def species(label, *args, **kwargs):
"""Load a species from an input file"""
global speciesDict, jobList
if label in speciesDict:
raise ValueError(
'Multiple occurrences of species with label {0!r}.'.format(label))
logging.info('Loading species {0}...'.format(label))
spec = Species(label=label)
speciesDict[label] = spec
path = None
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
logging.debug('Added species {0} to a stat mech job.'.format(label))
jobList.append(job)
elif len(args) > 1:
raise InputError('species {0} can only have two non-keyword argument '
'which should be the species label and the '
'path to a quantum file.'.format(spec.label))
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spinMultiplicity = 0
opticalIsomers = 1
molecularWeight = None
collisionModel = None
energyTransferModel = None
thermo = None
reactive = True
for key, value in kwargs.items():
if key == 'structure':
structure = value
elif key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'molecularWeight':
molecularWeight = value
elif key == 'collisionModel':
collisionModel = value
elif key == 'energyTransferModel':
energyTransferModel = value
elif key == 'thermo':
thermo = value
elif key == 'reactive':
reactive = value
else:
raise TypeError(
'species() got an unexpected keyword argument {0!r}.'.
format(key))
if structure:
spec.molecule = [structure]
spec.conformer = Conformer(E0=E0,
modes=modes,
spinMultiplicity=spinMultiplicity,
opticalIsomers=opticalIsomers)
if molecularWeight is not None:
spec.molecularWeight = molecularWeight
elif spec.molecularWeight is None and is_pdep(jobList):
# If a structure was given, simply calling spec.molecularWeight will calculate the molecular weight
# If one of the jobs is pdep and no molecular weight is given or calculated, raise an error
raise ValueError(
"No molecularWeight was entered for species {0}. Since a structure wasn't given"
" as well, the molecularWeight, which is important for pressure dependent jobs,"
" cannot be reconstructed.".format(spec.label))
spec.transportData = collisionModel
spec.energyTransferModel = energyTransferModel
spec.thermo = thermo
spec.reactive = reactive
if spec.reactive and path is None and spec.thermo is None and spec.conformer.E0 is None:
if not spec.molecule:
raise InputError(
'Neither thermo, E0, species file path, nor structure specified, cannot estimate'
' thermo properties of species {0}'.format(spec.label))
try:
db = getDB('thermo')
if db is None:
raise DatabaseError('Thermo database is None.')
except DatabaseError:
logging.warn(
"The database isn't loaded, cannot estimate thermo for {0}. "
"If it is a bath gas, set reactive = False to avoid generating thermo."
.format(spec.label))
else:
logging.info(
'No E0 or thermo found, estimating thermo and E0 of species {0} using'
' RMG-Database...'.format(spec.label))
spec.thermo = db.getThermoData(spec)
if spec.thermo.E0 is None:
th = spec.thermo.toWilhoit()
spec.conformer.E0 = th.E0
spec.thermo.E0 = th.E0
else:
spec.conformer.E0 = spec.thermo.E0
if spec.reactive and spec.thermo and not spec.hasStatMech(
) and structure is not None:
# generate stat mech info if it wasn't provided before
spec.generateStatMech()
if not energyTransferModel:
# default to RMG's method of generating energyTransferModel
spec.generateEnergyTransferModel()
return spec
def species(label, *args, **kwargs):
global speciesDict, jobList
if label in speciesDict:
raise ValueError('Multiple occurrences of species with label {0!r}.'.format(label))
logging.info('Loading species {0}...'.format(label))
spec = Species(label=label)
speciesDict[label] = spec
path = None
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
logging.debug('Added species {0} to a stat mech job.'.format(label))
jobList.append(job)
elif len(args) > 1:
raise InputError('species {0} can only have two non-keyword argument '
'which should be the species label and the '
'path to a quantum file.'.format(spec.label))
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spinMultiplicity = 0
opticalIsomers = 1
molecularWeight = None
collisionModel = None
energyTransferModel = None
thermo = None
reactive = True
for key, value in kwargs.items():
if key == 'structure':
structure = value
elif key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'molecularWeight':
molecularWeight = value
elif key == 'collisionModel':
collisionModel = value
elif key == 'energyTransferModel':
energyTransferModel = value
elif key == 'thermo':
thermo = value
elif key == 'reactive':
reactive = value
else:
raise TypeError('species() got an unexpected keyword argument {0!r}.'.format(key))
if structure:
spec.molecule = [structure]
spec.conformer = Conformer(E0=E0, modes=modes, spinMultiplicity=spinMultiplicity, opticalIsomers=opticalIsomers)
if molecularWeight is not None:
spec.molecularWeight = molecularWeight
elif spec.molecularWeight is None and is_pdep(jobList):
# If a structure was given, simply calling spec.molecularWeight will calculate the molecular weight
# If one of the jobs is pdep and no molecular weight is given or calculated, raise an error
raise ValueError("No molecularWeight was entered for species {0}. Since a structure wasn't given"
" as well, the molecularWeight, which is important for pressure dependent jobs,"
" cannot be reconstructed.".format(spec.label))
spec.transportData = collisionModel
spec.energyTransferModel = energyTransferModel
spec.thermo = thermo
spec.reactive = reactive
if spec.reactive and path is None and spec.thermo is None and spec.conformer.E0 is None:
if not spec.molecule:
raise InputError('Neither thermo, E0, species file path, nor structure specified, cannot estimate'
' thermo properties of species {0}'.format(spec.label))
try:
db = getDB('thermo')
if db is None:
raise DatabaseError('Thermo database is None.')
except DatabaseError:
logging.warn("The database isn't loaded, cannot estimate thermo for {0}. "
"If it is a bath gas, set reactive = False to avoid generating thermo.".format(spec.label))
else:
logging.info('No E0 or thermo found, estimating thermo and E0 of species {0} using'
' RMG-Database...'.format(spec.label))
spec.thermo = db.getThermoData(spec)
if spec.thermo.E0 is None:
th = spec.thermo.toWilhoit()
spec.conformer.E0 = th.E0
spec.thermo.E0 = th.E0
else:
spec.conformer.E0 = spec.thermo.E0
if spec.reactive and spec.thermo and not spec.hasStatMech() and structure is not None:
# generate stat mech info if it wasn't provided before
spec.generateStatMech()
if not energyTransferModel:
# default to RMG's method of generating energyTransferModel
spec.generateEnergyTransferModel()
return spec
