fix(arkane): make PDep sensitivity meaningful for ILT-based path reactions - #2990
fix(arkane): make PDep sensitivity meaningful for ILT-based path reactions#2990alongd wants to merge 2 commits into
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Regression Testing Results
Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:00:42 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)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s3_4_5_ene_3) + polycyclic(s3_5_5_ene_1) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentane) + radical(cyclopentene-allyl) Non-identical thermo! ❌
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_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl) Non-identical kinetics! ❌
kinetics: 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): | 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)
liquid_oxidation Passed Observable Testing ✅
Regression test nitrogen:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:44
Current: Execution time (DD:HH:MM:SS): 00:00:00:56
Reference: Memory used: 914.42 MB
Current: Memory used: 920.14 MB
nitrogen Passed Core Comparison ✅
Original model has 41 species.
Test model has 41 species. ✅
Original model has 359 reactions.
Test model has 359 reactions. ✅
nitrogen Failed Edge Comparison ❌
Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 981 reactions. ✅
Non-identical thermo! ❌
original: O1[C]=N1
tested: O1[C]=N1
| Hf(300K) | S(300K) | Cp(300K) | Cp(400K) | Cp(500K) | Cp(600K) | Cp(800K) | Cp(1000K) | Cp(1500K) |
|---|---|---|---|---|---|---|---|---|
| 141.64 | 58.66 | 12.26 | 12.27 | 12.09 | 11.96 | 12.26 | 12.72 | 12.15 |
| 116.46 | 53.90 | 11.62 | 12.71 | 13.49 | 13.96 | 14.14 | 13.85 | 13.58 |
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)
Non-identical kinetics! ❌
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
| k(1bar) | 300K | 400K | 500K | 600K | 800K | 1000K | 1500K | 2000K |
|---|---|---|---|---|---|---|---|---|
| k(T): | -66.25 | -46.19 | -34.19 | -26.21 | -16.28 | -10.36 | -2.54 | 1.31 |
| k(T): | -49.54 | -33.65 | -24.16 | -17.85 | -10.01 | -5.35 | 0.80 | 3.82 |
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.
Errors occurred during edge comparison ⚠️
ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py nitrogen-edge stable_regression_results/nitrogen/chemkin/chem_edge_annotated.inp stable_regression_results/nitrogen/chemkin/species_edge_dictionary.txt test/regression/nitrogen/chemkin/chem_edge_annotated.inp test/regression/nitrogen/chemkin/species_edge_dictionary.txt` failed. (See above for error)
nitrogen Passed Observable Testing ✅
Regression test oxidation:
Reference: Execution time (DD:HH:MM:SS): 00:00:01:10
Current: Execution time (DD:HH:MM:SS): 00:00:01:31
Reference: Memory used: 799.14 MB
Current: Memory used: 795.92 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. ✅
oxidation Passed Observable Testing ✅
Errors occurred during observable testing ⚠️
WARNING: Initial mole fractions do not sum to one; normalizing.
Regression test sulfur:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:30
Current: Execution time (DD:HH:MM:SS): 00:00:00:36
Reference: Memory used: 911.36 MB
Current: Memory used: 914.26 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)
sulfur Passed Observable Testing ✅
Regression test superminimal:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:18
Current: Execution time (DD:HH:MM:SS): 00:00:00:23
Reference: Memory used: 986.91 MB
Current: Memory used: 957.87 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): 00:00:01:51
Current: Execution time (DD:HH:MM:SS): 00:00:02:44
Reference: Memory used: 2422.47 MB
Current: Memory used: 2524.87 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. ✅
RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅
Regression test RMS_CSTR_liquid_oxidation:
Reference: Execution time (DD:HH:MM:SS): 00:00:15:22
Current: Execution time (DD:HH:MM:SS): 00:00:11:40
Reference: Memory used: 3312.12 MB
Current: Memory used: 2785.91 MB
RMS_CSTR_liquid_oxidation Failed Core Comparison ❌
Original model has 35 species.
Test model has 35 species. ✅
Original model has 132 reactions.
