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Fix Li atom type defs #2845

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Merged
JacksonBurns merged 3 commits into from
Sep 7, 2025
Merged

Fix Li atom type defs #2845

JacksonBurns merged 3 commits into from
Sep 7, 2025

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@alongd alongd commented Sep 6, 2025

Minor fixes to Li atom type definitions, added tests
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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): 00:00:00:51
Current: Execution time (DD:HH:MM:SS): 00:00:00:49
Reference: Memory used: 747.12 MB
Current: Memory used: 747.45 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: C1=CC2C=CC=1C=C2
tested: C1=CC2C=CC=1C=C2

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
164.90 80.93 22.21 28.97 35.25 40.69 48.70 53.97 64.36
129.39 79.85 22.98 30.09 36.61 42.21 50.22 55.39 65.95

thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(124cyclohexatriene)
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(1,4-Cyclohexadiene)

Non-identical kinetics! ❌
original:
rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [c]1ccccc1(3) + C1=CC2C=C[C]1C=C2(49) <=> benzene(1) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -3.00 -0.74 0.70 1.71 3.07 3.97 5.33 6.15
k(T): 4.24 4.69 5.05 5.33 5.79 6.14 6.78 7.23

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(9.943,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 38.5 to 41.6 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [H](4) + C1=CC2C=C[C]1C=C2(49) <=> [H][H](11) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -7.44 -4.08 -2.05 -0.69 1.02 2.06 3.46 4.18
k(T): 5.77 5.83 5.88 5.92 5.97 6.02 6.10 6.16

kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(18.137,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(4.06926e+10,'cm^3/(mol*s)'), n=0.47, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 75.2 to 75.9 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [CH]=C(7) + C1=CC2C=C[C]1C=C2(49) <=> C=C(13) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -7.17 -3.66 -1.56 -0.16 1.60 2.65 4.05 4.75
k(T): 4.06 4.76 5.18 5.46 5.81 6.02 6.30 6.44

kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(19.262,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(7.23e+12,'cm^3/(mol*s)'), n=0, Ea=(3.841,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_N-Sp-6R!H-4CHNS in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2CC2=C1(27) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.48 -21.35 -15.79 -12.03 -7.23 -4.28 -0.16 2.03
k(T): -4.55 -1.90 -0.23 0.94 2.49 3.50 5.02 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.063,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=C2C1(29) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -31.23 -21.91 -16.23 -12.40 -7.51 -4.50 -0.31 1.91
k(T): -5.30 -2.46 -0.68 0.57 2.21 3.28 4.87 5.80

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(48.686,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(13.089,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 53.5 to 54.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 202.2 to 203.7 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 53.5 to 54.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [CH]1C2=CC=CC12(8) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2=CC2C1(28) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -27.24 -18.91 -13.84 -10.40 -6.02 -3.30 0.48 2.51
k(T): -1.38 0.48 1.67 2.52 3.68 4.45 5.66 6.39

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(43.208,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(7.718,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 180.2 to 180.8 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation
tested:
rxn: [CH]=CC=C(15) + C1=CC2C=C[C]1C=C2(49) <=> C=CC=C(17) + C1=CC2C=CC=1C=C2(79)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -11.95 -7.61 -5.01 -3.27 -1.10 0.20 1.93 2.80
k(T): -0.49 0.99 1.87 2.46 3.19 3.64 4.23 4.52

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(23.821,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(8.084,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16)origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]=Cc1ccccc1(12) <=> C1=CC2C=CC=1C=C2(79) + C=Cc1ccccc1(16)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -12.28 -7.86 -5.21 -3.44 -1.23 0.10 1.87 2.75
k(T): -0.66 0.85 1.76 2.37 3.13 3.58 4.19 4.49

kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(24.273,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
kinetics: Arrhenius(A=(2.529e+11,'cm^3/(mol*s)'), n=0, Ea=(8.328,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0""")
Identical kinetics comments:
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-6R!H-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69)origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C1)C2(69)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.44 -21.32 -15.76 -12.01 -7.22 -4.26 -0.16 2.03
k(T): -4.51 -1.87 -0.20 0.96 2.51 3.52 5.03 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.606,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.01,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 46.5 to 50.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 195.1 to 199.2 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 46.5 to 50.2 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70)origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC(=C2)C1(70)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -32.11 -22.57 -16.76 -12.84 -7.84 -4.76 -0.49 1.78
k(T): -6.18 -3.12 -1.20 0.13 1.88 3.01 4.70 5.67

