def species(label='', E0=None, states=None, thermo=None, lennardJones=None, molecularWeight=0.0, SMILES='', InChI=''):
global speciesDict
if label == '': raise InputError('Missing "label" attribute in species() block.')
if E0 is not None: E0 = processQuantity(E0)[0]
else: E0 = 0.0
spec = Species(label=label, states=states, thermo=thermo, E0=E0, lennardJones=lennardJones)
if InChI != '':
spec.molecule = [Molecule(InChI=InChI)]
elif SMILES != '':
spec.molecule = [Molecule(SMILES=SMILES)]
spec.molecularWeight = processQuantity(molecularWeight)[0]
speciesDict[label] = spec
logging.debug('Found species "%s"' % spec)
# If the molecular weight was not specified but the structure was, then
# get the molecular weight from the structure
if spec.molecularWeight == 0.0 and spec.molecule is not None and len(spec.molecule) > 0:
spec.molecularWeight = spec.molecule[0].getMolecularWeight()
def species(label='', E0=None, states=None, lennardJones=None, molecularWeight=0.0):
global speciesDict
if E0 is not None: E0 = processQuantity(E0)[0]
else: E0 = 0.0
spec = Species(label=label, states=states, E0=E0, lennardJones=lennardJones)
spec.molecularWeight = processQuantity(molecularWeight)[0]
speciesDict[label] = spec
logging.debug('Found species "%s"' % spec)
elif data[0].lower() == 'grainsize':
assert data[2] == 'J/mol'
Ngrains = 0
grainSize = float(data[2])
network = Network()
# Read collision model
data = readMeaningfulLine(f).split()
assert data[0].lower() == 'singleexpdown'
assert data[1] == 'J/mol'
network.collisionModel = SingleExponentialDownModel(alpha0=float(data[2]), T0=298, n=0.0)
# Read bath gas parameters
bathGas = Species()
bathGas.molecularWeight = float(readMeaningfulLine(f).split()[1]) / 1000.0
bathGas.lennardJones = LennardJones(sigma=float(readMeaningfulLine(f).split()[1]), epsilon=float(readMeaningfulLine(f).split()[1]))
# Read species data
Nspec = int(readMeaningfulLine(f))
speciesDict = {}
for i in range(Nspec):
spec = Species()
# Read species label
spec.label = readMeaningfulLine(f)
speciesDict[spec.label] = spec
if spec.label in moleculeDict:
spec.molecule = [moleculeDict[spec.label]]
# Read species E0
data = readMeaningfulLine(f).split()
assert data[0] == 'J/mol'
