ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Error related to model chemistries
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Description
I don't really have time to look at this now, but so this doesn't get lost I'll put it down here now. I ran the ARC reaction notebook, except giving the TS in the yaml to it as an initial guess. I believe this issue is related to the fact that I set sp_level='B3LYP/6-311++G(3df,3pd)' in the ARC object construction.
Loading statistical mechanics parameters for TS...
Exception Traceback (most recent call last)
in ()
30 arc_rxn_list=arc_rxn_list, sp_level='B3LYP/6-311++G(3df,3pd)',
31 use_bac=False,scan_rotors=False, fine=False,ess_settings={"gaussian":"pharos"})
---> 32 arc0.execute()
/Users/mattjohnson/RMGCODE/ARC/arc/main.pyc in execute(self)
564 lib_long_desc=self.lib_long_desc, rmgdatabase=self.rmgdb, t_min=self.t_min, t_max=self.t_max,
565 t_count=self.t_count)
--> 566 prc.process()
567 self.summary()
568 self.log_footer()
/Users/mattjohnson/RMGCODE/ARC/arc/processor.pyc in process(self)
220 stat_mech_job.modelChemistry = self.model_chemistry
221 stat_mech_job.frequencyScaleFactor = assign_frequency_scale_factor(self.model_chemistry)
--> 222 stat_mech_job.execute(outputFile=None, plot=False)
223 for spc in rxn.r_species + rxn.p_species:
224 if spc.label not in arkane_spc_dict.keys():
/Users/mattjohnson/RMGCODE/RMG-Py/arkane/statmech.pyc in execute(self, outputFile, plot, pdep)
187 logging.error("pdep loading:")
188 logging.error(pdep)
--> 189 self.load(pdep)
190 if outputFile is not None:
191 self.save(outputFile)
/Users/mattjohnson/RMGCODE/RMG-Py/arkane/statmech.pyc in load(self, pdep)
418 atomEnergies=self.atomEnergies,
419 applyAtomEnergyCorrections=self.applyAtomEnergyCorrections,
--> 420 applyBondEnergyCorrections=self.applyBondEnergyCorrections)
421 if len(number) > 1:
422 ZPE = statmechLog.loadZeroPointEnergy() * self.frequencyScaleFactor
/Users/mattjohnson/RMGCODE/RMG-Py/arkane/statmech.pyc in applyEnergyCorrections(E0, modelChemistry, atoms, bonds, atomEnergies, applyAtomEnergyCorrections, applyBondEnergyCorrections)
774
775 else:
--> 776 raise Exception('Unknown model chemistry "{}".'.format(modelChemistry))
777
778 for symbol, count in atoms.items():
Exception: Unknown model chemistry "".
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Research direction
Reproduce the ARC reaction notebook using a TS from YAML and sp_level='B3LYP/6-311++G(3df,3pd)'. Trace model chemistry from arc/main.pyc and arc/processor.pyc into arkane/statmech.pyc, especially load() and applyEnergyCorrections(). Done means the run no longer reaches the unknown empty model chemistry exception.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100