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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): 00:00:00:55 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(s3_5_5_ene_1) - ring(Cyclobutene) - ring(Cyclopentane) - ring(Cyclopentene) + radical(cyclopentene-allyl) 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(Cyclopropane) - ring(Cyclopentane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(1,4-Cyclohexadiene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(1,3-Cyclohexadiene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl) Non-identical thermo! ❌
Identical thermo comments: 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): 00:00:01:56 liquid_oxidation Failed 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): 00:00:01:01 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): 00:00:01:43 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): 00:00:00:39 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): 00:00:00:25 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): 00:00:02:51 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): 00:00:14:43 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 77 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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Pull request overview
Adds a new YAML configuration file defining recommended thermo/kinetics/transport library sets for use by RMG’s “auto” library selection mode (including specialized sets for PAH formation, surface, halogens, and electrochemistry).
Changes:
- Introduces
input/recommended_libraries.ymlwith curated recommended library lists per chemistry type. - Adds additional categorization for CH pyrolysis vs PAH formation and includes surface/electrochem recommendations.
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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): 00:00:00:55 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(Cyclopropane) - ring(Cyclopentane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(1,4-Cyclohexadiene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(1,3-Cyclohexadiene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl) 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): 00:00:01:56 liquid_oxidation Failed 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): 00:00:01:01 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): 00:00:01:43 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): 00:00:00:39 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): 00:00:00:25 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): 00:00:02:51 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): 00:00:14:43 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 77 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 🤖 |
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 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): 00:00:01:56 liquid_oxidation Failed 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): 00:00:01:01 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): 00:00:01:43 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): 00:00:00:39 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): 00:00:00:25 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): 00:00:02:51 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): 00:00:14:43 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 77 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 🤖 |
JacksonBurns
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I don't know enough about the specifics of the chemistry to really comment on that, but I will say that adding some documentation about why these libraries were chosen for these types of chemistry would be helpful for users. I don't know the best place for, but I think inline comments on this file or further additions to the docs as you started in the Pair PR here would be good.
mjohnson541
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Here's at least an initial look over.
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| oxidation: | ||
| thermo: | ||
| - FFCM1(-) |
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Why FFCM1(-) here for oxidation and Klippenstein_Glarborg2016 for CH_pyrolysis_core?
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right, I think I can remove Klippenstein_Glarborg2016, it's superseded by NOx2018
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| - NOx2018 | ||
| - Butadiene_Dimerization | ||
| - CurranPentane |
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CurranPentane and some of these other libraries beg the question for me: How safe do we want to play these recommendations? Some these are libraries are not rock solid, but are much more likely to help than hurt...but users aren't going to inherently know which of these libraries are pure-calculations, which are super well validated and which involve lots of estimates so they may assume that what we recommended is rock solid.
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Excellent question. And a hard one.
For a mid-grade model, we can use some of these libraries, but for a high-grade model we shouldn't.
I removed CurranPentane, which is a model library and not a computed chemical subset library.
The philosophy I take is providing high-grade libraries, users may add the low-grade ones if they want, of course they don't always know what to add. It's hard to strike a balance. I'll try to add some more explanation in the docs in the RMG PR.
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| surface: | ||
| thermo: |
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If we're running on Pt111 is RMG smart enough to ignore surfaceThermoLi?
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I have no idea re surface libs, @rwest, could you please comment?
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I tried this out and no, RMG does not ignore surfaceThermoLi.
I think we should remove surfaceThermoLi from this list because surfaceThermoLi only contains a vacant site.
Even though both vacant sites are all zeros, I think it would confuse users if they try to build a mechanism and see the vacant site coming from Li and all the other thermo based on Pt.
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| - surfaceThermoNi111 | ||
| kinetics: | ||
| - name: Surface/CPOX_Pt/Deutschmann2006_adjusted |
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Do we think these surface kinetics libraries are safe enough to put in our recommendations?
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Yeah, I don't think so. Initially, I thought there is no harm in just adding them to the recommended list. However, this would suggest that we actually believe that the kinetic data from these microkinetic models is better or more accurate than anything that is out there. Of course, this is not true, but it might appear so to new users. There is nothing wrong with any of these microkinetic models. They were created in very different ways and have different parameters, which will change the generated mechanisms. Honestly, I would not recommend any of them, but instead advise the users to work with them at their own risk or create their own library. What do others think @mjohnson541 @kirkbadger18 @rwest @cfgoldsmith ? If we definitely want to add one of the libraries as a recommendation, I would add all to not discriminate against any of these studies.
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I agree, if there are BEP rules then those are probably good enough for a first pass mechanism, I doubt there will be real additional gains by using previous results with a mix of functionals/settings. There are some reactions however, like O2 adsorption, which I believe BEP rules do not work for, and are always added as a library value.
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I agree with what Bjarne and Kirk have said.
Also, like Kirk mentioned, RMG cannot currently find O2 dissociative adsorption by itself (or CO adsorption) because it lacks the families.
I think at least one of these libraries (or a dedicated O2 + CO library) is needed as a seed to build a reasonable mechanism, specifically to include O2 and CO adsorption.
