Use eigh (not eig) for moment-of-inertia diagonalization#2954
Conversation
The CI test test_co2_linear_rotor has been failing sporadically with
"TypeError: '<' not supported between instances of 'complex' and 'complex'"
raised from arkane/common.py:get_principal_moments_of_inertia. CO2 (and any
linear molecule) has a doubly-degenerate eigenvalue in its inertia tensor,
and np.linalg.eig's generic routine occasionally returns a complex128 array
with tiny imaginary noise on degenerate spectra. The downstream sorted()
call then chokes on complex comparison. Whether the noise is exactly zero
depends on input rounding, which is why the failure is flaky.
The inertia tensor is real and symmetric by construction so np.linalg.eigh
is the right routine: it is specialised
for symmetric/Hermitian matrices, guarantees real eigenvalues, and is what
arkane/statmech.py already uses for analogous diagonalisations. The fix is
applied in two places that had the same latent bug:
* arkane/common.py:get_principal_moments_of_inertia — directly hits the
sort and is the path that triggered the CI failure.
* rmgpy/statmech/conformer.pyx:Conformer.get_principal_moments_of_inertia
— same construction, same risk; would silently return complex-typed
moments for linear species and pass them to downstream consumers.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Regression Testing Results
Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:00:56 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Failed Edge Comparison ❌Original model has 106 species. Non-identical thermo! ❌
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! ❌
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 kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: 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)
|
| 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): 00:00:01:00
Current: Execution time (DD:HH:MM:SS): 00:00:00:55
Reference: Memory used: 904.72 MB
Current: Memory used: 905.01 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): 00:00:01:36
Current: Execution time (DD:HH:MM:SS): 00:00:01:33
Reference: Memory used: 778.39 MB
Current: Memory used: 779.90 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): 00:00:00:40
Current: Execution time (DD:HH:MM:SS): 00:00:00:38
Reference: Memory used: 899.58 MB
Current: Memory used: 899.87 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): 00:00:00:25
Current: Execution time (DD:HH:MM:SS): 00:00:00:23
Reference: Memory used: 976.34 MB
Current: Memory used: 972.51 MB
superminimal Passed Core Comparison ✅
Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅
superminimal Passed Edge Comparison ✅
Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅
Regression test RMS_constantVIdealGasReactor_superminimal:
Reference: Execution time (DD:HH:MM:SS): 00:00:02:17
Current: Execution time (DD:HH:MM:SS): 00:00:01:59
Reference: Memory used: 2274.41 MB
Current: Memory used: 2452.17 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): 00:00:18:42
Current: Execution time (DD:HH:MM:SS): 00:00:12:15
Reference: Memory used: 2705.08 MB
Current: Memory used: 3100.41 MB
RMS_CSTR_liquid_oxidation Failed Core Comparison ❌
Original model has 35 species.
Test model has 35 species. ✅
Original model has 146 reactions.
Test model has 128 reactions. ❌
The original model has 5 species that the tested model does not have. ❌
spc: CCCCCO
spc: CC=CC(C)OO(88)
spc: CC=O(93)
spc: [CH2]CCC(C)O(99)
spc: CC(CC(C)OO)OO
The tested model has 5 species that the original model does not have. ❌
spc: CCH2
spc: C=CC(18)
spc: C[CH]C(CC)OO(31)
spc: CC[CH]C(C)OO(35)
spc: [CH2]C(CCC)OO(36)
The original model has 51 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: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: C[CH]CC(C)OO(34) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](26) + [OH](26) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](41) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](26) + H2O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
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(34) origin: H_Abstraction
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> H2O(42) + CCCC(C)[O](41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [OH](26) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [O]O(13) + H2O(42) + CCCC(C)[O](41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](26) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)[O](41) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + CC=CC(C)OO(88) origin: Disproportionation
