search

ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
Other
400 stars 228 forks source link

Remove kinetic group additivity methods from code and documentation #2612

Closed jonwzheng closed 9 months ago

jonwzheng commented 9 months ago

Motivation or Problem

See #2605. We have decided to remove group additivity as a valid estimator for kinetics. Now, only rate rules will be supported moving forward. A previous commit (9f293bec90a093cf23b42089bb7bb0b14e05a2a7) removed the main group additivity estimator methods. However, there were still a few references to kinetic group additivity, including as the default method for get_kinetics if kinetics_estimator is not provided. There were also some mentions in the documentation and docstrings that suggest group additivity is supported.

Description of Changes

This PR removes most mentions of kinetic group additivity from the code, documentation, and docstrings.

However, this commit does not remove the KineticsGroup class (see rmgpy/data/kinetics/groups.py), which is used extensively in the definition of a KineticsFamily. I would welcome some discussion on whether we should remove those and rewrite the kinetics family code as well, or if we want to keep it for compatibility / future reference/use etc.

Testing

A local version of RMG-website using this commit hash seems to return the same kinetics as is currently returned on RMG-Py.

github-actions[bot] commented 9 months ago

Regression Testing Results

⚠️ One or more regression tests failed. Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results. ### Regression test aromatics: Reference: Execution time (DD:HH:MM:SS): 00:00:01:06 Current: Execution time (DD:HH:MM:SS): 00:00:01:06 Reference: Memory used: 3034.91 MB Current: Memory used: 3039.76 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)
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): 00:00:02:09 Current: Execution time (DD:HH:MM:SS): 00:00:02:12 Reference: Memory used: 3165.03 MB Current: Memory used: 3163.90 MB
liquid_oxidation Passed Core Comparison ✅ Original model has 37 species. Test model has 37 species. ✅ Original model has 216 reactions. Test model has 216 reactions. ✅
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. ✅ Non-identical kinetics! ❌ original: rxn: `CCCCCO[O](104) + CC(CC(C)OO)O[O](103) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129)` origin: Peroxyl_Disproportionation 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): 00:00:01:23 Current: Execution time (DD:HH:MM:SS): 00:00:01:22 Reference: Memory used: 3153.61 MB Current: Memory used: 3158.35 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): 00:00:02:29 Current: Execution time (DD:HH:MM:SS): 00:00:02:27 Reference: Memory used: 3018.44 MB Current: Memory used: 3020.22 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): 00:00:00:54 Current: Execution time (DD:HH:MM:SS): 00:00:00:54 Reference: Memory used: 3133.89 MB Current: Memory used: 3124.73 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): 00:00:00:34 Current: Execution time (DD:HH:MM:SS): 00:00:00:34 Reference: Memory used: 3224.31 MB Current: Memory used: 3227.66 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): 00:00:02:31 Current: Execution time (DD:HH:MM:SS): 00:00:02:24 Reference: Memory used: 3698.25 MB Current: Memory used: 3711.41 MB
RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅ Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅
RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅ Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅
Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison ✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅
### Regression test RMS_CSTR_liquid_oxidation: Reference: Execution time (DD:HH:MM:SS): 00:00:06:08 Current: Execution time (DD:HH:MM:SS): 00:00:05:44 Reference: Memory used: 3659.85 MB Current: Memory used: 3620.97 MB
RMS_CSTR_liquid_oxidation Failed Core Comparison ❌ Original model has 37 species. Test model has 35 species. ❌ Original model has 232 reactions. Test model has 211 reactions. ❌ The original model has 2 species that the tested model does not have. ❌ spc: CCC(38) spc: C[CH]OCCC(126) The original model has 21 reactions that the tested model does not have. ❌ rxn: `CC=O(99) + [CH2]CC(5) <=> C[CH]OCCC(126)` origin: R_Addition_MultipleBond rxn: `[CH2]CC(5) + pentane(2) <=> CCC(38) + CC[CH]CC(7)` origin: H_Abstraction rxn: `[CH2]CC(5) + pentane(2) <=> CCC(38) + C[CH]CCC(11)` origin: H_Abstraction rxn: `CCC(38) + [CH2]CCCC(12) <=> [CH2]CC(5) + pentane(2)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCC(C)OO(58) <=> CCC(38) + CCCC(C)O[O](33)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCC(C)OO(58) <=> CCC(38) + C[CH]CC(C)OO(52)` origin: H_Abstraction rxn: `[CH2]CC(5) + C[CH]CCC(11) <=> CCC(38) + C=CCCC(25)` origin: Disproportionation rxn: `[CH2]CC(5) + CCC(CC)OO(23) <=> CCC(38) + CCC(CC)O[O](19)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCCCOO(89) <=> CCC(38) + CCCCCO[O](69)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCOO(59) <=> CCCO[O](35) + CCC(38)` origin: H_Abstraction rxn: `OO(20) + [CH2]CC(5) <=> [O]O(13) + CCC(38)` origin: H_Abstraction rxn: `[OH](21) + CCC(38) <=> O(40) + [CH2]CC(5)` origin: H_Abstraction rxn: `[O]O(13) + [CH2]CC(5) <=> oxygen(1) + CCC(38)` origin: H_Abstraction rxn: `[CH2]CC(5) + [CH2]CCCC(12) <=> CCC(38) + C=CCCC(25)` origin: Disproportionation rxn: `[CH2]CC(5) + CCC(CC)OO(23) <=> CCC(38) + C[CH]C(CC)OO(31)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCCC(C)OO(58) <=> CCC(38) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `[CH2]CC(5) + C[CH]CCC(11) <=> CCC(38) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]CC(5) + CC[CH]CC(7) <=> CCC(38) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]CC(5) + CC(CC(C)OO)OO(171) <=> CCC(38) + CC(CC(C)OO)O[O](148)` origin: H_Abstraction rxn: `CCO[O](34) + C[CH]CCC(11) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `CCO[O](34) + CC[CH]CC(7) <=> CCOO(71) + 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(38) + C=CCCC(25)` origin: Disproportionation rxn: `CCO[O](34) + C[CH]CCC(11) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `CCO[O](34) + CC[CH]CC(7) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2](3) + C[CH]OCC(136) <=> C[CH]OCCC(126)` origin: 1,2_Insertion_carbene rxn: `[CH2](3) + C[CH]OCC(136) <=> C[CH]OCCC(126)` origin: 1,2_Insertion_carbene rxn: `[H](8) + C=COCCC(137) <=> C[CH]OCCC(126)` origin: R_Addition_MultipleBond rxn: `[CH2]COCCC(138) <=> C[CH]OCCC(126)` origin: intra_H_migration rxn: `CC[CH]OCC(139) <=> C[CH]OCCC(126)` origin: intra_H_migration rxn: `C[CH]COCC(140) <=> C[CH]OCCC(126)` origin: intra_H_migration rxn: `[CH2]CCOCC(141) <=> C[CH]OCCC(126)` origin: intra_H_migration rxn: `[CH2](3) + CC(37) <=> CCC(38)` origin: 1,2_Insertion_carbene rxn: `[CH2](3) + CC(37) <=> CCC(38)` origin: 1,2_Insertion_carbene rxn: `[CH3](10) + C[CH2](6) <=> CCC(38)` origin: R_Recombination rxn: `[H](8) + C[CH]C(28) <=> CCC(38)` origin: R_Recombination rxn: `[H](8) + [CH2]CC(5) <=> CCC(38)` origin: R_Recombination rxn: `oxygen(1) + CCC(38) <=> [O]O(13) + C[CH]C(28)` origin: H_Abstraction rxn: `CC[CH]CC(7) + CCCOCC(149) <=> C[CH]OCCC(126) + pentane(2)` origin: H_Abstraction rxn: `C[CH]CCC(11) + CCCOCC(149) <=> C[CH]OCCC(126) + pentane(2)` origin: H_Abstraction rxn: `[CH2]CCCC(12) + CCCOCC(149) <=> C[CH]OCCC(126) + pentane(2)` origin: H_Abstraction rxn: `C[CH]C(28) + pentane(2) <=> CCC(38) + C[CH]CCC(11)` origin: H_Abstraction rxn: `[O]O(13) + CCC(38) <=> OO(20) + C[CH]C(28)` origin: H_Abstraction rxn: `C[CH]C(28) + pentane(2) <=> CCC(38) + CC[CH]CC(7)` origin: H_Abstraction rxn: `[CH2]CC(5) + CCC(38) <=> C[CH]C(28) + CCC(38)` origin: H_Abstraction rxn: `C[CH]C(28) + CCC(CC)OO(23) <=> CCC(38) + CCC(CC)O[O](19)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCC(C)OO(58) <=> CCC(38) + CCCC(C)O[O](33)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCOO(59) <=> CCCO[O](35) + CCC(38)` origin: H_Abstraction rxn: `CCC(38) + [CH2]CCCC(12) <=> C[CH]C(28) + pentane(2)` origin: H_Abstraction rxn: `C[CH]C(28) + [CH2]CCCC(12) <=> CCC(38) + C=CCCC(25)` origin: Disproportionation rxn: `C[CH]C(28) + C[CH]CCC(11) <=> CCC(38) + C=CCCC(25)` origin: Disproportionation rxn: `[OH](21) + CC=O(99) <=> O(40) + C=C[O](120)` origin: H_Abstraction rxn: `[OH](21) + CC=O(99) <=> O(40) + C[C]=O(121)` origin: H_Abstraction rxn: `[OH](21) + CC=O(99) <=> C[CH]OO(62)` origin: R_Addition_MultipleBond rxn: `[OH](21) + CC=O(99) <=> CC([O])O(150)` origin: R_Addition_MultipleBond rxn: `[OH](21) + CCC(38) <=> O(40) + C[CH]C(28)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCCCOO(89) <=> CCC(38) + CCCCCO[O](69)` origin: H_Abstraction rxn: `C[CH]O(122) + CCO[O](34) <=> CC=O(99) + CCOO(71)` origin: Disproportionation rxn: `CC[O](96) + CCO[O](34) <=> CC=O(99) + CCOO(71)` origin: Disproportionation rxn: `C[CH]O(122) + C[CH]OO(62) <=> CC=O(99) + CCOO(71)` origin: Disproportionation rxn: `CC[O](96) + C[CH]OO(62) <=> CC=O(99) + CCOO(71)` origin: Disproportionation rxn: `C[CH]O(122) + [CH2]COO(68) <=> CC=O(99) + CCOO(71)` origin: Disproportionation rxn: `CC[O](96) + [CH2]COO(68) <=> CC=O(99) + CCOO(71)` origin: Disproportionation rxn: `CC=O(99) + CCCC(C)[O](61) <=> C=C[O](120) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CC=O(99) + CCCC(C)[O](61) <=> C[C]=O(121) + CCCC(C)O(107)` origin: H_Abstraction rxn: `C[CH]C(28) + CCCC(C)O(107) <=> CCC(38) + CCCC(C)[O](61)` origin: H_Abstraction rxn: `CCC(38) + CCCC(C)[O](61) <=> [CH2]CC(5) + CCCC(C)O(107)` origin: H_Abstraction rxn: `C[CH]O(122) + C[CH]C(28) <=> CC=O(99) + CCC(38)` origin: Disproportionation rxn: `C[CH]O(122) + [CH2]CC(5) <=> CC=O(99) + CCC(38)` origin: Disproportionation rxn: `CC[O](96) + C[CH]C(28) <=> CC=O(99) + CCC(38)` origin: Disproportionation rxn: `CC[O](96) + [CH2]CC(5) <=> CC=O(99) + CCC(38)` origin: Disproportionation rxn: `C[CH]C(28) + CCCC(C)OO(58) <=> CCC(38) + C[CH]CC(C)OO(52)` origin: H_Abstraction rxn: `C[CH]CC(C)OO(52) + 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(52) + CC(CC(C)OO)O[O](148) <=> C=CCC(C)OO(146) + CC(CC(C)OO)OO(171)` origin: Disproportionation rxn: `CCC(38) + C[CH]C(CC)OO(31) <=> C[CH]C(28) + CCC(CC)OO(23)` origin: H_Abstraction rxn: `CCC(38) + CC[CH]C(C)OO(50) <=> C[CH]C(28) + CCCC(C)OO(58)` origin: H_Abstraction rxn: `C[CH]C(28) + CC(CC(C)OO)OO(171) <=> CCC(38) + CC(CC(C)OO)O[O](148)` origin: H_Abstraction rxn: `CCC(CC)OOO(114) + 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(109) + 