ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-Py

Regression test model comparison tool attributes wrong reaction family?

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bug
Dominant language
Python
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Forks
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Avg merge
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Merged PRs (30d)
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Description

Bug Description

The regression test is reporting for liquid_oxidation-core.log

Test model has 37 species.
Original model has 37 species.
Test model has 216 reactions.
Original model has 215 reactions.
The tested model has 1 reactions that the original model does not have.
rxn: CCO[O](29) <=> [OH](22) + CC=O(69)		origin: intra_H_migration

similarly for liquid_oidation-edge.log

The original model has 1 reactions that the tested model does not have.
rxn: CCO[O](29) <=> C[CH]OO(73)		origin: intra_H_migration
The tested model has 1 reactions that the original model does not have.
rxn: CCO[O](29) <=> [OH](22) + CC=O(69)		origin: intra_H_migration

The family intra_H_migration is meant to be intra-molecular Hydrogen migration, meaning a hydrogen atom migrates within a molecule. It should be a unimolecular reaction. The image is
intra_H_migration

The reaction above has two products:

CCO[O](29) <=> [OH](22) + CC=O(69)

Clearly it shouldn't come from intra_H_migration, like it claims.

Perhaps it comes from a pressure dependent network, one reaction of which is intra_H_migration?

So maybe the bug is just in the comparer tool used by the regression testing misinterpreting the comments on the reaction? Or perhaps the comments are being written incorrectly?

Anyway, there's a bug somewhere.

How To Reproduce

Run the liquid_oxidation regression test.
Could also inspect the logs in the artifacts of any recent test run, eg. full results (31mb) or just the diff (15kb).

I suggest looking at the annotated chemkin file from the full logs to see what comment is being put on that reaction.

Expected Behavior

The results of the model diff wouldn't be confusingly attributing a bimolecular reaction to origin: intra_H_migration.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Run the liquid_oxidation regression test and inspect its full logs, diff artifacts, and annotated chemkin file. Trace the reaction comparison and annotation shown for CCOO and determine where the intra_H_migration origin is assigned or interpreted. Done means the model diff no longer attributes the bimolecular reaction to that unimolecular family.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, testing-qa
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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