rxn: [CH2]CC(CC)OO(38) + 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(38) origin: H_Abstraction
rxn: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: [OH](26) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + H2O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> H2O(42) + CCC([O])CC(44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + H2O(42) + CCC([O])CC(44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
The tested model has 33 reactions that the original model does not have. ❌
rxn: C[CH]C(CC)OO(31) <=> CCC(CC)O[O](22) origin: intra_H_migration
rxn: [O]O(13) + C[CH]C(CC)OO(31) <=> oxygen(1) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + pentane(2) <=> C[CH]CCC(11) + CCC(CC)OO(27) origin: H_Abstraction
rxn: OO(23) + C[CH]C(CC)OO(31) <=> [O]O(13) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + pentane(2) <=> CC[CH]CC(7) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC(CC)OO(27) <=> C[CH]C(CC)OO(31) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]C(CC)OO(31) <=> C=CCCC(17) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]C(CC)OO(31) <=> C=CCCC(17) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]C(C)OO(35) <=> CCCC(C)O[O](20) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]C(C)OO(35) <=> oxygen(1) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(24) origin: H_Abstraction
rxn: OO(23) + CC[CH]C(C)OO(35) <=> [O]O(13) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCC(C)OO(24) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)OO(24) <=> CC[CH]C(C)OO(35) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]C(C)OO(35) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]C(C)OO(35) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2) origin: R_Recombination
rxn: C[CH]CCC(11) <=> C[CH2](6) + C=CC(18) origin: R_Addition_MultipleBond
rxn: CCCC(C)O[O](20) <=> [CH2]C(CCC)OO(36) origin: intra_H_migration
rxn: [O]O(13) + [CH2]C(CCC)OO(36) <=> oxygen(1) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(24) origin: H_Abstraction
rxn: OO(23) + [CH2]C(CCC)OO(36) <=> [O]O(13) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)OO(24) origin: H_Abstraction
rxn: [O]O(13) + C=CCCC(17) <=> [CH2]C(CCC)OO(36) origin: R_Addition_MultipleBond
rxn: [CH2]CCCC(12) + [CH2]C(CCC)OO(36) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]C(CCC)OO(36) <=> C=CCCC(17) + CCCC(C)OO(24) origin: Disproportionation
Errors occurred during core comparison ⚠️
ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-core stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt` failed. (See above for error)
RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌
Original model has 99 species.
Test model has 77 species. ❌
Original model has 384 reactions.
Test model has 254 reactions. ❌
The original model has 22 species that the tested model does not have. ❌
spc: CCCCCO
spc: [CH2]COO(80)
spc: [CH2]CCOO(81)
spc: [CH2]OO(82)
spc: [CH2]CCCOO(83)
spc: CCCC[CH]OO(84)
spc: C[CH]CCOO(85)
spc: [CH2]C(C)C(C)OO(86)
spc: CC1CC(C)O1(87)
spc: CC=CC(C)OO(88)
spc: C=CCC(C)OO(89)
spc: CC([O])CC(C)O(90)
spc: CCCCO
spc: CCC(C)O
spc: CC=O(93)
spc: CCCC=O(94)
spc: CCCCO(95)
spc: CC[CH]C(C)O(96)
spc: [CH2]C(O)CCC(97)
spc: C[CH]CC(C)O(98)
spc: [CH2]CCC(C)O(99)
spc: CC(CC(C)OO)OO
The original model has 130 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: CCCC(C)O[O](21) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: C[CH]CC(C)OO(34) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](26) + [OH](26) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: CC=O(93) + [CH2]CC(5) <=> CCCC(C)[O](41) origin: R_Addition_MultipleBond
rxn: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](26) + H2O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
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(34) origin: H_Abstraction
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> H2O(42) + CCCC(C)[O](41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [OH](26) + H2O(42) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(25) <=> [O]O(13) + H2O(42) + CCCC(C)[O](41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](26) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](26) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)[O](41) <=> [CH2]CCC(C)O(99) origin: intra_H_migration
