Add thermo and kinetics data for electrocatalytic CO2 reduction#677
Add thermo and kinetics data for electrocatalytic CO2 reduction#677ssun30 wants to merge 7 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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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)
| entry( | ||
| index = 204, | ||
| label = "dummy solvent", | ||
| molecule = "O", |
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Isn't this going to show up as having the molecular structure of H2O?
| shortDesc = u""" """, | ||
| longDesc = | ||
| u""" | ||
| Abraham parameters: fitted by Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., |
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Can we remove or at least separate all of these whitespace changes?
| } | ||
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| # CO2RR families | ||
| surface_CO2 = { |
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This isn't mentioned in the commit title. What's the difference between this set and surface?
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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)
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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.