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Update extract_source_from_comments to grab library object in addition to library name#2963

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Update extract_source_from_comments to grab library object in addition to library name#2963
sevyharris wants to merge 5 commits into
ReactionMechanismGenerator:mainfrom
sevyharris:expand_lib_extract_source

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@sevyharris sevyharris commented May 27, 2026 •
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Motivation or Problem: we need this to implement grabbing rank for UQ (not part of RMG 4 paper)

Right now extract_source_from_comments

RMG-Py/rmgpy/data/thermo.py

Line 2838 in 8a0b7fe

def extract_source_from_comments(self, species):

only grabs the library name instead of the library entry object. This causes problems downstream in the uncertainty estimation tool because get_partial_uncertainty_value

RMG-Py/rmgpy/tools/uncertainty.py

Line 91 in 8a0b7fe

def get_partial_uncertainty_value(self, source, corr_source_type, corr_param=None, corr_group_type=None):

only has access to what gets saved in the source, and it's a total pain extracting things like the species structure or rank, which could have been added in extract_source_from_comments and are added for Rate Rules, but never got implemented for Libraries.

This PR updates extract_source_from_comments to use the actual library entry objects, and then modifies the downstream code in rmgpy.tools.uncertainty to use that information.

Description of Changes (each bullet is a commit)

  • Add extra tests for uncertainty's assign_intermediate_uncertainties to make sure we don't break this later on
  • New uncertainty test to make sure we reference the correct library entries when using radical or adsorption correction
  • Refactor thermo's extract_source_from_comments to use helper functions (_parse_gav_groups is almost an exact copy of the last section of the old extract_source_from_comments) and also return specific library entry objects instead of just the library name. Update thermoTest to handle this change in library source format.
  • Update kinetics db's extract_source_from_comments to return specific library entry objects instead of just the library name. Update kineticsTest to handle the change in library source format.
  • Update the uncertainty tool to use specific library entry objects instead library names. This allows us to delete a lot of code, including the extra_species property, which I found especially confusing.

Testing

  • added extra tests for assign_intermediate_uncertainties to make sure we don't break it. You can check out that first commit to see that it works before we add all these changes and then still works after.
  • added a new uncertainty test to make sure the correct library entries are being correlated when one species uses a Library source and the other uses the same Library source + a radical correction.
  • this passes the thermo database and kinetics database tests
  • TODO: rerun previous uncertainty demo notebooks

Reviewer Tips

¯_(ツ)_/¯

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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): 00:00:00:52
Current: Execution time (DD:HH:MM:SS): 00:00:00:51
Reference: Memory used: 823.87 MB
Current: Memory used: 822.81 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)
169.15 73.17 31.27 38.45 44.76 50.28 59.14 65.47 72.92
167.21 73.60 28.78 36.79 44.00 50.25 59.65 65.52 74.04

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)
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)

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)
144.84 79.03 29.08 35.37 40.95 45.86 53.89 59.79 67.35
125.44 71.45 27.43 34.15 40.42 46.18 56.01 63.43 71.86

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)
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)

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)
98.15 66.21 25.82 33.30 40.19 46.24 55.47 61.34 70.49
100.48 61.70 25.50 33.41 40.70 47.02 56.22 61.78 71.32

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)
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)

Non-identical thermo! ❌
original: C=CC1C=CC2=CC1C=C2
tested: C=CC1C=CC2=CC1C=C2

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

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

Non-identical 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): -47.51 -31.51 -21.94 -15.56 -7.62 -2.87 3.42 6.54
k(T): -46.27 -30.58 -21.19 -14.94 -7.15 -2.49 3.67 6.72

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.""")
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.""")
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): -37.76 -25.37 -17.92 -12.96 -6.74 -3.01 1.98 4.49
k(T): -27.05 -17.33 -11.49 -7.60 -2.72 0.21 4.13 6.10

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.""")
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.""")
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): -14.18 -7.68 -3.77 -1.16 2.10 4.07 6.70 8.03
k(T): -15.17 -8.42 -4.36 -1.66 1.73 3.77 6.50 7.88

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.""")
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.""")
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): -8.00 -2.50 0.81 3.02 5.79 7.46 9.70 10.83
k(T): -8.89 -3.16 0.28 2.58 5.46 7.19 9.52 10.69

