ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

Receiving KeyError: `conformers` when attempting to `arcrestart`

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#622 4 comments 0 reactions 0 assignees View on GitHub

A pull request for this has already been merged.

  • #621 by @alongd — merged
Type: Bug
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

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

restart.zip

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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

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

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