Test model has 147 reactions. ❌
The original model has 5 species that the tested model does not have. ❌
spc: CH3
spc: C=CC(18)
spc: CC[CH]C(C)OO(32)
spc: [CH2]C(CCC)OO(33)
spc: C[CH]C(CC)OO(37)
The tested model has 5 species that the original model does not have. ❌
spc: CCCCCO
spc: CC=O(87)
spc: CC1CC(C)O1(96)
spc: CC=CC(C)OO(97)
spc: CC(CC(C)OO)OO
The original model has 34 reactions that the tested model does not have. ❌
rxn: C[CH]C(CC)OO(37) <=> CCC(CC)O[O](22) origin: intra_H_migration
rxn: [O]O(13) + C[CH]C(CC)OO(37) <=> oxygen(1) + CCC(CC)OO(27) origin: H_Abstraction
rxn: OO(23) + C[CH]C(CC)OO(37) <=> [O]O(13) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + pentane(2) <=> C[CH]CCC(11) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + pentane(2) <=> CC[CH]CC(7) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCCC(C)OO(26) <=> CCCC(C)O[O](21) + CCC(CC)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(37) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCC(CC)OO(27) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC(CC)OO(27) <=> C[CH]C(CC)OO(37) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]C(CC)OO(37) <=> C=CCCC(17) + CCC(CC)OO(27) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]C(CC)OO(37) <=> C=CCCC(17) + CCC(CC)OO(27) origin: Disproportionation
rxn: CC[CH]C(C)OO(32) <=> CCCC(C)O[O](21) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]C(C)OO(32) <=> oxygen(1) + CCCC(C)OO(26) origin: H_Abstraction
rxn: OO(23) + CC[CH]C(C)OO(32) <=> [O]O(13) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCCC(C)OO(26) <=> CCCC(C)O[O](21) + CCCC(C)OO(26) origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)OO(26) <=> CC[CH]C(C)OO(32) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]C(C)OO(32) <=> C=CCCC(17) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]C(C)OO(32) <=> C=CCCC(17) + CCCC(C)OO(26) origin: Disproportionation
rxn: CC[CH]C(C)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
rxn: C[CH]CCC(11) <=> C[CH2](6) + C=CC(18) origin: R_Addition_MultipleBond
rxn: CCCC(C)O[O](21) <=> [CH2]C(CCC)OO(33) origin: intra_H_migration
rxn: [O]O(13) + [CH2]C(CCC)OO(33) <=> oxygen(1) + CCCC(C)OO(26) origin: H_Abstraction
rxn: OO(23) + [CH2]C(CCC)OO(33) <=> [O]O(13) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCCC(C)OO(26) <=> CCCC(C)O[O](21) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [O]O(13) + C=CCCC(17) <=> [CH2]C(CCC)OO(33) origin: R_Addition_MultipleBond
rxn: [CH2]CCCC(12) + [CH2]C(CCC)OO(33) <=> C=CCCC(17) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]C(CCC)OO(33) <=> C=CCCC(17) + CCCC(C)OO(26) origin: Disproportionation
rxn: [CH2]C(CCC)OO(33) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction
The tested model has 49 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](25) + [OH](25) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: CC=O(87) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](25) + CCC(CC)OO(24) <=> H2O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](25) + H2O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + CCCC(C)O[O](22) origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCC(C)OO(27) + CCCCCOO(78) <=> H2O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [OH](25) + H2O(42) + CCCC(C)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [O]O(13) + H2O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](25) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](25) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(97) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [OH](25) + CCC(CC)OO(24) <=> H2O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [OH](25) + 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(27) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCCC(C)O[O](22) 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: [O]O(13) + C[CH]CCCOO(75) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(75) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(75) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCCOO(76) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(76) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(76) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(76) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(76) origin: H_Abstraction
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> H2O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + H2O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
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) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(74) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(74) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(74) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) <=> [OH](25) + CC1CC(C)O1(96) origin: Cyclic_Ether_Formation
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 77 species.
Test model has 99 species. ❌
Original model has 260 reactions.
Test model has 384 reactions. ❌
The tested model has 22 species that the original 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: CCCCO
spc: CCC(C)O
spc: CC=O(87)
spc: CCCC=O(88)
spc: CCCCO(89)
spc: CC[CH]C(C)O(90)
spc: [CH2]C(O)CCC(91)
spc: C[CH]CC(C)O(92)
spc: [CH2]CCC(C)O(93)
spc: C[CH]CCOO(94)
spc: [CH2]C(C)C(C)OO(95)
spc: CC1CC(C)O1(96)
spc: CC=CC(C)OO(97)
spc: C=CCC(C)OO(98)
spc: CC([O])CC(C)O(99)
spc: CC(CC(C)OO)OO
The tested model has 124 reactions that the original model does not have. ❌
rxn: CCC(CC)O[O](20) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCC(12) <=> CCCCCOO(78) origin: R_Recombination
rxn: [OH](25) + [OH](25) <=> OO(23) origin: R_Recombination
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCCCCO[O](61) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(18) origin: Disproportionation
rxn: CC=O(87) + [CH2]CC(5) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [OH](25) + CCC(CC)OO(24) <=> H2O(42) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](25) + H2O(42) + CCC(CC)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + CCCC(C)O[O](22) origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCC(C)OO(27) + CCCCCOO(78) <=> H2O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [OH](25) + H2O(42) + CCCC(C)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [O]O(13) + H2O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CCCCCO[O](61) origin: H_Abstraction
rxn: OO(23) + CCCCCOO(78) <=> [OH](25) + H2O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](25) + [O]O(13) + H2O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](100) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(97) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [OH](25) + CCC(CC)OO(24) <=> H2O(42) + [CH2]CC(CC)OO(32) origin: H_Abstraction
rxn: [OH](25) + 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(27) + CCCCCOO(78) <=> H2O(42) + CCCCC[O](79) + CCCC(C)O[O](22) 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: [O]O(13) + C[CH]CCCOO(75) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(75) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(75) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + C[CH]CCCOO(75) origin: H_Abstraction
rxn: [O]O(13) + [CH2]CCCCOO(76) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(76) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(76) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(76) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + [CH2]CCCCOO(76) origin: H_Abstraction
