ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Weird rotor scan troubleshooting
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- Dominant language
- Python
- Stars
- 51
- Forks
- 25
- Avg merge
- 4d 5h
- Merged PRs (30d)
- 15
Description
This is a special case where a ring flip is involved. The molecule is CC1([CH]CO)COO1.
The red rotor is the rotor being scanned, rotors in other colors are those being frozen. The strategy is proposed by the latest troubleshooting module. The 4-member-ring flipped during the previous scan, looks similar to this:
The output file I got is output.out.zip
The error got is
New curvilinear step not converged.
Error imposing constraints
Error termination via Lnk1e in /cm/shared/c3ddb/gaussian/09.d01/g09/l103.exe at Wed May 6 06:25:10 2020.
So it seems like ARC is over-constraining the molecule for its scan. But I cannot really tell how it is over-constrained. My guess is the ring is over-constrained but cannot tell why and how. Let me know your thoughts and I really appreciate your help. Thanks
Contributor guide
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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
Start with output.out.zip and the troubleshooting module's proposed scan strategy, focusing on the reported ring flip and the Gaussian constraint errors. Reproduce the case for CC1([CH]CO)COO1 and trace how the red rotor and frozen rotors are constrained; done means identifying the over-constraint or documenting why the scan cannot proceed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100