ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
Other
382 stars 226 forks source link

ValueError: Unable to generate identifier type inchi with backend rdkit-first. #1728

Closed AH9316 closed 1 year ago

AH9316 commented 4 years ago

Topic

General area which your question is related to.

Context

I am trying to run aniline pyrolysis simulation with quantum calculation and I meet an error as below:

Traceback (most recent call last):
  File "rmg.py", line 173, in <module>
    main()
  File "rmg.py", line 167, in main
    rmg.execute(**kwargs)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/rmg/main.py", line 860, in execute
    trimolecularReact=self.trimolecularReact)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/rmg/model.py", line 617, in enlarge
    self.applyThermoToSpecies(procnum)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/rmg/model.py", line 813, in applyThermoToSpecies
    quantumMechanics.runJobs(self.newSpeciesList, procnum=procnum)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/qm/main.py", line 255, in runJobs
    map(_write_QMfiles_star, qm_arg_list)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/qm/main.py", line 266, in _write_QMfiles_star
    return _write_QMfiles(*args)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/qm/main.py", line 273, in _write_QMfiles
    quantumMechanics.getThermoData(mol)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/qm/main.py", line 212, in getThermoData
    qm_molecule_calculator = rmgpy.qm.mopac.MopacMolPM3(molecule, self.settings)
  File "/home/rcf-40/anguohu/.conda/envs/rmg_env/lib/python2.7/site-packages/rmgpy/qm/molecule.py", line 254, in __init__
    self.uniqueIDlong = self.molecule.toAugmentedInChI()
  File "rmgpy/molecule/molecule.py", line 1633, in rmgpy.molecule.molecule.Molecule.toAugmentedInChI
  File "rmgpy/molecule/molecule.py", line 1640, in rmgpy.molecule.molecule.Molecule.toAugmentedInChI
  File "rmgpy/molecule/translator.py", line 142, in rmgpy.molecule.translator.toInChI
  File "rmgpy/molecule/translator.py", line 168, in rmgpy.molecule.translator.toInChI
  File "rmgpy/molecule/translator.py", line 158, in rmgpy.molecule.translator.toInChI
  File "rmgpy/molecule/translator.py", line 537, in rmgpy.molecule.translator._write
ValueError: Unable to generate identifier type inchi with backend rdkit-first.

I did not meet this issue when I run aniline pyrolysis without quantum calculation so I guess the quantum calculation may be the reason for this case. However, I run an aniline oxidation simulation with quantum calculation at the same time and it is still running now.

Question

Is that because of RMG generated an unreasonable species that rdkit cannot draw the inchi for it?

github-actions[bot] commented 1 year ago

This issue is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant issue, otherwise it will automatically be closed in 30 days.