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.lennardJones = collisionModel
spec.energyTransferModel = energyTransferModel
spec.thermo = thermo
return spec
def loadFAMEInput(path, moleculeDict=None):
"""
Load the contents of a FAME input file into the MEASURE object. FAME
is an early version of MEASURE written in Fortran and used by RMG-Java.
This script enables importing FAME input files into MEASURE so we can
use the additional functionality that MEASURE provides. Note that it
is mostly designed to load the FAME input files generated automatically
by RMG-Java, and may not load hand-crafted FAME input files. If you
specify a `moleculeDict`, then this script will use it to associate
the species with their structures.
"""
def readMeaningfulLine(f):
line = f.readline()
while line != '':
line = line.strip()
if len(line) > 0 and line[0] != '#':
return line
else:
line = f.readline()
return ''
moleculeDict = moleculeDict or {}
logging.info('Loading file "{0}"...'.format(path))
f = open(path)
job = PressureDependenceJob(network=None)
# Read method
method = readMeaningfulLine(f).lower()
if method == 'modifiedstrongcollision':
job.method = 'modified strong collision'
elif method == 'reservoirstate':
job.method = 'reservoir state'
# Read temperatures
Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split()
job.Tmin = Quantity(float(Tmin), Tunits)
job.Tmax = Quantity(float(Tmax), Tunits)
job.Tcount = int(Tcount)
Tlist = []
for i in range(int(Tcount)):
Tlist.append(float(readMeaningfulLine(f)))
job.Tlist = Quantity(Tlist, Tunits)
# Read pressures
Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split()
job.Pmin = Quantity(float(Pmin), Punits)
job.Pmax = Quantity(float(Pmax), Punits)
job.Pcount = int(Pcount)
Plist = []
for i in range(int(Pcount)):
Plist.append(float(readMeaningfulLine(f)))
job.Plist = Quantity(Plist, Punits)
# Read interpolation model
model = readMeaningfulLine(f).split()
if model[0].lower() == 'chebyshev':
job.model = ['chebyshev', int(model[1]), int(model[2])]
elif model[0].lower() == 'pdeparrhenius':
job.model = ['pdeparrhenius']
# Read grain size or number of grains
job.grainCount = 0
job.grainSize = Quantity(0.0, "J/mol")
for i in range(2):
data = readMeaningfulLine(f).split()
if data[0].lower() == 'numgrains':
job.grainCount = int(data[1])
elif data[0].lower() == 'grainsize':
job.grainSize = Quantity(float(data[2]), data[1])
# Create the Network
job.network = Network()
# Read collision model
data = readMeaningfulLine(f)
assert data.lower() == 'singleexpdown'
alpha0units, alpha0 = readMeaningfulLine(f).split()
T0units, T0 = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
energyTransferModel = SingleExponentialDown(
alpha0 = Quantity(float(alpha0), alpha0units),
T0 = Quantity(float(T0), T0units),
n = float(n),
)
speciesDict = {}
# Read bath gas parameters
bathGas = Species(label='bath_gas', energyTransferModel=energyTransferModel)
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
bathGas.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
bathGas.lennardJones = LennardJones(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
job.network.bathGas = {bathGas: 1.0}
# Read species data
Nspec = int(readMeaningfulLine(f))
for i in range(Nspec):
species = Species()
species.conformer = Conformer()
# Read species label
species.label = readMeaningfulLine(f)
speciesDict[species.label] = species
if species.label in moleculeDict:
species.molecule = [moleculeDict[species.label]]
# Read species E0
E0units, E0 = readMeaningfulLine(f).split()
species.conformer.E0 = Quantity(float(E0), E0units)
species.conformer.E0.units = 'kJ/mol'
# Read species thermo data
H298units, H298 = readMeaningfulLine(f).split()
S298units, S298 = readMeaningfulLine(f).split()
Cpcount, Cpunits = readMeaningfulLine(f).split()
Cpdata = []
for i in range(int(Cpcount)):
Cpdata.append(float(readMeaningfulLine(f)))
if S298units == 'J/mol*K': S298units = 'J/(mol*K)'
if Cpunits == 'J/mol*K': Cpunits = 'J/(mol*K)'
species.thermo = ThermoData(
H298 = Quantity(float(H298), H298units),
S298 = Quantity(float(S298), S298units),
Tdata = Quantity([300,400,500,600,800,1000,1500], "K"),
Cpdata = Quantity(Cpdata, Cpunits),
)
# Read species collision parameters
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
species.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
species.lennardJones = LennardJones(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
# Read species vibrational frequencies
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
species.conformer.modes.append(HarmonicOscillator(
frequencies = Quantity(frequencies, freqUnits),
))
# Read species external rotors
rotCount, rotUnits = readMeaningfulLine(f).split()
if int(rotCount) > 0:
raise NotImplementedError('Cannot handle external rotational modes in FAME input.')
