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ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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FIx Handling of Initial Species with Seed Mechanisms #2653

Closed mjohnson541 closed 7 months ago

mjohnson541 commented 7 months ago

In #2649 it seems like we are having issues with adding seed mechanism containing a matching initial species while the initial species are in the edge.

Because of how we process creating the initial core-edge and running estimation we add the initial species to the edge first later add the seed mechanisms and reaction libraries and lastly add the initial species to core and react them.

In #2649 we run into a problem because the function for adding seed mechanisms searches for "site" and finds it (it is in the edge), since it finds it, it seems to assume it doesn't need to do anything which becomes a problem when it tries to add the associated reaction directly to core since "site" isn't in the core.

I have modified add_seed_mechanism_to_core to track species that are in the edge and add them to core before adding the reactions. I have modified enlarge to be okay with reacting a species that has already been added to core.

github-actions[bot] commented 7 months ago

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): 00:00:01:08 Current: Execution time (DD:HH:MM:SS): 00:00:01:06 Reference: Memory used: 2774.43 MB Current: Memory used: 2769.08 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: `C=CC1C=CC2=CC1C=C2` tested: `C=CC1C=CC2=CC1C=C2` |Hf(300K) |S(300K) |Cp(300K) |Cp(400K) |Cp(500K) |Cp(600K) |Cp(800K) |Cp(1000K) |Cp(1500K) | |----------|----------|----------|----------|----------|----------|----------|----------|----------| | 83.22| 84.16| 35.48| 45.14| 53.78| 61.40| 73.58| 82.20| 95.08| | 83.22| 82.78| 35.48| 45.14| 53.78| 61.40| 73.58| 82.20| 95.08| Identical thermo comments: thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,3-Cyclohexadiene) + ring(Cyclopentadiene) 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 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 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 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 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 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 Multiplied by reaction path degeneracy 3.0""")` kinetics: Estimated from node Root_Ext-1R!H-R_N-4R->O 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Multiplied by reaction path degeneracy 9.0
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): 00:00:02:16 Current: Execution time (DD:HH:MM:SS): 00:00:02:10 Reference: Memory used: 2907.43 MB Current: Memory used: 2907.41 MB
liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 37 species. ✅ Original model has 216 reactions. Test model has 215 reactions. ❌ The original model has 1 reactions that the tested model does not have. ❌ rxn: `CCO[O](30) <=> [OH](22) + CC=O(69)` origin: intra_H_migration
liquid_oxidation Failed Edge Comparison ❌ Original model has 202 species. Test model has 202 species. ✅ Original model has 1610 reactions. Test model has 1610 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: `CCO[O](30) <=> [OH](22) + CC=O(69)` origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCO[O](29) <=> C[CH]OO(70)` origin: intra_H_migration Non-identical kinetics! ❌ original: rxn: `CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](128) + CC([O])CC(C)OO(127)` origin: Peroxyl_Disproportionation tested: rxn: `CCCCCO[O](104) + CC(CC(C)OO)O[O](103) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129)` origin: Peroxyl_Disproportionation |k(1bar)|300K |400K |500K |600K |800K |1000K |1500K |2000K | |-------|-------|-------|-------|-------|-------|-------|-------|-------| |k(T): | 3.52| 4.27| 4.71| 5.01| 5.39| 5.61| 5.91| 6.06| |k(T): | 7.79| 7.46| 7.21| 7.00| 6.67| 6.41| 5.94| 5.60| kinetics: `Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.096,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")` kinetics: `Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0.053,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.""")` kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.
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): 00:00:01:26 Current: Execution time (DD:HH:MM:SS): 00:00:01:22 Reference: Memory used: 2901.14 MB Current: Memory used: 2903.68 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 132 species. Test model has 132 species. ✅ Original model has 997 reactions. Test model has 997 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""")` 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""")` Identical kinetics comments: kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H
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): 00:00:02:26 Current: Execution time (DD:HH:MM:SS): 00:00:02:23 Reference: Memory used: 2774.68 MB Current: Memory used: 2763.48 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. ✅
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 ✅
### Regression test sulfur: Reference: Execution time (DD:HH:MM:SS): 00:00:00:57 Current: Execution time (DD:HH:MM:SS): 00:00:00:54 Reference: Memory used: 2890.40 MB Current: Memory used: 2873.02 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
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): 00:00:00:37 Current: Execution time (DD:HH:MM:SS): 00:00:00:35 Reference: Memory used: 2960.56 MB Current: Memory used: 2987.04 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): 00:00:02:34 Current: Execution time (DD:HH:MM:SS): 00:00:02:25 Reference: Memory used: 3441.29 MB Current: Memory used: 3459.11 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. ✅
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): 00:00:06:28 Current: Execution time (DD:HH:MM:SS): 00:00:06:07 Reference: Memory used: 3372.10 MB Current: Memory used: 3378.24 MB
RMS_CSTR_liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 37 species. ✅ Original model has 232 reactions. Test model has 233 reactions. ❌ The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCO[O](35) <=> [OH](22) + CC=O(62)` origin: intra_H_migration
RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌ Original model has 206 species. Test model has 206 species. ✅ Original model has 1508 reactions. Test model has 1508 reactions. ✅ The original model has 2 reactions that the tested model does not have. ❌ rxn: `CCCO[O](34) <=> CC[CH]OO(45)` origin: intra_H_migration rxn: `CCO[O](35) <=> C[CH]OO(62)` origin: intra_H_migration The tested model has 2 reactions that the original model does not have. ❌ rxn: `CCO[O](35) <=> [OH](22) + CC=O(62)` origin: intra_H_migration rxn: `CCCO[O](34) <=> [OH](22) + CCC=O(44)` origin: intra_H_migration Non-identical kinetics! ❌ original: rxn: `CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](96) + CCCC(C)[O](61)` origin: Peroxyl_Disproportionation tested: rxn: `CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](98) + CCCC(C)[O](65)` origin: Peroxyl_Disproportionation |k(1bar)|300K |400K |500K |600K |800K |1000K |1500K |2000K | |-------|-------|-------|-------|-------|-------|-------|-------|-------| |k(T): | 3.69| 4.39| 4.82| 5.10| 5.45| 5.66| 5.94| 6.08| |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=(3.866,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")` 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""")` kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
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): 00:00:00:42 Current: Execution time (DD:HH:MM:SS): 00:00:00:40 Reference: Memory used: 2702.34 MB Current: Memory used: 2699.47 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. ✅
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 ✅
### Regression test RMS_constantVIdealGasReactor_fragment: Reference: Execution time (DD:HH:MM:SS): 00:00:03:16 Current: Execution time (DD:HH:MM:SS): 00:00:03:06 Reference: Memory used: 3603.35 MB Current: Memory used: 3584.96 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. ✅
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 ✅

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mjohnson541 commented 7 months ago

I tested this on the example in #2649 and it doesn't seem to be doing anything notable in the regression tests. However, this is a rather sensitive and opaque part of RMG.