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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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Deprecate the nomkl mutex metapackage #2723

Closed ssun30 closed 1 month ago

ssun30 commented 1 month ago

Motivation or Problem

Resolves issue #2722 .

Description of Changes

github-actions[bot] commented 1 month 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. ⚠️ 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): 00:00:01:05 Reference: Memory used: 2756.55 MB Current: Memory used: 2759.07 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): 00:00:02:08 Current: Execution time (DD:HH:MM:SS): 00:00:02:09 Reference: Memory used: 2888.18 MB Current: Memory used: 2895.43 MB
liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 37 species. ✅ Original model has 216 reactions. Test model has 215 reactions. ❌ The original model has 1 reactions that the tested model does not have. ❌ rxn: `CCO[O](30) <=> [OH](22) + CC=O(69)` origin: intra_H_migration
liquid_oxidation Failed Edge Comparison ❌ Original model has 202 species. Test model has 202 species. ✅ Original model has 1613 reactions. Test model has 1613 reactions. ✅ The original model has 1 reactions that the tested model does not have. ❌ rxn: `CCO[O](30) <=> [OH](22) + CC=O(69)` origin: intra_H_migration The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCO[O](30) <=> C[CH]OO(73)` origin: intra_H_migration Non-identical kinetics! ❌ original: rxn: `CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129)` origin: Peroxyl_Disproportionation tested: rxn: `CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](128) + CC([O])CC(C)OO(127)` origin: Peroxyl_Disproportionation |k(1bar)|300K |400K |500K |600K |800K |1000K |1500K |2000K | |-------|-------|-------|-------|-------|-------|-------|-------|-------| |k(T): | 7.79| 7.46| 7.21| 7.00| 6.67| 6.41| 5.94| 5.60| |k(T): | 3.52| 4.27| 4.71| 5.01| 5.39| 5.61| 5.91| 6.06| kinetics: `Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0.053,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.""")` kinetics: `Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.096,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")` kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction. kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R
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): 00:00:01:25 Current: Execution time (DD:HH:MM:SS): 00:00:01:23 Reference: Memory used: 2894.83 MB Current: Memory used: 2886.13 MB
nitrogen Failed Core Comparison ❌ Original model has 41 species. Test model has 41 species. ✅ Original model has 359 reactions. Test model has 360 reactions. ❌ The tested model has 1 reactions that the original model does not have. ❌ rxn: `HNO(48) + HCO(13) <=> NO(38) + CH2O(18)` origin: H_Abstraction
nitrogen Failed Edge Comparison ❌ Original model has 133 species. Test model has 133 species. ✅ Original model has 981 reactions. Test model has 983 reactions. ❌ Non-identical thermo! ❌ original: `O1[C]=N1` tested: `O1[C]=N1` |Hf(300K) |S(300K) |Cp(300K) |Cp(400K) |Cp(500K) |Cp(600K) |Cp(800K) |Cp(1000K) |Cp(1500K) | |----------|----------|----------|----------|----------|----------|----------|----------|----------| | 116.46| 53.90| 11.62| 12.71| 13.49| 13.96| 14.14| 13.85| 13.58| | 141.64| 58.66| 12.26| 12.27| 12.09| 11.96| 12.26| 12.72| 12.15| thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO) thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO) The tested model has 2 reactions that the original model does not have. ❌ rxn: `HNO(48) + HCO(13) <=> NO(38) + CH2O(18)` origin: H_Abstraction rxn: `HON(T)(83) + HCO(13) <=> NO(38) + CH2O(18)` origin: Disproportionation Non-identical kinetics! ❌ original: rxn: `NCO(66) <=> O1[C]=N1(126)` origin: Intra_R_Add_Endocyclic tested: rxn: `NCO(66) <=> O1[C]=N1(126)` origin: Intra_R_Add_Endocyclic |k(1bar)|300K |400K |500K |600K |800K |1000K |1500K |2000K | |-------|-------|-------|-------|-------|-------|-------|-------|-------| |k(T): | -49.54| -33.65| -24.16| -17.85| -10.01| -5.35| 0.80| 3.82| |k(T): | -66.25| -46.19| -34.19| -26.21| -16.28| -10.36| -2.54| 1.31| kinetics: `Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")` kinetics: `Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")` Identical kinetics comments: kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H
Observables Test Case: NC Comparison ✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions! nitrogen Passed Observable Testing ✅
### Regression test oxidation: Reference: Execution time (DD:HH:MM:SS): 00:00:02:24 Current: Execution time (DD:HH:MM:SS): 00:00:02:21 Reference: Memory used: 2751.85 MB Current: Memory used: 2759.57 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): 00:00:00:54 Reference: Memory used: 2853.45 MB Current: Memory used: 2857.36 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: 2945.25 MB Current: Memory used: 2942.22 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): 00:00:02:21 Current: Execution time (DD:HH:MM:SS): 00:00:02:22 Reference: Memory used: 3444.51 MB Current: Memory used: 3433.87 MB
RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅ Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅
RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅ Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅
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): 00:00:05:50 Current: Execution time (DD:HH:MM:SS): 00:00:05:59 Reference: Memory used: 3376.57 MB Current: Memory used: 3352.67 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](34) <=> [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: `CCCO[O](35) <=> CC[CH]OO(51)` origin: intra_H_migration rxn: `CCO[O](36) <=> C[CH]OO(62)` origin: intra_H_migration The tested model has 2 reactions that the original model does not have. ❌ rxn: `CCO[O](34) <=> [OH](21) + CC=O(62)` origin: intra_H_migration rxn: `CCCO[O](35) <=> [OH](21) + CCC=O(44)` origin: intra_H_migration Non-identical kinetics! ❌ original: rxn: `CCCO[O](35) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](94) + CCCC(C)[O](61)` origin: Peroxyl_Disproportionation tested: rxn: `CCCO[O](35) + 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): | 3.69| 4.39| 4.82| 5.10| 5.45| 5.66| 5.94| 6.08| |k(T): | 7.83| 7.49| 7.23| 7.02| 6.68| 6.42| 5.95| 5.61| kinetics: `Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.866,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")` kinetics: `Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")` kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
Observables Test Case: RMS_CSTR_liquid_oxidation Comparison ✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_CSTR_liquid_oxidation Passed Observable Testing ✅
### Regression test fragment: Reference: Execution time (DD:HH:MM:SS): 00:00:00:40 Current: Execution time (DD:HH:MM:SS): 00:00:00:40 Reference: Memory used: 2689.15 MB Current: Memory used: 2678.82 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): 00:00:03:01 Current: Execution time (DD:HH:MM:SS): 00:00:02:58 Reference: Memory used: 3584.09 MB Current: Memory used: 3579.01 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): 00:00:00:43 Current: Execution time (DD:HH:MM:SS): 00:00:00:43 Reference: Memory used: 2851.99 MB Current: Memory used: 2857.11 MB
minimal_surface Passed Core Comparison ✅ Original model has 11 species. Test model has 11 species. ✅ Original model has 3 reactions. Test model has 3 reactions. ✅
minimal_surface Passed Edge Comparison ✅ Original model has 38 species. Test model has 38 species. ✅ Original model has 38 reactions. Test model has 38 reactions. ✅
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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