Add thermo and kinetics data for electrocatalytic CO2 reduction#677
Add thermo and kinetics data for electrocatalytic CO2 reduction#677ssun30 wants to merge 11 commits intoReactionMechanismGenerator:mainfrom
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Regression Testing ResultsWARNING:root:Initial mole fractions do not sum to one; normalizing. Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:01:07 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Passed Edge Comparison ✅Original model has 106 species. DetailsObservables 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): 00:00:02:20 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 214 species. Non-identical kinetics! ❌
kinetics: DetailsObservables 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): 00:00:01:27 nitrogen Failed Core Comparison ❌Original model has 41 species. nitrogen Failed Edge Comparison ❌Original model has 133 species. DetailsObservables 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): 00:00:02:27 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species. DetailsObservables 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 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species. DetailsObservables 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): 00:00:00:39 superminimal Passed Core Comparison ✅Original model has 13 species. superminimal Passed Edge Comparison ✅Original model has 18 species. Regression test RMS_constantVIdealGasReactor_superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:02:23 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species. DetailsObservables 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): 00:00:06:16 RMS_CSTR_liquid_oxidation Passed Core Comparison ✅Original model has 37 species. RMS_CSTR_liquid_oxidation Passed Edge Comparison ✅Original model has 248 species. DetailsObservables 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 ✅beep boop this comment was written by a bot 🤖 |
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JacksonBurns
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You have some tests failing because of bad adjacency lists:
ERROR test/database/databaseTest.py::TestDatabase::test_kinetics - rmgpy.exceptions.InvalidAdjacencyListError: Error in adjacency list:
XCHOH
1 O u0 p2 c0 {2,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,D}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 X u0 p0 c0 {2,S}
Found bonds between 2 and 5, but of different orders "['D']" and "['S']".
ERROR test/database/databaseTest.py::TestDatabase::test_thermo - rmgpy.exceptions.InvalidAdjacencyListError: Error in adjacency list:
XCHOH
1 O u0 p2 c0 {2,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,D}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 X u0 p0 c0 {2,S}
Found bonds between 2 and 5, but of different orders "['D']" and "['S']".
ERROR test/database/databaseTest.py::TestDatabase::test_solvation - rmgpy.exceptions.InvalidAdjacencyListError: Error in adjacency list:
XCHOH
1 O u0 p2 c0 {2,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,D}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 X u0 p0 c0 {2,S}
Found bonds between 2 and 5, but of different orders "['D']" and "['S']".
ERROR test/database/databaseTest.py::TestDatabase::test_statmech - rmgpy.exceptions.InvalidAdjacencyListError: Error in adjacency list:
XCHOH
1 O u0 p2 c0 {2,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,D}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 X u0 p0 c0 {2,S}
Found bonds between 2 and 5, but of different orders "['D']" and "['S']".
ERROR test/database/databaseTest.py::TestDatabase::test_transport - rmgpy.exceptions.InvalidAdjacencyListError: Error in adjacency list:
XCHOH
1 O u0 p2 c0 {2,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,D}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 X u0 p0 c0 {2,S}
Found bonds between 2 and 5, but of different orders "['D']" and "['S']".
ERROR test/database/databaseTest.py::TestDatabase::test_metal_libraries - rmgpy.exceptions.InvalidAdjacencyListError: Error in adjacency list:
XCHOH
1 O u0 p2 c0 {2,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,D}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 X u0 p0 c0 {2,S}
Found bonds between 2 and 5, but of different orders "['D']" and "['S']".
This should be pretty straightforward to fix (I hope)
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@mjohnson541 @JacksonBurns I'm changing this back to WIP since we recently got some adsorbate data for Cu(111) and Cu3Sn(0001) and I'd like the check the validity of these. I would also need to cleanup the whitespace changes and re-generate the descriptions to match existing entries. |
to Liquid Thermo Library. This prevents RMG from applying solvent corrections twice.
on Cu(111) and Cu3Sn(0001)
families for CO2RR
Fixed an issue with bond orders in the CO2RR DFT Ag111 kinetics library
Undid trailing whitespace changes to solvent.py
JacksonBurns
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Assuming the tests pass, this looks good as all of the comments have been addressed. I think a second approval from @mjohnson541 would be good, but otherwise this is good to go.
Regression Testing ResultsWARNING:root:Initial mole fractions do not sum to one; normalizing. Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:00:55 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Failed Edge Comparison ❌Original model has 106 species. Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s3_4_5_ene_3) + polycyclic(s2_4_5_diene_1_5) + polycyclic(s2_5_5_diene_1_5) - ring(Cyclobutene) - ring(Cyclopentene) - ring(Cyclopentene) + radical(cyclopentene-allyl) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5) Non-identical thermo! ❌
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(1,4-Cyclohexadiene) + ring(124cyclohexatriene) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,3-Cyclohexadiene) Non-identical thermo! ❌
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(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,3-Cyclohexadiene) + radical(Cds_P) Non-identical thermo! ❌
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(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,3-Cyclohexadiene) Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: DetailsObservables 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): 00:00:02:01 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 214 species. DetailsObservables Test Case: liquid_oxidation Comparison✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! liquid_oxidation Passed Observable Testing ✅Regression test nitrogen:Reference: Execution time (DD:HH:MM:SS): 00:00:01:04 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 133 species. DetailsObservables Test Case: NC Comparison✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions! nitrogen Passed Observable Testing ✅Regression test oxidation:Reference: Execution time (DD:HH:MM:SS): 00:00:01:47 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species. DetailsObservables 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): 00:00:00:42 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species. DetailsObservables Test Case: SO2 ComparisonThe following observables did not match: ❌ Observable species O=S=O varied by more than 0.100 on average between old model SO2(15) and new model SO2(15) in condition 1.
sulfur Failed Observable Testing ❌Regression test superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:00:26 superminimal Passed Core Comparison ✅Original model has 13 species. superminimal Passed Edge Comparison ✅Original model has 18 species. Regression test RMS_constantVIdealGasReactor_superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:02:19 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species. DetailsObservables 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): 00:00:22:24 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 99 species. DetailsObservables 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 ✅beep boop this comment was written by a bot 🤖 |
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Raw DFT data calculated by Manish Kumar Kothakonda and Colin Gallagher from Northeastern University. Converted to RMG data format by Su Sun.