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(49.895,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(14.299,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 56.6 to 59.8 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 205.2 to 208.8 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 56.6 to 59.8 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71)origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + [CH]1C2=CC=CC1C=C2(48) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2=CC(C=C2)C1(71)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -33.97 -23.97 -17.88 -13.77 -8.54 -5.32 -0.86 1.50
k(T): -8.04 -4.52 -2.32 -0.81 1.18 2.46 4.32 5.39

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(52.457,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(16.86,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 214.4 to 219.5 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 65.8 to 70.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82)origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1C=C2(82)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -30.48 -21.35 -15.79 -12.03 -7.23 -4.28 -0.16 2.03
k(T): -4.55 -1.90 -0.23 0.94 2.49 3.50 5.02 5.92

kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(47.659,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(17.1699,'cm^3/(mol*s)'), n=3.635, Ea=(12.063,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 3.0 Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 195.4 to 199.4 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 3.0
Ea raised from 46.8 to 50.5 kJ/mol to match endothermicity of reaction.

Non-identical kinetics! ❌
original:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83)origin: Disproportionation
tested:
rxn: C1=CC2C=C[C]1C=C2(49) + C1=CC2C=C[C]1C=C2(49) <=> C1=CC2C=CC=1C=C2(79) + C1=CC2C=CC1=CC2(83)origin: Disproportionation

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -19.49 -12.98 -9.00 -6.29 -2.81 -0.64 2.42 4.08
k(T): 3.96 4.60 5.07 5.43 5.98 6.39 7.11 7.60

kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(33.226,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 9.0 Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(51.5097,'cm^3/(mol*s)'), n=3.635, Ea=(1.036,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation. Multiplied by reaction path degeneracy 9.0""")
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 9.0
Ea raised from 133.4 to 139.0 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O_Sp-5R!H=1R!H_Ext-4CHNS-R_Ext-4CHNS-R in family Disproportionation.
Multiplied by reaction path degeneracy 9.0

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): 00:00:02:04
Current: Execution time (DD:HH:MM:SS): 00:00:01:57
Reference: Memory used: 845.44 MB
Current: Memory used: 848.05 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 1593 reactions.
Test model has 1593 reactions. ✅
The original model has 4 reactions that the tested model does not have. ❌
rxn: C[CH]CC(C)OO(32) <=> CCC[C](C)OO(81)origin: intra_H_migration
rxn: CCCC[CH]OO(102) <=> C[CH]CCCOO(48)origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(CCC=O)OO(116)origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(=O)CCCOO(112)origin: intra_H_migration
The tested model has 4 reactions that the original model does not have. ❌
rxn: C[CH]CC(C)OO(31) <=> [OH](22) + CCCC(C)=O(28)origin: intra_H_migration
rxn: C[CH]CCCOO(63) <=> [OH](22) + CCCCC=O(60)origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> CC(CC[CH]OO)OO(133)origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> C[C](CCCOO)OO(132)origin: intra_H_migration

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

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): 7.83 7.49 7.23 7.02 6.68 6.42 5.95 5.61
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,'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.

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): 00:00:01:04
Current: Execution time (DD:HH:MM:SS): 00:00:01:02
Reference: Memory used: 848.18 MB
Current: Memory used: 847.92 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 Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 983 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)

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): 00:00:01:51
Current: Execution time (DD:HH:MM:SS): 00:00:01:50
Reference: Memory used: 734.59 MB
Current: Memory used: 733.88 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): 00:00:00:40
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 842.17 MB
Current: Memory used: 841.44 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: 928.74 MB
Current: Memory used: 933.56 MB

superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:55
Current: Execution time (DD:HH:MM:SS): 00:00:02:56
Reference: Memory used: 2287.13 MB
Current: Memory used: 2406.36 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): 00:00:17:24
Current: Execution time (DD:HH:MM:SS): 00:00:13:29
Reference: Memory used: 2759.88 MB
Current: Memory used: 2698.96 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 35 species.
Test model has 35 species. ✅
Original model has 141 reactions.
Test model has 130 reactions. ❌
The original model has 7 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=O(93)
spc: [CH2]CCC(C)O(99)
spc: CC(CC(C)OO)OO
The tested model has 7 species that the original model does not have. ❌
spc: CCH2
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)
spc: CC[CH]CCOO(64)
The original model has 45 reactions that the tested model does not have. ❌
rxn: CCCC(C)O[O](22) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)origin: H_Abstraction
rxn: C[CH]CC(C)OO(34) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)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(93) + [CH2]CC(5) <=> CCCC(C)[O](41)origin: R_Addition_MultipleBond
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + CCCC(C)O[O](22)origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + C[CH]CC(C)OO(34)origin: H_Abstraction
rxn: CCCC(C)OO(27) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](41) + CCCCCO[O](61)origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [OH](25) + O(42) + CCCC(C)O[O](22)origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [O]O(13) + O(42) + CCCC(C)[O](41)origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCC(CC)OO(24) <=> O(42) + CCC(CC)O[O](20)origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](25) + O(42) + CCC(CC)O[O](20)origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + CCCCCO[O](61)origin: H_Abstraction
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(34) <=> CC(CC(C)OO)O[O](100)origin: R_Recombination
rxn: CCCC(C)[O](41) <=> [CH2]CCC(C)O(99)origin: intra_H_migration
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + CC=CC(C)OO(88)origin: Disproportionation
rxn: [OH](25) + CCC(CC)OO(24) <=> O(42) + [CH2]CC(CC)OO(38)origin: H_Abstraction
rxn: [OH](25) + CCCCC[O](79) <=> CCCCCOO(78)origin: R_Recombination
rxn: CCCC(C)OO(27) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](22)origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)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: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78)origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78)origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + C[CH]CCCOO(65)origin: H_Abstraction
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCC([O])CC(44) + CCCCCO[O](61)origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + O(42) + CCC([O])CC(44)origin: Bimolec_Hydroperoxide_Decomposition
rxn: C[CH]CC(C)OO(34) <=> [OH](25) + CC1CC(C)O1(87)origin: Cyclic_Ether_Formation
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78)origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78)origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + [CH2]CCCCOO(66)origin: H_Abstraction
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + C=CCC(C)OO(89)origin: Disproportionation
The tested model has 34 reactions that the original 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]CCOO(64) <=> CCCCCO[O](61)origin: intra_H_migration
rxn: C[CH2](6) + [CH2]CC(5) <=> pentane(2)origin: R_Recombination
rxn: C[CH]CCC(11) <=> C[CH2](6) + C=CC(18)origin: R_Addition_MultipleBond
rxn: CCCC(C)O[O](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