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""")
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""")
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): 00:00:01:50
Reference: Memory used: 907.79 MB
Current: Memory used: 906.56 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 1588 reactions.
Test model has 1588 reactions. ✅
The original model has 2 reactions that the tested 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
The tested model has 2 reactions that the original 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

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): 00:00:00:56
Current: Execution time (DD:HH:MM:SS): 00:00:00:55
Reference: Memory used: 907.83 MB
Current: Memory used: 910.81 MB

nitrogen Passed Core Comparison ✅

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

nitrogen Passed Edge Comparison ✅

Original model has 133 species.
Test model has 133 species. ✅
Original model has 983 reactions.
Test model has 983 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 ✅
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): 00:00:01:31
Current: Execution time (DD:HH:MM:SS): 00:00:01:32
Reference: Memory used: 792.61 MB
Current: Memory used: 791.79 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 ⚠️ 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): 00:00:00:36
Reference: Memory used: 905.16 MB
Current: Memory used: 903.78 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 ⚠️ 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
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): 00:00:00:21
Reference: Memory used: 967.06 MB
Current: Memory used: 971.46 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): 00:00:02:17
Current: Execution time (DD:HH:MM:SS): 00:00:02:37
Reference: Memory used: 2304.96 MB
Current: Memory used: 2511.59 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): 00:00:24:55
Current: Execution time (DD:HH:MM:SS): 00:00:18:33
Reference: Memory used: 3526.41 MB
Current: Memory used: 3661.74 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 134 reactions.
Test model has 132 reactions. ❌
The original model has 1 species that the tested model does not have. ❌
spc: CC1CC(C)O1(87)
The tested model has 1 species that the original model does not have. ❌
spc: CCH2
The original model has 3 reactions that the tested 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]CC(C)OO(37) <=> [OH](26) + CC1CC(C)O1(87) origin: Cyclic_Ether_Formation
The tested model has 1 reactions that the original model does not have. ❌
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2) origin: R_Recombination

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 100 species.
Test model has 99 species. ❌
Original model has 385 reactions.
Test model has 380 reactions. ❌
The original model has 1 species that the tested model does not have. ❌
spc: CCCCCOOOO
The original model has 5 reactions that the tested 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: 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

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): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:30
Reference: Memory used: 753.75 MB
Current: Memory used: 752.32 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): 00:00:02:43
Current: Execution time (DD:HH:MM:SS): 00:00:03:00
Reference: Memory used: 2425.29 MB
Current: Memory used: 2579.28 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 ⚠️ 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): 00:00:00:30
Current: Execution time (DD:HH:MM:SS): 00:00:00:29
Reference: Memory used: 910.72 MB
Current: Memory used: 910.70 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 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
/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 sevyharris force-pushed the expand_lib_extract_source branch 7 times, most recently from daa9af4 to a167215 Compare May 28, 2026 20:22
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@sevyharris sevyharris force-pushed the expand_lib_extract_source branch from a167215 to b9eeaf0 Compare May 28, 2026 20:30
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@sevyharris sevyharris force-pushed the expand_lib_extract_source branch from b9eeaf0 to 1e43cf9 Compare May 28, 2026 21:14
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Pull request overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Comments suppressed due to low confidence (1)

rmgpy/tools/uncertainty.py:78

  • get_uncertainty_value() constructs the covariance lookup label as f'Surface_Library {source["Surface_Library"][2]}', but source['Surface_Library'][2] is already intended to be the full parameter label (e.g., Surface_Library CH4(16)), so this will duplicate the prefix and fail to match keys in other_covariances. Use the stored label directly (and ensure extract_sources_from_model() stores it in the same format used when building covariance labels).
            varG += self.dG_library * self.dG_library
        if 'Surface_Library' in source:
            surf_lib_varG = self.dG_surf_lib * self.dG_surf_lib
            # covariance libraries should overrule the default uncertainties when available,
            if self.other_covariances is not None:
                label = f'Surface_Library {source["Surface_Library"][2]}'  # match the covariance dict label format
                cov_label = (label, label)
                if cov_label in self.other_covariances:
                    surf_lib_varG = self.other_covariances[cov_label]
            varG += surf_lib_varG  # Add the variance of the surface library parameter if covariance is not specified in the covariance libraries

Comment thread rmgpy/tools/uncertainty.py
Comment thread rmgpy/tools/uncertainty.py Outdated
Comment thread rmgpy/data/thermo.py
Comment thread rmgpy/data/thermo.py
Comment thread rmgpy/data/kinetics/database.py
Comment thread test/rmgpy/tools/uncertaintyTest.py
@sevyharris sevyharris force-pushed the expand_lib_extract_source branch 6 times, most recently from a0dfbfd to 6b61784 Compare May 28, 2026 21:58
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Pull request overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated 5 comments.