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> H2O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + H2O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
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) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(74) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(74) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(74) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) <=> [OH](25) + CC1CC(C)O1(96) origin: Cyclic_Ether_Formation
rxn: CC[C](CC)OO(53) + 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: 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(74) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]OO(82) + [CH2]CCC(9) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + CCC[CH]COO(73) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH3](10) + [CH2]CCCOO(83) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + C[CH]CCCOO(75) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + CCCC[CH]OO(84) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + [CH2]CCCCOO(76) <=> CCCCCOO(78) origin: R_Recombination
rxn: H(8) + [O]O(13) <=> OO(23) origin: R_Recombination
rxn: CH2(S)(3) + CCCC[O](85) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: CH2(S)(3) + CCC(C)[O](86) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: CH2(S)(3) + CCC(C)[O](86) <=> CCCC(C)[O](44) origin: 1,2_Insertion_carbene
rxn: H(8) + CCCC(C)=O(34) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: [CH3](10) + CCCC=O(88) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](44) <=> CCC[C](C)O(89) origin: intra_H_migration
rxn: CC[CH]C(C)O(90) <=> CCCC(C)[O](44) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> [CH2]C(O)CCC(91) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> C[CH]CC(C)O(92) origin: intra_H_migration
rxn: CCCC(C)[O](44) <=> [CH2]CCC(C)O(93) origin: intra_H_migration
rxn: CH2(S)(3) + C[CH]CCOO(94) <=> C[CH]CC(C)OO(37) origin: 1,2_Insertion_carbene
rxn: [CH2]C(C)C(C)OO(95) <=> C[CH]CC(C)OO(37) origin: 1,2_shiftC
rxn: H(8) + CC=CC(C)OO(97) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: H(8) + C=CCC(C)OO(98) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: C[CH]OO(56) + C=CC(19) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: CC[CH]C(C)OO(35) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: [CH2]CCC(C)OO(38) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CCC[C](C)OO(58) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> [CH2]C(CCC)OO(36) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CC([O])CC(C)O(99) origin: intra_OH_migration
rxn: [O]O(13) + CCC[CH]COO(73) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC[CH]OO(84) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: oxygen(1) + CCCC(C)[O](44) <=> [O]O(13) + CCCC(C)=O(34) origin: Disproportionation
rxn: oxygen(1) + CCCC(C)[O](44) <=> CCCC(C)OO[O](49) origin: R_Recombination
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + C=CCC(C)OO(98) origin: Disproportionation
rxn: CCCC(C)[O](44) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)O(47) origin: H_Abstraction
rxn: OO(23) + CCC[CH]COO(73) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCOO(78) <=> OO(23) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78) origin: H_Abstraction
rxn: [OH](25) + CCC(CC)OO(24) <=> H2O(42) + CC[C](CC)OO(53) origin: H_Abstraction
rxn: [OH](25) + CCC(CC)OO(24) <=> H2O(42) + C[CH]C(CC)OO(31) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> CC[C](CC)OO(53) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> C[CH]C(CC)OO(31) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCC(CC)OO(24) <=> [CH2]CC(CC)OO(32) + CCCC(C)O(47) origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + CCC[C](C)OO(58) origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + CC[CH]C(C)OO(35) origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + [CH2]C(CCC)OO(36) origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> H2O(42) + [CH2]CCC(C)OO(38) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(27) <=> CCC[C](C)OO(58) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(27) <=> CC[CH]C(C)OO(35) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(27) <=> [CH2]C(CCC)OO(36) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)OO(27) <=> [CH2]CCC(C)OO(38) + CCCC(C)O(47) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC[CH]COO(73) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC[CH]COO(73) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CCC[CH]COO(73) origin: H_Abstraction
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CCCC[CH]OO(84) 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(74) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCC[CH]COO(73) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> C[CH]CCCOO(75) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> CCCC[CH]OO(84) + CCCC(C)O(47) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCOO(78) <=> [CH2]CCCCOO(76) + CCCC(C)O(47) origin: H_Abstraction
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)
RMS_CSTR_liquid_oxidation Passed Observable Testing ✅
Regression test fragment:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:26
Current: Execution time (DD:HH:MM:SS): 00:00:00:31
Reference: Memory used: 758.73 MB
Current: Memory used: 758.18 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. ✅
fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️
WARNING: Initial mole fractions do not sum to one; normalizing.
Regression test RMS_constantVIdealGasReactor_fragment:
Reference: Execution time (DD:HH:MM:SS): 00:00:02:14
Current: Execution time (DD:HH:MM:SS): 00:00:03:06
Reference: Memory used: 2443.54 MB
Current: Memory used: 2552.80 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. ✅
RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️
WARNING: Initial mole fractions do not sum to one; normalizing.
Regression test minimal_surface:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:23
Current: Execution time (DD:HH:MM:SS): 00:00:00:29
Reference: Memory used: 922.80 MB
Current: Memory used: 915.28 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. ✅
minimal_surface Passed Observable Testing ✅
beep boop this comment was written by a bot 🤖
…tions
PDepSensitivity perturbs only conformer.E0. For a path reaction whose
microcanonical rate k(E) comes from an inverse Laplace transform of the
high-pressure-limit kinetics rather than from RRKM theory, that perturbation is a
structural no-op, so the reported sensitivity coefficient is identically zero.
This is the common case for RMG-generated networks: RMG synthesizes a transition
state with E0 = sum(E0 reactants) + Ea and no statmech modes, so Reaction.can_tst()
is False and rmgpy/pdep/reaction.pyx takes the ILT branch. There, the TS E0 is
referenced only inside the n < 0.25 branch -- and typical rate-rule / group-additivity
kinetics have n of roughly 0.3 to 2.5 -- while the result is subsequently renormalized
to kf_expected, which is the high-pressure-limit Arrhenius and independent of the TS E0.
Perturb the barrier at its source instead. Since E0(TS) = sum(E0 reactants) + Ea by
construction, shifting Ea by the same amount as E0 is the physically consistent
perturbation, and it reaches both the ILT convolution and the renormalization target.