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(115) + CC(CC(C)OO)OO(171) <=> O(40) + CCCCCO[O](69) + CC(CC(C)OO)O[O](148)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `CCCO[O](35) + CC(CC(C)OO)O[O](148) <=> oxygen(1) + CCC[O](94) + CC([O])CC(C)OO(172)` origin: Peroxyl_Disproportionation rxn: `CCCO[O](35) + CC(CC(C)OO)O[O](148) <=> oxygen(1) + CCC=O(128) + CC(O)CC(C)OO(173)` origin: Peroxyl_Termination rxn: `CCCO[O](35) + CC(CC(C)OO)O[O](148) <=> oxygen(1) + CCCO(127) + CC(=O)CC(C)OO(166)` origin: Peroxyl_Termination rxn: `[OH](21) + CC=CCC(16) <=> O(40) + C[CH]C=CC(178)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + [CH2]CC=CC(179)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + [CH2]C=CCC(77)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + CC=[C]CC(181)` origin: H_Abstraction rxn: `[OH](21) + CC=CCC(16) <=> O(40) + C[C]=CCC(182)` 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(102)` origin: R_Addition_MultipleBond rxn: `[OH](21) + CCC1OC1C(153) <=> O(40) + CC[C]1OC1C(189)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(153) <=> O(40) + CCC1O[C]1C(191)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(153) <=> O(40) + C[CH]C1OC1C(193)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(153) <=> O(40) + [CH2]C1OC1CC(194)` origin: H_Abstraction rxn: `[OH](21) + CCC1OC1C(153) <=> O(40) + [CH2]CC1OC1C(195)` origin: H_Abstraction rxn: `[OH](21) + CC(CC(C)OO)OO(171) <=> O(40) + C[C](CC(C)OO)OO(198)` 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: `C[CH]OO(62) + C[CH]CCC(11) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `C[CH]OO(62) + CC[CH]CC(7) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]COO(68) + C[CH]CCC(11) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `[CH2]COO(68) + CC[CH]CC(7) <=> CCOO(71) + CC=CCC(16)` origin: Disproportionation rxn: `CC=CCC(16) + CCCC(C)[O](61) <=> C[CH]C=CC(178) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CC=CCC(16) + CCCC(C)[O](61) <=> [CH2]CC=CC(179) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CC=CCC(16) + CCCC(C)[O](61) <=> [CH2]C=CCC(77) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CC=[C]CC(181) + CCCC(C)O(107) <=> CC=CCC(16) + CCCC(C)[O](61)` origin: H_Abstraction rxn: `C[C]=CCC(182) + CCCC(C)O(107) <=> CC=CCC(16) + CCCC(C)[O](61)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CCCC(C)[O](61) <=> CC[C]1OC1C(189) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CCCC(C)[O](61) <=> CCC1O[C]1C(191) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CCCC(C)[O](61) <=> C[CH]C1OC1C(193) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CCCC(C)[O](61) <=> [CH2]C1OC1CC(194) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CCCC(C)[O](61) <=> [CH2]CC1OC1C(195) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCCC(C)[O](61) + CC(CC(C)OO)OO(171) <=> CC(CC(C)OO)O[O](148) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCCC(C)[O](61) + CC(CC(C)OO)OO(171) <=> C[C](CC(C)OO)OO(198) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCCC(C)[O](61) + CC(CC(C)OO)OO(171) <=> CC([CH]C(C)OO)OO(167) + CCCC(C)O(107)` origin: H_Abstraction rxn: `CCCC(C)[O](61) + CC(CC(C)OO)OO(171) <=> [CH2]C(CC(C)OO)OO(168) + CCCC(C)O(107)` origin: H_Abstraction rxn: `C[CH]C(28) + C[CH]CCC(11) <=> CCC(38) + CC=CCC(16)` origin: Disproportionation rxn: `C[CH]C(28) + CC[CH]CC(7) <=> CCC(38) + CC=CCC(16)` origin: Disproportionation rxn: `CC=CCC(16) + CC[CH]C(C)OO(50) <=> C[CH]C=CC(178) + CCCC(C)OO(58)` origin: H_Abstraction rxn: `[CH2]CC=CC(179) + CCCC(C)OO(58) <=> CC=CCC(16) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `CC=CCC(16) + CC[CH]C(C)OO(50) <=> [CH2]C=CCC(77) + CCCC(C)OO(58)` origin: H_Abstraction rxn: `CC=[C]CC(181) + CCCC(C)OO(58) <=> CC=CCC(16) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `C[C]=CCC(182) + CCCC(C)OO(58) <=> CC=CCC(16) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CC[CH]C(C)OO(50) <=> CC[C]1OC1C(189) + CCCC(C)OO(58)` origin: H_Abstraction rxn: `CCC1OC1C(153) + CC[CH]C(C)OO(50) <=> CCC1O[C]1C(191) + CCCC(C)OO(58)` origin: H_Abstraction rxn: `C[CH]C1OC1C(193) + CCCC(C)OO(58) <=> CCC1OC1C(153) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `[CH2]C1OC1CC(194) + CCCC(C)OO(58) <=> CCC1OC1C(153) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `[CH2]CC1OC1C(195) + CCCC(C)OO(58) <=> CCC1OC1C(153) + CC[CH]C(C)OO(50)` origin: H_Abstraction rxn: `CC[CH]C(C)OO(50) + CC(CC(C)OO)OO(171) <=> C[C](CC(C)OO)OO(198) + CCCC(C)OO(58)` origin: H_Abstraction rxn: `CC([CH]C(C)OO)OO(167) + CCCC(C)OO(58) <=> CC[CH]C(C)OO(50) + CC(CC(C)OO)OO(171)` origin: H_Abstraction rxn: `[CH2]C(CC(C)OO)OO(168) + CCCC(C)OO(58) <=> CC[CH]C(C)OO(50) + CC(CC(C)OO)OO(171)` origin: H_Abstraction rxn: `OOO(113) + CCCOO(59) <=> [O]O(13) + O(40) + CCCO[O](35)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `OO(20) + CCCOOO(135) <=> [O]O(13) + O(40) + CCCO[O](35)` origin: Bimolec_Hydroperoxide_Decomposition rxn: `OOO(113) + 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](61) + CC[CH]C(C)OO(52) <=> CCC=C(C)OO(111) + CCCC(C)O(128)` origin: Disproportionation rxn: `CCCC(C)[O](61) + CC[CH]C(C)OO(52) <=> CC=CC(C)OO(112) + CCCC(C)O(128)` origin: Disproportionation rxn: `CCCC(C)[O](61) + CC[CH]C(C)OO(52) <=> CCCC(C)=O(51) + CCCC(C)OO(59)` origin: Disproportionation rxn: `CCCC(C)[O](61) + C[CH]CC(C)OO(54) <=> CC=CC(C)OO(112) + CCCC(C)O(128)` origin: Disproportionation rxn: `CCCC(C)[O](61) + C[CH]CC(C)OO(54) <=> C=CCC(C)OO(118) + CCCC(C)O(128)` origin: Disproportionation rxn: `CCCC(C)[O](61) + C[CH]CC(C)OO(54) <=> CCCC(C)=O(51) + CCCC(C)OO(59)` origin: Disproportionation rxn: `CCCC(C)[O](61) + C[CH]C(CC)OO(31) <=> CC=C(CC)OO(120) + CCCC(C)O(128)` origin: Disproportionation rxn: `CCCC(C)[O](61) + C[CH]C(CC)OO(31) <=> C=CC(CC)OO(121) + CCCC(C)O(128)` origin: Disproportionation rxn: `CCCC(C)[O](61) + C[CH]C(CC)OO(31) <=> CCCC(C)=O(51) + CCC(CC)OO(23)` origin: Disproportionation rxn: `[CH2]CC(5) + CC(CC(C)OO)O[O](126) <=> C=CC(26) + CC(CC(C)OO)OO(131)` origin: Disproportionation 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](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](96) + CCCC(C)[O](61)` 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 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): 00:00:00:41 Current: Execution time (DD:HH:MM:SS): 00:00:00:40 Reference: Memory used: 2949.43 MB Current: Memory used: 2951.07 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): 00:00:03:06 Current: Execution time (DD:HH:MM:SS): 00:00:03:05 Reference: Memory used: 3844.16 MB Current: Memory used: 3827.71 MB
RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅ Original model has 10 species. Test model has 10 species. ✅ Original model has 2 reactions. Test model has 2 reactions. ✅
RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅ Original model has 27 species. Test model has 27 species. ✅ Original model has 24 reactions. Test model has 24 reactions. ✅
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 ✅