I think the easiest thing would be to pick Deutschmann_adjusted as the seed (it's already the one used in RMG's official catalysis example), keep all libraries in to avoid showing favoritism, and mention in a comment that BEP rules probably work better but you have to put O2 and CO adsorption in your seed or RMG won't find them.
Alternatively, @bjkreitz and @kirkbadger18 , if either of you have favorite/trusted O2 and CO adsorption reactions to use as a seed, we could add that and recommend it instead?
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I need to check these thermo libraries in more detail.
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@rwest, could you please take a look at the recommended surface libraries? @JacksonBurns, I added inline comments to the core chemistry so that the comments live with the data Thanks! |
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): 00:00:00:56 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(s3_5_5_ene_1) - ring(Cyclobutene) - ring(Cyclopentane) - ring(Cyclopentene) + radical(cyclopentene-allyl) 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): 00:00:02:00 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): 00:00:01:46 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): 00:00:00:41 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): 00:00:03:02 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): 00:00:34:48 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 100 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 🤖 |
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)(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(Cyclopropane) - ring(Cyclopentane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_diene_0_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(1,4-Cyclohexadiene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,4-Cyclohexadiene) + radical(cyclopentene-4) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_diene_1_3) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(1,3-Cyclohexadiene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(1,3-Cyclohexadiene) + radical(cyclopentene-allyl) Non-identical thermo! ❌
Identical thermo comments: 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): 00:00:01:57 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 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): 00:00:01:47 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): 00:00:00:41 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): 00:00:02:56 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): 00:00:15:21 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 77 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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@kirkbadger18 @bjkreitz and @sevyharris please could you look at the surface families? @sevyharris also check the combustion? @Nora-Khalil please could you tackle halogens? Many views are valuable here. |
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@rwest happy to add to the list for halogens! However, I have some new libraries that I have been using for halogen chemistry. Do you suggest also adding in those new libraries to input/kinetics/libraries and input/thermo/libraries in this PR, or a separate one? |
Adding new libraries should be a separate PR(s). And if it merges after this then that PR should also add them to this list. |
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): 00:00:00:54 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): 00:00:01:59 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): 00:00:01:03 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): 00:00:01:45 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): 00:00:00:40 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): 00:00:00:25 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): 00:00:02:18 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): 00:00:30:23 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 107 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 🤖 |
| thermo: | ||
| - surfaceThermoLi | ||
| - surfaceThermoPt111 | ||
| - surfaceThermoNi111 |
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I'm not sure if I would recommend the Ni111 library. @cfgoldsmith and @rwest constructed this for the initial RMG-cat paper and I think a lot of the thermo might be rough estimates.
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I agree with Bjarne. I would not recommend this library. It is more of an historical artifact at this point.
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Thanks! Removed.
All other comments are welcome!
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): 00:00:00:54 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(Cyclopropane) - ring(Cyclopentane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_ene_1) + polycyclic(s3_5_6_diene_1_5) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-4) 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(s2_4_5_diene_1_5) + 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-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_ene_1) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(Cyclohexene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-allyl) 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 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: 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): 00:00:01:59 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): 00:00:01:03 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(oxirene) + 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): 00:00:01:45 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): 00:00:00:40 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): 00:00:00:25 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): 00:00:02:18 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): 00:00:30:23 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 107 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 🤖 |
| kinetics: | ||
| - name: Surface/CPOX_Pt/Deutschmann2006_adjusted | ||
| seed: false | ||
| - Surface/Methane/Deutschmann_Pt |
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I think Surface/Methane/Deutschmann_Pt should be removed from this list because it's the same as Surface/CPOX_Pt/Deutschmann2006_adjusted but without reaction barriers raised to the endothermicity of the reaction.
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Thanks, @sevyharris! |
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): 00:00:00:54 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-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_ene_1) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(Cyclohexene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-allyl) 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 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: 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): 00:00:01:59 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): 00:00:01:03 nitrogen Failed Core Comparison ❌Original model has 41 species. 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: 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(oxirene) + radical(CdJ-NdO) 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: 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): 00:00:01:45 oxidation Failed Core Comparison ❌Original model has 59 species. 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: 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: oxidation Failed Edge Comparison ❌Original model has 230 species. 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: 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: 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: 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: Oxidation ComparisonThe following observables did not match: ❌ Observable species [OH] varied by more than 0.500 on average between old model OH(5) and new model OH(5) in condition 1.
oxidation Failed Observable Testing ❌Regression test sulfur:Reference: Execution time (DD:HH:MM:SS): 00:00:00:40 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species. Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: 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): 00:00:00:25 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): 00:00:02:18 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): 00:00:30:23 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 107 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 🤖 |
To be used with the auto database feature ReactionMechanismGenerator/RMG-Py#2909
Reviewers: Please see that this PR makes sense in terms of the chemistry and library correctness, let me know if you have other recommendations. Also, please double check the details of the surface libraries implementation in this file, I'm not fluent inthat.
(Also, I see that we have a
LithiumSurfaceas well as asurfaceThermoLithermo library. It's confusing, maybe rename or unite [in another PR]?)