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 99 species.
Test model has 77 species. ❌
Original model has 382 reactions.
Test model has 256 reactions. ❌
The original model has 22 species that the tested model does not have. ❌
spc: CCCCCO
spc: [CH2]COO(80)
spc: [CH2]CCOO(81)
spc: [CH2]OO(82)
spc: [CH2]CCCOO(83)
spc: CCCC[CH]OO(84)
spc: C[CH]CCOO(85)
spc: [CH2]C(C)C(C)OO(86)
spc: CC1CC(C)O1(87)
spc: CC=CC(C)OO(88)
spc: C=CCC(C)OO(89)
spc: CC([O])CC(C)O(90)
spc: CCCCO
spc: CCC(C)O
spc: CC=O(93)
spc: CCCC=O(94)
spc: CCCCO(95)
spc: CC[CH]C(C)O(96)
spc: [CH2]C(O)CCC(97)
spc: C[CH]CC(C)O(98)
spc: [CH2]CCC(C)O(99)
spc: CC(CC(C)OO)OO
The original model has 126 reactions that the tested model does not have. ❌
rxn: CCCC(C)O[O](22) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)origin: H_Abstraction
rxn: C[CH]CC(C)OO(34) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)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(93) + [CH2]CC(5) <=> CCCC(C)[O](41)origin: R_Addition_MultipleBond
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + CCCC(C)O[O](22)origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + C[CH]CC(C)OO(34)origin: H_Abstraction
rxn: CCCC(C)OO(27) + CCCCCOO(78) <=> O(42) + CCCC(C)[O](41) + CCCCCO[O](61)origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [OH](25) + O(42) + CCCC(C)O[O](22)origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCCC(C)OO(27) <=> [O]O(13) + O(42) + CCCC(C)[O](41)origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCC(CC)OO(24) <=> O(42) + CCC(CC)O[O](20)origin: H_Abstraction
rxn: OO(23) + CCC(CC)OO(24) <=> [OH](25) + O(42) + CCC(CC)O[O](20)origin: Bimolec_Hydroperoxide_Decomposition
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + CCCCCO[O](61)origin: H_Abstraction
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(34) <=> CC(CC(C)OO)O[O](100)origin: R_Recombination
rxn: CCCC(C)[O](41) <=> [CH2]CCC(C)O(99)origin: intra_H_migration
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + CC=CC(C)OO(88)origin: Disproportionation
rxn: [OH](25) + CCC(CC)OO(24) <=> O(42) + [CH2]CC(CC)OO(38)origin: H_Abstraction
rxn: [OH](25) + CCCCC[O](79) <=> CCCCCOO(78)origin: R_Recombination
rxn: CCCC(C)OO(27) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCCC(C)O[O](22)origin: Bimolec_Hydroperoxide_Decomposition
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCCCC[O](79) + CCC(CC)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: [O]O(13) + C[CH]CCCOO(65) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: OO(23) + C[CH]CCCOO(65) <=> [O]O(13) + CCCCCOO(78)origin: H_Abstraction
rxn: C[CH]CCCOO(65) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78)origin: H_Abstraction
rxn: [CH2]CCCC(12) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + C[CH]CCCOO(65) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + C[CH]CCCOO(65)origin: H_Abstraction
rxn: CCC(CC)OO(24) + CCCCCOO(78) <=> O(42) + CCC([O])CC(44) + CCCCCO[O](61)origin: Bimolec_Hydroperoxide_Decomposition
rxn: OO(23) + CCC(CC)OO(24) <=> [O]O(13) + O(42) + CCC([O])CC(44)origin: Bimolec_Hydroperoxide_Decomposition
rxn: C[CH]CC(C)OO(34) <=> [OH](25) + CC1CC(C)O1(87)origin: Cyclic_Ether_Formation
rxn: [O]O(13) + [CH2]CCCCOO(66) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: OO(23) + [CH2]CCCCOO(66) <=> [O]O(13) + CCCCCOO(78)origin: H_Abstraction
rxn: [CH2]CCCCOO(66) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78)origin: H_Abstraction
rxn: [CH2]CCCC(12) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + [CH2]CCCCOO(66) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + [CH2]CCCCOO(66)origin: H_Abstraction
rxn: oxygen(1) + C[CH]CC(C)OO(34) <=> [O]O(13) + C=CCC(C)OO(89)origin: Disproportionation
rxn: CCC[C](C)OO(54) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)origin: H_Abstraction
rxn: CC[CH]C(C)OO(32) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)origin: H_Abstraction
rxn: [CH2]C(CCC)OO(33) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)origin: H_Abstraction
rxn: [CH2]CCC(C)OO(35) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)OO(27)origin: H_Abstraction
rxn: [CH2](3) + CCCCOO(50) <=> CCCCCOO(78)origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCCCOO(50) <=> CCCCCOO(78)origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCCCO[O](61) <=> CCCCCOO(78)origin: R_Recombination
rxn: [CH2]COO(80) + [CH2]CC(5) <=> CCCCCOO(78)origin: R_Recombination
rxn: C[CH2](6) + [CH2]CCOO(81) <=> CCCCCOO(78)origin: R_Recombination
rxn: [H](8) + CC[CH]CCOO(64) <=> CCCCCOO(78)origin: R_Recombination
rxn: [CH2]OO(82) + [CH2]CCC(9) <=> CCCCCOO(78)origin: R_Recombination
rxn: [H](8) + CCC[CH]COO(63) <=> CCCCCOO(78)origin: R_Recombination
rxn: [CH3](10) + [CH2]CCCOO(83) <=> CCCCCOO(78)origin: R_Recombination
rxn: [H](8) + C[CH]CCCOO(65) <=> CCCCCOO(78)origin: R_Recombination
rxn: [H](8) + CCCC[CH]OO(84) <=> CCCCCOO(78)origin: R_Recombination
rxn: [H](8) + [CH2]CCCCOO(66) <=> CCCCCOO(78)origin: R_Recombination
