ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Receiving KeyError: `conformers` when attempting to `arcrestart`
A pull request for this has already been merged.
- #621 by @alongd — merged
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- Python
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Description
Describe the bug
!!! Warning !!! Distance between atoms 5 and 4 (0.970541 A) is suspicious.
Warning: Isomorphism check for all conformers of species r_82_[O-][Np][=O]O failed at wb97xd/def2svp. Attempting to troubleshoot using a different level.
Traceback (most recent call last):
File "/Local/ce_dana/Code/ARC//ARC.py", line 69, in <module>
main()
File "/Local/ce_dana/Code/ARC//ARC.py", line 65, in main
arc_object.execute()
File "/Local/ce_dana/Code/ARC/arc/main.py", line 583, in execute
fine_only=self.fine_only,
File "/Local/ce_dana/Code/ARC/arc/scheduler.py", line 484, in __init__
self.schedule_jobs()
File "/Local/ce_dana/Code/ARC/arc/scheduler.py", line 494, in schedule_jobs
self.determine_most_stable_conformer(species.label)
File "/Local/ce_dana/Code/ARC/arc/scheduler.py", line 2001, in determine_most_stable_conformer
self.troubleshoot_conformer_isomorphism(label=label)
File "/Local/ce_dana/Code/ARC/arc/scheduler.py", line 3317, in troubleshoot_conformer_isomorphism
job = self.job_dict[label]['conformers'][0]
KeyError: 'conformers'
(arc_env) calvinp@tech-ui02:/storage/ce_dana/calvinp/runs/nn_arc/low_level/50_rows_71_to_120_r$
How to reproduce
I have an input file with 50 reactions to check and when attempting to restart the run due another issue, it then reports a KeyError: conformers
Here is the restart.yml
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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 arc/scheduler.py, especially determine_most_stable_conformer and troubleshoot_conformer_isomorphism, then inspect how the supplied restart.yml becomes self.job_dict. Reproduce the arcrestart failure using restart.zip and verify that the run handles this restart state without raising KeyError: 'conformers'.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100