Thanks!

JacksonBurns · 2026-05-11T22:54:37Z

Thanks @sevyharris, I will review tonight and start the release, assuming all looks good (which from a quick glance, it does)!

github-actions · 2026-05-12T11:32:16Z

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): 00:00:00:54
Current: Execution time (DD:HH:MM:SS): 00:00:00:56
Reference: Memory used: 810.75 MB
Current: Memory used: 816.66 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: [CH]1C2=CC3C1C=CC23
tested: [CH]1C2=CC3C1C=CC23

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
167.21	73.60	28.78	36.79	44.00	50.25	59.65	65.52	74.04
169.15	73.17	31.27	38.45	44.76	50.28	59.14	65.47	72.92

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s2_5_5_diene_1_5) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentene) + radical(cyclopentene-allyl)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s3_5_5_ene_1) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentane) + radical(cyclopentene-allyl)

Non-identical thermo! ❌
original: [CH]1C2C=CC3C(=C2)C13
tested: [CH]1C2C=CC3C(=C2)C13

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
125.44	71.45	27.43	34.15	40.42	46.18	56.01	63.43	71.86
144.84	79.03	29.08	35.37	40.95	45.86	53.89	59.79	67.35

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_ene_1) + polycyclic(s3_5_6_diene_1_5) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-4)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,4-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4)

Non-identical thermo! ❌
original: [CH]1C2=CC3C1C3C=C2
tested: [CH]1C2=CC3C1C3C=C2

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
100.48	61.70	25.50	33.41	40.70	47.02	56.22	61.78	71.32
98.15	66.21	25.82	33.30	40.19	46.24	55.47	61.34	70.49

thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_ene_1) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(Cyclohexene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-allyl)
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl)

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C=CC23(62) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C=CC23(62) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-46.27	-30.58	-21.19	-14.94	-7.15	-2.49	3.67	6.72
k(T):	-47.51	-31.51	-21.94	-15.56	-7.62	-2.87	3.42	6.54

kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(86.724,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.08454e+19,'s^-1'), n=-0.859, Ea=(88.43,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone1_2R!H-inRing_1R!H-inRing in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC3C(=C2)C13(63) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2C=CC3C(=C2)C13(63) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-27.05	-17.33	-11.49	-7.60	-2.72	0.21	4.13	6.10
k(T):	-37.76	-25.37	-17.92	-12.96	-6.74	-3.01	1.98	4.49

kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(53.177,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(67.891,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic
tested:
rxn: [CH]1C2=CC=CC1C=C2(48) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-15.17	-8.42	-4.36	-1.66	1.73	3.77	6.50	7.88
k(T):	-14.18	-7.68	-3.77	-1.16	2.10	4.07	6.70	8.03

kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(36.869,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(1.12e+11,'s^-1'), n=0.26, Ea=(35.513,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone3_Sp-4R!H=1R!H_Sp-3R!H-2R!H_Sp-2R!H-1R!H_Ext-2R!H-R in family Intra_R_Add_Endocyclic.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic
tested:
rxn: C1=CC2C=C[C]1C=C2(49) <=> [CH]1C2=CC3C1C3C=C2(67) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-8.89	-3.16	0.28	2.58	5.46	7.19	9.52	10.69
k(T):	-8.00	-2.50	0.81	3.02	5.79	7.46	9.70	10.83

kinetics: Arrhenius(A=(1.49409e+13,'s^-1'), n=0.283, Ea=(31.249,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(1.49409e+13,'s^-1'), n=0.283, Ea=(30.033,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Backbone2_Sp-3R!H=1R!H_N-4R!H->S_2R!H-inRing_5R!H-inRing_Ext-5R!H-R_Ext-6R!H-R_Ext-7R!H-R_1R!H-inRing in family Intra_R_Add_Endocyclic.
Multiplied by reaction path degeneracy 3.0

