RMG-Py v4.0.0 stable#736
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Glarborg's original thesis has the entry as CH3CHOOH -> CH3CHO + OH. The previous entry was malformed (a symmetric reaction). https://backend.orbit.dtu.dk/ws/portalfiles/portal/4727804/PhDThesis_CLR_Printing.pdf (see Ch. 5.3 Table 5.4 pg. 133, entry 182).
Chore: update CI to RMG-Py Py311 Version
Add the FormicAcid thermo and kinetics libraries
There is a PR in progress to enable RMG to read coverage dependent thermo from libraries ReactionMechanismGenerator/RMG-Py#2646, but we have none in RMG-database to use as examples, so this adds a library with Jongyoon's CO coverage dependence corrections on Pt applied on top of the current surfaceThermoPt111 entry for XCO. This will make it much easier to share examples of using coverage dependent thermo in RMG.
Added recommended_libraries.yml
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
Add thermo and kinetics data for electrocatalytic CO2 reduction
Using conda env create --clone fails because of some caching issue for one package. This forces the workflow to create a fresh environment and then run with the more robust conda run -n in case the conda activate command fails. See ReactionMechanismGenerator/RMG-Py#2944 for more details
…istry and to resolve bugs in computing the values previously
… were duplicated, but children were not
drop this commit before merging, and merge at the same time as ReactionMechanismGenerator/RMG-Py#2706
… is used The CI workflow checks out the RMG-Py branch named by an env var, but the env var was renamed to RMG_PYBRANCH (one underscore) in a4a0c62. The reference therefore resolved to an empty string, and actions/checkout silently fell back to the default branch (main) instead of the requested branch. Restore the matching name RMG_PY_BRANCH (both underscores) on the definition so the ref expression resolves and the intended branch is checked out. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
this is not actual revert, since that previous commit (ReactionMechanismGenerator/RMG-Py@5e967e6) also fixed a typo in this variable name
Formate families
Adding four vdW Bidentates to the thermoPt111 library
RMG-database v4.0.0 🎉
Regression Testing ResultsERROR conda.cli.main_run:execute(148): 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)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopentane) - ring(Cyclopropane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclohexane) - ring(Cyclopentane) + ring(1,4-Cyclohexadiene) + ring(Cyclopentene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4) 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(124cyclohexatriene) + ring(124cyclohexatriene) 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:
✅ 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): 00:00:01:52 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 214 species.
✅ 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): 00:00:00:55 nitrogen Failed Core Comparison ❌Original model has 41 species. nitrogen Failed Edge Comparison ❌Original model has 133 species.
✅ 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): 00:00:01:32 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species.
✅ 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): 00:00:00:39 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species.
✅ 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): 00:00:00:23 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.
✅ 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): 00:00:10:52 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 90 species.
✅ 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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