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + CC=CC(C)OO(88) origin: Disproportionation
rxn: [CH2]CC(CC)OO(38) + 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(38) origin: H_Abstraction
rxn: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(65) origin: H_Abstraction
rxn: [OH](26) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(25) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCCC(C)O[O](21) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + H2O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> H2O(42) + CCC([O])CC(44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + H2O(42) + CCC([O])CC(44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(66) origin: H_Abstraction
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](26) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
rxn: CC[C](CC)OO(52) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CCC[C](C)OO(58) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(25) origin: H_Abstraction
rxn: CH2(S)(3) + CCCCOO(55) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: CH2(S)(3) + CCCCOO(55) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: H(8) + CCCCCO[O](61) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]COO(80) + [CH2]CC(5) <=> CCCCCOO(78) origin: R_Recombination
rxn: C[CH2](6) + [CH2]CCOO(81) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + CC[CH]CCOO(64) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]OO(82) + [CH2]CCC(9) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + CCC[CH]COO(63) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH3](10) + [CH2]CCCOO(83) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + C[CH]CCCOO(65) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + CCCC[CH]OO(84) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + [CH2]CCCCOO(66) <=> CCCCCOO(78) origin: R_Recombination
rxn: CH2(S)(3) + C[CH]CCOO(85) <=> C[CH]CC(C)OO(34) origin: 1,2_Insertion_carbene
rxn: [CH2]C(C)C(C)OO(86) <=> C[CH]CC(C)OO(34) origin: 1,2_shiftC
rxn: C[CH]CC(C)OO(34) <=> [OH](26) + CC1CC(C)O1(87) origin: Cyclic_Ether_Formation
rxn: H(8) + CC=CC(C)OO(88) <=> C[CH]CC(C)OO(34) origin: R_Addition_MultipleBond
rxn: H(8) + C=CCC(C)OO(89) <=> C[CH]CC(C)OO(34) origin: R_Addition_MultipleBond
rxn: C[CH]OO(56) + C=CC(19) <=> C[CH]CC(C)OO(34) origin: R_Addition_MultipleBond
rxn: CC[CH]C(C)OO(32) <=> C[CH]CC(C)OO(34) origin: intra_H_migration
rxn: [CH2]CCC(C)OO(35) <=> C[CH]CC(C)OO(34) origin: intra_H_migration
rxn: C[CH]CC(C)OO(34) <=> CCC[C](C)OO(58) origin: intra_H_migration
rxn: C[CH]CC(C)OO(34) <=> [CH2]C(CCC)OO(33) origin: intra_H_migration
rxn: C[CH]CC(C)OO(34) <=> CC([O])CC(C)O(90) origin: intra_OH_migration
rxn: H(8) + [O]O(13) <=> OO(23) origin: R_Recombination
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: [O]O(13) + CCC[CH]COO(63) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC[CH]OO(84) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + C=CCC(C)OO(89) origin: Disproportionation
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: 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: 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: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + CC[C](CC)OO(52) origin: H_Abstraction
rxn: [OH](26) + CCC(CC)OO(24) <=> H2O(42) + C[CH]C(CC)OO(37) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> CC[C](CC)OO(52) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> C[CH]C(CC)OO(37) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> [CH2]CC(CC)OO(38) + CCCC(C)O(46) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + CCC[C](C)OO(58) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + CC[CH]C(C)OO(32) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + [CH2]C(CCC)OO(33) origin: H_Abstraction
rxn: [OH](26) + CCCC(C)OO(25) <=> H2O(42) + [CH2]CCC(C)OO(35) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(25) <=> CCCC(C)O[O](21) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(25) <=> CCC[C](C)OO(58) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(25) <=> CC[CH]C(C)OO(32) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(25) <=> C[CH]CC(C)OO(34) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(25) <=> [CH2]C(CCC)OO(33) + CCCC(C)O(46) origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(25) <=> [CH2]CCC(C)OO(35) + CCCC(C)O(46) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC[CH]COO(63) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC[CH]COO(63) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
