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Load spin multiplicity into the Arkane Species Molecule if given explicitly in the main Arkane input file #2854

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jonwzheng merged 1 commit into from
Oct 30, 2025
Merged

Load spin multiplicity into the Arkane Species Molecule if given explicitly in the main Arkane input file #2854

jonwzheng merged 1 commit into from
Oct 30, 2025
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@alongd alongd commented Oct 27, 2025

Motivation or Problem

Running thermo in the same ARC/Arkane job for [CH2]CCO[CH2] singlet and [CH2]CCO[CH2] triplet failed with:

rmgpy.exceptions.DatabaseError: Adjacency list and multiplicity of [CH2]CCO[CH2][T] matches that of existing molecule [CH2]CCO[CH2][S] in thermo library thermo. Please correct your library.

despite defining the multiplicity correctly in the respective Arkane main ouput and in the species .py files.

For example, this input file results in the above error:

modelChemistry = LevelOfTheory(method='ccsd(t)f12',basis='ccpvtzf12',software='molpro')

frequencyScaleFactor = 0.988
useHinderedRotors = True
useAtomCorrections = True
useBondCorrections = True
bondCorrectionType = 'p'

species('[CH2]CCO[CH2][S]', '[CH2]CCO[CH2][S].py', structure=SMILES('[CH2]CCO[CH2]'), spinMultiplicity=1)
species('[CH2]CCO[CH2][T]', '[CH2]CCO[CH2][T].py', structure=SMILES('[CH2]CCO[CH2]'), spinMultiplicity=3)

thermo('[CH2]CCO[CH2][S]', 'NASA')
thermo('[CH2]CCO[CH2][T]', 'NASA')

Description of Changes

We now load the reserved keyword spinMultiplicity in the Arkane input file into the created molecule object.

Testing

Run the following ARC job before and after this implementaiton:

project: test_arkane_s_t

level_of_theory: CCSD(T)-F12/cc-pVTZ-F12//wb97xd/def2tzvp

species:
  - label: '[CH2]CCO[CH2](S)'
    smiles: '[CH2]CCO[CH2]'
    multiplicity: 1
    number_of_radicals: 2
  - label: '[CH2]CCO[CH2](T)'
    smiles: '[CH2]CCO[CH2]'
    multiplicity: 3
    number_of_radicals: 2

@alongd alongd mentioned this pull request Oct 27, 2025
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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): 00:00:00:50
Current: Execution time (DD:HH:MM:SS): 00:00:00:50
Reference: Memory used: 746.75 MB
Current: Memory used: 746.64 MB

aromatics Passed Core Comparison ✅

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

aromatics Passed Edge Comparison ✅

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

Details Observables Test Case: Aromatics Comparison

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

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:57
Current: Execution time (DD:HH:MM:SS): 00:00:01:58
Reference: Memory used: 847.95 MB
Current: Memory used: 847.55 MB

liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 241 reactions.
Test model has 241 reactions. ✅

liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1590 reactions.
Test model has 1593 reactions. ❌
The original model has 2 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> [OH](22) + CCCC(C)=O(29) origin: intra_H_migration
rxn: C[CH]CCCOO(51) <=> [OH](22) + CCCCC=O(48) origin: intra_H_migration
The tested model has 5 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(31) <=> CCC[C](C)OO(78) origin: intra_H_migration
rxn: CCCC[CH]OO(96) <=> C[CH]CCCOO(48) origin: intra_H_migration
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC([O])CC(C)OO(110) + CC([O])CCCOO(123) origin: Peroxyl_Disproportionation
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CC(C)OO(105) + CC(O)CCCOO(152) origin: Peroxyl_Termination
rxn: CC(CC(C)OO)O[O](90) + CC(CCCOO)O[O](108) <=> oxygen(1) + CC(=O)CCCOO(115) + CC(O)CC(C)OO(143) origin: Peroxyl_Termination

Non-identical kinetics! ❌
original:
rxn: CCC(CC)O[O](35) + CCCCCO[O](37) <=> oxygen(1) + CCC([O])CC(67) + CCCCC[O](69) origin: Peroxyl_Disproportionation
tested:
rxn: CCC(CC)O[O](37) + CCCCCO[O](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): 7.83 7.49 7.23 7.02 6.68 6.42 5.95 5.61

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,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing in family Peroxyl_Disproportionation.""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R in family Peroxyl_Disproportionation.
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing in family Peroxyl_Disproportionation.