Scoped carefully:
- Only when the synthetic relation actually holds. A hand-authored modeless TS may
carry an independent, physically meaningful E0; for those, moving Ea too would be
wrong, so only E0 is perturbed and the reason is logged. The check is written to be
invariant across a perturb/unperturb pair, so a reaction can never be perturbed
without being restored.
- For every path reaction sharing the TS object, not just the first. An Arkane input
may point several reaction blocks at one transitionState label; the E0 perturbation
already affects all of them, so the Ea perturbation must match that blast radius or
the two representations of the same barrier desynchronize.
- Not for RRKM-based reactions, which genuinely use the TS E0 and sum of states;
perturbing both would double-count.
- MultiArrhenius is not handled: apply_inverse_laplace_transform_method is Cython-typed
for Arrhenius, so such a reaction cannot reach the ILT path at all.
The output text now says plainly that ILT TS rows are a derivative along the coordinate
that raises the synthetic barrier, rather than a plain dln(r)/dE0. The YAML key format
is unchanged.
Measured on two RMG-generated networks, holding everything else fixed:
network1_1 (MSC) before: 4/4 TS coefficients exactly 0.0
after: 0/4 zero, max |coefficient| 1.15e-4
network4_1 (MSC) before: 300/300 TS coefficients exactly 0.0
after: 0/300 zero, max |coefficient| 1.16e-4
which is the same order as the well coefficients, and as the TS coefficients an
Arkane job with genuine statmech data already produced.
Regression Testing Results
Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:00:55 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-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_4_4_ene_1) + polycyclic(s3_4_6_ene_1) + Estimated bicyclic component: polycyclic(s2_4_6_ane) - ring(Cyclohexane) - ring(Cyclobutane) + ring(Cyclohexene) + ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclobutene) - ring(Cyclohexene) + radical(cyclobutane) Non-identical kinetics! ❌
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)
liquid_oxidation Passed Observable Testing ✅
Regression test nitrogen:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:56
Current: Execution time (DD:HH:MM:SS): 00:00:00:45
Reference: Memory used: 910.72 MB
Current: Memory used: 909.86 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. ✅
nitrogen Passed Observable Testing ✅
Regression test oxidation:
Reference: Execution time (DD:HH:MM:SS): 00:00:01:32
Current: Execution time (DD:HH:MM:SS): 00:00:01:10
Reference: Memory used: 792.60 MB
Current: Memory used: 793.04 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. ✅
oxidation Passed Observable Testing ✅
Errors occurred during observable testing ⚠️
WARNING: Initial mole fractions do not sum to one; normalizing.
Regression test sulfur:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:36
Current: Execution time (DD:HH:MM:SS): 00:00:00:29
Reference: Memory used: 905.36 MB
Current: Memory used: 908.41 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
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.
Condition 1:
Reactor Type: IdealGasReactor
Reaction Time: 0.01 s
T0: 900 K
P0: 30 bar
Initial Mole Fractions: {'S': 0.000756, '[O][O]': 0.00129, 'N#N': 0.997954}
sulfur Failed Observable Testing ❌
Errors occurred during observable testing ⚠️
ERROR conda.cli.main_run:execute(148): `conda run python rmgpy/tools/regression.py test/regression/sulfur/regression_input.py stable_regression_results/sulfur/chemkin test/regression/sulfur/chemkin` failed. (See above for error)
Regression test superminimal:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:23
Current: Execution time (DD:HH:MM:SS): 00:00:00:18
Reference: Memory used: 967.62 MB
Current: Memory used: 985.94 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): 00:00:02:23
Reference: Memory used: 2336.50 MB
Current: Memory used: 2492.39 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. ✅
RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅
Regression test RMS_CSTR_liquid_oxidation:
Reference: Execution time (DD:HH:MM:SS): 00:00:18:44
Current: Execution time (DD:HH:MM:SS): 00:00:22:48
Reference: Memory used: 3509.74 MB
Current: Memory used: 3507.85 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 176 reactions. ❌
The original model has 1 species that the tested model does not have. ❌
spc: CC[CH]CCOO(64)
The tested model has 1 species that the original model does not have. ❌
spc: CCCC=O(88)
The original model has 7 reactions that the tested model does not have. ❌
rxn: CC[CH]CCOO(64) <=> CCCCCO[O](61) origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(24) <=> CCCC(C)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> H2O(42) + CC[CH]CCOO(64) origin: H_Abstraction
The tested model has 37 reactions that the original model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](25) + [O]O(13) origin: H_Abstraction
rxn: [OH](25) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: [OH](25) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: [OH](25) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: [CH3](10) + CCCC=O(88) <=> CCCC(C)[O](44) origin: R_Addition_MultipleBond
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](22) <=> CC=CCC(16) + CCCC(C)OO(27) 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(27) 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](22) <=> CC=CCC(16) + CCCC(C)OO(27) 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(27) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](20) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCC(CC)OO(24) origin: Disproportionation
rxn: CCCC(C)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCCC(C)OO(27) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](25) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](20) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
Errors occurred during core comparison ⚠️
ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py RMS_CSTR_liquid_oxidation-core stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp stable_regression_results/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt test/regression/RMS_CSTR_liquid_oxidation/chemkin/chem_annotated.inp test/regression/RMS_CSTR_liquid_oxidation/chemkin/species_dictionary.txt` failed. (See above for error)
RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌
Original model has 99 species.
