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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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Patch for surface regression diffmodels #2656

Closed sevyharris closed 6 months ago

sevyharris commented 7 months ago

Patch for surface regression diffmodels

Motivation or Problem

The .github actions script calling scripts/checkModels.py does not use the correct arguments or filenames for checking a surface model. So this adds a check for whether the existence of surface files to rmgpy/tools/diffmodels.py

Description of Changes

Rather than changing this part of https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/.github/workflows/CI.yml ...

# Compare the edge and core
            if python-jl scripts/checkModels.py \
                "$regr_test-core" \
                $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
                $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
                test/regression/"$regr_test"/chemkin/chem_annotated.inp \
                test/regression/"$regr_test"/chemkin/species_dictionary.txt
            then

... I think it would be easier to add a check in Python to see if the surface files exist and chem_annotated.inp does not, and then make appropriate changes from there.

Testing

I ran the checkModels.py script locally and confirmed these changes fix the problem for the minimal_surface example without breaking the minimal example.

Even if this fix works, the minimal_surface regression test for this PR is not expected to pass because there are no stable regression edge files to compare against.

Reviewer Tips

Let me know if you have thoughts about the level at which this bug should be fixed. In theory, we could rewrite the CI.yml to call the surface tests separately from the others, but that sounds like a pain. Alternatively, we could move the check for surface files inside the checkModels.py script instead of adding it to rmgpy/tools/diffmodels.py

github-actions[bot] commented 7 months ago

Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing. WARNING:root:Initial mole fractions do not sum to one; normalizing. WARNING:root:Initial mole fractions do not sum to one; normalizing. Traceback (most recent call last): File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/diffmodels.py", line 365, in execute surface_path1 = kwargs['surface_path1'] KeyError: 'surface_path1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main python(vars(ns)) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python scope = runpy.run_path(script, run_name="main") File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path pkg_name=pkg_name, script_name=fname) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "scripts/checkModels.py", line 308, in error = main() File "scripts/checkModels.py", line 78, in main error = check(name, bench_chemkin, bench_species_dict, test_chemkin, test_species_dict) File "scripts/checkModels.py", line 92, in check execute(benchChemkin, benchSpeciesDict, bench_thermo, testChemkin, testSpeciesDict, test_thermo, kwargs) File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/diffmodels.py", line 375, in execute model1.species, model1.reactions = load_chemkin_file(chemkin1, species_dict1, thermo_path=thermo1) File "rmgpy/chemkin.pyx", line 982, in rmgpy.chemkin.load_chemkin_file species_dict = load_species_dictionary(dictionary_path, generate_resonance_structures=generate_resonance_structures) File "rmgpy/chemkin.pyx", line 872, in rmgpy.chemkin.load_species_dictionary with open(path, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'stable_regression_results/minimal_surface/chemkin/species_edge_dictionary.txt' ⚠️ 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): 00:00:01:05 Current: Execution time (DD:HH:MM:SS): 00:00:01:08 Reference: Memory used: 2782.56 MB Current: Memory used: 2780.55 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 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): 00:00:02:10 Current: Execution time (DD:HH:MM:SS): 00:00:02:12 Reference: Memory used: 2914.40 MB Current: Memory used: 2907.60 MB
liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 37 species. ✅ Original model has 215 reactions. Test model has 216 reactions. ❌ The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCO[O](31) <=> [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](29) <=> C[CH]OO(70)` origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCO[O](31) <=> [OH](22) + CC=O(69)` origin: intra_H_migration
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): 00:00:01:21 Current: Execution time (DD:HH:MM:SS): 00:00:01:24 Reference: Memory used: 2907.08 MB Current: Memory used: 2913.60 MB
nitrogen Passed Core Comparison ✅ Original model has 41 species. Test model has 41 species. ✅ Original model has 360 reactions. Test model has 360 reactions. ✅
nitrogen Passed Edge Comparison ✅ Original model has 132 species. Test model has 132 species. ✅ Original model has 997 reactions. Test model has 997 reactions. ✅
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): 00:00:02:20 Current: Execution time (DD:HH:MM:SS): 00:00:02:25 Reference: Memory used: 2773.59 MB Current: Memory used: 2777.12 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): 00:00:00:53 Current: Execution time (DD:HH:MM:SS): 00:00:00:56 Reference: Memory used: 2870.85 MB Current: Memory used: 2882.14 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): 00:00:00:35 Current: Execution time (DD:HH:MM:SS): 00:00:00:36 Reference: Memory used: 2953.68 MB Current: Memory used: 2988.34 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): 00:00:02:22 Current: Execution time (DD:HH:MM:SS): 00:00:02:27 Reference: Memory used: 3450.77 MB Current: Memory used: 3452.96 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): 00:00:05:56 Current: Execution time (DD:HH:MM:SS): 00:00:06:10 Reference: Memory used: 3392.12 MB Current: Memory used: 3369.44 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](21) + 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 1 reactions that the tested model does not have. ❌ rxn: `CCO[O](36) <=> C[CH]OO(63)` origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCO[O](35) <=> [OH](21) + CC=O(62)` origin: intra_H_migration Non-identical kinetics! ❌ original: rxn: `CCCO[O](35) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](91) + CCCC(C)[O](62)` origin: Peroxyl_Disproportionation tested: rxn: `CCCO[O](36) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](95) + CCCC(C)[O](65)` 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): | 3.69| 4.39| 4.82| 5.10| 5.45| 5.66| 5.94| 6.08| 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: `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: 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
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): 00:00:00:40 Current: Execution time (DD:HH:MM:SS): 00:00:00:42 Reference: Memory used: 2699.84 MB Current: Memory used: 2685.60 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): 00:00:02:59 Current: Execution time (DD:HH:MM:SS): 00:00:03:10 Reference: Memory used: 3592.57 MB Current: Memory used: 3591.37 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 ✅
### Regression test minimal_surface: Reference: Execution time (DD:HH:MM:SS): 00:00:01:05 Current: Execution time (DD:HH:MM:SS): 00:00:01:08 Reference: Memory used: 2892.65 MB Current: Memory used: 2891.83 MB
minimal_surface Failed Core Comparison ❌ Original model has 30 species. Test model has 30 species. ✅ Original model has 136 reactions. Test model has 136 reactions. ✅ Non-identical thermo! ❌ original: `X` tested: `X` |Hf(300K) |S(300K) |Cp(300K) |Cp(400K) |Cp(500K) |Cp(600K) |Cp(800K) |Cp(1000K) |Cp(1500K) | |----------|----------|----------|----------|----------|----------|----------|----------|----------| | 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| | 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| Identical thermo comments: thermo: Thermo library: surfaceThermoPt111
minimal_surface Failed Edge Comparison ❌
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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github-actions[bot] commented 6 months ago

Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing. WARNING:root:Initial mole fractions do not sum to one; normalizing. WARNING:root:Initial mole fractions do not sum to one; normalizing. Traceback (most recent call last): File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/diffmodels.py", line 365, in execute surface_path1 = kwargs['surface_path1'] KeyError: 'surface_path1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main python(vars(ns)) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python scope = runpy.run_path(script, run_name="main") File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path pkg_name=pkg_name, script_name=fname) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "scripts/checkModels.py", line 308, in error = main() File "scripts/checkModels.py", line 78, in main error = check(name, bench_chemkin, bench_species_dict, test_chemkin, test_species_dict) File "scripts/checkModels.py", line 92, in check execute(benchChemkin, benchSpeciesDict, bench_thermo, testChemkin, testSpeciesDict, test_thermo, kwargs) File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/diffmodels.py", line 375, in execute model1.species, model1.reactions = load_chemkin_file(chemkin1, species_dict1, thermo_path=thermo1) File "rmgpy/chemkin.pyx", line 982, in rmgpy.chemkin.load_chemkin_file species_dict = load_species_dictionary(dictionary_path, generate_resonance_structures=generate_resonance_structures) File "rmgpy/chemkin.pyx", line 872, in rmgpy.chemkin.load_species_dictionary with open(path, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'stable_regression_results/minimal_surface/chemkin/species_edge_dictionary.txt' ⚠️ 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): 00:00:01:06 Current: Execution time (DD:HH:MM:SS): 00:00:01:09 Reference: Memory used: 2783.62 MB Current: Memory used: 2769.30 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| 82.78| 35.48| 45.14| 53.78| 61.40| 73.58| 82.20| 95.08| | 83.22| 84.16| 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): 00:00:02:10 Current: Execution time (DD:HH:MM:SS): 00:00:02:12 Reference: Memory used: 2918.24 MB Current: Memory used: 2904.07 MB
liquid_oxidation Passed Core Comparison ✅ Original model has 37 species. Test model has 37 species. ✅ Original model has 215 reactions. Test model has 215 reactions. ✅
liquid_oxidation Failed Edge Comparison ❌ Original model has 202 species. Test model has 202 species. ✅ Original model has 1613 reactions. Test model has 1618 reactions. ❌ The tested model has 5 reactions that the original model does not have. ❌ rxn: `[CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(36) + CC[CH]CCOO(114)` origin: H_Abstraction rxn: `[CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(36) + CCC[CH]COO(113)` origin: H_Abstraction rxn: `[CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(36) + C[CH]CCCOO(115)` origin: H_Abstraction rxn: `[CH2]CCOO(70) + CCCCCOO(105) <=> CCCOO(36) + CCCC[CH]OO(137)` origin: H_Abstraction rxn: `CCCOO(36) + [CH2]CCCCOO(116) <=> [CH2]CCOO(70) + CCCCCOO(105)` origin: H_Abstraction
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): 00:00:01:22 Current: Execution time (DD:HH:MM:SS): 00:00:01:23 Reference: Memory used: 2915.50 MB Current: Memory used: 2905.32 MB
nitrogen Passed Core Comparison ✅ Original model has 41 species. Test model has 41 species. ✅ Original model has 360 reactions. Test model has 360 reactions. ✅
nitrogen Passed Edge Comparison ✅ Original model has 132 species. Test model has 132 species. ✅ Original model has 997 reactions. Test model has 997 reactions. ✅
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): 00:00:02:22 Current: Execution time (DD:HH:MM:SS): 00:00:02:23 Reference: Memory used: 2777.05 MB Current: Memory used: 2772.11 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): 00:00:00:55 Current: Execution time (DD:HH:MM:SS): 00:00:00:54 Reference: Memory used: 2875.62 MB Current: Memory used: 2876.72 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): 00:00:00:35 Current: Execution time (DD:HH:MM:SS): 00:00:00:36 Reference: Memory used: 2987.18 MB Current: Memory used: 2984.77 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): 00:00:02:22 Current: Execution time (DD:HH:MM:SS): 00:00:02:24 Reference: Memory used: 3433.43 MB Current: Memory used: 3444.22 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): 00:00:05:54 Current: Execution time (DD:HH:MM:SS): 00:00:06:00 Reference: Memory used: 3372.45 MB Current: Memory used: 3371.54 MB
RMS_CSTR_liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 37 species. ✅ Original model has 233 reactions. Test model has 232 reactions. ❌ The original model has 1 reactions that the tested model does not have. ❌ rxn: `CCO[O](36) <=> [OH](21) + 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: `CCO[O](36) <=> [OH](21) + CC=O(62)` origin: intra_H_migration rxn: `CCCO[O](34) <=> [OH](21) + CCC=O(44)` origin: intra_H_migration The tested model has 2 reactions that the original model does not have. ❌ rxn: `CCCO[O](34) <=> CC[CH]OO(45)` origin: intra_H_migration rxn: `CCO[O](36) <=> C[CH]OO(62)` origin: intra_H_migration
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): 00:00:00:40 Current: Execution time (DD:HH:MM:SS): 00:00:00:41 Reference: Memory used: 2698.92 MB Current: Memory used: 2701.63 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): 00:00:03:02 Current: Execution time (DD:HH:MM:SS): 00:00:03:04 Reference: Memory used: 3595.05 MB Current: Memory used: 3598.64 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 ✅
### Regression test minimal_surface: Reference: Execution time (DD:HH:MM:SS): 00:00:01:06 Current: Execution time (DD:HH:MM:SS): 00:00:01:07 Reference: Memory used: 2892.71 MB Current: Memory used: 2892.37 MB
minimal_surface Failed Core Comparison ❌ Original model has 30 species. Test model has 30 species. ✅ Original model has 136 reactions. Test model has 136 reactions. ✅ Non-identical thermo! ❌ original: `X` tested: `X` |Hf(300K) |S(300K) |Cp(300K) |Cp(400K) |Cp(500K) |Cp(600K) |Cp(800K) |Cp(1000K) |Cp(1500K) | |----------|----------|----------|----------|----------|----------|----------|----------|----------| | 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| | 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| Identical thermo comments: thermo: Thermo library: surfaceThermoPt111
minimal_surface Failed Edge Comparison ❌
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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github-actions[bot] commented 6 months ago

Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing. WARNING:root:Initial mole fractions do not sum to one; normalizing. WARNING:root:Initial mole fractions do not sum to one; normalizing. Traceback (most recent call last): File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/diffmodels.py", line 365, in execute surface_path1 = kwargs['surface_path1'] KeyError: 'surface_path1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main python(vars(ns)) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python scope = runpy.run_path(script, run_name="main") File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path pkg_name=pkg_name, script_name=fname) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "/usr/share/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "scripts/checkModels.py", line 308, in error = main() File "scripts/checkModels.py", line 78, in main error = check(name, bench_chemkin, bench_species_dict, test_chemkin, test_species_dict) File "scripts/checkModels.py", line 92, in check execute(benchChemkin, benchSpeciesDict, bench_thermo, testChemkin, testSpeciesDict, test_thermo, kwargs) File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/tools/diffmodels.py", line 375, in execute model1.species, model1.reactions = load_chemkin_file(chemkin1, species_dict1, thermo_path=thermo1) File "rmgpy/chemkin.pyx", line 982, in rmgpy.chemkin.load_chemkin_file species_dict = load_species_dictionary(dictionary_path, generate_resonance_structures=generate_resonance_structures) File "rmgpy/chemkin.pyx", line 872, in rmgpy.chemkin.load_species_dictionary with open(path, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'stable_regression_results/minimal_surface/chemkin/species_edge_dictionary.txt' ⚠️ 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): 00:00:01:06 Current: Execution time (DD:HH:MM:SS): 00:00:01:06 Reference: Memory used: 2783.62 MB Current: Memory used: 2769.24 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. ✅
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): 00:00:02:10 Current: Execution time (DD:HH:MM:SS): 00:00:02:12 Reference: Memory used: 2918.24 MB Current: Memory used: 2908.54 MB
liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 37 species. ✅ Original model has 215 reactions. Test model has 215 reactions. ✅ Non-identical kinetics! ❌ original: rxn: `CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](128)` origin: Peroxyl_Disproportionation tested: rxn: `CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128)` 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): | 3.77| 4.45| 4.86| 5.14| 5.48| 5.68| 5.96| 6.09| 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: `Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""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 kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R
liquid_oxidation Failed Edge Comparison ❌ Original model has 202 species. Test model has 202 species. ✅ Original model has 1613 reactions. Test model has 1610 reactions. ❌ The original model has 4 reactions that the tested model does not have. ❌ rxn: `C[CH]CCCO(157) + CCCCCO[O](103) <=> CC=CCCO(183) + CCCCCOO(105)` origin: Disproportionation rxn: `C[CH]CCCO(157) + CCCCCO[O](103) <=> C=CCCCO(184) + CCCCCOO(105)` origin: Disproportionation rxn: `C[CH]CCCO(157) + C[CH]CCCO(157) <=> CC=CCCO(183) + CCCCCO(130)` origin: Disproportionation rxn: `C[CH]CCCO(157) + C[CH]CCCO(157) <=> C=CCCCO(184) + CCCCCO(130)` origin: Disproportionation The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCCCCO[O](104) + CCCCCO[O](104) <=> oxygen(1) + CCCCC=O(120) + CCCCCO(130)` origin: Peroxyl_Termination Non-identical kinetics! ❌ original: rxn: `CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](128)` origin: Peroxyl_Disproportionation tested: rxn: `CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128)` 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): | 3.77| 4.45| 4.86| 5.14| 5.48| 5.68| 5.96| 6.09| 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: `Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""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 kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R
