ReactionMechanismGenerator / ARC

ARC - Automatic Rate Calculator
https://reactionmechanismgenerator.github.io/ARC/index.html
MIT License
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Don't trsh conformer isomorphism if no XYZ is given #611

Closed alongd closed 1 year ago

alongd commented 1 year ago

I got the following trace when running C2H5NO2 (smiles [O-][N+](=O)CC) at CBS-QB3:

Warning: Isomorphism check for all conformers of species C2H5NO2 failed at wb97xd/def2svp. Attempting to troubleshoot using a different level.
Troubleshooting conformer job in gaussian using wb97xd/def2TZVP for species C2H5NO2
Traceback (most recent call last):
  File "/Code/ARC/ARC.py", line 69, in <module>
    main()
  File "/Code/ARC/ARC.py", line 65, in main
    arc_object.execute()
  File "/Code/ARC/arc/main.py", line 583, in execute
    fine_only=self.fine_only,
  File "/Code/ARC/arc/scheduler.py", line 481, in __init__
    self.schedule_jobs()
  File "/Code/ARC/arc/scheduler.py", line 534, in schedule_jobs
    self.determine_most_stable_conformer(label)  # also checks isomorphism
  File "/Code/ARC/arc/scheduler.py", line 2004, in determine_most_stable_conformer
    self.troubleshoot_conformer_isomorphism(label=label)
  File "/Code/ARC/arc/scheduler.py", line 3340, in troubleshoot_conformer_isomorphism
    xyz = self.species_dict[label].conformers_before_opt[conformer]

Some debugging exposed that ARC tried to troubleshoot the second conformer (index 1), but the Species .conformers_before_opt attribute contained only a tuple of length 1 with XYZ.

A check for the iterator was now added to avoid crashing.

codecov[bot] commented 1 year ago

Codecov Report

Merging #611 (b5a765b) into main (a41eb1e) will increase coverage by 0.00%. The diff coverage is 0.00%.

@@           Coverage Diff           @@
##             main     #611   +/-   ##
=======================================
  Coverage   72.16%   72.16%           
=======================================
  Files          97       97           
  Lines       25562    25564    +2     
  Branches     5391     5392    +1     
=======================================
+ Hits        18447    18449    +2     
- Misses       5756     5757    +1     
+ Partials     1359     1358    -1     
Impacted Files Coverage Δ
arc/scheduler.py 20.24% <0.00%> (-0.03%) :arrow_down:

... and 1 file with indirect coverage changes

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