Test model has 107 species. ❌
Original model has 384 reactions.
Test model has 545 reactions. ❌
The tested model has 8 species that the original model does not have. ❌
spc: CCCCCOOOO(101)
spc: CCCC(C)OOO(102)
spc: CCCCCO(103)
spc: CCC[CH]CO(104)
spc: CCCCCOOO
spc: OOO(106)
spc: CCC(CC)OOO(107)
spc: CCCCCOOO(108)
The tested model has 161 reactions that the original model does not have. ❌
rxn: oxygen(1) + H2O(42) <=> [OH](25) + [O]O(13) origin: H_Abstraction
rxn: [OH](25) + OO(23) <=> [O]O(13) + H2O(42) origin: H_Abstraction
rxn: [OH](25) + [CH2]CCCC(12) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
rxn: [OH](25) + C[CH]CCC(11) <=> H2O(42) + C=CCCC(18) origin: Disproportionation
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](22) <=> CC=CCC(16) + CCCC(C)OO(27) 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(27) 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](22) <=> CC=CCC(16) + CCCC(C)OO(27) 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(27) origin: Disproportionation
rxn: [CH2]CC(CC)OO(32) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(24) origin: H_Abstraction
rxn: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + pentane(2) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + pentane(2) origin: Disproportionation
rxn: CCC(CC)O[O](20) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCC(CC)OO(24) origin: Disproportionation
rxn: CCCC(C)O[O](22) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCCC(C)OO(27) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCCCCOO(78) origin: Disproportionation
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> C[CH]CCCOO(75) + pentane(2) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCCOO(75) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + [OH](25) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)[O](44) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC[O](79) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: CCC(CC)O[O](20) + CCCCCO[O](61) <=> oxygen(1) + CCC([O])CC(41) + CCCCC[O](79) origin: Peroxyl_Disproportionation
rxn: [CH2]CCCCOO(76) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + pentane(2) <=> [CH2]CCCC(12) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCCOO(76) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: H(8) + [OH](25) <=> H2O(42) origin: R_Recombination
rxn: C=CCCC(18) + CC[CH]CC(7) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(18) + CC[CH]CC(7) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(18) + CC[CH]CC(7) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(18) + CC[CH]CC(7) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(18) + CC[CH]CC(7) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> CC[CH]CC(7) + CCCCCOO(78) origin: H_Abstraction
rxn: CC[CH]CC(7) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: CC[CH]CC(7) + 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: CC[CH]CC(7) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(98) + pentane(2) origin: Disproportionation
rxn: [O]O(13) + CCCCCO[O](61) <=> oxygen(1) + H2O(42) + CCCCC=O(72) origin: Peroxyl_Termination
rxn: [O]O(13) + CCCCCO[O](61) <=> CCCCCOOOO(101) origin: R_Recombination
rxn: [O]O(13) + CCCC(C)[O](44) <=> OO(23) + CCCC(C)=O(34) origin: Disproportionation
rxn: [O]O(13) + CCCC(C)[O](44) <=> oxygen(1) + CCCC(C)O(47) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)[O](44) <=> CCCC(C)OOO(102) origin: R_Recombination
rxn: C=CC[CH]C(64) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=CCCC(18) + C[CH]CCC(11) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(18) + C[CH]CCC(11) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + pentane(2) <=> C[CH]CCC(11) + CCCCCOO(78) origin: H_Abstraction
rxn: C[CH]CCC(11) + 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: C[CH]CCC(11) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(98) + pentane(2) origin: Disproportionation
rxn: C=CC[CH]C(64) + 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(66) + CCC(CC)OO(24) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCC(CC)OO(24) <=> C=CCCC(18) + CCC(CC)O[O](20) origin: H_Abstraction
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(72) + CCC(O)CC(46) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + 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: CCCC(C)[O](44) + CCC(CC)O[O](20) <=> CCCC(C)=O(34) + CCC(CC)OO(24) origin: Disproportionation
rxn: CCC(CC)O[O](20) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(98) + CCC(CC)OO(24) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCC(C)OO(27) <=> C=CCCC(18) + CCCC(C)O[O](22) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)O[O](22) <=> [CH2]C=CCC(66) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(27) <=> C=CCCC(18) + CCCC(C)O[O](22) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(27) <=> C=CCCC(18) + CCCC(C)O[O](22) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(27) <=> C=CCCC(18) + CCCC(C)O[O](22) origin: H_Abstraction
rxn: CCCC(C)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCC(C)=O(34) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CCCC(C)O[O](22) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCC(C)O(47) origin: Peroxyl_Termination
rxn: CCCC(C)[O](44) + CCCC(C)O[O](22) <=> CCCC(C)=O(34) + CCCC(C)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](22) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(98) + CCCC(C)OO(27) origin: Disproportionation
rxn: C[CH]CC(C)OO(37) + CCCC(C)OO(27) <=> CCC[C](C)OO(54) + CCCC(C)OO(27) origin: H_Abstraction
