ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

ConverterError in a species from the RMGDB

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Module: Converter Module: Species Type: Bug
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

Description

Describe the bug
while performing 1D scans on a list of species from the RMGDB, I encountered an error:

Traceback (most recent call last):
  File f"{arc_path}/ARC.py", line 69, in <module>
    main()
  File f"{arc_path}/ARC.py", line 65, in main
    arc_object.execute()
  File f"{arc_path}/arc/main.py", line 583, in execute
    fine_only=self.fine_only,
  File f"{arc_path}/arc/scheduler.py", line 484, in __init__
    self.schedule_jobs()
  File f"{arc_path}/arc/scheduler.py", line 500, in schedule_jobs
    self.run_conformer_jobs()
  File f"{arc_path}/arc/scheduler.py", line 1030, in run_conformer_jobs
    self.process_conformers(label)
  File f"{arc_path}/arc/scheduler.py", line 1736, in process_conformers
    is_ts=False,
  File f"{arc_path}/arc/plotter.py", line 935, in save_conformers_file
    b_mol = molecules_from_xyz(xyz, multiplicity=multiplicity, charge=charge)[1]
  File f"{arc_path}/arc/species/converter.py", line 1417, in molecules_from_xyz
    set_multiplicity(mol_s1_updated, mol_bo.multiplicity, charge, radical_map=mol_bo)
  File f"{arc_path}//arc/species/converter.py", line 1451, in set_multiplicity
    set_radicals_by_map(mol, radical_map)
  File f"{arc_path}/arc/species/converter.py", line 1566, in set_radicals_by_map
    '{0} is not {1}.'.format(atom.element.symbol, radical_map.atoms[i].symbol))
arc.exceptions.ConverterError: Atom order in mol and radical_map in set_radicals_by_map() do not match. O is not C.

How to reproduce

allow_nonisomorphic_2d: true
compute_thermo: false
job_types:
  bde: false
  conformers: false
  fine: false
  freq: false
  opt: true
  rotors: true
  sp: true
level_of_theory: wb97xd/def2tzvp
project: 1d
species:
- directed_rotors: &id001
    cont_opt:
    - all
  label: '796'
  smiles: '[O]OS(O)(C)C'
trsh_ess_jobs: false

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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

Reproduce the issue with the YAML configuration and species '[O]OS(O)(C)C'. Start in arc/species/converter.py at molecules_from_xyz(), set_multiplicity(), and set_radicals_by_map(), following the traceback. Done means the reproduced species no longer raises the atom-order ConverterError during the workflow.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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