ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

DatabaseError with Thermo Parameters

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Python
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Description

Hello,

I am encountering a DatabaseError related to thermo parameter estimation for fluorine-containing molecules in RMG-Py. Specifically, the error message is:
DatabaseError: Unable to determine thermo parameters for atom {'*': <Atom 'F'>} in molecule <Molecule "OOC(F)F">: no data for node R or any of its ancestors in database group.

I encounter this issue both with and without a seed mechanism. For instance, when using a seed mechanism, I receive the following error:
DatabaseError: Unable to determine thermo parameters for atom {'*': <Atom 'F'>} in molecule <Molecule "OCF">: no data for node R or any of its ancestors in database group.
Could anyone provide guidance on how to rectify this issue? Are there specific updates or database modifications needed to include data for fluorine-containing molecules?

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  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

Start with RMG-Py thermo parameter estimation and the database group lookup reported for fluorine-containing molecules such as OOC(F)F and OCF. Compare the failures with and without a seed mechanism, then determine whether the database lacks the required fluorine entries; done means the reported molecules receive thermo parameters or the required database update is clearly identified.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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