Comment thread rmgpy/data/thermo.py Outdated
Comment thread rmgpy/data/thermo.py
Comment thread rmgpy/data/kinetics/database.py
Comment thread rmgpy/data/kinetics/database.py
Comment thread rmgpy/tools/uncertainty.py
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@sevyharris sevyharris force-pushed the expand_lib_extract_source branch 3 times, most recently from 41ada7e to 438222f Compare May 29, 2026 14:18
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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): 00:00:00:52
Current: Execution time (DD:HH:MM:SS): 00:00:00:51
Reference: Memory used: 823.10 MB
Current: Memory used: 822.61 MB

aromatics Passed Core Comparison ✅

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

aromatics Passed Edge Comparison ✅

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

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): 00:00:01:50
Current: Execution time (DD:HH:MM:SS): 00:00:01:50
Reference: Memory used: 904.00 MB
Current: Memory used: 904.07 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 1588 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(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
The tested model has 5 reactions that the original 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
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(95) + 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(112) + CC(O)CC(C)OO(143) origin: Peroxyl_Termination

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

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

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: 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: 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.

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): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:55
Reference: Memory used: 911.55 MB
Current: Memory used: 909.10 MB

nitrogen Passed Core Comparison ✅

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

nitrogen Passed Edge Comparison ✅

Original model has 133 species.
Test model has 133 species. ✅
Original model has 983 reactions.
Test model has 983 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 ✅
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): 00:00:01:31
Reference: Memory used: 791.17 MB
Current: Memory used: 789.65 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): 00:00:00:39
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 907.11 MB
Current: Memory used: 906.92 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): 00:00:00:22
Current: Execution time (DD:HH:MM:SS): 00:00:00:23
Reference: Memory used: 969.45 MB
Current: Memory used: 966.20 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): 00:00:02:55
Current: Execution time (DD:HH:MM:SS): 00:00:02:58
Reference: Memory used: 2529.25 MB
Current: Memory used: 2546.18 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