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): 00:00:00:34
Current: Execution time (DD:HH:MM:SS): 00:00:00:32
Reference: Memory used: 744.77 MB
Current: Memory used: 744.57 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): 00:00:02:27
Reference: Memory used: 2512.18 MB
Current: Memory used: 2552.58 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): 00:00:00:32
Current: Execution time (DD:HH:MM:SS): 00:00:00:30
Reference: Memory used: 899.68 MB
Current: Memory used: 908.05 MB
minimal_surface Failed Core Comparison ❌
Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅
Non-identical thermo! ❌
original: COX
tested: COX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -66.92 | 7.42 | 8.12 | 8.95 | 9.53 | 9.95 | 10.55 | 10.93 | 11.41 |
| -56.52 | 7.42 | 8.12 | 8.95 | 9.53 | 9.95 | 10.55 | 10.93 | 11.41 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: OX
tested: OX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -31.99 | 2.89 | 4.40 | 5.00 | 5.33 | 5.51 | 5.70 | 5.78 | 5.87 |
| -25.24 | 2.89 | 4.40 | 5.00 | 5.33 | 5.51 | 5.70 | 5.78 | 5.87 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CH4X
tested: CH4X
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -20.44 | 35.53 | 10.29 | 11.53 | 12.92 | 14.33 | 16.88 | 19.00 | 22.51 |
| -25.70 | 35.53 | 10.29 | 11.53 | 12.92 | 14.33 | 16.88 | 19.00 | 22.51 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Errors occurred during core comparison ⚠️
ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py minimal_surface-core stable_regression_results/minimal_surface/chemkin/chem_annotated.inp stable_regression_results/minimal_surface/chemkin/species_dictionary.txt test/regression/minimal_surface/chemkin/chem_annotated.inp test/regression/minimal_surface/chemkin/species_dictionary.txt` failed. (See above for error)
minimal_surface Failed Edge Comparison ❌
Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅
Non-identical thermo! ❌
original: COX
tested: COX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -66.92 | 7.42 | 8.12 | 8.95 | 9.53 | 9.95 | 10.55 | 10.93 | 11.41 |
| -56.52 | 7.42 | 8.12 | 8.95 | 9.53 | 9.95 | 10.55 | 10.93 | 11.41 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: OX
tested: OX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -31.99 | 2.89 | 4.40 | 5.00 | 5.33 | 5.51 | 5.70 | 5.78 | 5.87 |
| -25.24 | 2.89 | 4.40 | 5.00 | 5.33 | 5.51 | 5.70 | 5.78 | 5.87 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: HX
tested: HX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -6.37 | 1.01 | 2.49 | 3.51 | 4.19 | 4.64 | 5.16 | 5.43 | 5.70 |
| -8.60 | 1.01 | 2.49 | 3.51 | 4.19 | 4.64 | 5.16 | 5.43 | 5.70 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CH3X
tested: CH3X
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -11.28 | 9.22 | 8.64 | 10.56 | 12.16 | 13.49 | 15.61 | 17.25 | 19.89 |
| -14.31 | 9.22 | 8.64 | 10.56 | 12.16 | 13.49 | 15.61 | 17.25 | 19.89 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: HOX
tested: HOX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -35.92 | 17.09 | 8.24 | 8.88 | 9.24 | 9.46 | 9.76 | 10.02 | 10.61 |
| -34.90 | 17.55 | 5.70 | 6.36 | 6.80 | 7.11 | 7.54 | 7.88 | 8.55 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CX
tested: CX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| 14.02 | 1.46 | 3.22 | 4.16 | 4.73 | 5.07 | 5.44 | 5.61 | 5.79 |
| 17.67 | 1.46 | 3.22 | 4.16 | 4.73 | 5.07 | 5.44 | 5.61 | 5.79 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CH2X
tested: CH2X
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| 0.19 | 5.32 | 6.86 | 8.73 | 10.08 | 11.08 | 12.55 | 13.62 | 15.33 |
| -0.61 | 5.32 | 6.86 | 8.73 | 10.08 | 11.08 | 12.55 | 13.62 | 15.33 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CHX
tested: CHX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -5.51 | 2.75 | 5.28 | 6.78 | 7.74 | 8.38 | 9.22 | 9.78 | 10.64 |
| -4.09 | 2.75 | 5.28 | 6.78 | 7.74 | 8.38 | 9.22 | 9.78 | 10.64 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CH4X
tested: CH4X
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -20.44 | 35.53 | 10.29 | 11.53 | 12.92 | 14.33 | 16.88 | 19.00 | 22.51 |
