def loadFAMEInput(self, 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.
"""
from network import Network
from collision import SingleExponentialDown
from rmgpy.species import Species, TransitionState
from rmgpy.reaction import Reaction
from rmgpy.species import LennardJones
from rmgpy.statmech import HarmonicOscillator, HinderedRotor, StatesModel
from rmgpy.thermo import ThermoData
from rmgpy.kinetics import Arrhenius
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)
# Read method
method = readMeaningfulLine(f).lower()
if method == 'modifiedstrongcollision':
self.method = 'modified strong collision'
elif method == 'reservoirstate':
self.method = 'reservoir state'
# Read temperatures
Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split()
self.Tmin = Quantity(float(Tmin), Tunits)
self.Tmax = Quantity(float(Tmax), Tunits)
self.Tcount = int(Tcount)
Tlist = []
for i in range(int(Tcount)):
Tlist.append(float(readMeaningfulLine(f)))
self.Tlist = Quantity(Tlist, Tunits)
# Read pressures
Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split()
self.Pmin = Quantity(float(Pmin), Punits)
self.Pmax = Quantity(float(Pmax), Punits)
self.Pcount = int(Pcount)
Plist = []
for i in range(int(Pcount)):
Plist.append(float(readMeaningfulLine(f)))
self.Plist = Quantity(Plist, Punits)
# Read interpolation model
model = readMeaningfulLine(f).split()
if model[0].lower() == 'chebyshev':
self.model = ['chebyshev', int(model[1]), int(model[2])]
elif model[0].lower() == 'pdeparrhenius':
self.model = ['pdeparrhenius']
# Read grain size or number of grains
data = readMeaningfulLine(f).split()
if data[0].lower() == 'numgrains':
self.grainCount = int(data[1])
self.grainSize = Quantity(0.0, "J/mol")
elif data[0].lower() == 'grainsize':
self.grainCount = 0
self.grainSize = Quantity(float(data[2]), data[1])
# Create the Network
self.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)
collisionModel = SingleExponentialDown(
alpha0 = Quantity(float(alpha0), alpha0units),
T0 = Quantity(float(T0), T0units),
n = Quantity(float(n)),
)
speciesDict = {}
# Read bath gas parameters
bathGas = Species(label='bath_gas', collisionModel=collisionModel)
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'g/mol'
bathGas.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
bathGas.lennardJones = LennardJones(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ), epsilonLJunits),
)
self.network.bathGas = {bathGas: 1.0}
# Read species data
Nspec = int(readMeaningfulLine(f))
for i in range(Nspec):
species = Species()
# 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.E0 = Quantity(float(E0), E0units)
# 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)))
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 = 'g/mol'
species.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
species.lennardJones = LennardJones(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ), epsilonLJunits),
)
species.states = StatesModel()
# Read species vibrational frequencies
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
species.states.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.states.modes.append(HinderedRotor(
inertia = Quantity(I,"kg*m^2"),
barrier = Quantity(V0,barrUnits),
symmetry = 1,
))
# Read overall symmetry number
species.states.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'
self.network.isomers.append(speciesDict[data[1]])
for i in range(Nreac):
data = readMeaningfulLine(f).split()
assert data[0] == '2'
self.network.reactants.append([speciesDict[data[1]], speciesDict[data[2]]])
for i in range(Nprod):
data = readMeaningfulLine(f).split()
if data[0] == '1':
self.network.products.append([speciesDict[data[1]]])
elif data[0] == '2':
self.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)
self.network.pathReactions.append(reaction)
# Read reactant and product indices
data = readMeaningfulLine(f).split()
reac = int(data[0]) - 1
prod = int(data[1]) - 1
if reac < Nisom:
reaction.reactants = [self.network.isomers[reac]]
elif reac < Nisom+Nreac:
reaction.reactants = self.network.reactants[reac-Nisom]
else:
reaction.reactants = self.network.products[reac-Nisom-Nreac]
if prod < Nisom:
reaction.products = [self.network.isomers[prod]]
elif prod < Nisom+Nreac:
reaction.products = self.network.reactants[prod-Nisom]
else:
reaction.products = self.network.products[prod-Nisom-Nreac]
# Read reaction E0
E0units, E0 = readMeaningfulLine(f).split()
reaction.transitionState.E0 = Quantity(float(E0), E0units)
# 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)),
)
f.close()
def loadFAMEInput(self, 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.