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

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

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

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): 00:00:10:24
Current: Execution time (DD:HH:MM:SS): 00:00:31:15
Reference: Memory used: 3784.35 MB
Current: Memory used: 2646.48 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 127 reactions.
Test model has 176 reactions. ❌
The original model has 4 species that the tested model does not have. ❌
spc: CCH2
spc: CC[CH]CCOO(74)
spc: CC1CC(C)O1(87)
spc: C=CCC(C)OO(89)
The tested model has 4 species that the original model does not have. ❌
spc: CH3
spc: CC=O(93)
spc: CCCC=O(94)
spc: [CH2]CCC(C)O(99)
The original model has 7 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(37) <=> [OH](26) + CC1CC(C)O1(87) origin: Cyclic_Ether_Formation
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + C=CCC(C)OO(89) origin: Disproportionation
rxn: CC[CH]CCOO(74) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(74) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(74) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(74) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
The tested model has 56 reactions that the original model does not have. ❌
rxn: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) 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) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: [OH](26) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: [OH](26) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: [OH](26) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: CC[CH]CC(7) + CCC(CC)O[O](20) <=> CC=CCC(16) + CCC(CC)OO(24) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(25) 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(25) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](20) <=> CC=CCC(16) + CCC(CC)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(25) 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(25) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](20) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(24) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(25) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH3](10) + CCCC=O(94) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(65) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + pentane(2) <=> C[CH]CCC(11) + 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) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(65) + pentane(2) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
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) <=> H2O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](26) + 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: [CH2]CCCCOO(66) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC(CC)O[O](20) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_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 90 species.
Test model has 107 species. ❌
Original model has 305 reactions.
Test model has 545 reactions. ❌
The tested model has 17 species that the original model does not have. ❌
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: 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 tested model has 240 reactions that the original model does not have. ❌
rxn: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) 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) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: [OH](26) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: [OH](26) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: [OH](26) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: CC[CH]CC(7) + CCC(CC)O[O](20) <=> CC=CCC(16) + CCC(CC)OO(24) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(25) 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(25) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC(CC)O[O](20) <=> CC=CCC(16) + CCC(CC)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC(C)O[O](21) <=> CC=CCC(16) + CCCC(C)OO(25) 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(25) origin: Disproportionation
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](20) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCC(CC)OO(24) origin: Disproportionation
rxn: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCC(C)OO(25) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(88) + CCCCCOO(78) origin: Disproportionation
rxn: [CH3](10) + CCCC=O(94) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(65) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + pentane(2) <=> C[CH]CCC(11) + 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) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(65) + pentane(2) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
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) <=> H2O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](26) + 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: [CH2]CCCCOO(66) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC(CC)O[O](20) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC[C](C)OO(54) + 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: CC[C](CC)OO(58) + 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: C=CC[CH]C(69) + [CH2]CCCC(12) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: C=CC[CH]C(69) + C[CH]CCC(11) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: [CH2]C=CCC(71) + [CH2]CCCC(12) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: [CH2]C=CCC(71) + C[CH]CCC(11) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: [CH2]CCC=C(72) + [CH2]CCCC(12) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: [CH2]CCC=C(72) + C[CH]CCC(11) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: C=[C]CCC(73) + [CH2]CCCC(12) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: C=[C]CCC(73) + C[CH]CCC(11) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: [CH]=CCCC(74) + [CH2]CCCC(12) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: [CH]=CCCC(74) + C[CH]CCC(11) <=> C=CCCC(18) + C=CCCC(18) origin: Disproportionation
rxn: CH2(S)(3) + CCCC[O](91) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: CH2(S)(3) + CCC(C)[O](92) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: CH2(S)(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: 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: C=CCCC(18) + CC[CH]CC(7) <=> C=CC[CH]C(69) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(18) + CC[CH]CC(7) <=> [CH2]C=CCC(71) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + pentane(2) <=> C=CCCC(18) + CC[CH]CC(7) origin: H_Abstraction
rxn: C=[C]CCC(73) + pentane(2) <=> C=CCCC(18) + CC[CH]CC(7) origin: H_Abstraction
rxn: [CH]=CCCC(74) + pentane(2) <=> C=CCCC(18) + CC[CH]CC(7) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + 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(69) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=CCCC(18) + C[CH]CCC(11) <=> [CH2]C=CCC(71) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=[C]CCC(73) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: [CH]=CCCC(74) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + 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(18) + CCCC(C)O(47) origin: Disproportionation
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + H2O(42) + CCCCC=O(62) origin: Peroxyl_Termination
rxn: [O]O(13) + CCCCCO[O](61) <=> CCCCCOOOO(101) origin: R_Recombination