| -25.70 | 35.53 | 10.29 | 11.53 | 12.92 | 14.33 | 16.88 | 19.00 | 22.51 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CO2XX
tested: CO2XX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -129.65 | 10.75 | 10.69 | 12.48 | 14.02 | 15.18 | 16.38 | 16.72 | 17.85 |
| -90.85 | 9.47 | 9.51 | 10.97 | 12.29 | 13.36 | 14.62 | 15.09 | 16.09 |
thermo: Gas phase thermo for CO2 from Thermo library: thermo_DFT_CCSDTF12_BAC. Adsorption correction: + Thermo group additivity estimation: adsorptionPt111(CO)
thermo: Gas phase thermo for CO2 from Thermo library: thermo_DFT_CCSDTF12_BAC. Adsorption correction: + Thermo group additivity estimation: adsorptionPt111(C-XRO-X)
Non-identical thermo! ❌
original: COXX
tested: COXX
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -105.34 | 1.78 | 7.40 | 8.36 | 9.29 | 10.05 | 10.84 | 11.05 | 11.91 |
| -73.25 | 2.61 | 5.89 | 6.67 | 7.51 | 8.22 | 8.91 | 9.01 | 9.83 |
thermo: Gas phase thermo for CO from Thermo library: primaryThermoLibrary. Adsorption correction: + Thermo group additivity estimation: adsorptionPt111(R*bidentate)
thermo: Gas phase thermo for CO from Thermo library: primaryThermoLibrary. Adsorption correction: + Thermo group additivity estimation: adsorptionPt111(RXbidentate)
Non-identical thermo! ❌
original: XOXO
tested: XOXO
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -25.60 | 9.14 | 9.12 | 10.07 | 10.65 | 10.99 | 11.37 | 11.55 | 11.74 |
| -13.14 | 10.90 | 9.10 | 10.02 | 10.59 | 10.94 | 11.34 | 11.53 | 11.73 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: O2(S)X
tested: O2(S)X
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| 9.16 | 19.16 | 8.74 | 9.20 | 9.57 | 9.87 | 10.33 | 10.66 | 11.08 |
| 9.64 | 18.24 | 6.40 | 6.79 | 7.23 | 7.64 | 8.16 | 8.38 | 8.91 |
thermo: Gas phase thermo for O2(S) from Thermo library: primaryThermoLibrary. Adsorption correction: + Thermo group additivity estimation: adsorptionPt111(R*vdW)
thermo: Gas phase thermo for O2(S) from Thermo library: primaryThermoLibrary. Adsorption correction: + Thermo group additivity estimation: adsorptionPt111(RXvdW)
Non-identical thermo! ❌
original: HC(O)XO
tested: HC(O)XO
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -88.44 | 16.37 | 12.74 | 14.53 | 16.02 | 17.25 | 19.06 | 20.27 | 21.90 |
| -73.52 | 16.37 | 12.74 | 14.53 | 16.02 | 17.25 | 19.06 | 20.27 | 21.90 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: XCHO
tested: XCHO
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -53.80 | 14.59 | 9.35 | 10.71 | 11.79 | 12.66 | 13.97 | 14.88 | 16.19 |
| -45.63 | 14.59 | 9.35 | 10.71 | 11.79 | 12.66 | 13.97 | 14.88 | 16.19 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: CH3XCO
tested: CH3XCO
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -69.07 | 26.52 | 13.22 | 15.97 | 18.33 | 20.33 | 23.43 | 25.69 | 29.07 |
| -61.70 | 26.52 | 13.22 | 15.97 | 18.33 | 20.33 | 23.43 | 25.69 | 29.07 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical thermo! ❌
original: XOCH3
tested: XOCH3
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| -37.74 | 21.40 | 10.09 | 12.19 | 14.08 | 15.75 | 18.42 | 20.42 | 23.48 |
| -35.47 | 23.21 | 10.17 | 12.28 | 14.20 | 15.89 | 18.58 | 20.59 | 23.63 |
Identical thermo comments:
thermo: Thermo library: surfaceThermoPt111
Non-identical kinetics! ❌
original:
rxn: X(3) + CO2X(4) <=> CO2XX(23) origin: Surface_vdW_to_Bidentate
tested:
rxn: X(3) + CO2X(4) <=> CO2XX(23) origin: Surface_vdW_to_Bidentate
| k(1bar) | 300K | 400K | 500K | 600K | 800K | 1000K | 1500K | 2000K |
|---|---|---|---|---|---|---|---|---|
| k(T): | 17.60 | 17.60 | 17.60 | 17.60 | 17.60 | 17.60 | 17.60 | 17.60 |
| k(T): | 15.04 | 15.68 | 16.07 | 16.32 | 16.64 | 16.83 | 17.09 | 17.22 |
kinetics: SurfaceArrhenius(A=(4e+21,'cm^2/(mol*s)'), n=0, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1 used for Combined;VacantSite Exact match found for rate rule [Combined;VacantSite] Euclidian distance = 0 Multiplied by reaction path degeneracy 4.0 family: Surface_vdW_to_Bidentate""")
kinetics: SurfaceArrhenius(A=(4e+21,'cm^2/(mol*s)'), n=0, Ea=(3.515,'kcal/mol'), T0=(1,'K'), comment="""From training reaction 1 used for Combined;VacantSite Exact match found for rate rule [Combined;VacantSite] Euclidian distance = 0 Multiplied by reaction path degeneracy 4.0 family: Surface_vdW_to_Bidentate Ea raised from 0.0 to 14.7 kJ/mol to match endothermicity of reaction.""")
