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Fix bug with loading molecule statmech during Rate jobs #73

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Mar 4, 2019
Merged

Fix bug with loading molecule statmech during Rate jobs #73

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15 changes: 8 additions & 7 deletions arc/processor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@ def process(self):
species_list_for_thermo_parity = list()
species_for_thermo_lib = list()
for species in self.species_dict.values():
if species.generate_thermo and not species.is_ts and 'ALL converged' in self.output[species.label]['status']:
if not species.is_ts and 'ALL converged' in self.output[species.label]['status']:
species_for_thermo_lib.append(species)
output_file_path = self._generate_arkane_species_file(species)
arkane_spc = arkane_species(str(species.label), species.arkane_file)
Expand All @@ -185,10 +185,11 @@ def process(self):
stat_mech_job.modelChemistry = self.model_chemistry
stat_mech_job.frequencyScaleFactor = assign_frequency_scale_factor(self.model_chemistry)
stat_mech_job.execute(outputFile=output_file_path, plot=False)
thermo_job = ThermoJob(arkane_spc, 'NASA')
thermo_job.execute(outputFile=output_file_path, plot=False)
species.thermo = arkane_spc.getThermoData()
plotter.log_thermo(species.label, path=output_file_path)
if species.generate_thermo:
thermo_job = ThermoJob(arkane_spc, 'NASA')
thermo_job.execute(outputFile=output_file_path, plot=False)
species.thermo = arkane_spc.getThermoData()
plotter.log_thermo(species.label, path=output_file_path)

species.rmg_species = Species(molecule=[species.mol])
species.rmg_species.reactive = True
Expand All @@ -200,8 +201,8 @@ def process(self):
logging.info('Could not retrieve RMG thermo for species {0}, possibly due to missing 2D structure '
'(bond orders). Not including this species in the parity plots.'.format(species.label))
else:
species_list_for_thermo_parity.append(species)

if species.generate_thermo:
species_list_for_thermo_parity.append(species)
# Kinetics:
rxn_list_for_kinetics_plots = list()
arkane_spc_dict = dict() # a dictionary with all species and the TSs
Expand Down