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: [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: CCC(CC)O[O](20) + CCCCCO[O](61) <=> oxygen(1) + CCC(=O)CC(30) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCC(CC)O[O](20) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(62) + CCC(O)CC(46) origin: Peroxyl_Termination
rxn: C=CC[CH]C(69) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: C=CCCC(18) + CCC(CC)O[O](20) <=> [CH2]C=CCC(71) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: C=[C]CCC(73) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: [CH]=CCCC(74) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC(CC)O[O](20) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCC(CC)OO(24) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCC(CC)O[O](20) <=> CCCC(C)=O(34) + CCC(CC)OO(24) origin: Disproportionation
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(62) + CCCC(C)O(47) origin: Peroxyl_Termination
rxn: C=CC[CH]C(69) + CCCC(C)OO(25) <=> C=CCCC(18) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)O[O](21) <=> [CH2]C=CCC(71) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + CCCC(C)OO(25) <=> C=CCCC(18) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: C=[C]CCC(73) + CCCC(C)OO(25) <=> C=CCCC(18) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: [CH]=CCCC(74) + CCCC(C)OO(25) <=> C=CCCC(18) + CCCC(C)O[O](21) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + 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: CCCC(C)O[O](21) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(89) + CCCC(C)OO(25) origin: Disproportionation
rxn: CCCC(C)[O](44) + CCCC(C)O[O](21) <=> CCCC(C)=O(34) + CCCC(C)OO(25) origin: Disproportionation
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + CCC[C](C)OO(54) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + CC[CH]C(C)OO(35) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + [CH2]C(CCC)OO(36) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + [CH2]CCC(C)OO(38) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCC(C)OO(25) <=> CCC[C](C)OO(54) + CCCC(C)OO(25) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(25) 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(54) + 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) + CCC(CC)OO(24) <=> H2O(42) + CC[C](CC)OO(58) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + C[CH]C(CC)OO(31) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCC(CC)OO(24) <=> CC[C](CC)OO(58) + CCCC(C)OO(25) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(24) 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(58) + 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: C=CCCC(18) + [CH2]CCCC(12) <=> C=CC[CH]C(69) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(18) + [CH2]CCCC(12) <=> [CH2]C=CCC(71) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + pentane(2) <=> C=CCCC(18) + [CH2]CCCC(12) origin: H_Abstraction
rxn: C=[C]CCC(73) + pentane(2) <=> C=CCCC(18) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH]=CCCC(74) + pentane(2) <=> C=CCCC(18) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CC[CH]CCOO(64) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCC[CH]COO(63) + 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(18) + CCCC(C)O(47) origin: Disproportionation
rxn: [OH](26) + C=CCCC(18) <=> H2O(42) + C=CC[CH]C(69) origin: H_Abstraction
rxn: [OH](26) + C=CCCC(18) <=> H2O(42) + [CH2]C=CCC(71) origin: H_Abstraction
rxn: [OH](26) + C=CCCC(18) <=> H2O(42) + [CH2]CCC=C(72) origin: H_Abstraction
rxn: [OH](26) + C=CCCC(18) <=> H2O(42) + C=[C]CCC(73) origin: H_Abstraction
rxn: [OH](26) + C=CCCC(18) <=> H2O(42) + [CH]=CCCC(74) origin: H_Abstraction
rxn: [OH](26) + C=CCCC(18) <=> [CH2]C(O)CCC(97) origin: R_Addition_MultipleBond
rxn: [OH](26) + C=CCCC(18) <=> CCC[CH]CO(104) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCC[CH]COO(63) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)[O](44) <=> H2O(42) + CCCC(C)=O(34) origin: Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(62) + CCCCCO(103) origin: Peroxyl_Termination
rxn: C=CC[CH]C(69) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=CCCC(18) + CCCCCO[O](61) <=> [CH2]C=CCC(71) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=[C]CCC(73) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: [CH]=CCCC(74) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + 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: H2O(42) + C=CCCC(18) <=> CCCCCO(103) origin: 1,3_Insertion_ROR
rxn: H2O(42) + C=CCCC(18) <=> CCCC(C)O(47) origin: 1,3_Insertion_ROR
rxn: C=CC[CH]C(69) + CCCC(C)OO(25) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(18) + C[CH]CC(C)OO(37) <=> [CH2]C=CCC(71) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]CCC=C(72) + CCCC(C)OO(25) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=[C]CCC(73) + CCCC(C)OO(25) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [CH]=CCCC(74) + CCCC(C)OO(25) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)[O](44) <=> C=CC[CH]C(69) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)[O](44) <=> [CH2]C=CCC(71) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)[O](44) <=> [CH2]CCC=C(72) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=[C]CCC(73) + CCCC(C)O(47) <=> C=CCCC(18) + CCCC(C)[O](44) origin: H_Abstraction
rxn: [CH]=CCCC(74) + CCCC(C)O(47) <=> C=CCCC(18) + CCCC(C)[O](44) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)O(47) <=> H2O(42) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(63) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
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
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CCCC(C)=O(34) + CCCC(C)OO(25) 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: [O]O(13) + CCCC(C)O(47) <=> OO(23) + CCCC(C)[O](44) origin: H_Abstraction
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](20) 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(24) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OOO(107) <=> [O]O(13) + H2O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OOO(106) + CCCC(C)OO(25) <=> [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(24) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](20) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(25) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](20) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCC(C)OOO(102) <=> H2O(42) + CCC(CC)O[O](20) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](20) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCCCOOO(108) <=> H2O(42) + CCC(CC)O[O](20) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(25) + 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(25) + 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): 00:00:00:32
Reference: Memory used: 753.25 MB
Current: Memory used: 753.85 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): 00:00:03:23
Current: Execution time (DD:HH:MM:SS): 00:00:03:23
Reference: Memory used: 2630.30 MB
Current: Memory used: 2572.70 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): 00:00:00:31
Reference: Memory used: 912.06 MB
Current: Memory used: 910.74 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 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
/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 sevyharris force-pushed the expand_lib_extract_source branch from aedb962 to 7836926 Compare May 29, 2026 19:58
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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: 823.95 MB
Current: Memory used: 823.19 MB