Details Observables Test Case: liquid_oxidation Comparison

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

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:03
Current: Execution time (DD:HH:MM:SS): 00:00:01:02
Reference: Memory used: 850.02 MB
Current: Memory used: 843.27 MB

nitrogen Failed Core Comparison ❌

Original model has 41 species.
Test model has 41 species. ✅
Original model has 359 reactions.
Test model has 360 reactions. ❌
The tested model has 1 reactions that the original model does not have. ❌
rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction

nitrogen Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 981 reactions.
Test model has 983 reactions. ❌

Non-identical thermo! ❌
original: O1[C]=N1
tested: O1[C]=N1

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
116.46 53.90 11.62 12.71 13.49 13.96 14.14 13.85 13.58
141.64 58.66 12.26 12.27 12.09 11.96 12.26 12.72 12.15

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
The tested model has 2 reactions that the original model does not have. ❌
rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction
rxn: HON(T)(83) + HCO(13) <=> NO(38) + CH2O(18) origin: Disproportionation

Non-identical kinetics! ❌
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -49.54 -33.65 -24.16 -17.85 -10.01 -5.35 0.80 3.82
k(T): -66.25 -46.19 -34.19 -26.21 -16.28 -10.36 -2.54 1.31

kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.""")
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H in family Intra_R_Add_Endocyclic.

Details Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:48
Current: Execution time (DD:HH:MM:SS): 00:00:01:48
Reference: Memory used: 732.75 MB
Current: Memory used: 733.60 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 1526 reactions.
Test model has 1526 reactions. ✅

Details Observables Test Case: Oxidation Comparison

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

oxidation Passed Observable Testing ✅
Errors occurred during observable testing ⚠️ WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:39
Current: Execution time (DD:HH:MM:SS): 00:00:00:40
Reference: Memory used: 842.49 MB
Current: Memory used: 842.49 MB

sulfur Passed Core Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 74 reactions.
Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species.
Test model has 89 species. ✅
Original model has 227 reactions.
Test model has 227 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary
The tested model has 1 reactions that the original model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Details Observables Test Case: SO2 Comparison

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

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:25
Current: Execution time (DD:HH:MM:SS): 00:00:00:25
Reference: Memory used: 932.48 MB
Current: Memory used: 936.97 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): 00:00:02:15
Current: Execution time (DD:HH:MM:SS): 00:00:02:56
Reference: Memory used: 2301.03 MB
Current: Memory used: 2440.61 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

