def run_statmech(
self,
arkane_species: Type[Species],
arkane_file_path: str,
arkane_output_path: str = None,
bac_type: Optional[str] = None,
sp_level: Optional[Level] = None,
plot: bool = False,
) -> bool:
"""
A helper function for running an Arkane statmech job.
Args:
arkane_species (arkane_input_species): An instance of an Arkane species() object.
arkane_file_path (str): The path to the Arkane species file (either in .py or YAML form).
arkane_output_path (str): The path to the folder in which the Arkane output.py file will be saved.
bac_type (str, optional): The bond additivity correction type. 'p' for Petersson- or 'm' for Melius-type BAC.
``None`` to not use BAC.
sp_level (Level, optional): The level of theory used for energy corrections.
plot (bool): A flag indicating whether to plot a PDF of the calculated thermo properties (True to plot)
Returns:
bool: Whether the statmech job was successful.
"""
success = True
stat_mech_job = StatMechJob(arkane_species, arkane_file_path)
stat_mech_job.applyBondEnergyCorrections = bac_type is not None and sp_level is not None
if bac_type is not None:
stat_mech_job.bondEnergyCorrectionType = bac_type
if sp_level is None:
# if this is a kinetics computation and we don't have a valid model chemistry, don't bother about it
stat_mech_job.applyAtomEnergyCorrections = False
else:
stat_mech_job.level_of_theory = sp_level.to_arkane_level_of_theory(
)
stat_mech_job.frequencyScaleFactor = self.freq_scale_factor
try:
stat_mech_job.execute(output_directory=arkane_output_path,
plot=plot)
except Exception as e:
logger.error(
f'Arkane statmech job for species {arkane_species.label} failed with the error message:\n{e}'
)
if stat_mech_job.applyBondEnergyCorrections \
and 'missing' in str(e).lower() and 'bac parameters for model chemistry' in str(e).lower():
# try executing Arkane w/o BACs
logger.warning('Trying to run Arkane without BACs')
stat_mech_job.applyBondEnergyCorrections = False
try:
stat_mech_job.execute(output_directory=arkane_output_path,
plot=plot)
except Exception as e:
logger.error(
f'Arkane statmech job for {arkane_species.label} failed with the error message:\n{e}'
)
success = False
else:
success = False
return success
def test_specifying_absolute_file_paths(self):
"""Test specifying absolute file paths of statmech files"""
h2o2_input = """#!/usr/bin/env python
# -*- coding: utf-8 -*-
bonds = {{'H-O': 2, 'O-O': 1}}
externalSymmetry = 2
spinMultiplicity = 1
opticalIsomers = 1
energy = {{'b3lyp/6-311+g(3df,2p)': Log('{energy}')}}
geometry = Log('{freq}')
frequencies = Log('{freq}')
rotors = [HinderedRotor(scanLog=Log('{scan}'), pivots=[1, 2], top=[1, 3], symmetry=1, fit='fourier')]
"""
abs_arkane_path = os.path.abspath(os.path.dirname(
__file__)) # this is the absolute path to `.../RMG-Py/arkane`
energy_path = os.path.join('arkane', 'data', 'H2O2', 'sp_a19032.out')
freq_path = os.path.join('arkane', 'data', 'H2O2', 'freq_a19031.out')
scan_path = os.path.join('arkane', 'data', 'H2O2', 'scan_a19034.out')
h2o2_input = h2o2_input.format(energy=energy_path,
freq=freq_path,
scan=scan_path)
h2o2_path = os.path.join(abs_arkane_path, 'data', 'H2O2', 'H2O2.py')
if not os.path.exists(os.path.dirname(h2o2_path)):
os.makedirs(os.path.dirname(h2o2_path))
with open(h2o2_path, 'w') as f:
f.write(h2o2_input)
h2o2 = Species(label='H2O2', smiles='OO')
self.assertIsNone(h2o2.conformer)
statmech_job = StatMechJob(species=h2o2, path=h2o2_path)
statmech_job.level_of_theory = LevelOfTheory('b3lyp',
'6-311+g(3df,2p)')
statmech_job.load(pdep=False, plot=False)
self.assertAlmostEqual(h2o2.conformer.E0.value_si, -146031.49933673252)
os.remove(h2o2_path)