aromatics Passed Core Comparison ✅

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

aromatics Failed Edge Comparison ❌

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

Non-identical thermo! ❌
original: C=CC1C=CC2=CC1C=C2
tested: C=CC1C=CC2=CC1C=C2

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

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

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): 00:00:01:48
Current: Execution time (DD:HH:MM:SS): 00:00:01:49
Reference: Memory used: 906.51 MB
Current: Memory used: 905.01 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 1588 reactions.
Test model has 1588 reactions. ✅

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

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): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:57
Reference: Memory used: 909.48 MB
Current: Memory used: 909.16 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 ✅
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): 00:00:01:29
Current: Execution time (DD:HH:MM:SS): 00:00:01:33
Reference: Memory used: 792.84 MB
Current: Memory used: 790.82 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): 00:00:00:36
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 905.15 MB
Current: Memory used: 904.01 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): 00:00:00:22
Current: Execution time (DD:HH:MM:SS): 00:00:00:24
Reference: Memory used: 964.50 MB
Current: Memory used: 967.11 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): 00:00:02:18
Current: Execution time (DD:HH:MM:SS): 00:00:02:59
Reference: Memory used: 2393.58 MB
Current: Memory used: 2508.70 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): 00:00:09:08
Current: Execution time (DD:HH:MM:SS): 00:00:21:32
Reference: Memory used: 2668.97 MB
Current: Memory used: 3701.47 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 142 reactions.
Test model has 137 reactions. ❌
The original model has 3 species that the tested model does not have. ❌
spc: CCH2
spc: CC[CH]CCOO(74)
spc: C=CCC(C)OO(89)
The tested model has 3 species that the original model does not have. ❌
spc: CH3
spc: CC=O(93)
spc: [CH2]CCC(C)O(99)
The original model has 14 reactions that the tested model does not have. ❌
rxn: CCCCCO[O](61) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + 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: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(74) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(74) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(74) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCCC(C)OO(26) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(74) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(74) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2) origin: R_Recombination
The tested model has 9 reactions that the original model does not have. ❌
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](41) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + CCCC(C)O[O](20) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + C[CH]CC(C)OO(34) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(25) <=> H2O(42) + CCC(CC)O[O](21) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: CCCC(C)[O](41) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: [OH](26) + CCC(CC)OO(25) <=> H2O(42) + [CH2]CC(CC)OO(38) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(66) 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 90 species.
Test model has 99 species. ❌
Original model has 342 reactions.
Test model has 375 reactions. ❌
The tested model has 9 species that the original model does not have. ❌
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)
The original model has 15 reactions that the tested model does not have. ❌
rxn: CCCCCO[O](61) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: H(8) + [OH](24) <=> H2O(42) origin: R_Recombination
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[C](C)OO(54) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[C](CC)OO(58) + 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
The tested model has 48 reactions that the original model does not have. ❌
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](41) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + CCCC(C)O[O](20) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + C[CH]CC(C)OO(34) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(25) <=> H2O(42) + CCC(CC)O[O](21) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: CCCC(C)[O](41) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: [OH](26) + CCC(CC)OO(25) <=> H2O(42) + [CH2]CC(CC)OO(38) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: CH2(S)(3) + CCCC[O](91) <=> CCCC(C)[O](41) origin: 1,2_Insertion_carbene
rxn: CH2(S)(3) + CCC(C)[O](92) <=> CCCC(C)[O](41) origin: 1,2_Insertion_carbene
rxn: CH2(S)(3) + CCC(C)[O](92) <=> CCCC(C)[O](41) origin: 1,2_Insertion_carbene
rxn: H(8) + CCCC(C)=O(31) <=> CCCC(C)[O](41) origin: R_Addition_MultipleBond
rxn: [CH3](10) + CCCC=O(94) <=> CCCC(C)[O](41) origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](41) <=> CCC[C](C)O(95) origin: intra_H_migration
rxn: CC[CH]C(C)O(96) <=> CCCC(C)[O](41) origin: intra_H_migration
rxn: CCCC(C)[O](41) <=> [CH2]C(O)CCC(97) origin: intra_H_migration
rxn: CCCC(C)[O](41) <=> C[CH]CC(C)O(98) origin: intra_H_migration
rxn: oxygen(1) + CCCC(C)[O](41) <=> [O]O(13) + CCCC(C)=O(31) origin: Disproportionation
rxn: oxygen(1) + CCCC(C)[O](41) <=> CCCC(C)OO[O](48) origin: R_Recombination
rxn: CCCC(C)[O](41) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)O(46) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + CCC[C](C)OO(54) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + CC[CH]C(C)OO(32) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + [CH2]C(CCC)OO(33) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(24) <=> H2O(42) + [CH2]CCC(C)OO(35) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(24) <=> CCC[C](C)OO(54) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(24) <=> CC[CH]C(C)OO(32) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(24) <=> C[CH]CC(C)OO(34) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(24) <=> [CH2]C(CCC)OO(33) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(24) <=> [CH2]CCC(C)OO(35) + CCCC(C)O(46) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(25) <=> H2O(42) + CC[C](CC)OO(59) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(25) <=> H2O(42) + C[CH]C(CC)OO(37) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(25) <=> CCC(CC)O[O](21) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(25) <=> CC[C](CC)OO(59) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(25) <=> C[CH]C(CC)OO(37) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(25) <=> [CH2]CC(CC)OO(38) + CCCC(C)O(46) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCC[CH]COO(63) origin: H_Abstraction
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CC[CH]CCOO(64) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CCC[CH]COO(63) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> C[CH]CCCOO(65) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CCCC[CH]OO(84) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> [CH2]CCCCOO(66) + CCCC(C)O(46) origin: H_Abstraction