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py aromatics-edge stable_regression_results/aromatics/chemkin/chem_edge_annotated.inp stable_regression_results/aromatics/chemkin/species_edge_dictionary.txt test/regression/aromatics/chemkin/chem_edge_annotated.inp test/regression/aromatics/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/aromatics/regression_input.py"... INFO:root:options( title = 'Aromatics', tolerance = 0.5, )

observables

observable(
label = 'benzene',
structure=SMILES('c1ccccc1'),
)

species definition used in the reactor setup specification

species(
label = 'benzene',
structure=SMILES('c1ccccc1'),
)

species(
label = 'ethyne',
structure=SMILES('C#C'),
)

reactor setups

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([100],'s'),
initialMoleFractionsList=[{
"benzene": 0.2,
"ethyne": 0.8,
}],
temperatures=([1500.0],'K'),
pressures=([1.0],'bar'),
)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:53
Current: Execution time (DD:HH:MM:SS): 00:00:01:55
Reference: Memory used: 888.78 MB
Current: Memory used: 901.55 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 239 reactions.
Test model has 239 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1591 reactions.
Test model has 1588 reactions. ❌
The original model has 7 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> CCC[C](C)OO(78) origin: intra_H_migration
rxn: CCCC[CH]OO(96) <=> C[CH]CCCOO(63) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> CC(CC[CH]OO)OO(133) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> C[C](CCCOO)OO(132) origin: intra_H_migration
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC([O])CC(C)OO(110) + CC([O])CCCOO(122) origin: Peroxyl_Disproportionation
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CC(C)OO(105) + CC(O)CCCOO(152) origin: Peroxyl_Termination
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CCCOO(115) + CC(O)CC(C)OO(143) origin: Peroxyl_Termination
The tested model has 4 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(33) <=> [OH](22) + CCCC(C)=O(30) origin: intra_H_migration
rxn: C[CH]CCCOO(63) <=> [OH](22) + CCCCC=O(60) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(CCC=O)OO(116) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(=O)CCCOO(112) origin: intra_H_migration

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py liquid_oxidation-edge stable_regression_results/liquid_oxidation/chemkin/chem_edge_annotated.inp stable_regression_results/liquid_oxidation/chemkin/species_edge_dictionary.txt test/regression/liquid_oxidation/chemkin/chem_edge_annotated.inp test/regression/liquid_oxidation/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/liquid_oxidation/regression_input.py"... INFO:root:options( title='liquid_oxidation', tolerance=0.1 )

observable(
label='pentane',
structure=SMILES('CCCCC')
)

species(
label='oxygen',
structure=SMILES('[O][O]'),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([1e3], 's'),
initialMoleFractionsList=[{
'pentane': 0.9,
'oxygen': 0.1,
}],
temperatures=([600], 'K'),
pressures=([1.0], 'bar'),
)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:57
Current: Execution time (DD:HH:MM:SS): 00:00:00:58
Reference: Memory used: 896.82 MB
Current: Memory used: 903.81 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

Errors occurred during core comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-core stable_regression_results/nitrogen/chemkin/chem_annotated.inp stable_regression_results/nitrogen/chemkin/species_dictionary.txt test/regression/nitrogen/chemkin/chem_annotated.inp test/regression/nitrogen/chemkin/species_dictionary.txt` failed. (See above for error)

nitrogen Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 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)
141.64	58.66	12.26	12.27	12.09	11.96	12.26	12.72	12.15
116.46	53.90	11.62	12.71	13.49	13.96	14.14	13.85	13.58

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + 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):	-66.25	-46.19	-34.19	-26.21	-16.28	-10.36	-2.54	1.31
k(T):	-49.54	-33.65	-24.16	-17.85	-10.01	-5.35	0.80	3.82

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 in family Intra_R_Add_Endocyclic.""")
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 in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-edge stable_regression_results/nitrogen/chemkin/chem_edge_annotated.inp stable_regression_results/nitrogen/chemkin/species_edge_dictionary.txt test/regression/nitrogen/chemkin/chem_edge_annotated.inp test/regression/nitrogen/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/nitrogen/regression_input.py"... INFO:root: options( title='NC', tolerance=0.2 )

observable(
label='NC',
structure=SMILES("NC"),
)

observable(
label='OH',
structure=SMILES("[OH]"),
)

species(
label='O2',
structure=SMILES("[O][O]"),
)

species(
label='Ar',
structure=adjacencyList('1 Ar u0 p4 c0'),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([0.002],'s'),
initialMoleFractionsList=[{
"NC": 0.0005,
"O2": 0.002,
"Ar": 0.9975,
}],
temperatures=([1500],'K'),
pressures=([1.],'atm'),
)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:32
Current: Execution time (DD:HH:MM:SS): 00:00:01:33
Reference: Memory used: 773.62 MB
Current: Memory used: 779.76 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 1524 reactions.
Test model has 1524 reactions. ✅