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): 00:00:01:22 Current: Execution time (DD:HH:MM:SS): 00:00:01:23 Reference: Memory used: 2915.50 MB Current: Memory used: 2906.44 MB
nitrogen Passed Core Comparison ✅ Original model has 41 species. Test model has 41 species. ✅ Original model has 360 reactions. Test model has 360 reactions. ✅
nitrogen Passed Edge Comparison ✅ Original model has 132 species. Test model has 132 species. ✅ Original model has 997 reactions. Test model has 997 reactions. ✅
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): 00:00:02:22 Current: Execution time (DD:HH:MM:SS): 00:00:02:22 Reference: Memory used: 2777.05 MB Current: Memory used: 2763.55 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): 00:00:00:55 Current: Execution time (DD:HH:MM:SS): 00:00:00:54 Reference: Memory used: 2875.62 MB Current: Memory used: 2876.09 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): 00:00:00:35 Current: Execution time (DD:HH:MM:SS): 00:00:00:35 Reference: Memory used: 2987.18 MB Current: Memory used: 2954.10 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): 00:00:02:22 Current: Execution time (DD:HH:MM:SS): 00:00:02:23 Reference: Memory used: 3433.43 MB Current: Memory used: 3447.14 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): 00:00:05:54 Current: Execution time (DD:HH:MM:SS): 00:00:05:34 Reference: Memory used: 3372.45 MB Current: Memory used: 3362.96 MB
RMS_CSTR_liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 35 species. ❌ Original model has 233 reactions. Test model has 212 reactions. ❌ The original model has 2 species that the tested model does not have. ❌ spc: CCC(37) spc: C[CH]OCCC(127) The original model has 21 reactions that the tested model does not have. ❌ rxn: `[CH2]CC(5) + pentane(2) <=> CCC(37) + CC[CH]CC(7)` origin: H_Abstraction rxn: `[CH2]CC(5) + pentane(2) <=> CCC(37) + C[CH]CCC(11)` origin: H_Abstraction rxn: `CCC(37) + [CH2]CCCC(12) <=> [CH2]CC(5) + pentane(2)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCC(C)OO(60) <=> CCC(37) + CCCC(C)O[O](33)` origin: H_Abstraction rxn: `[CH2]CC(5) + C[CH]CCC(11) <=> CCC(37) + C=CCCC(25)` origin: Disproportionation rxn: `[CH2]CC(5) + CCC(CC)OO(23) <=> CCC(37) + CCC(CC)O[O](19)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCCCOO(91) <=> CCC(37) + CCCCCO[O](72)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCOO(59) <=> CCCO[O](34) + CCC(37)` origin: H_Abstraction rxn: `OO(20) + [CH2]CC(5) <=> [O]O(13) + CCC(37)` origin: H_Abstraction rxn: `[OH](21) + CCC(37) <=> O(40) + [CH2]CC(5)` origin: H_Abstraction rxn: `CC=O(62) + [CH2]CC(5) <=> C[CH]OCCC(127)` origin: R_Addition_MultipleBond rxn: `[CH2]CC(5) + CCCC(C)OO(60) <=> CCC(37) + C[CH]CC(C)OO(51)` origin: H_Abstraction rxn: `[O]O(13) + [CH2]CC(5) <=> oxygen(1) + CCC(37)` origin: H_Abstraction rxn: `[CH2]CC(5) + [CH2]CCCC(12) <=> CCC(37) + C=CCCC(25)` origin: Disproportionation rxn: `[CH2]CC(5) + CCCC(C)OO(60) <=> CCC(37) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCC(CC)OO(23) <=> CCC(37) + C[CH]C(CC)OO(31)` origin: H_Abstraction rxn: `[CH2]CC(5) + CC(CC(C)OO)OO(171) <=> CCC(37) + CC(CC(C)OO)O[O](148)` origin: H_Abstraction rxn: `[CH2]CC(5) + C[CH]CCC(11) <=> CCC(37) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]CC(5) + CC[CH]CC(7) <=> CCC(37) + CC=CCC(16)` origin: Disproportionation rxn: `CCO[O](36) + C[CH]CCC(11) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `CCO[O](36) + CC[CH]CC(7) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation
RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌ Original model has 206 species. Test model has 197 species. ❌ Original model has 1508 reactions. Test model has 1406 reactions. ❌ The original model has 9 species that the tested model does not have. ❌ spc: C[CH]OCC(136) spc: C=COCCC(137) spc: [CH2]COCCC(138) spc: CC[CH]OCC(139) spc: C[CH]COCC(140) spc: [CH2]CCOCC(141) spc: CCCOCC(149) spc: CC([O])O(150) spc: C[CH]C(O)CC(202) The original model has 112 reactions that the tested model does not have. ❌ rxn: `[CH2]CC(5) + [CH2]CCCC(12) <=> CCC(37) + C=CCCC(25)` origin: Disproportionation rxn: `CCO[O](36) + C[CH]CCC(11) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `CCO[O](36) + CC[CH]CC(7) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2](3) + CC(38) <=> CCC(37)` origin: 1,2_Insertion_carbene rxn: `[CH2](3) + CC(38) <=> CCC(37)` origin: 1,2_Insertion_carbene rxn: `[CH3](10) + C[CH2](6) <=> CCC(37)` origin: R_Recombination rxn: `[H](8) + C[CH]C(28) <=> CCC(37)` origin: R_Recombination rxn: `[H](8) + [CH2]CC(5) <=> CCC(37)` origin: R_Recombination rxn: `[CH2](3) + C[CH]OCC(136) <=> C[CH]OCCC(127)` origin: 1,2_Insertion_carbene rxn: `[CH2](3) + C[CH]OCC(136) <=> C[CH]OCCC(127)` origin: 1,2_Insertion_carbene rxn: `[H](8) + C=COCCC(137) <=> C[CH]OCCC(127)` origin: R_Addition_MultipleBond rxn: `[CH2]COCCC(138) <=> C[CH]OCCC(127)` origin: intra_H_migration rxn: `CC[CH]OCC(139) <=> C[CH]OCCC(127)` origin: intra_H_migration rxn: `C[CH]COCC(140) <=> C[CH]OCCC(127)` origin: intra_H_migration rxn: `[CH2]CCOCC(141) <=> C[CH]OCCC(127)` origin: intra_H_migration rxn: `oxygen(1) + CCC(37) <=> [O]O(13) + C[CH]C(28)` origin: H_Abstraction rxn: `CC[CH]CC(7) + CCCOCC(149) <=> C[CH]OCCC(127) + pentane(2)` origin: H_Abstraction rxn: `C[CH]CCC(11) + CCCOCC(149) <=> C[CH]OCCC(127) + pentane(2)` origin: H_Abstraction rxn: `[CH2]CCCC(12) + CCCOCC(149) <=> C[CH]OCCC(127) + pentane(2)` origin: H_Abstraction rxn: `C[CH]C(28) + pentane(2) <=> CCC(37) + C[CH]CCC(11)` origin: H_Abstraction rxn: `[O]O(13) + CCC(37) <=> OO(20) + C[CH]C(28)` origin: H_Abstraction rxn: `C[CH]C(28) + pentane(2) <=> CCC(37) + CC[CH]CC(7)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCC(37) <=> C[CH]C(28) + CCC(37)` origin: H_Abstraction rxn: `C[CH]C(28) + CCC(CC)OO(23) <=> CCC(37) + CCC(CC)O[O](19)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCOO(59) <=> CCCO[O](34) + CCC(37)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCC(C)OO(60) <=> CCC(37) + CCCC(C)O[O](33)` origin: H_Abstraction rxn: `CCC(37) + [CH2]CCCC(12) <=> C[CH]C(28) + pentane(2)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCCCOO(91) <=> CCC(37) + CCCCCO[O](72)` origin: H_Abstraction rxn: `[OH](21) + CC=O(62) <=> O(40) + C=C[O](121)` origin: H_Abstraction rxn: `[OH](21) + CC=O(62) <=> O(40) + C[C]=O(122)` origin: H_Abstraction rxn: `[OH](21) + CC=O(62) <=> C[CH]OO(66)` origin: R_Addition_MultipleBond rxn: `[OH](21) + CC=O(62) <=> CC([O])O(150)` origin: R_Addition_MultipleBond rxn: `[OH](21) + CCC(37) <=> O(40) + C[CH]C(28)` origin: H_Abstraction rxn: `C[CH]C(28) + [CH2]CCCC(12) <=> CCC(37) + C=CCCC(25)` origin: Disproportionation rxn: `C[CH]C(28) + C[CH]CCC(11) <=> CCC(37) + C=CCCC(25)` origin: Disproportionation rxn: `C[CH]O(123) + CCO[O](36) <=> CC=O(62) + CCOO(73)` origin: Disproportionation rxn: `CC[O](93) + CCO[O](36) <=> CC=O(62) + CCOO(73)` origin: Disproportionation rxn: `C[CH]O(123) + C[CH]OO(66) <=> CC=O(62) + CCOO(73)` origin: Disproportionation rxn: `CC[O](93) + C[CH]OO(66) <=> CC=O(62) + CCOO(73)` origin: Disproportionation rxn: `C[CH]O(123) + [CH2]COO(63) <=> CC=O(62) + CCOO(73)` origin: Disproportionation rxn: `CC[O](93) + [CH2]COO(63) <=> CC=O(62) + CCOO(73)` origin: Disproportionation rxn: `CC=O(62) + CCCC(C)[O](65) <=> C=C[O](121) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CC=O(62) + CCCC(C)[O](65) <=> C[C]=O(122) + CCCC(C)O(108)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCC(C)O(108) <=> CCC(37) + CCCC(C)[O](65)` origin: H_Abstraction rxn: `CCC(37) + CCCC(C)[O](65) <=> [CH2]CC(5) + CCCC(C)O(108)` origin: H_Abstraction rxn: `C[CH]O(123) + C[CH]C(28) <=> CC=O(62) + CCC(37)` origin: Disproportionation rxn: `C[CH]O(123) + [CH2]CC(5) <=> CC=O(62) + CCC(37)` origin: Disproportionation rxn: `CC[O](93) + C[CH]C(28) <=> CC=O(62) + CCC(37)` origin: Disproportionation rxn: `CC[O](93) + [CH2]CC(5) <=> CC=O(62) + CCC(37)` origin: Disproportionation rxn: `C[CH]C(28) + CCCC(C)OO(60) <=> CCC(37) + C[CH]CC(C)OO(51)` origin: H_Abstraction rxn: `CCC(37) + CC[CH]C(C)OO(49) <=> C[CH]C(28) + CCCC(C)OO(60)` origin: H_Abstraction rxn: `CCC(37) + C[CH]C(CC)OO(31) <=> C[CH]C(28) + CCC(CC)OO(23)` origin: H_Abstraction rxn: `C[CH]C(28) + CC(CC(C)OO)OO(171) <=> CCC(37) + CC(CC(C)OO)O[O](148)` origin: H_Abstraction rxn: `C[CH]CC(C)OO(51) + CC(CC(C)OO)O[O](148) <=> CC=CC(C)OO(145) + CC(CC(C)OO)OO(171)` origin: Disproportionation rxn: `C[CH]CC(C)OO(51) + CC(CC(C)OO)O[O](148) <=> C=CCC(C)OO(146) + CC(CC(C)OO)OO(171)` origin: Disproportionation rxn: `CCC(CC)OOO(115) + CC(CC(C)OO)OO(171) <=> O(40) + CCC(CC)O[O](19) + CC(CC(C)OO)O[O](148)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `CCCC(C)OOO(110) + CC(CC(C)OO)OO(171) <=> O(40) + CCCC(C)O[O](33) + CC(CC(C)OO)O[O](148)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `CCCCCOOO(116) + CC(CC(C)OO)OO(171) <=> O(40) + CCCCCO[O](72) + CC(CC(C)OO)O[O](148)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `CCCO[O](34) + CC(CC(C)OO)O[O](148) <=> oxygen(1) + CCC[O](98) + CC([O])CC(C)OO(172)` origin: Peroxyl_Disproportionation rxn: `CCCO[O](34) + CC(CC(C)OO)O[O](148) <=> oxygen(1) + CCC=O(44) + CC(O)CC(C)OO(173)` origin: Peroxyl_Termination rxn: `CCCO[O](34) + CC(CC(C)OO)O[O](148) <=> oxygen(1) + CCCO(128) + CC(=O)CC(C)OO(166)` origin: Peroxyl_Termination rxn: `[OH](21) + CCC1OC1C(154) <=> O(40) + CC[C]1OC1C(179)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(154) <=> O(40) + CCC1O[C]1C(181)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(154) <=> O(40) + C[CH]C1OC1C(183)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(154) <=> O(40) + [CH2]C1OC1CC(184)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(154) <=> O(40) + [CH2]CC1OC1C(185)` origin: H_Abstraction rxn: `[OH](21) + CC(CC(C)OO)OO(171) <=> O(40) + C[C](CC(C)OO)OO(188)` origin: H_Abstraction rxn: `[OH](21) + CC(CC(C)OO)OO(171) <=> O(40) + CC([CH]C(C)OO)OO(167)` origin: H_Abstraction rxn: `[OH](21) + CC(CC(C)OO)OO(171) <=> O(40) + [CH2]C(CC(C)OO)OO(168)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + C[CH]C=CC(193)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + [CH2]CC=CC(194)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + [CH2]C=CCC(84)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + CC=[C]CC(196)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + C[C]=CCC(197)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> C[CH]C(O)CC(202)` origin: R_Addition_MultipleBond rxn: `[OH](21) + CC=CCC(16) <=> CC[CH]C(C)O(103)` origin: R_Addition_MultipleBond rxn: `C[CH]OO(66) + C[CH]CCC(11) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `C[CH]OO(66) + CC[CH]CC(7) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]COO(63) + C[CH]CCC(11) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]COO(63) + CC[CH]CC(7) <=> CCOO(73) + CC=CCC(16)` origin: Disproportionation rxn: `CCC1OC1C(154) + CCCC(C)[O](65) <=> CC[C]1OC1C(179) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCC1OC1C(154) + CCCC(C)[O](65) <=> CCC1O[C]1C(181) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCC1OC1C(154) + CCCC(C)[O](65) <=> C[CH]C1OC1C(183) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCC1OC1C(154) + CCCC(C)[O](65) <=> [CH2]C1OC1CC(184) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCC1OC1C(154) + CCCC(C)[O](65) <=> [CH2]CC1OC1C(185) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCCC(C)[O](65) + CC(CC(C)OO)OO(171) <=> CC(CC(C)OO)O[O](148) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCCC(C)[O](65) + CC(CC(C)OO)OO(171) <=> C[C](CC(C)OO)OO(188) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCCC(C)[O](65) + CC(CC(C)OO)OO(171) <=> CC([CH]C(C)OO)OO(167) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CCCC(C)[O](65) + CC(CC(C)OO)OO(171) <=> [CH2]C(CC(C)OO)OO(168) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CC=CCC(16) + CCCC(C)[O](65) <=> C[CH]C=CC(193) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CC=CCC(16) + CCCC(C)[O](65) <=> [CH2]CC=CC(194) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CC=CCC(16) + CCCC(C)[O](65) <=> [CH2]C=CCC(84) + CCCC(C)O(108)` origin: H_Abstraction rxn: `CC=[C]CC(196) + CCCC(C)O(108) <=> CC=CCC(16) + CCCC(C)[O](65)` origin: H_Abstraction rxn: `C[C]=CCC(197) + CCCC(C)O(108) <=> CC=CCC(16) + CCCC(C)[O](65)` origin: H_Abstraction rxn: `C[CH]C(28) + C[CH]CCC(11) <=> CCC(37) + CC=CCC(16)` origin: Disproportionation rxn: `C[CH]C(28) + CC[CH]CC(7) <=> CCC(37) + CC=CCC(16)` origin: Disproportionation rxn: `CCC1OC1C(154) + CC[CH]C(C)OO(49) <=> CC[C]1OC1C(179) + CCCC(C)OO(60)` origin: H_Abstraction rxn: `CCC1OC1C(154) + CC[CH]C(C)OO(49) <=> CCC1O[C]1C(181) + CCCC(C)OO(60)` origin: H_Abstraction rxn: `C[CH]C1OC1C(183) + CCCC(C)OO(60) <=> CCC1OC1C(154) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `[CH2]C1OC1CC(184) + CCCC(C)OO(60) <=> CCC1OC1C(154) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `[CH2]CC1OC1C(185) + CCCC(C)OO(60) <=> CCC1OC1C(154) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `CC[CH]C(C)OO(49) + CC(CC(C)OO)OO(171) <=> C[C](CC(C)OO)OO(188) + CCCC(C)OO(60)` origin: H_Abstraction rxn: `CC([CH]C(C)OO)OO(167) + CCCC(C)OO(60) <=> CC[CH]C(C)OO(49) + CC(CC(C)OO)OO(171)` origin: H_Abstraction rxn: `[CH2]C(CC(C)OO)OO(168) + CCCC(C)OO(60) <=> CC[CH]C(C)OO(49) + CC(CC(C)OO)OO(171)` origin: H_Abstraction rxn: `CC=CCC(16) + CC[CH]C(C)OO(49) <=> C[CH]C=CC(193) + CCCC(C)OO(60)` origin: H_Abstraction rxn: `[CH2]CC=CC(194) + CCCC(C)OO(60) <=> CC=CCC(16) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `CC=CCC(16) + CC[CH]C(C)OO(49) <=> [CH2]C=CCC(84) + CCCC(C)OO(60)` origin: H_Abstraction rxn: `CC=[C]CC(196) + CCCC(C)OO(60) <=> CC=CCC(16) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `C[C]=CCC(197) + CCCC(C)OO(60) <=> CC=CCC(16) + CC[CH]C(C)OO(49)` origin: H_Abstraction rxn: `OOO(114) + CCCOO(59) <=> [O]O(13) + O(40) + CCCO[O](34)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `OO(20) + CCCOOO(135) <=> [O]O(13) + O(40) + CCCO[O](34)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `OOO(114) + CC(CC(C)OO)OO(171) <=> [O]O(13) + O(40) + CC(CC(C)OO)O[O](148)` origin: Bimolec_Hydroperoxide_Decomposition The tested model has 10 reactions that the original model does not have. ❌ rxn: `CCCC(C)[O](65) + C[CH]CC(C)OO(48) <=> CC=CC(C)OO(110) + CCCC(C)O(129)` origin: Disproportionation rxn: `CCCC(C)[O](65) + C[CH]CC(C)OO(48) <=> C=CCC(C)OO(111) + CCCC(C)O(129)` origin: Disproportionation rxn: `CCCC(C)[O](65) + C[CH]CC(C)OO(48) <=> CCCC(C)=O(45) + CCCC(C)OO(59)` origin: Disproportionation rxn: `CCCC(C)[O](65) + C[CH]C(CC)OO(29) <=> CC=C(CC)OO(116) + CCCC(C)O(129)` origin: Disproportionation rxn: `CCCC(C)[O](65) + C[CH]C(CC)OO(29) <=> C=CC(CC)OO(117) + CCCC(C)O(129)` origin: Disproportionation rxn: `CCCC(C)[O](65) + C[CH]C(CC)OO(29) <=> CCCC(C)=O(45) + CCC(CC)OO(21)` origin: Disproportionation rxn: `CCCC(C)[O](65) + CC[CH]C(C)OO(46) <=> CCC=C(C)OO(121) + CCCC(C)O(129)` origin: Disproportionation rxn: `CCCC(C)[O](65) + CC[CH]C(C)OO(46) <=> CC=CC(C)OO(110) + CCCC(C)O(129)` origin: Disproportionation rxn: `CCCC(C)[O](65) + CC[CH]C(C)OO(46) <=> CCCC(C)=O(45) + CCCC(C)OO(59)` origin: Disproportionation rxn: `[CH2]CC(5) + CC(CC(C)OO)O[O](126) <=> C=CC(26) + CC(CC(C)OO)OO(132)` origin: Disproportionation Non-identical kinetics! ❌ original: rxn: `CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](98) + CCCC(C)[O](65)` origin: Peroxyl_Disproportionation tested: rxn: `CCCO[O](35) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](92) + CCCC(C)[O](65)` 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): | 3.69| 4.39| 4.82| 5.10| 5.45| 5.66| 5.94| 6.08| 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: `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: 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
Observables Test Case: RMS_CSTR_liquid_oxidation Comparison The following observables did not match: ❌ Observable species CCCCC varied by more than 0.100 on average between old model pentane(2) and new model pentane(2) in condition 1. ⚠️ The following reaction conditions had some discrepancies: Condition 1: Reactor Type: IdealGasReactor Reaction Time: 1000 s T0: 600 K P0: 1 bar Initial Mole Fractions: {'CCCCC': 0.9, '[O][O]': 0.1} RMS_CSTR_liquid_oxidation Failed Observable Testing ❌
### Regression test fragment: Reference: Execution time (DD:HH:MM:SS): 00:00:00:40 Current: Execution time (DD:HH:MM:SS): 00:00:00:40 Reference: Memory used: 2698.92 MB Current: Memory used: 2698.89 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): 00:00:03:02 Current: Execution time (DD:HH:MM:SS): 00:00:02:59 Reference: Memory used: 3595.05 MB Current: Memory used: 3584.25 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 ✅
### Regression test minimal_surface: Reference: Execution time (DD:HH:MM:SS): 00:00:01:06 Current: Execution time (DD:HH:MM:SS): 00:00:01:07 Reference: Memory used: 2892.71 MB Current: Memory used: 2890.47 MB
minimal_surface Failed Core Comparison ❌ Original model has 30 species. Test model has 30 species. ✅ Original model has 136 reactions. Test model has 136 reactions. ✅ Non-identical thermo! ❌ original: `X` tested: `X` |Hf(300K) |S(300K) |Cp(300K) |Cp(400K) |Cp(500K) |Cp(600K) |Cp(800K) |Cp(1000K) |Cp(1500K) | |----------|----------|----------|----------|----------|----------|----------|----------|----------| | 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| | 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| 0.00| Identical thermo comments: thermo: Thermo library: surfaceThermoPt111
minimal_surface Failed Edge Comparison ❌ Please specify 2 surface input files if you are comparing a surface mechanism
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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sevyharris commented 6 months ago

Although this is still failing with:

FileNotFoundError: [Errno 2] No such file or directory: 'stable_regression_results/minimal_surface/chemkin/species_edge_dictionary.txt'

This failure is expected because the last run of the regression tests on main didn't produce the edge files. It's the same expected error as when we first pushed the minimal_surface regression test, so I think this is ready for review.

sevyharris commented 6 months ago

Also, the surface regression test is still failing because of this issue https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2657, but I'll make a separate PR for that.

JacksonBurns commented 6 months ago

If we merge this PR would that enable #2657 to pass normally (assuming the bug can be fixed)?

sevyharris commented 6 months ago

If we merge this PR would that enable #2657 to pass normally (assuming the bug can be fixed)?

Yes. And then https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2658 is my fix for that bug.

JacksonBurns commented 6 months ago

Great - will send this in now.