Vdw bonds#2706
Conversation
bjkreitz
added
Complexity: Medium
Topic: Catalysis
Status: WIP
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 Failed Edge Comparison ❌Original model has 106 species. 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: 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): 00:00:02:11 liquid_oxidation Failed Core Comparison ❌Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 202 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): 00:00:01:27 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): 00:00:02:26 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): 00:00:00:56 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): 00:00:00:40 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): 00:00:05:53 RMS_CSTR_liquid_oxidation Passed Core Comparison ✅Original model has 37 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 206 species. Non-identical kinetics! ❌
kinetics: 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 ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:43 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species. DetailsObservables 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): 00:00:03:04 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species. DetailsObservables 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 🤖 |
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
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): 00:00:01:05 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)(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(1,4-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: 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): 00:00:02:09 liquid_oxidation Failed Core Comparison ❌Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 202 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): 00:00:01:25 nitrogen Failed Core Comparison ❌Original model has 41 species. nitrogen Failed Edge Comparison ❌Original model has 133 species. Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO) Non-identical kinetics! ❌
kinetics: 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): 00:00:02:28 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): 00:00:00:54 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): 00:00:00:36 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): 00:00:02:26 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): 00:00:05:59 RMS_CSTR_liquid_oxidation Passed Core Comparison ✅Original model has 37 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 206 species. Non-identical kinetics! ❌
kinetics: 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 ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:42 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species. DetailsObservables 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 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species. DetailsObservables 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): 00:00:00:44 minimal_surface Passed Core Comparison ✅Original model has 11 species. minimal_surface Passed Edge Comparison ✅Original model has 38 species. DetailsObservables 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 ✅beep boop this comment was written by a bot 🤖 |
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): 00:00:01:08 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Failed Edge Comparison ❌Original model has 106 species. Non-identical thermo! ❌
Identical thermo comments: 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: 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): 00:00:02:24 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): 00:00:01:29 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): 00:00:02:33 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): 00:00:00:58 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): 00:00:00:37 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): 00:00:02:26 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): 00:00:06:17 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 ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:42 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species. DetailsObservables 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): 00:00:03:05 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species. DetailsObservables 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): 00:00:00:45 minimal_surface Passed Core Comparison ✅Original model has 11 species. minimal_surface Passed Edge Comparison ✅Original model has 38 species. DetailsObservables 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 ✅beep boop this comment was written by a bot 🤖 |
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
github-actions
Bot
added
the
abandoned
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): 00:00:01:06 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): 00:00:02:21 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): 00:00:01:25 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Failed Edge Comparison ❌Original model has 133 species. Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO) Non-identical kinetics! ❌
kinetics: 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): 00:00:02:28 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): 00:00:00:38 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): 00:00:06:10 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 ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:41 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species. DetailsObservables 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): 00:00:03:04 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species. DetailsObservables 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): 00:00:00:44 minimal_surface Passed Core Comparison ✅Original model has 11 species. minimal_surface Passed Edge Comparison ✅Original model has 38 species. DetailsObservables 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 ✅beep boop this comment was written by a bot 🤖 |
github-actions
Bot
removed
abandoned
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
github-actions
Bot
added
the
abandoned
We don't need to check if it's multidentate and THEN check if there's a covalent surface bond. Knowing that there's a covalent surface bond will suffice, and still only involves looping through the atoms once each. (same as counting the X atoms). And if we haven't returned early, we should remove the bonds.
The optimized is_multidentate now short-circuits on the second surface site, and avoids building an intermediate list.
If we declare these things as Atoms and Bonds then Cython can directly access the methods like .is_surface_site() and .is_van_der_waals() I noticed the pxd declares a whole ton of things as Vertex instead of Atom. This should probably also be fixed, if I'm right.
…fied. Suggested by copilot: Previously, populate_resonance_algorithms() adds generate_formate_resonance_structures only in the features['is_multidentate'] branch, but it is not included in the default (features=None) method list. This means call sites that iterate populate_resonance_algorithms() without passing features (e.g., the isomorphic-resonance enumeration later in this module) will never generate the new formate resonance structures. Consider adding the new generator to the features is None list as well to keep behavior consistent.
…rmate_resonance_structures Just so all the adsorbate things start with similar names.
Should NOT remove vdW if there's also a covalent bond to the surface.
For checking multi-dentate vdW things. I'm about to refactor, and want to first document what the current code does, then change how we do it in the next commit.
Lifts is_multidentate() into the outer guard (short-circuits on the second surface atom,
so it's cheaper than get_num_atoms('X') > 1 which counts all atoms).
Replaces the surface_sites list + all(... == 'Xv') check with
`not has_covalent_surface_bond()`.
Drops the now-unused surface_sites = [] initializer.
Also add tests for it, and use it in reaction family is_molecule_forbidden method.
The has_vdw_surface_bond now ALSO returns True for has LACK OF a bond (but an X and one other thing). I guess if you were to give it an adjacency list with just X atoms, this would return True, which may seem weird. (But so would the old test which was just for the presence of an Xv atom type)
Since Python 3.8 we can do this "walrus" operator :=
drop this commit before merging to main. merge at same time as ReactionMechanismGenerator/RMG-database#729
The dispatch else-branch in kinetics_check_sample_can_react raised a terse
ValueError ("Family had N reactants?: ...") that named neither the family nor
the underlying cause, making CI failures hard to diagnose. This branch is
reached whenever the number of reactant roots that produced at least one usable
sample molecule does not match the family
template, and it raised before the
logging loop ran, discarding any per-sample errors already queued.
Add an explicit check comparing the number of reactant roots that
yielded samples against the family template's reactant count. On a mismatch,
append a descriptive, per-root message logged together with
the queued per-sample errors (and then raises the standard
"Error Occurred. See log for details."), naming the family and the specific
reactant root(s) with no usable sample.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This reverts commit 5e967e6.
JacksonBurns
left a comment
JacksonBurns
left a comment
There was a problem hiding this comment.
Was previously approved by @kirkbadger18 (approval was dismissed for an unrelated reason). Approving and automerging.
Motivation or Problem
There are a couple of species that we currently cannot handle in RMG when generating mechanisms for heterogeneously catalyzed reactions, because we have no way to represent them in RMG. One of these species is bidentate formate *OC(H)*O.
This adsorbate is a bidentate species, where both oxygen adatoms have the same distance to the surface. Formate is an important intermediate in many reactions mechanisms, like methanation or methanol synthesis. The only way to draw a Lewis structure for this species is to assume a resonance structure, where one of the oxygens doesn't have a bond to the surface. It is necessary to tell RMG that this is a bidentate species and that both oxygen atoms are coordinated with the surface atoms. There is also a stable monodentate formate species and our Lewis structure for the bidentate needs to be different from the monodentate.
Description of Changes
I adjusted RMG to handle this structure (and similar adsorbates) by introducing a vdW bond between the oxygen and the surface atom. This tells RMG that the oxygen and the surface atom are connected.
These vdW bonds occur only in multidentate adsorbates that have another covalent bond with the surface. If a reaction recipe leads to a species with only vdW bonds to the surface, RMG still removes those and forms a physisorbed structure.
Testing
I was able to generate a mechanism with the bidentate formate and it can also participate in reactions, when I provide new reaction families that can form and break this bond.
Reviewer Tips
This is still a work in progress and requires further updates. I'm just looking for initial thoughts on whether this approach is the right one to address this issue.