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/oxidation/regression_input.py"... INFO:root:options( title = 'Oxidation', tolerance = 0.5, )

observables

observable(
label = 'OH',
structure=SMILES('[OH]'),
)

species definition used in the reactor setup specification

species(
label = 'OH',
structure=SMILES('[OH]'),
)

species(
label = 'N2',
structure=SMILES("N#N"),
)

species(
label = 'O2',
structure=SMILES('[O][O]'),
)

species(
label = 'propane',
structure=SMILES('CCC'),
)

reactor setups

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([100.0],'s'),
initialMoleFractionsList=[{
"propane": 2.0/7.0,
"O2": 1.0,
"N2":4.0,
}],
temperatures=([725.0],'K'),
pressures=([10.0],'bar'),
)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
WARNING:root:Initial mole fractions do not sum to one; normalizing.
INFO:root:
INFO:root:Original composition:
INFO:root:propane = 0.2857142857142857
INFO:root:O2 = 1.0
INFO:root:N2 = 4.0
INFO:root:
INFO:root:Normalized mole fractions:
INFO:root:propane = 0.05405405405405405
INFO:root:O2 = 0.1891891891891892
INFO:root:N2 = 0.7567567567567568
INFO:root:

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:37
Current: Execution time (DD:HH:MM:SS): 00:00:00:40
Reference: Memory used: 893.35 MB
Current: Memory used: 900.77 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

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py sulfur-edge stable_regression_results/sulfur/chemkin/chem_edge_annotated.inp stable_regression_results/sulfur/chemkin/species_edge_dictionary.txt test/regression/sulfur/chemkin/chem_edge_annotated.inp test/regression/sulfur/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/sulfur/regression_input.py"... INFO:root: options( title='SO2', tolerance=0.1 )

observable(
label='SO2',
structure=SMILES("O=S=O"),
)
species(
label='H2S',
structure=SMILES("S"),
)

species(
label='O2',
structure=SMILES("[O][O]"),
)

species(
label='N2',
structure=SMILES("N#N"),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([0.01],'s'),
initialMoleFractionsList=[{
"H2S": 0.000756,
"O2": 0.001290,
"N2": 0.997954}],
temperatures=([900],'K'),
pressures=([30.],'bar'),
)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:23
Current: Execution time (DD:HH:MM:SS): 00:00:00:24
Reference: Memory used: 961.34 MB
Current: Memory used: 977.88 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): 00:00:02:03
Current: Execution time (DD:HH:MM:SS): 00:00:02:58
Reference: Memory used: 2420.87 MB
Current: Memory used: 2341.77 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. ✅

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/RMS_constantVIdealGasReactor_superminimal/regression_input.py"... INFO:root: options( title='RMS_constantVIdealGasReactor_superminimal', tolerance=0.1 )

observable(
label='H2',
structure=SMILES("[H][H]"),
)

observable(
label='O2',
structure=SMILES("[O][O]"),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([0.01],'s'),
initialMoleFractionsList=[{
'H2':.67,
'O2':.33,
}],
temperatures=([1000],'K'),
pressures=([1.0],'bar'),
)
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:20:15
Current: Execution time (DD:HH:MM:SS): 00:00:13:13
Reference: Memory used: 2609.38 MB
Current: Memory used: 3068.06 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 176 reactions.
Test model has 147 reactions. ❌
The original model has 2 species that the tested model does not have. ❌
spc: CH3
spc: [CH2]CCC(C)O(99)
The tested model has 2 species that the original model does not have. ❌
spc: CC[CH]CCOO(64)
spc: C=CCC(C)OO(89)
The original model has 37 reactions that the tested model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](24) + [O]O(13) origin: H_Abstraction
rxn: [OH](24) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: [OH](24) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: [OH](24) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](24) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
The tested model has 8 reactions that the original model does not have. ❌
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + C=CCC(C)OO(89) origin: Disproportionation
rxn: CC[CH]CCOO(64) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation

Errors occurred during core comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-core stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt` failed. (See above for error)

