ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database
Labelling bugs with importChemkinLibrary.py
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- Dominant language
- Python
- Stars
- 127
- Forks
- 160
- Avg merge
- 6d 2h
- Merged PRs (30d)
- 2
Description
I recently tried to use the importChemkinLibrary script on a merged mechanism and noticed a couple bugs that made it so the user couldn't use the libraries without making modifications:
For kinetics library:
- dictionary.txt saved different names from reactions.py. The dictionary removed the parenthetical indicies, but reactions.py did not (e.g. in reactions.py labels CH3(1)+CH3(1) <=> C2H6(2), whereas dictionary.txt has only CH3 and C2H6).
- Does not catch if species name had an "=", which causes parsing errors in kinetics library
For thermo library:
RMG needs thermo values at 298K, but the script faithfully copies over temperature ranges that are in the chemkin file. We probably should have it throw an error, instead of changing the temperature range.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate importChemkinLibrary.py and inspect how it generates dictionary.txt, reactions.py, and thermo library entries from a Chemkin file. Reproduce the reported parsing and temperature-range cases, then verify that names stay consistent, invalid '=' species are handled, and incompatible thermo ranges are rejected.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- databases, tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100