Пример #1
0
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.interpolationModel = ('chebyshev', int(model[1]), int(model[2]))
    elif model[0].lower() == 'pdeparrhenius':
        job.interpolationModel = ('pdeparrhenius',)
    
    # Read grain size or number of grains
    job.minimumGrainCount = 0
    job.maximumGrainSize = None
    for i in range(2):
        data = readMeaningfulLine(f).split()
        if data[0].lower() == 'numgrains':
            job.minimumGrainCount = int(data[1])
        elif data[0].lower() == 'grainsize':
            job.maximumGrainSize = (float(data[2]), data[1])

    # A FAME file is almost certainly created during an RMG job, so use RMG mode
    job.rmgmode = True

    # 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.transportData = TransportData(
        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()
        species.energyTransferModel = energyTransferModel
        
        # 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),
            Cp0 = (Cpdata[0], Cpunits),
            CpInf = (Cpdata[-1], 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.transportData = TransportData(
            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,
                semiclassical = False,
            ))
            
        # 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
Пример #2
0
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