rxn: CC[CH]C(C)OO(35) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]C(CCC)OO(36) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(38) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCC(C)OO(27) origin: H_Abstraction
rxn: C[CH]CC(C)OO(37) + CCC(CC)OO(24) <=> CC[C](CC)OO(58) + CCCC(C)OO(27) origin: H_Abstraction
rxn: C[CH]C(CC)OO(31) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCC(CC)OO(24) origin: H_Abstraction
rxn: C=CCCC(18) + [CH2]CCCC(12) <=> C=CC[CH]C(64) + pentane(2) origin: H_Abstraction
rxn: C=CCCC(18) + [CH2]CCCC(12) <=> [CH2]C=CCC(66) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + pentane(2) <=> C=CCCC(18) + [CH2]CCCC(12) origin: H_Abstraction
rxn: C=[C]CCC(68) + pentane(2) <=> C=CCCC(18) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH]=CCCC(69) + pentane(2) <=> C=CCCC(18) + [CH2]CCCC(12) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CC[CH]CCOO(74) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCC[CH]COO(73) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCCCOO(78) <=> CCCC[CH]OO(84) + pentane(2) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + pentane(2) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC(C)[O](44) <=> C=CCCC(18) + CCCC(C)O(47) origin: Disproportionation
rxn: C=CC[CH]C(64) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=CCCC(18) + CCCCCO[O](61) <=> [CH2]C=CCC(66) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCCCOO(78) <=> C=CCCC(18) + CCCCCO[O](61) origin: H_Abstraction
rxn: [OH](25) + C=CCCC(18) <=> H2O(42) + C=CC[CH]C(64) origin: H_Abstraction
rxn: [OH](25) + C=CCCC(18) <=> H2O(42) + [CH2]C=CCC(66) origin: H_Abstraction
rxn: [OH](25) + C=CCCC(18) <=> H2O(42) + [CH2]CCC=C(67) origin: H_Abstraction
rxn: [OH](25) + C=CCCC(18) <=> H2O(42) + C=[C]CCC(68) origin: H_Abstraction
rxn: [OH](25) + C=CCCC(18) <=> H2O(42) + [CH]=CCCC(69) origin: H_Abstraction
rxn: [OH](25) + C=CCCC(18) <=> [CH2]C(O)CCC(91) origin: R_Addition_MultipleBond
rxn: [OH](25) + C=CCCC(18) <=> CCC[CH]CO(104) origin: R_Addition_MultipleBond
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=CCCC(18) + CCCC(C)[O](44) <=> C=CC[CH]C(64) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)[O](44) <=> [CH2]C=CCC(66) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=CCCC(18) + CCCC(C)[O](44) <=> [CH2]CCC=C(67) + CCCC(C)O(47) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)O(47) <=> C=CCCC(18) + CCCC(C)[O](44) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)O(47) <=> C=CCCC(18) + CCCC(C)[O](44) origin: H_Abstraction
rxn: C=CC[CH]C(64) + CCCC(C)OO(27) <=> 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(66) + CCCC(C)OO(27) origin: H_Abstraction
rxn: [CH2]CCC=C(67) + CCCC(C)OO(27) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: C=[C]CCC(68) + CCCC(C)OO(27) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: [CH]=CCCC(69) + CCCC(C)OO(27) <=> C=CCCC(18) + C[CH]CC(C)OO(37) origin: H_Abstraction
rxn: CCCCCO[O](61) + CCCCCO[O](61) <=> oxygen(1) + CCCCC=O(72) + CCCCCO(103) origin: Peroxyl_Termination
rxn: CC[CH]CCOO(74) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCCCO[O](61) <=> CCCC(C)=O(34) + CCCCCOO(78) origin: Disproportionation
rxn: CCCCCO[O](61) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(98) + CCCCCOO(78) origin: Disproportionation
rxn: [OH](25) + CCCC(C)[O](44) <=> H2O(42) + CCCC(C)=O(34) origin: Disproportionation
rxn: [OH](25) + CCCC(C)O(47) <=> H2O(42) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CC[CH]CCOO(74) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCC[CH]COO(73) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: CCCC[CH]OO(84) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(37) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC(C)O(47) <=> OO(23) + CCCC(C)[O](44) origin: H_Abstraction
rxn: CCCC(C)[O](44) + CCCC(C)[O](44) <=> CCCC(C)=O(34) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CC=CC(C)OO(97) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> C=CCC(C)OO(98) + CCCC(C)O(47) origin: Disproportionation
rxn: CCCC(C)[O](44) + C[CH]CC(C)OO(37) <=> CCCC(C)=O(34) + CCCC(C)OO(27) origin: Disproportionation
rxn: CCCC(C)O[O](22) + CCC(CC)OO[O](48) <=> oxygen(1) + CCCC(C)[O](44) + CCC(CC)O[O](20) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](22) + CCCC(C)OO[O](49) <=> oxygen(1) + CCCC(C)[O](44) + CCCC(C)O[O](22) origin: Peroxyl_Disproportionation
rxn: CCCC(C)O[O](22) + 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(27) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OOO(102) <=> [O]O(13) + H2O(42) + CCCC(C)O[O](22) 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(27) + CCC(CC)OOO(107) <=> H2O(42) + CCC(CC)O[O](20) + CCCC(C)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCC(C)OOO(102) <=> H2O(42) + CCC(CC)O[O](20) + CCCC(C)O[O](22) 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(27) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](22) + CCCC(C)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCC(C)OOO(102) <=> H2O(42) + CCCC(C)O[O](22) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(27) + CCCCCOOO(108) <=> H2O(42) + CCCC(C)O[O](22) + 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)
RMS_CSTR_liquid_oxidation Passed Observable Testing ✅
Regression test fragment:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:24
Reference: Memory used: 753.36 MB
Current: Memory used: 755.33 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. ✅
fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️
WARNING: Initial mole fractions do not sum to one; normalizing.