rxn: [CH2](3) + C[CH]CCOO(85) <=> C[CH]CC(C)OO(34)origin: 1,2_Insertion_carbene
rxn: [CH2]C(C)C(C)OO(86) <=> C[CH]CC(C)OO(34)origin: 1,2_shiftC
rxn: [H](8) + CC=CC(C)OO(88) <=> C[CH]CC(C)OO(34)origin: R_Addition_MultipleBond
rxn: [H](8) + C=CCC(C)OO(89) <=> C[CH]CC(C)OO(34)origin: R_Addition_MultipleBond
rxn: C[CH]OO(52) + C=CC(19) <=> C[CH]CC(C)OO(34)origin: R_Addition_MultipleBond
rxn: CC[CH]C(C)OO(32) <=> C[CH]CC(C)OO(34)origin: intra_H_migration
rxn: [CH2]CCC(C)OO(35) <=> C[CH]CC(C)OO(34)origin: intra_H_migration
rxn: C[CH]CC(C)OO(34) <=> CCC[C](C)OO(54)origin: intra_H_migration
rxn: C[CH]CC(C)OO(34) <=> [CH2]C(CCC)OO(33)origin: intra_H_migration
rxn: C[CH]CC(C)OO(34) <=> CC([O])CC(C)O(90)origin: intra_OH_migration
rxn: [H](8) + [O]O(13) <=> OO(23)origin: R_Recombination
rxn: [CH2](3) + CCCC[O](91) <=> CCCC(C)[O](41)origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCC(C)[O](92) <=> CCCC(C)[O](41)origin: 1,2_Insertion_carbene
rxn: [CH2](3) + CCC(C)[O](92) <=> CCCC(C)[O](41)origin: 1,2_Insertion_carbene
rxn: [H](8) + CCCC(C)=O(31) <=> CCCC(C)[O](41)origin: R_Addition_MultipleBond
rxn: [CH3](10) + CCCC=O(94) <=> CCCC(C)[O](41)origin: R_Addition_MultipleBond
rxn: CCCC(C)[O](41) <=> CCC[C](C)O(95)origin: intra_H_migration
rxn: CC[CH]C(C)O(96) <=> CCCC(C)[O](41)origin: intra_H_migration
rxn: CCCC(C)[O](41) <=> [CH2]C(O)CCC(97)origin: intra_H_migration
rxn: CCCC(C)[O](41) <=> C[CH]CC(C)O(98)origin: intra_H_migration
rxn: [O]O(13) + CC[CH]CCOO(64) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: [O]O(13) + CCC[CH]COO(63) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: [O]O(13) + CCCC[CH]OO(84) <=> oxygen(1) + CCCCCOO(78)origin: H_Abstraction
rxn: oxygen(1) + CCCC(C)[O](41) <=> [O]O(13) + CCCC(C)=O(31)origin: Disproportionation
rxn: oxygen(1) + CCCC(C)[O](41) <=> CCCC(C)OO[O](48)origin: R_Recombination
rxn: CCCC(C)[O](41) + pentane(2) <=> CC[CH]CC(7) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + pentane(2) <=> C[CH]CCC(11) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + pentane(2) <=> [CH2]CCCC(12) + CCCC(C)O(46)origin: H_Abstraction
rxn: OO(23) + CC[CH]CCOO(64) <=> [O]O(13) + CCCCCOO(78)origin: H_Abstraction
rxn: OO(23) + CCC[CH]COO(63) <=> [O]O(13) + CCCCCOO(78)origin: H_Abstraction
rxn: [O]O(13) + CCCCCOO(78) <=> OO(23) + CCCC[CH]OO(84)origin: H_Abstraction
rxn: CC[CH]CCOO(64) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCCCOO(78)origin: H_Abstraction
rxn: CCC[CH]COO(63) + 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) + CCCC(C)OO(27) <=> O(42) + CCC[C](C)OO(54)origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + CC[CH]C(C)OO(32)origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + [CH2]C(CCC)OO(33)origin: H_Abstraction
rxn: [OH](25) + CCCC(C)OO(27) <=> O(42) + [CH2]CCC(C)OO(35)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(27) <=> CCCC(C)O[O](22) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(27) <=> CCC[C](C)OO(54) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(27) <=> CC[CH]C(C)OO(32) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(27) <=> C[CH]CC(C)OO(34) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(27) <=> [CH2]C(CCC)OO(33) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCC(C)OO(27) <=> [CH2]CCC(C)OO(35) + CCCC(C)O(46)origin: H_Abstraction
rxn: [OH](25) + CCC(CC)OO(24) <=> O(42) + CC[C](CC)OO(59)origin: H_Abstraction
rxn: [OH](25) + CCC(CC)OO(24) <=> O(42) + C[CH]C(CC)OO(37)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> CCC(CC)O[O](20) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> CC[C](CC)OO(59) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> C[CH]C(CC)OO(37) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCC(CC)OO(24) <=> [CH2]CC(CC)OO(38) + CCCC(C)O(46)origin: H_Abstraction
rxn: [CH2]CCCC(12) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [CH2]CCCC(12) + CCC[CH]COO(63) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [CH2]CCCC(12) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + CC[CH]CCOO(64) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + CCC[CH]COO(63) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: C[CH]CCC(11) + CCCC[CH]OO(84) <=> C=CCCC(18) + CCCCCOO(78)origin: Disproportionation
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + CC[CH]CCOO(64)origin: H_Abstraction
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + CCC[CH]COO(63)origin: H_Abstraction
rxn: [OH](25) + CCCCCOO(78) <=> O(42) + CCCC[CH]OO(84)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CCCCCO[O](61) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CC[CH]CCOO(64) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CCC[CH]COO(63) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> C[CH]CCCOO(65) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> CCCC[CH]OO(84) + CCCC(C)O(46)origin: H_Abstraction
rxn: CCCC(C)[O](41) + CCCCCOO(78) <=> [CH2]CCCCOO(66) + CCCC(C)O(46)origin: H_Abstraction