"""
from network import Network
from collision import SingleExponentialDown
from rmgpy.species import Species, TransitionState
from rmgpy.reaction import Reaction
from rmgpy.transport import TransportData
from rmgpy.statmech import HarmonicOscillator, HinderedRotor, StatesModel
from rmgpy.thermo import ThermoData
from rmgpy.kinetics import Arrhenius
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)
# Read method
method = readMeaningfulLine(f).lower()
if method == 'modifiedstrongcollision':
self.method = 'modified strong collision'
elif method == 'reservoirstate':
self.method = 'reservoir state'
# Read temperatures
Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split()
self.Tmin = Quantity(float(Tmin), Tunits)
self.Tmax = Quantity(float(Tmax), Tunits)
self.Tcount = int(Tcount)
Tlist = []
for i in range(int(Tcount)):
Tlist.append(float(readMeaningfulLine(f)))
self.Tlist = Quantity(Tlist, Tunits)
# Read pressures
Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split()
self.Pmin = Quantity(float(Pmin), Punits)
self.Pmax = Quantity(float(Pmax), Punits)
self.Pcount = int(Pcount)
Plist = []
for i in range(int(Pcount)):
Plist.append(float(readMeaningfulLine(f)))
self.Plist = Quantity(Plist, Punits)
# Read interpolation model
model = readMeaningfulLine(f).split()
if model[0].lower() == 'chebyshev':
self.model = ['chebyshev', int(model[1]), int(model[2])]
elif model[0].lower() == 'pdeparrhenius':
self.model = ['pdeparrhenius']
# Read grain size or number of grains
self.grainCount = 0
self.grainSize = Quantity(0.0, "J/mol")
for i in range(2):
data = readMeaningfulLine(f).split()
if data[0].lower() == 'numgrains':
self.grainCount = int(data[1])
elif data[0].lower() == 'grainsize':
self.grainSize = Quantity(float(data[2]), data[1])
# Create the Network
self.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)
collisionModel = SingleExponentialDown(
alpha0 = Quantity(float(alpha0), alpha0units),
T0 = Quantity(float(T0), T0units),
n = Quantity(float(n)),
)
speciesDict = {}
# Read bath gas parameters
bathGas = Species(label='bath_gas', collisionModel=collisionModel)
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'g/mol'
bathGas.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
bathGas.transportData = TransportData(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ), epsilonLJunits),
)
self.network.bathGas = {bathGas: 1.0}
# Read species data
Nspec = int(readMeaningfulLine(f))
for i in range(Nspec):
species = Species()
# 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.E0 = Quantity(float(E0), E0units)
# 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)))
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 = 'g/mol'
species.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
species.transportData = TransportData(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ), epsilonLJunits),
)
species.states = StatesModel()
# Read species vibrational frequencies
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
species.states.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.states.modes.append(HinderedRotor(
inertia = Quantity(I,"kg*m^2"),
barrier = Quantity(V0,barrUnits),
symmetry = 1,
))
# Read overall symmetry number
species.states.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'
self.network.isomers.append(speciesDict[data[1]])
for i in range(Nreac):
data = readMeaningfulLine(f).split()
assert data[0] == '2'
self.network.reactants.append([speciesDict[data[1]], speciesDict[data[2]]])
for i in range(Nprod):
data = readMeaningfulLine(f).split()
if data[0] == '1':
self.network.products.append([speciesDict[data[1]]])
elif data[0] == '2':
self.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)
self.network.pathReactions.append(reaction)
# Read reactant and product indices
data = readMeaningfulLine(f).split()
reac = int(data[0]) - 1
prod = int(data[1]) - 1
if reac < Nisom:
reaction.reactants = [self.network.isomers[reac]]
elif reac < Nisom+Nreac:
reaction.reactants = self.network.reactants[reac-Nisom]
else:
reaction.reactants = self.network.products[reac-Nisom-Nreac]
if prod < Nisom:
reaction.products = [self.network.isomers[prod]]
elif prod < Nisom+Nreac:
reaction.products = self.network.reactants[prod-Nisom]
else:
reaction.products = self.network.products[prod-Nisom-Nreac]
# Read reaction E0
E0units, E0 = readMeaningfulLine(f).split()
reaction.transitionState.E0 = Quantity(float(E0), E0units)
# 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)),
)
f.close()