Regression test RMS_constantVIdealGasReactor_fragment:
Reference: Execution time (DD:HH:MM:SS): 00:00:02:41
Current: Execution time (DD:HH:MM:SS): 00:00:02:41
Reference: Memory used: 2539.89 MB
Current: Memory used: 2597.55 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. ✅
RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️
WARNING: Initial mole fractions do not sum to one; normalizing.
Regression test minimal_surface:
Reference: Execution time (DD:HH:MM:SS): 00:00:00:30
Current: Execution time (DD:HH:MM:SS): 00:00:00:25
Reference: Memory used: 909.45 MB
Current: Memory used: 914.69 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. ✅
minimal_surface Passed Observable Testing ✅
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| # re-derive can_tst() per reaction. Labels match the '(TS) <label>' keys used below. | ||
| ilt_ts_labels = [] | ||
| for rxn in self.job.network.path_reactions: | ||
| if rxn.transition_state is not None and not rxn.can_tst(): |
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Whilst this gate is not rxn.can_tst(), perturb() at lime 436 also requires isinstance(kinetics,Arrhenius) before it actually shifts to Ea. When they disagree, the YAML lists a ts under ilt_trainsition_stats and the header promises a combined E0+Ea derivative, whilst its Ea is never touched.
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Fixed. save()'s ilt_transition_states gate now also requires isinstance(kinetics, Arrhenius), matching what perturb() actually does — a TS is marked ILT only when its Ea was really shifted, so the header/metadata no longer promise the combined E0+Ea semantics for a row whose Ea was untouched. (In the reachable universe this is a no-op, since non-Arrhenius ILT can't occur — see the thread on line 444 — but it makes the defensive branch honest.) The ILT/contaminated classification is now a single helper, _classify_ilt_transition_states(), shared by save() and plot(), so the table, YAML and figure can't disagree.
| ts_label = '(TS) ' + rxn.transition_state.label | ||
| if ts_label not in ilt_ts_labels: | ||
| ilt_ts_labels.append(ts_label) | ||
| sa_data['metadata'] = {'ilt_transition_states': ilt_ts_labels} |
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sa_coefficients.yml previously had on structures plus reaction strings. Anything looping over th etop-level keys now hits a dict it cannot parse.
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structures was already a top-level non-reaction dict, so a consumer blindly iterating top-level keys as reactions was already broken before this PR (reaction keys are distinguishable by containing " <=> "). To remove any regression for the common case, metadata is now only written when it carries content, so an all-RRKM network's YAML keeps the pre-existing shape (structures + reaction strings) byte-for-byte.
| # TS row belonging to an ILT-based path reaction it is a derivative along the | ||
| # coordinate that raises E0 and Ea together, not a plain dln(k)/dE0(TS) (see save()). | ||
| # The coefficient has units of mol/J (the reciprocal of the perturbed energy). | ||
| axis.set_xlabel(r'Sensitivity coefficient ($\frac{mol}{J}$)') |
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two different derivatives now share one bar chart and the label was made generic so nothing in the figure distinguishes them. also check KineticSensitivity.plot() for the wrong label units that you corrected here.
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Fixed both. PDepSensitivity.plot() now annotates the TS tick labels — (E0+Ea) for ILT rows and (E0+Ea, contaminated) for shared-kinetics rows — so the two derivative types on the shared axis are distinguishable. And KineticsSensitivity.plot()'s inverted units are corrected to mol/J on both the forward and reverse xlabels.
| continue | ||
| perturbed_kinetics.add(id(kinetics)) | ||
| kinetics.Ea = quantity.Energy(kinetics.Ea.value_si + perturbation, 'J/mol') | ||
| else: |
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two things:
- this will fire twice due to lack of aliasing guard like you have for
if not unperturb - also this isn't reachable in a real run -
apply_inverse_laplace_transform_methodhas a Cython typedArrhenius kineticsparamter, so a non-arrhenius ILT raises aTypeErrorinnetwork.pybefore sensitivity runs.
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-
Fixed — the warning is now guarded by
not unperturb, so it fires once per perturbation instead of on both the perturb and unperturb passes. Addedtest_unsupported_kinetics_warning_not_duplicated_on_unperturb, confirmed red against the unguarded branch first. -
Confirmed.
apply_inverse_laplace_transform_methodis Cython-typedArrhenius kinetics, and the unperturbed base run in__init__executes before any perturbation, so a non-Arrhenius ILT reaction raisesTypeErrorthere first — the branch is unreachable in a real run. Keeping it as documented defensive-only code (tests pin the warning forMultiArrhenius/Chebyshev), now with an inline comment stating the unreachability.
| and not rxn.can_tst()): | ||
| other_kinetics = rxn.kinetics if rxn.network_kinetics is None else rxn.network_kinetics | ||
| if id(other_kinetics) in perturbed_kinetics: | ||
| logging.warning( |
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when shared kinetics is detected, the contaminated coefficicents are still written to the table and the yaml with no marker.
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Fixed — contamination is now surfaced in the output, not just the log. Contaminated TS rows are flagged with (!) in the text table (with an explanatory legend) and listed under metadata.contaminated_transition_states in sa_coefficients.yml. Detection is static (an Arrhenius object mapped to more than one distinct TS among ILT path reactions), via the shared _classify_ilt_transition_states() helper, with unit tests for both the ILT gate and contamination detection.
