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fix(arkane): make PDep sensitivity meaningful for ILT-based path reactions - #2990

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fix(arkane): make PDep sensitivity meaningful for ILT-based path reactions#2990
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@alongd alongd commented Jul 28, 2026

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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) + Ea by construction, this perturbs Ea by 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.

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alongd marked this pull request as ready for review July 28, 2026 05:06
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Regression Testing Results

⚠️ One or more regression tests failed.
Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:42
Current: Execution time (DD:HH:MM:SS): 00:00:00:52
Reference: Memory used: 829.40 MB
Current: Memory used: 829.74 MB

aromatics Passed Core Comparison ✅

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

aromatics Failed Edge Comparison ❌

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

Non-identical thermo! ❌
original: [CH]1C2=CC3C1C=CC23
tested: [CH]1C2=CC3C1C=CC23

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Errors occurred during edge comparison ⚠️ ERROR conda.cli.main_run:execute(148): `conda run python scripts/checkModels.py aromatics-edge stable_regression_results/aromatics/chemkin/chem_edge_annotated.inp stable_regression_results/aromatics/chemkin/species_edge_dictionary.txt test/regression/aromatics/chemkin/chem_edge_annotated.inp test/regression/aromatics/chemkin/species_edge_dictionary.txt` failed. (See above for error)
✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions! aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:28
Current: Execution time (DD:HH:MM:SS): 00:00:01:52
Reference: Memory used: 911.97 MB
Current: Memory used: 911.66 MB

liquid_oxidation Passed Core Comparison ✅

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

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1591 reactions.
Test model has 1591 reactions. ✅

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

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

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

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)
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:44
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)
✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions! nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:10
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. ✅

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions! oxidation Passed Observable Testing ✅
Errors occurred during observable testing ⚠️ WARNING: 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)
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:18
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. ✅

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

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:15:22
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)
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:26
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. ✅

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️ WARNING: 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. ✅

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️ WARNING: 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. ✅

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

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@alongd alongd mentioned this pull request Jul 29, 2026
Draft
alongd added 2 commits July 31, 2026 17:25
@alongd
fix(arkane): make PDep sensitivity meaningful for ILT-based path reac…
ac4fbf1 
…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.
@alongd
fix(arkane): make the ILT Ea-perturbation gate structural, not arithm…
e720866 
…etic

The previous commit perturbed an ILT-based path reaction's Arrhenius Ea alongside
the TS E0 only when the "synthetic" relation E0(TS) = sum(E0(reactants)) + Ea held
to within 1 kJ/mol (`_ts_e0_is_synthetic`). That guard is broken on real RMG output:
across 400 real RMG-written networks, only 24 of the 6,434 path reactions with a
resolvable species E0 satisfy the relation (0.4%), with a median miss of 146 kJ/mol
against the 1 kJ/mol tolerance. The relation is generally unrecoverable from a
written network file: RMG mutates Ea via `fix_barrier_height(force_positive=True)`
just before synthesizing E0(TS) (rmgpy/rmg/pdep.py), and Arkane strips
`energy_correction` when writing the file (arkane/pdep.py), so the file does not
carry the information the arithmetic check needs. In practice the guard therefore
reverted essentially every real network to the old behaviour: a structurally zero
TS sensitivity coefficient (~1e-14 mol/J of numerical noise, nine orders below the
well rows).

Replace the arithmetic gate with the structural condition that actually identifies
"ILT is the only path": `not rxn.can_tst()` (no TS statmech modes, so RRKM is
impossible) and the kinetics in use (`network_kinetics` if set, else `kinetics`)
being an `Arrhenius`. This also drops the carve-out for hand-authored modeless TSs
with an "independent" E0, deliberately: for an ILT-based reaction the TS E0 is never
referenced by `apply_inverse_laplace_transform_method` when n >= 0.25, acts only as
a grain-threshold cutoff when n < 0.25, and in every case the resulting k(E) is
renormalized so its canonical average reproduces the high-pressure-limit Arrhenius
k(T) (rmgpy/pdep/network.py), which depends on Ea and not on E0(TS). So the old
"protection" gave those inputs a meaningless structural zero, not a correct
dln(r)/dE0; the joint E0+Ea coordinate is the only meaningful "raise this barrier"
derivative for any ILT reaction, whatever the provenance of its E0.
`_ts_e0_is_synthetic` and its tolerance constant are deleted outright (not demoted
to a log line): the relation carries no decision weight, and warning about a
relation that fails for 99.6% of real networks would only mislead. The structural
condition is trivially invariant across a perturb/unperturb pair -- it depends only
on the presence of statmech modes and the kinetics type, neither of which the
perturbation touches -- so Ea can never be left shifted.

Verified on a real RMG-written T3 network (network13_2, CH2CNH <=> CH3CN, ILT
barrier with n=0, E0(TS) missing the relation by 137 kJ/mol): TS coefficients move
from +5e-16..+2.5e-14 mol/J (noise) to -1.7e-5..-9.1e-5 mol/J at the four
sensitivity conditions, negative as expected (raising the barrier slows the
reaction), identical in both direction keys (the equilibrium constant is
barrier-independent), and of the same order as -1/RT; the well rows
(1.0e-7..3.8e-6 mol/J) are unchanged.

Test updates, and why each new expectation is correct:

- test_modeless_ts_with_independent_e0_is_not_perturbed_for_ea is replaced by
  test_ilt_reaction_with_unrelated_ts_e0_still_perturbs_ea, a regression test
  using the real network13_2 energies: the old test asserted the guard's carve-out
  (Ea untouched when the relation fails), which is exactly the defect; the new
  contract is that Ea moves for every ILT/Arrhenius reaction.
- test_ts_e0_is_synthetic_tries_products_side_when_reactants_side_fails and
  test_ts_e0_is_synthetic_tolerance_boundary are deleted with the function they
  tested.
- test_ilt_reaction_perturbs_e0_and_ea and test_network_kinetics_is_perturbed_when_present
  no longer arrange species E0s to satisfy the relation, since it is no longer read.
- The tst_ilt_mixed fixture's 'entrance1' TS E0 moves from 0.0 to 2.0 kcal/mol so it
  no longer satisfies the relation. The fixture previously satisfied it trivially
  (every energy involved was 0.0), which is precisely why the earlier revision's
  integration test passed while real networks failed; the integration test now
  asserts the relation is broken and that the ILT TS coefficients are within two
  orders of magnitude of the well coefficients, not just nonzero.
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