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 107 species.
Test model has 99 species. ❌
Original model has 545 reactions.
Test model has 384 reactions. ❌
The original model has 8 species that the tested model does not have. ❌
spc: CCCCCOOOO(101)
spc: CCCC(C)OOO(102)
spc: CCCCCO(103)
spc: CCC[CH]CO(104)
spc: CCCCCOOO
spc: OOO(106)
spc: CCC(CC)OOO(107)
spc: CCCCCOOO(108)
The original model has 161 reactions that the tested model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](24) + [O]O(13) origin: H_Abstraction
rxn: [OH](24) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: [OH](24) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: [OH](24) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(17) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + CCC(CC)O[O](22) <=> CC=CCC(16) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]CC(7) + [CH2]CCCC(12) <=> CC=CCC(16) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCO[O](61) <=> CC=CCC(16) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CCC(16) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](24) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: H(8) + [OH](24) <=> H2O(42) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + H2O(42) + CCCCC=O(72) origin: Peroxyl_Termination
rxn: [O]O(13) + CCCCCO[O](61) <=> CCCCCOOOO(101) origin: R_Recombination
rxn: [O]O(13) + CCCC(C)[O](44) <=> OO(23) + CCCC(C)=O(34) origin: Disproportionation
rxn: [O]O(13) + CCCC(C)[O](44) <=> oxygen(1) + CCCC(C)O(47) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)[O](44) <=> CCCC(C)OOO(102) origin: R_Recombination
rxn: C=CC[CH]C(64) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=CCCC(17) + C[CH]CCC(11) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + C[CH]CCC(11) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> CC=CCC(16) + CCCC(C)O(47) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)[O](44) <=> C=CCCC(17) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CCCC(17) + CC[CH]CC(7) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(17) + CC[CH]CC(7) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + CC[CH]CC(7) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)[O](44) <=> CC=CCC(16) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: C=CCCC(17) + CCC(CC)O[O](22) <=> [CH2]C=CCC(66) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCC(CC)OO(27) <=> C=CCCC(17) + CCC(CC)O[O](22) origin: H_Abstraction
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCC(=O)CC(30) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCC(CC)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCC(O)CC(46) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC(CC)O[O](22) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCC(CC)OO(27) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCC(CC)O[O](22) <=> CCCC(C)=O(34) + CCC(CC)OO(27) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)O[O](21) <=> [CH2]C=CCC(66) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(26) <=> C=CCCC(17) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)=O(34) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](21) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCC(C)O(47) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)O[O](21) <=> CCCC(C)=O(34) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CC(C)OO(37) + CCC(CC)OO(27) <=> CC[C](CC)OO(52) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCC(C)OO(26) <=> CCC[C](C)OO(57) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C=CCCC(17) + [CH2]CCCC(12) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(17) + [CH2]CCCC(12) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(17) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CC[CH]CCOO(74) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCC[CH]COO(73) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> C=CCCC(17) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=CCCC(17) + CCCCCO[O](61) <=> [CH2]C=CCC(66) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCCCOO(78) <=> C=CCCC(17) + CCCCCO[O](61) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + C=CC[CH]C(64) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH2]C=CCC(66) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH2]CCC=C(67) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + C=[C]CCC(68) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> H2O(42) + [CH]=CCCC(69) origin: H_Abstraction
rxn: [OH](24) + C=CCCC(17) <=> [CH2]C(O)CCC(97) origin: R_Addition_MultipleBond
rxn: [OH](24) + C=CCCC(17) <=> CCC[CH]CO(104) origin: R_Addition_MultipleBond
rxn: H2O(42) + C=CCCC(17) <=> CCCCCO(103) origin: 1,3_Insertion_ROR
rxn: H2O(42) + C=CCCC(17) <=> CCCC(C)O(47) origin: 1,3_Insertion_ROR
rxn: C=CC[CH]C(64) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(17) + C[CH]CC(C)OO(37) <=> [CH2]C=CCC(66) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(26) <=> C=CCCC(17) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> C=CC[CH]C(64) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> [CH2]C=CCC(66) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(17) + CCCC(C)[O](44) <=> [CH2]CCC=C(67) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)O(47) <=> C=CCCC(17) + CCCC(C)[O](44) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)O(47) <=> C=CCCC(17) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCCCOO(78) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCCCO[O](61) <=> CCCC(C)=O(34) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](24) + CCCC(C)[O](44) <=> H2O(42) + CCCC(C)=O(34) origin: Disproportionation
rxn: [OH](24) + CCCC(C)O(47) <=> H2O(42) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(26) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)O(47) <=> OO(23) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CCCC(C)=O(34) + CCCC(C)OO(26) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)O[O](21) + CCC(CC)OO[O](48) <=> oxygen(1) + CCCC(C)[O](44) + CCC(CC)O[O](22) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCC(C)OO[O](49) <=> oxygen(1) + CCCC(C)[O](44) + CCCC(C)O[O](21) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](21) + CCCCCOO[O](105) <=> oxygen(1) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Peroxyl_Disproportionation
rxn: OO(23) + OOO(106) <=> [O]O(13) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCC(CC)OO(27) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OOO(107) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCC(C)OO(26) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OOO(102) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCCCOO(78) <=> [O]O(13) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOOO(108) <=> [O]O(13) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCC(C)OOO(102) <=> H2O(42) + CCC(CC)O[O](22) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCCCOOO(108) <=> H2O(42) + CCC(CC)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](21) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](21) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(26) + CCCCCOOO(108) <=> H2O(42) + CCCC(C)O[O](21) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOOO(108) <=> H2O(42) + CCCCCO[O](61) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition

Errors occurred during edge comparison ⚠️

ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-edge stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_edge_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_edge_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_edge_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_edge_dictionary.txt` failed. (See above for error)

Details

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 ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/RMS_CSTR_liquid_oxidation/regression_input.py"... INFO:root:options( title='RMS_CSTR_liquid_oxidation', tolerance=0.1 )

observable(
label='pentane',
structure=SMILES('CCCCC')
)

species(
label='oxygen',
structure=SMILES('[O][O]'),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([1e3], 's'),
initialMoleFractionsList=[{
'pentane': 0.9,
'oxygen': 0.1,
}],
temperatures=([600], 'K'),
pressures=([1.0], 'bar'),
)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:32
Current: Execution time (DD:HH:MM:SS): 00:00:00:34
Reference: Memory used: 738.01 MB
Current: Memory used: 744.23 MB

fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Details

Observables Test Case: fragment Comparison

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

fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/fragment/regression_input.py"... INFO:root: options( title='fragment', tolerance=0.1 )

observable(
label="LCCCC",
structure=fragment_adj(
"""1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 L u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
12 H u0 p0 c0 {4,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
"""
),
)

species(
label="LCCCC",
structure=fragment_adj(
"""1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 L u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
12 H u0 p0 c0 {4,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
"""
),
)

species(
label="RCCCC",
structure=fragment_adj(
"""1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 R u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
12 H u0 p0 c0 {4,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
"""
),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([0.01],'s'),
initialMoleFractionsList=[{
"LCCCC": 1,
"RCCCC": 1,
}],
temperatures=([1600],'K'),
pressures=([40.0],'bar'),
)
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
WARNING:root:Initial mole fractions do not sum to one; normalizing.
INFO:root:
INFO:root:Original composition:
INFO:root:LCCCC = 1
INFO:root:RCCCC = 1
INFO:root:
INFO:root:Normalized mole fractions:
INFO:root:LCCCC = 0.5
INFO:root:RCCCC = 0.5
INFO:root:

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:32
Current: Execution time (DD:HH:MM:SS): 00:00:03:33
Reference: Memory used: 2584.82 MB
Current: Memory used: 2638.93 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

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

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/RMS_constantVIdealGasReactor_fragment/regression_input.py"... INFO:root: options( title='RMS_constantVIdealGasReactor_fragment', tolerance=0.1 )

observable(
label="LCCCC",
structure=fragment_adj(
"""1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 L u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
12 H u0 p0 c0 {4,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
"""
),
)

species(
label="LCCCC",
structure=fragment_adj(
"""1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 L u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
12 H u0 p0 c0 {4,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
"""
),
)

species(
label="RCCCC",
structure=fragment_adj(
"""1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 R u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
12 H u0 p0 c0 {4,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
"""
),
)

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([0.01],'s'),
initialMoleFractionsList=[{
"LCCCC": 1,
"RCCCC": 1,
}],
temperatures=([1600],'K'),
pressures=([40.0],'bar'),
)
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
WARNING:root:Initial mole fractions do not sum to one; normalizing.
INFO:root:
INFO:root:Original composition:
INFO:root:LCCCC = 1
INFO:root:RCCCC = 1
INFO:root:
INFO:root:Normalized mole fractions:
INFO:root:LCCCC = 0.5
INFO:root:RCCCC = 0.5
INFO:root:

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:33
Reference: Memory used: 898.96 MB
Current: Memory used: 899.40 MB

minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Details

Observables Test Case: minimal_surface Comparison

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

minimal_surface Passed Observable Testing ✅

Errors occurred during observable testing ⚠️

INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/minimal_surface/regression_input.py"... INFO:root:options( title = 'minimal_surface', tolerance = 0.5, )

observables

observable(
label = 'CH4',
structure=SMILES('C'),
)

observable(
label = 'O2',
structure=SMILES('[O][O]'),
)

observable(
label = 'X',
structure=adjacencyList(
"""
1 X u0 p0 c0
"""),
)

List of species

species(
label='CH4',
structure=SMILES("[CH4]"),
)
species(
label='O2',
structure=adjacencyList(
"""
1 O u1 p2 c0 {2,S}
2 O u1 p2 c0 {1,S}
"""),
)
species(
label='N2',
structure=SMILES("N#N"),
)
species(
label='X',
structure=adjacencyList(
"""
1 X u0 p0 c0
"""),
)

reactor setups

reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([1.0], 's'),
initialMoleFractionsList=[{
'CH4': 0.15,
'O2': 0.15,
'N2': 0.7,
}],
initialSurfaceMoleFractionsList=[{
'X': 1.0,
}],

temperatures=([1000.0], 'K'),
pressures=([1.0], 'bar'),

)

INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has no default temperature ranges
INFO:root:(The line it would be on is ' 300.000 1000.000 5000.000\n' but that is not formatted as such)
INFO:root:(It should have Tmin in columns 1-10, Tmid in columns 11-20, and Tmax in columns 21-30)
INFO:root:Ignoring short but non-empty line: ' 300.000 1000.000 5000.000\n'
INFO:root:Thermo file has no default temperature ranges
INFO:root:(The line it would be on is ' 300.000 1000.000 5000.000\n' but that is not formatted as such)
INFO:root:(It should have Tmin in columns 1-10, Tmid in columns 11-20, and Tmax in columns 21-30)
INFO:root:Ignoring short but non-empty line: ' 300.000 1000.000 5000.000\n'
/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/canteramodel.py:550: UserWarning: ReactorSurface::syncState: Behavior changed in Cantera 3.2 for consistency with ReactorBase. To set SurfPhase state from ReactorSurface object, use restoreState().
species_data.append(np.concatenate((cantera_reactor.thermo[species_names_list].X, rsurf.kinetics.coverages)))

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sevyharris force-pushed the uncertainty_export_beef branch from af58f3a to 486dd7d Compare April 28, 2026 12:22

sevyharris force-pushed the uncertainty_export_beef branch from 486dd7d to 99e9c48 Compare May 3, 2026 16:38

sevyharris closed this May 10, 2026

sevyharris force-pushed the uncertainty_export_beef branch from 99e9c48 to 731b402 Compare May 10, 2026 17:56

sevyharris reopened this May 10, 2026

sevyharris force-pushed the uncertainty_export_beef branch 2 times, most recently from 1ea52dd to d3cdba0 Compare May 10, 2026 23:48

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sevyharris force-pushed the uncertainty_export_beef branch 7 times, most recently from ce0d01d to 1d14c25 Compare May 11, 2026 19:36

add ability to load BEEF correlations for UQ

2ffa731

sevyharris force-pushed the uncertainty_export_beef branch from 1d14c25 to 2ffa731 Compare May 11, 2026 21:05

zero out negative contributions to local uncertainty

1e4c425

When loading covariance matrices, it is possible to have negative correlations. This can lead to a negative contribution to the overall variance, but this will screw up the plotting functions, so for now we set it to zero.

sevyharris requested a review from JacksonBurns May 11, 2026 22:02

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Merge branch 'main' into uncertainty_export_beef

a7c87c4

sevyharris merged commit ce3bb55 into ReactionMechanismGenerator:main May 12, 2026
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sevyharris commented Apr 24, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Dependencies:

Not dependent but will need to rerun the covariance calculation script after these get merged:

Motivation or Problem

Description of Changes

Testing

Reviewer Tips

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github-actions Bot commented Apr 24, 2026

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:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

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github-actions Bot commented Apr 29, 2026

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:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

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github-actions Bot commented May 10, 2026

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:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

Uh oh!

github-actions Bot commented May 11, 2026

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:

Regression test fragment:

Regression test RMS_constantVIdealGasReactor_fragment:

Regression test minimal_surface:

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sevyharris commented Apr 24, 2026 •

edited

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sevyharris commented May 11, 2026 •

edited

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