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): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:31
Reference: Memory used: 753.18 MB
Current: Memory used: 753.59 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): 00:00:02:44
Current: Execution time (DD:HH:MM:SS): 00:00:03:27
Reference: Memory used: 2432.39 MB
Current: Memory used: 2506.72 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): 00:00:00:29
Current: Execution time (DD:HH:MM:SS): 00:00:00:30
Reference: Memory used: 908.89 MB
Current: Memory used: 911.87 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 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
/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)))

beep boop this comment was written by a bot 🤖

sevyharris added 4 commits May 29, 2026 17:38
@sevyharris
Add tests for UQ assign_intermediate_uncertainties
2ee436f
@sevyharris
Add uncertainty tests for correlated library match
33b5fa0 
Add some tests to make sure the correct index is referenced when assembling thermo sources that use libraries. For example, if CH3 is estimated from a CH4 library + a radical correction, we want to make sure the uncertainty source points to CH4 as the index for the library value used (as opposed to CH3)
@sevyharris
refactor thermo extract_source_from_comments
6f5a3ea 
This refactors the extract_source_from_comments function and changes library sources so that a tuple of the library name and the library entry object is returned instead of just the library name. It also returns a tuple of QM method and molecule used for the case of QM sources.
@sevyharris
return kinetic library entry when parsing comments
210f585 
Before this, the kinetics version of extract_source_from_comment returned the library name, but now it returns a tuple of the library name and the library entry. This makes things much easier downstream in the uncertainty tool.
@sevyharris sevyharris force-pushed the expand_lib_extract_source branch from 7836926 to e523aa9 Compare May 29, 2026 21:40
@sevyharris
update uncertainty tool to use library entry objects instead of names
004d62c 
When the library sources only included the name of the library, the uncertainty code had to compensate by adding extra species that are not in the model. Now that we're using library entry objects we are able to remove the complexity of the uncertainty.extra_species object.
@sevyharris sevyharris force-pushed the expand_lib_extract_source branch from e523aa9 to 004d62c Compare May 29, 2026 21:52
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