beep boop this comment was written by a bot :robot:

codecov[bot] commented 9 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (f9246f9) 55.14% compared to head (c0ea448) 55.16%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #2612 +/- ## ========================================== + Coverage 55.14% 55.16% +0.01% ========================================== Files 125 125 Lines 37036 37019 -17 ========================================== - Hits 20424 20421 -3 + Misses 16612 16598 -14 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

JacksonBurns commented 9 months ago

Re-running CI in the hope that the failures were spurious Julia dependency stuff.

JacksonBurns commented 9 months ago

Branch was outdated - rebased.

JacksonBurns commented 9 months ago

@jonwzheng I think there is just a simple formatting error in this table: https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/7932965819/job/21660635035?pr=2612#step:9:335

jonwzheng commented 9 months ago

@jonwzheng I think there is just a simple formatting error in this table: https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/7932965819/job/21660635035?pr=2612#step:9:335

fixed this in the latest commit!

github-actions[bot] commented 9 months ago

Regression Testing Results

⚠️ One or more regression tests failed. Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results. ### Regression test aromatics: Reference: Execution time (DD:HH:MM:SS): 00:00:01:05 Current: Execution time (DD:HH:MM:SS): 00:00:01:07 Reference: Memory used: 3058.56 MB Current: Memory used: 3056.47 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): 00:00:02:09 Current: Execution time (DD:HH:MM:SS): 00:00:02:12 Reference: Memory used: 3162.01 MB Current: Memory used: 3170.59 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](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128)` origin: Peroxyl_Disproportionation tested: rxn: `CCCC(C)O[O](20) + CCCCCO[O](103) <=> 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 1618 reactions. Test model has 1610 reactions. ❌ The original model has 9 reactions that the tested model does not have. ❌ rxn: `[CH2]CCOO(79) + CCCCCOO(105) <=> CCCOO(36) + CC[CH]CCOO(122)` origin: H_Abstraction rxn: `[CH2]CCOO(79) + CCCCCOO(105) <=> CCCOO(36) + CCC[CH]COO(121)` origin: H_Abstraction rxn: `[CH2]CCOO(79) + CCCCCOO(105) <=> CCCOO(36) + C[CH]CCCOO(123)` origin: H_Abstraction rxn: `[CH2]CCOO(79) + CCCCCOO(105) <=> CCCOO(36) + CCCC[CH]OO(138)` origin: H_Abstraction rxn: `CCCOO(36) + [CH2]CCCCOO(124) <=> [CH2]CCOO(79) + CCCCCOO(105)` origin: H_Abstraction rxn: `C[CH]CCCO(157) + CCCCCO[O](104) <=> CC=CCCO(192) + CCCCCOO(105)` origin: Disproportionation rxn: `C[CH]CCCO(157) + CCCCCO[O](104) <=> C=CCCCO(193) + CCCCCOO(105)` origin: Disproportionation rxn: `C[CH]CCCO(157) + C[CH]CCCO(157) <=> CC=CCCO(192) + CCCCCO(130)` origin: Disproportionation rxn: `C[CH]CCCO(157) + C[CH]CCCO(157) <=> C=CCCCO(193) + CCCCCO(130)` origin: Disproportionation The tested model has 1 reactions that the original model does not have. ❌ rxn: `CCCCCO[O](103) + CCCCCO[O](103) <=> oxygen(1) + CCCCC=O(120) + CCCCCO(130)` origin: Peroxyl_Termination Non-identical kinetics! ❌ original: rxn: `CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128)` origin: Peroxyl_Disproportionation tested: rxn: `CCCC(C)O[O](20) + CCCCCO[O](103) <=> 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): 00:00:01:24 Current: Execution time (DD:HH:MM:SS): 00:00:01:23 Reference: Memory used: 3154.85 MB Current: Memory used: 3165.50 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 132 species. Test model has 132 species. ✅ Original model has 995 reactions. Test model has 997 reactions. ❌ 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