# Read species internal rotors
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
barrCount, barrUnits = readMeaningfulLine(f).split()
barriers = []
for j in range(int(barrCount)):
barriers.append(float(readMeaningfulLine(f)))
if barrUnits == 'cm^-1':
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.c * constants.Na * 100. for barr in barriers]
elif barrUnits in ['Hz', 's^-1']:
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.Na for barr in barriers]
elif barrUnits != 'J/mol':
raise Exception('Unexpected units "{0}" for hindered rotor barrier height.'.format(barrUnits))
inertia = [V0 / 2.0 / (nu * constants.c * 100.)**2 / constants.Na for nu, V0 in zip(frequencies, barriers)]
for I, V0 in zip(inertia, barriers):
species.conformer.modes.append(HinderedRotor(
inertia = Quantity(I,"kg*m^2"),
barrier = Quantity(V0,barrUnits),
symmetry = 1,
))
# Read overall symmetry number
species.conformer.spinMultiplicity = int(readMeaningfulLine(f))
# Read isomer, reactant channel, and product channel data
Nisom = int(readMeaningfulLine(f))
Nreac = int(readMeaningfulLine(f))
Nprod = int(readMeaningfulLine(f))
for i in range(Nisom):
data = readMeaningfulLine(f).split()
assert data[0] == '1'
job.network.isomers.append(speciesDict[data[1]])
for i in range(Nreac):
data = readMeaningfulLine(f).split()
assert data[0] == '2'
job.network.reactants.append([speciesDict[data[1]], speciesDict[data[2]]])
for i in range(Nprod):
data = readMeaningfulLine(f).split()
if data[0] == '1':
job.network.products.append([speciesDict[data[1]]])
elif data[0] == '2':
job.network.products.append([speciesDict[data[1]], speciesDict[data[2]]])
# Read path reactions
Nrxn = int(readMeaningfulLine(f))
for i in range(Nrxn):
# Read and ignore reaction equation
equation = readMeaningfulLine(f)
reaction = Reaction(transitionState=TransitionState(), reversible=True)
job.network.pathReactions.append(reaction)
reaction.transitionState.conformer = Conformer()
# Read reactant and product indices
data = readMeaningfulLine(f).split()
reac = int(data[0]) - 1
prod = int(data[1]) - 1
if reac < Nisom:
reaction.reactants = [job.network.isomers[reac]]
elif reac < Nisom+Nreac:
reaction.reactants = job.network.reactants[reac-Nisom]
else:
reaction.reactants = job.network.products[reac-Nisom-Nreac]
if prod < Nisom:
reaction.products = [job.network.isomers[prod]]
elif prod < Nisom+Nreac:
reaction.products = job.network.reactants[prod-Nisom]
else:
reaction.products = job.network.products[prod-Nisom-Nreac]
# Read reaction E0
E0units, E0 = readMeaningfulLine(f).split()
reaction.transitionState.conformer.E0 = Quantity(float(E0), E0units)
reaction.transitionState.conformer.E0.units = 'kJ/mol'
# Read high-pressure limit kinetics
data = readMeaningfulLine(f)
assert data.lower() == 'arrhenius'
Aunits, A = readMeaningfulLine(f).split()
if '/' in Aunits:
index = Aunits.find('/')
Aunits = '{0}/({1})'.format(Aunits[0:index], Aunits[index+1:])
Eaunits, Ea = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
reaction.kinetics = Arrhenius(
A = Quantity(float(A), Aunits),
Ea = Quantity(float(Ea), Eaunits),
n = Quantity(float(n)),
)
reaction.kinetics.Ea.units = 'kJ/mol'
f.close()
job.network.isomers = [Configuration(isomer) for isomer in job.network.isomers]
job.network.reactants = [Configuration(*reactants) for reactants in job.network.reactants]
job.network.products = [Configuration(*products) for products in job.network.products]
return job