…etic Gate the Ea perturbation on can_tst() and the kinetics type alone (structural, invariant across the perturb/unperturb pair), not on an E0/Ea/species-energy arithmetic relation that real RMG-written networks almost never satisfy. Harden the mechanism per review: - perturb Ea once per Arrhenius object, not once per owning path reaction, so a kinetics instance shared by several of a TS's reactions is not shifted twice; - warn when one Arrhenius object is shared across reactions of different transition states (an unsupported input that cross-contaminates their sensitivities); - qualify the 'E0 alone is a no-op' docstring: strictly true only for n>=0.25; for n<0.25 E0 is a live grain threshold, which is why moving it alongside Ea is correct rather than a double-count; - soften the plot xlabel and fix its inverted units to mol/J, since ILT TS rows are an E0+Ea derivative, not a plain dln(k)/dE0; - tag ILT TS rows in sa_coefficients.yml so consumers need not re-derive can_tst(); - cover the TS-identity scoping and the shared-kinetics dedupe with unit tests. Address a second review round (calvinp0): - match save()'s ilt_transition_states metadata gate to perturb()'s actual behavior: a TS is marked ILT only when its kinetics is Arrhenius (i.e. its Ea was really shifted), so the YAML/header/plot no longer over-promise the combined-E0+Ea semantics for a row that never got the Ea perturbation; - guard the unsupported-kinetics warning with `not unperturb` so it fires once per perturbation, not twice (perturb + unperturb), and document that the branch is defensive-only (a non-Arrhenius ILT reaction cannot reach SA -- apply_inverse_laplace_transform_method is Cython-typed for Arrhenius, so the base run would already have raised); - only emit the top-level `metadata` YAML key when it carries content, so an all-RRKM network's output keeps the pre-existing shape byte-for-byte; - surface shared-kinetics-across-TS contamination in the output, not just the log: mark affected rows with '(!)' in the text table and list them under metadata.contaminated_transition_states in the YAML; - annotate the PDep plot's TS tick labels (E0+Ea / contaminated) so the two derivative types drawn on one axis are distinguishable; - also fix the inverted units (J/mol -> mol/J) in KineticsSensitivity.plot(); - factor the ILT/contaminated row classification into one helper shared by save() and plot() so the table, YAML and figure never disagree, with unit tests for the gate and contamination detection.
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@calvinp0 addressed all five in
Classification is factored into one helper shared by |
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Pull request overview
This PR fixes Arkane’s pressure-dependence (PDep) sensitivity analysis for ILT-based path reactions by making TS perturbations meaningful: when a path reaction’s microcanonical rate is derived via inverse Laplace transform (ILT) rather than RRKM, the sensitivity perturbation now shifts the owning Arrhenius barrier (Ea) alongside the TS E0, matching the physical “raise the barrier” coordinate and avoiding structurally zero coefficients.
Changes:
- Update
arkane.sensitivity.PDepSensitivityto perturbEain addition to TSE0for ILT-based (not can_tst()) path reactions with Arrhenius kinetics, with safeguards for shared kinetics objects and metadata/labeling in outputs. - Add focused unit tests for
PDepSensitivity.perturb()and TS classification logic. - Add a functional integration test and a new Arkane network fixture containing mixed ILT + RRKM path reactions to validate non-zero, finite coefficients and emitted YAML metadata.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| arkane/sensitivity.py | Implements ILT-aware TS perturbation (E0+Ea), adds TS classification + YAML/plot/table annotations for ILT and contaminated rows, and corrects sensitivity units labeling. |
| test/arkane/sensitivityTest.py | New unit tests covering ILT vs RRKM perturb semantics, shared-TS behavior, shared-kinetics aliasing warnings, and ILT TS row classification. |
| test/arkane/arkanePdepTest.py | Adds a functional integration test that runs a real PDep sensitivity job on a mixed ILT/RRKM network and validates coefficient behavior + YAML metadata. |
| test/rmgpy/test_data/arkane/tst_ilt_mixed/pdep_sa_ilt_mixed.py | New Arkane input fixture (acetyl + O2) configured to include both ILT-based and RRKM-based path reactions with sensitivity conditions enabled. |
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| Perturb E0 of `entry` which could be either a :class:TransitionState or a :class:Configuration | ||
| In the latter case, only the first species in the Configuration.species list is perturbed. | ||
| The perturbation is done by addition of the energy amount in self.perturbation. | ||
| If unperturb is `False`, the perturbation is addition of the energy amount in self.perturbation. | ||
| If unperturb is `False`, this is done by subtracting. |
| reactants = [ | ||
| ('acetyl', 'oxygen'), | ||
| ('ketene', 'hydroperoxyl'), | ||
| ('lactone', 'hydroxyl') |
| yaml_path = os.path.join(self.directory, "sensitivity", "sa_coefficients.yml") | ||
| assert os.path.isfile(yaml_path) | ||
| with open(yaml_path, "r") as f: | ||
| sa_data = yaml.unsafe_load(f) | ||
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Arkane's PDep sensitivity analysis perturbs
conformer.E0. For path reactions whose k(E) comes from an inverse Laplace transform instead of RRKM, that does nothing at all — the sensitivity coefficients come back as exactly zero.Since
E0(TS) = Σ E0(reactants) + Eaby construction, this perturbsEaby the same amount alongside E0, which reaches both the ILT convolution and the renormalization target.A hand-authored modeless TS with a real E0 keeps the old behavior; applied to every path reaction sharing the TS object, matching the E0 perturbation's reach; and skipped for RRKM reactions, where it would double-count.