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): 00:00:02:30 Current: Execution time (DD:HH:MM:SS): 00:00:02:26 Reference: Memory used: 3030.34 MB Current: Memory used: 3036.75 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): 00:00:00:54 Current: Execution time (DD:HH:MM:SS): 00:00:00:55 Reference: Memory used: 3142.60 MB Current: Memory used: 3142.37 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): 00:00:00:34 Current: Execution time (DD:HH:MM:SS): 00:00:00:34 Reference: Memory used: 3240.11 MB Current: Memory used: 3246.84 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): 00:00:02:27 Current: Execution time (DD:HH:MM:SS): 00:00:02:28 Reference: Memory used: 3704.85 MB Current: Memory used: 3696.29 MB
RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅ Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅
RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅ Original model has 13 species. Test model has 13 species. ✅ Original model has 19 reactions. Test model has 19 reactions. ✅
Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison ✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅
### Regression test RMS_CSTR_liquid_oxidation: Reference: Execution time (DD:HH:MM:SS): 00:00:06:07 Current: Execution time (DD:HH:MM:SS): 00:00:06:10 Reference: Memory used: 3654.23 MB Current: Memory used: 3653.55 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](22) + CC=O(62)` origin: intra_H_migration
RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌ Original model has 206 species. Test model has 206 species. ✅ Original model has 1508 reactions. Test model has 1508 reactions. ✅ The original model has 2 reactions that the tested model does not have. ❌ rxn: `CCO[O](36) <=> [OH](22) + CC=O(62)` origin: intra_H_migration rxn: `CCCO[O](35) <=> [OH](22) + 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 Non-identical kinetics! ❌ original: rxn: `CCCO[O](35) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](98) + CCCC(C)[O](65)` origin: Peroxyl_Disproportionation tested: rxn: `CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](94) + CCCC(C)[O](61)` 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): 00:00:00:41 Current: Execution time (DD:HH:MM:SS): 00:00:00:40 Reference: Memory used: 2959.67 MB Current: Memory used: 2963.80 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): 00:00:03:08 Current: Execution time (DD:HH:MM:SS): 00:00:03:07 Reference: Memory used: 3840.01 MB Current: Memory used: 3835.76 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 ✅

beep boop this comment was written by a bot :robot:

JacksonBurns commented 9 months ago

@jonwzheng could you check the live docs pages online and see if the changes here are reflected there?

jonwzheng commented 9 months ago

The live docs don't show this yet; see this and this.

JacksonBurns commented 9 months ago

Ugh, the latest doc building action fixes still aren't working. @jonwzheng could you put another pair of eyes on this workflow file and tell me if you see what is wrong? https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/.github/workflows/docs.yml

Here is the workflow run from merging this PR, it seems like the building worked but then the push failed?? https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/7935329144/job/21668223608

jonwzheng commented 9 months ago

I'm looking into this and it looks like documentation build workflow has had this issue as early as last week: see this for example.

Yeah, it looks like it's something specifically with the push step even though the build works. I'm not too familiar with how the workflow automation works, so I don't see anything that strikes me as particularly wrong. The error nothing to commit, working tree clean is really weird. Is there any chance that the /build/html in the Publish documentation action is different from the build/html/ compiled during Make documentation - to publish? I'm not sure how else to explain that there's nothing to commit unless we're operating in the original (rather than re-created) directory.

rwest commented 9 months ago

I think there could be a difference between documentation/build/html and build/html ? Seem to be doing the git actions (checking out, committing, etc.) in the latter, but building the documentation in the former? Could add some path printing stuff to debug, or could try something like https://github.com/mxschmitt/action-tmate to poke around and see what's happening.