Unable to determine respresentative structures (resonance) #1578
Description
Bug Description
During mechanism generation, my RMG run comes to a screeching halt with the following behavior:
ResonanceError: Could not determine representative localized structures for species [O-][N+](=O)C1C=CC=CC=1[N]C1=CC=CC=C1
Traceback (most recent call last):
File "/home/fuller/Documents/CFG Lab/RMG/RMG-Py/rmg.py", line 173, in <module>
main()
File "/home/fuller/Documents/CFG Lab/RMG/RMG-Py/rmg.py", line 167, in main
rmg.execute(**kwargs)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/rmg/main.py", line 664, in execute
trimolecularReact=self.trimolecularReact)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/rmg/model.py", line 679, in enlarge
unimolecularReact, bimolecularReact, trimolecularReact=trimolecularReact)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/rmg/react.py", line 143, in reactAll
rxns = list(react(*spcTuples))
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/rmg/react.py", line 59, in react
spcTuples)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/scoop_framework/util.py", line 154, in map_
return map(WorkerWrapper(args[0]), *args[1:], **kwargs)
File "/home/fuller/miniconda2/envs/rmg_env/lib/python2.7/site-packages/scoop-0.7.2.0-py2.7.egg/scoop/fallbacks.py", line 49, in wrapper
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/scoop_framework/util.py", line 112, in __call__
return self.myfn(*args, **kwargs)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/rmg/react.py", line 75, in reactSpecies
reactions = getDB('kinetics').generate_reactions_from_families(speciesTuple)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/data/kinetics/database.py", line 521, in generate_reactions_from_families
reaction_list = find_degenerate_reactions(reaction_list, same_reactants, kinetics_database=self)
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/data/kinetics/common.py", line 279, in find_degenerate_reactions
rxn0.ensure_species()
File "rmgpy/reaction.py", line 1110, in rmgpy.reaction.Reaction.ensure_species
File "rmgpy/reaction.py", line 1130, in rmgpy.reaction.Reaction.ensure_species
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/data/kinetics/common.py", line 171, in ensure_species
new_item.generate_resonance_structures(keep_isomorphic=keep_isomorphic)
File "rmgpy/species.py", line 168, in rmgpy.species.Species.generate_resonance_structures
File "rmgpy/species.py", line 178, in rmgpy.species.Species.generate_resonance_structures
File "rmgpy/molecule/molecule.py", line 1831, in rmgpy.molecule.molecule.Molecule.generate_resonance_structures
File "rmgpy/molecule/molecule.py", line 1833, in rmgpy.molecule.molecule.Molecule.generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 151, in rmgpy.molecule.resonance.generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 240, in rmgpy.molecule.resonance.generate_resonance_structures
File "/home/fuller/Dropbox/Documents/CFG Lab/RMG/RMG-Py/rmgpy/molecule/filtration.py", line 76, in filter_structures
mol_list[0].toSMILES()))
rmgpy.exceptions.ResonanceError: Could not determine representative localized structures for species [O-][N+](=O)C1C=CC=CC=1[N]C1=CC=CC=C1
How To Reproduce
I ma attaching my input script and my two additional libraries
ResonanceErrorFiles.zip
Expected Behavior
These libraries have been used in the past (two years ago) to generate a similar mechanism, so I have no idea why this new error is occurring.
Installation Information
Describe your installation method and system information.
- OS: Fedora Linux (29)
- Installation method: conda
- RMG version information: source/developer install:
- RMG-Py: 2.1.0-1710-ga5ab75ce5
- RMG-database: 2.1.0-1710-ga5ab75ce5
Additional Context
Add any other context about the problem here.