Remove kinetic group additivity methods from code and documentation #2612
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Regression Testing Results
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 Failed Edge Comparison ❌Original model has 106 species. Non-identical thermo! ❌
Identical thermo comments:
Observables 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 Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 202 species. Non-identical kinetics! ❌
kinetics:
Observables 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): 00:00:01:23 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 132 species.
Observables 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): 00:00:02:29 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species.
Observables 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.
Observables 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): 00:00:00:34 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): 00:00:02:31 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species.
Observables 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): 00:00:06:08 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 37 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 206 species. Non-identical kinetics! ❌
kinetics:
Observables Test Case: RMS_CSTR_liquid_oxidation Comparison
The following observables did not match: ❌ Observable species CCCCC varied by more than 0.100 on average between old model pentane(2) and new model pentane(2) in condition 1.
RMS_CSTR_liquid_oxidation Failed 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.
Observables 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): 00:00:03:06 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species.
Observables 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 🤖 |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #2612 +/- ##
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+ Coverage 55.14% 55.16% +0.01%
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Files 125 125
Lines 37036 37019 -17
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- Hits 20424 20421 -3
+ Misses 16612 16598 -14 ☔ View full report in Codecov by Sentry. |
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Re-running CI in the hope that the failures were spurious Julia dependency stuff. |
We have decided to remove group additivity methods for kinetics estimation. This commit builds upon the commit from Aug. 2023 to remove additional references to kinetic estimation by group additivity, including docstring, such that the only valid kinetic estimator now is 'rate rules'.
…al of useful description of what data type is returned
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Branch was outdated - rebased. |
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@jonwzheng I think there is just a simple formatting error in this table: https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/7932965819/job/21660635035?pr=2612#step:9:335 |
fixed this in the latest commit! |
Regression Testing Results
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 Passed Edge Comparison ✅Original model has 106 species.
Observables 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. Non-identical kinetics! ❌
kinetics: liquid_oxidation Failed Edge Comparison ❌Original model has 202 species. Non-identical kinetics! ❌
kinetics:
Observables 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): 00:00:01:24 nitrogen Failed Core Comparison ❌Original model has 41 species. nitrogen Failed Edge Comparison ❌Original model has 132 species.
Observables 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): 00:00:02:30 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species.
Observables 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.
Observables 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): 00:00:00:34 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): 00:00:02:27 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species.
Observables 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): 00:00:06:07 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 37 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 206 species. Non-identical kinetics! ❌
kinetics:
Observables 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.
Observables 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.
Observables 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 🤖 |
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@jonwzheng could you check the live docs pages online and see if the changes here are reflected there? |
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Ugh, the latest doc building action fixes still aren't working. @jonwzheng could you put another pair of eyes on this workflow file and tell me if you see what is wrong? https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/.github/workflows/docs.yml Here is the workflow run from merging this PR, it seems like the building worked but then the push failed?? https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/7935329144/job/21668223608 |
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I'm looking into this and it looks like documentation build workflow has had this issue as early as last week: see this for example. Yeah, it looks like it's something specifically with the push step even though the build works. I'm not too familiar with how the workflow automation works, so I don't see anything that strikes me as particularly wrong. |
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I think there could be a difference between |
Motivation or Problem
See #2605. We have decided to remove group additivity as a valid estimator for kinetics. Now, only rate rules will be supported moving forward.
A previous commit (9f293be) removed the main group additivity estimator methods. However, there were still a few references to kinetic group additivity, including as the default method for
get_kineticsifkinetics_estimatoris not provided. There were also some mentions in the documentation and docstrings that suggest group additivity is supported.Description of Changes
This PR removes most mentions of kinetic group additivity from the code, documentation, and docstrings.
However, this commit does not remove the
KineticsGroupclass (seermgpy/data/kinetics/groups.py), which is used extensively in the definition of aKineticsFamily. I would welcome some discussion on whether we should remove those and rewrite the kinetics family code as well, or if we want to keep it for compatibility / future reference/use etc.Testing
A local version of RMG-website using this commit hash seems to return the same kinetics as is currently returned on RMG-Py.