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

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

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

Details Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

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

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:09:38
Current: Execution time (DD:HH:MM:SS): 00:00:08:44
Reference: Memory used: 3388.46 MB
Current: Memory used: 2715.37 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 136 reactions.
Test model has 125 reactions. ❌
The original model has 5 species that the tested model does not have. ❌
spc: CCCCCO
spc: CC1CC(C)O1(87)
spc: CC=CC(C)OO(88)
spc: C=CCC(C)OO(89)
spc: CC(CC(C)OO)OO
The tested model has 5 species that the original model does not have. ❌
spc: [CH2]CCC(9)
spc: CH3
spc: C=CC(18)
spc: [CH2]C(CCC)OO(33)
spc: [CH2]CCC(C)OO(35)
The original model has 36 reactions that the tested model does not have. ❌
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: OO(23) + CCC(CC)OO(27) <=> [OH](25) + O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [OH](25) + O(42) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(17) origin: Disproportionation
rxn: OO(23) + CCCCCOO(78) <=> [OH](25) + O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](25) + [O]O(13) + O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](91) origin: R_Recombination
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [O]O(13) + O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(88) origin: Disproportionation
rxn: [OH](25) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCC(CC)OO(27) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCCCOO(78) <=> O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(27) <=> [O]O(13) + O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CC(C)OO(37) <=> [OH](25) + CC1CC(C)O1(87) origin: Cyclic_Ether_Formation
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + C=CCC(C)OO(89) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [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: [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
The tested model has 25 reactions that the original model does not have. ❌
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
rxn: [CH3](10) + [CH2]CCC(9) <=> pentane(2) origin: R_Recombination
rxn: [CH2]CCC(C)OO(35) <=> CCCC(C)O[O](21) origin: intra_H_migration
rxn: [O]O(13) + [CH2]CCC(C)OO(35) <=> oxygen(1) + CCCC(C)OO(26) origin: H_Abstraction
rxn: OO(23) + [CH2]CCC(C)OO(35) <=> [O]O(13) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + CCCC(C)OO(26) <=> CCCC(C)O[O](21) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + CCC(CC)OO(27) <=> CCC(CC)O[O](22) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)OO(26) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCC(C)OO(35) <=> C=CCCC(17) + CCCC(C)OO(26) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCC(C)OO(35) <=> C=CCCC(17) + CCCC(C)OO(26) origin: Disproportionation
rxn: [CH2]CCC(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(26) origin: H_Abstraction

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 90 species.
Test model has 77 species. ❌
Original model has 330 reactions.
Test model has 262 reactions. ❌
The original model has 13 species that the tested model does not have. ❌
spc: CCCCCO
spc: [CH2]COO(80)
spc: [CH2]CCOO(81)
spc: [CH2]OO(82)
spc: [CH2]CCCOO(83)
spc: CCCC[CH]OO(84)
spc: C[CH]CCOO(85)
spc: [CH2]C(C)C(C)OO(86)
spc: CC1CC(C)O1(87)
spc: CC=CC(C)OO(88)
spc: C=CCC(C)OO(89)
spc: CC([O])CC(C)O(90)
spc: CC(CC(C)OO)OO
The original model has 68 reactions that the tested model does not have. ❌
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: OO(23) + CCC(CC)OO(27) <=> [OH](25) + O(42) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [OH](25) + O(42) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [CH2]CCCC(12) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCCCO[O](61) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCC(12) <=> OO(23) + C=CCCC(17) origin: Disproportionation
rxn: OO(23) + CCCCCOO(78) <=> [OH](25) + O(42) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + OO(23) <=> [OH](25) + [O]O(13) + O(42) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> CC(CC(C)OO)O[O](91) origin: R_Recombination
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](44) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(24) <=> [O]O(13) + O(42) + CCCC(C)[O](44) origin: Bimolec_Hydroperoxide_Decomposition
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + CC=CC(C)OO(88) origin: Disproportionation
rxn: [OH](25) + CCCCC[O](79) <=> CCCCCOO(78) origin: R_Recombination
rxn: CCC(CC)OO(27) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)O[O](22) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCC(C)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](20) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCCCCOO(78) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCCCOO(78) <=> [O]O(13) + O(42) + CCCCC[O](79) origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(27) + CCCCCOO(78) <=> O(42) + CCC([O])CC(41) + CCCCCO[O](61) origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(27) <=> [O]O(13) + O(42) + CCC([O])CC(41) origin: Bimolec_Hydroperoxide_Decomposition
rxn: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CC(C)OO(37) <=> [OH](25) + CC1CC(C)O1(87) origin: Cyclic_Ether_Formation
rxn: oxygen(1) + C[CH]CC(C)OO(37) <=> [O]O(13) + C=CCC(C)OO(89) origin: Disproportionation
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [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: [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: [CH2](3) + CCCCOO(55) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCCCOO(55) <=> CCCCCOO(78) origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCCCO[O](61) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]COO(80) + [CH2]CC(5) <=> CCCCCOO(78) origin: R_Recombination
rxn: C[CH2](6) + [CH2]CCOO(81) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CC[CH]CCOO(64) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH2]OO(82) + [CH2]CCC(9) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CCC[CH]COO(63) <=> CCCCCOO(78) origin: R_Recombination
rxn: [CH3](10) + [CH2]CCCOO(83) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + C[CH]CCCOO(65) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + CCCC[CH]OO(84) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + [CH2]CCCCOO(66) <=> CCCCCOO(78) origin: R_Recombination
rxn: [H](8) + [O]O(13) <=> OO(23) origin: R_Recombination
rxn: [CH2](3) + C[CH]CCOO(85) <=> C[CH]CC(C)OO(37) origin: 1,2_Insertion_carbene
rxn: [CH2]C(C)C(C)OO(86) <=> C[CH]CC(C)OO(37) origin: 1,2_shiftC
rxn: [H](8) + CC=CC(C)OO(88) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: [H](8) + C=CCC(C)OO(89) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: C[CH]OO(56) + C=CC(18) <=> C[CH]CC(C)OO(37) origin: R_Addition_MultipleBond
rxn: CC[CH]C(C)OO(35) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: [CH2]CCC(C)OO(38) <=> C[CH]CC(C)OO(37) origin: intra_H_migration
rxn: C[CH]CC(C)OO(37) <=> CCC[C](C)OO(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(90) origin: intra_OH_migration
rxn: [H](8) + [OH](25) <=> O(42) origin: R_Recombination
rxn: [O]O(13) + CCC[CH]COO(63) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCC[CH]OO(84) <=> oxygen(1) + CCCCCOO(78) origin: H_Abstraction
rxn: OO(23) + CCC[CH]COO(63) <=> [O]O(13) + CCCCCOO(78) origin: H_Abstraction
rxn: [O]O(13) + CCCCCOO(78) <=> OO(23) + CCCC[CH]OO(84) origin: H_Abstraction
rxn: [CH2]CCCC(12) + CCC[CH]COO(63) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC[CH]OO(84) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCC[CH]COO(63) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC[CH]OO(84) <=> C=CCCC(17) + CCCCCOO(78) origin: Disproportionation