kinetics: From training reaction 1 used for Combined;VacantSite
Exact match found for rate rule [Combined;VacantSite]
Euclidian distance = 0
Multiplied by reaction path degeneracy 4.0
family: Surface_vdW_to_Bidentate
kinetics: From training reaction 1 used for Combined;VacantSite
Exact match found for rate rule [Combined;VacantSite]
Euclidian distance = 0
Multiplied by reaction path degeneracy 4.0
family: Surface_vdW_to_Bidentate
Ea raised from 0.0 to 14.7 kJ/mol to match endothermicity of reaction.
Non-identical kinetics! ❌
original:
rxn: X(3) + X(3) + CO2(13) <=> OX(6) + COX(5) origin: Surface_Adsorption_Dissociative_Double
tested:
rxn: X(3) + X(3) + CO2(13) <=> OX(6) + COX(5) origin: Surface_Adsorption_Dissociative_Double
| k(1bar) | 300K | 400K | 500K | 600K | 800K | 1000K | 1500K | 2000K |
|---|
Errors occurred during edge comparison ⚠️
Traceback (most recent call last):
File "/home/runner/work/RMG-Py/RMG-Py/scripts/checkModels.py", line 301, in
error = main()
^^^^^^
File "/home/runner/work/RMG-Py/RMG-Py/scripts/checkModels.py", line 78, in main
error = check(name, bench_chemkin, bench_species_dict, test_chemkin, test_species_dict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/RMG-Py/RMG-Py/scripts/checkModels.py", line 99, in check
error_reactions = checkReactions(common_reactions, unique_reactions_test, unique_reactions_orig)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/RMG-Py/RMG-Py/scripts/checkModels.py", line 206, in checkReactions
[printRates(rxn) for rxn in [rxn1, rxn2]]
File "/home/runner/work/RMG-Py/RMG-Py/scripts/checkModels.py", line 206, in
[printRates(rxn) for rxn in [rxn1, rxn2]]
^^^^^^^^^^^^^^^
File "/home/runner/work/RMG-Py/RMG-Py/scripts/checkModels.py", line 236, in printRates
math.log10(rxn.kinetics.get_rate_coefficient(300, 1e5)),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "rmgpy/kinetics/model.pyx", line 195, in rmgpy.kinetics.model.KineticsModel.get_rate_coefficient
cpdef double get_rate_coefficient(self, double T, double P=0.0) except -1:
File "rmgpy/kinetics/model.pyx", line 201, in rmgpy.kinetics.model.KineticsModel.get_rate_coefficient
raise NotImplementedError('Unexpected call to KineticsModel.get_rate_coefficient(); '
NotImplementedError: Unexpected call to KineticsModel.get_rate_coefficient(); you should be using a class derived from KineticsModel.
ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py minimal_surface-edge stable_regression_results/minimal_surface/chemkin/chem_edge_annotated.inp stable_regression_results/minimal_surface/chemkin/species_edge_dictionary.txt test/regression/minimal_surface/chemkin/chem_edge_annotated.inp test/regression/minimal_surface/chemkin/species_edge_dictionary.txt` failed. (See above for error)
Details
Observables Test Case: minimal_surface ComparisonThe following observables did not match:
❌ Observable species [Pt] varied by more than 0.500 on average between old model X(3) and new model X(3) in condition 1.
