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
- 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
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