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: 698.95 MB
Current: Memory used: 699.52 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): 00:00:03:19
Current: Execution time (DD:HH:MM:SS): 00:00:03:29
Reference: Memory used: 2523.86 MB
Current: Memory used: 2564.71 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: 850.44 MB
Current: Memory used: 849.80 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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Copilot AI reviewed Sep 6, 2025
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Pull Request Overview

This PR fixes minor issues in lithium atom type definitions and adds corresponding test coverage. The changes correct the atom type label in the Li0 definition and fix an incorrect reference in the decrement_radical action.

  • Fix Li0 atom type constructor to use correct label 'Li0' instead of 'Li'
  • Correct decrement_radical action for Li0 from 'H0' to 'Li0'
  • Add test cases for lithium atom types Li+ and Li0

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File Description
rmgpy/molecule/atomtype.py Fixes Li0 atom type definition and corrects action mapping
test/rmgpy/molecule/atomtypeTest.py Adds test molecules and test method for lithium atom types

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rmgpy/molecule/atomtype.py

ATOMTYPES['Li'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Li'], break_bond=['Li'], increment_radical=['Li'], decrement_radical=['Li'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=['Li'], decrement_charge=['Li'])
ATOMTYPES['Li0'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Li0'], break_bond=['Li0'], increment_radical=['Li0'], decrement_radical=['H0'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=['Li+'], decrement_charge=[])
ATOMTYPES['Li0'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Li0'], break_bond=['Li0'], increment_radical=['Li0'], decrement_radical=['Li0'], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=['Li+'], decrement_charge=[])
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Copilot AI Sep 6, 2025

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The decrement_radical action was incorrectly referencing 'H0' instead of 'Li0'. This fix ensures that radical operations on Li0 atoms correctly transition to the Li0 atom type.
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rmgpy/molecule/atomtype.py
ATOMTYPES['Li'] = AtomType('Li', generic=['R', 'R!H', 'R!H!Val7'], specific=['Li0','Li+'],
single=[0,1], all_double=[0], r_double=[0], o_double=[0], s_double=[0], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[0], charge=[0,1])
ATOMTYPES['Li0'] = AtomType('Li', generic=['Li','R', 'R!H', 'R!H!Val7'], specific=[],
ATOMTYPES['Li0'] = AtomType('Li0', generic=['Li','R', 'R!H', 'R!H!Val7'], specific=[],
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Copilot AI Sep 6, 2025

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The AtomType constructor was incorrectly using 'Li' as the label instead of 'Li0'. This fix ensures the atom type has the correct label matching its key in the ATOMTYPES dictionary.
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@JacksonBurns JacksonBurns merged commit 6bdfa26 into main Sep 7, 2025
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@JacksonBurns JacksonBurns deleted the li_at_fixup branch September 7, 2025 21:51
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@alongd @JacksonBurns