def transitionState(label, *args, **kwargs):
global transitionStateDict
if label in transitionStateDict:
raise ValueError(
'Multiple occurrences of transition state with label {0!r}.'.
format(label))
logging.info('Loading transition state {0}...'.format(label))
ts = TransitionState(label=label)
transitionStateDict[label] = ts
if len(args) == 1 and len(kwargs) == 0:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=ts, path=path)
jobList.append(job)
elif len(args) == 0 and len(kwargs) > 0:
# The species parameters are given explicitly
E0 = None
modes = []
spinMultiplicity = 1
opticalIsomers = 1
frequency = None
for key, value in kwargs.items():
if key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'frequency':
frequency = value
else:
raise TypeError(
'transitionState() got an unexpected keyword argument {0!r}.'
.format(key))
ts.conformer = Conformer(E0=E0,
modes=modes,
spinMultiplicity=spinMultiplicity,
opticalIsomers=opticalIsomers)
ts.frequency = frequency
return ts
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
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
jobList.append(job)
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spinMultiplicity = 1
opticalIsomers = 1
molecularWeight = None
collisionModel = None
energyTransferModel = None
thermo = None
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
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)
spec.molecularWeight = molecularWeight
spec.transportData = collisionModel
spec.energyTransferModel = energyTransferModel
spec.thermo = thermo
return spec