Condition 1:
Reactor Type: IdealGasReactor
Reaction Time: 1 s
T0: 1000 K
P0: 1 bar
Initial Mole Fractions: {'C': 0.15, '[O][O]': 0.15, 'N#N': 0.7}
minimal_surface Failed Observable Testing ❌
Errors occurred during observable testing ⚠️
INFO:root:Reading input file "/home/runner/work/RMG-Py/RMG-Py/test/regression/minimal_surface/regression_input.py"...
INFO:root:options(
title = 'minimal_surface',
tolerance = 0.5,
)
observables
observable(
label = 'CH4',
structure=SMILES('C'),
)
observable(
label = 'O2',
structure=SMILES('[O][O]'),
)
observable(
label = 'X',
structure=adjacencyList(
"""
1 X u0 p0 c0
"""),
)
List of species
species(
label='CH4',
structure=SMILES("[CH4]"),
)
species(
label='O2',
structure=adjacencyList(
"""
1 O u1 p2 c0 {2,S}
2 O u1 p2 c0 {1,S}
"""),
)
species(
label='N2',
structure=SMILES("N#N"),
)
species(
label='X',
structure=adjacencyList(
"""
1 X u0 p0 c0
"""),
)
reactor setups
reactorSetups(
reactorTypes=['IdealGasReactor'],
terminationTimes=([1.0], 's'),
initialMoleFractionsList=[{
'CH4': 0.15,
'O2': 0.15,
'N2': 0.7,
}],
initialSurfaceMoleFractionsList=[{
'X': 1.0,
}],
temperatures=([1000.0], 'K'),
pressures=([1.0], 'bar'),
)
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
INFO:root:Thermo file has no default temperature ranges
INFO:root:(The line it would be on is ' 300.000 1000.000 5000.000\n' but that is not formatted as such)
INFO:root:(It should have Tmin in columns 1-10, Tmid in columns 11-20, and Tmax in columns 21-30)
INFO:root:Ignoring short but non-empty line: ' 300.000 1000.000 5000.000\n'
INFO:root:Thermo file has no default temperature ranges
INFO:root:(The line it would be on is ' 300.000 1000.000 5000.000\n' but that is not formatted as such)
INFO:root:(It should have Tmin in columns 1-10, Tmid in columns 11-20, and Tmax in columns 21-30)
INFO:root:Ignoring short but non-empty line: ' 300.000 1000.000 5000.000\n'
/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/canteramodel.py:550: UserWarning: ReactorSurface::syncState: Behavior changed in Cantera 3.2 for consistency with ReactorBase. To set SurfPhase state from ReactorSurface object, use restoreState().
species_data.append(np.concatenate((cantera_reactor.thermo[species_names_list].X, rsurf.kinetics.coverages)))
ERROR conda.cli.main_run:execute(148): conda run python rmgpy/tools/regression.py test/regression/minimal_surface/regression_input.py stable_regression_results/minimal_surface/chemkin test/regression/minimal_surface/chemkin failed. (See above for error)
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rwest
merged commit 4ab53c3
into
ReactionMechanismGenerator:main
2 participants
Motivation or Problem
The CI test test_co2_linear_rotor has been failing sporadically with "TypeError: '<' not supported between instances of 'complex' and 'complex'" raised from arkane/common.py:get_principal_moments_of_inertia. CO2 (and any linear molecule) has a doubly-degenerate eigenvalue in its inertia tensor, and np.linalg.eig's generic routine occasionally returns a complex128 array with tiny imaginary noise on degenerate spectra. The downstream sorted() call then chokes on complex comparison. Whether the noise is exactly zero depends on input rounding, which is why the failure is flaky.
Description of Changes
The inertia tensor is real and symmetric by construction so np.linalg.eigh is the right routine: it is specialised
for symmetric/Hermitian matrices, guarantees real eigenvalues, and is what arkane/statmech.py already uses for analogous diagonalisations. The fix is applied in two places that had the same latent bug:
Testing
Ran relevant tests locally. All passed.
Hopefully this clears the CI test suite.