Details Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

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

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:30
Current: Execution time (DD:HH:MM:SS): 00:00:00:30
Reference: Memory used: 698.86 MB
Current: Memory used: 699.16 MB

fragment Passed Core Comparison ✅

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

fragment Passed Edge Comparison ✅

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

Details Observables Test Case: fragment Comparison

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

fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️ WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:40
Current: Execution time (DD:HH:MM:SS): 00:00:03:25
Reference: Memory used: 2511.06 MB
Current: Memory used: 2516.63 MB

RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

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

RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

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

Details Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

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

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅
Errors occurred during observable testing ⚠️ WARNING:root:Initial mole fractions do not sum to one; normalizing.

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:31
Current: Execution time (DD:HH:MM:SS): 00:00:00:31
Reference: Memory used: 844.38 MB
Current: Memory used: 849.67 MB

minimal_surface Passed Core Comparison ✅

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

minimal_surface Passed Edge Comparison ✅

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

Details Observables Test Case: minimal_surface Comparison

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

minimal_surface Passed Observable Testing ✅

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@alongd alongd requested a review from jonwzheng October 30, 2025 07:36
jonwzheng
jonwzheng approved these changes Oct 30, 2025
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LGTM

@jonwzheng jonwzheng merged commit d65c5f3 into main Oct 30, 2025
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@jonwzheng jonwzheng deleted the arkane_spc_mult_input branch October 30, 2025 14:53
@alongd alongd changed the title Load spin multiplicity into the Arkane Species Molecule if give explicitly in the main Arkane input file Load spin multiplicity into the Arkane Species Molecule if given explicitly in the main Arkane input file Dec 3, 2025
alongd added a commit to ReactionMechanismGenerator/ARC that referenced this pull request Dec 31, 2025
@alongd
Send the species multiplicity to Arkane's input file (#804)
1039e88 
To allow Arkane to process (and differentiate between) singlet and
triplet forms of the same structure.
See ReactionMechanismGenerator/RMG-Py#2854
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