def liquidReactor(temperature,
initialConcentrations,
terminationConversion=None,
terminationTime=None,
sensitivity=None,
sensitivityThreshold=1e-3):
logging.debug('Found LiquidReactor reaction system')
T = Quantity(temperature)
for spec, conc in initialConcentrations.iteritems():
concentration = Quantity(conc)
# check the dimensions are ok
# convert to mol/m^3 (or something numerically nice? or must it be SI)
initialConcentrations[spec] = concentration.value_si
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if len(termination) == 0:
raise InputError(
'No termination conditions specified for reaction system #{0}.'.
format(len(rmg.reactionSystems) + 2))
sensitiveSpecies = []
if sensitivity:
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
system = LiquidReactor(T, initialConcentrations, termination,
sensitiveSpecies, sensitivityThreshold)
rmg.reactionSystems.append(system)
def simpleReactor(temperature,
pressure,
initialMoleFractions,
terminationConversion=None,
terminationTime=None,
sensitivity=None,
sensitivityThreshold=1e-3):
logging.debug('Found SimpleReactor reaction system')
for value in initialMoleFractions.values():
if value < 0:
raise InputError('Initial mole fractions cannot be negative.')
for spec in initialMoleFractions:
initialMoleFractions[spec] = float(initialMoleFractions[spec])
totalInitialMoles = sum(initialMoleFractions.values())
if totalInitialMoles != 1:
logging.warning(
'Initial mole fractions do not sum to one; normalizing.')
logging.info('')
logging.info('Original composition:')
for spec, molfrac in initialMoleFractions.iteritems():
logging.info("{0} = {1}".format(spec, molfrac))
for spec in initialMoleFractions:
initialMoleFractions[spec] /= totalInitialMoles
logging.info('')
logging.info('Normalized mole fractions:')
for spec, molfrac in initialMoleFractions.iteritems():
logging.info("{0} = {1}".format(spec, molfrac))
T = Quantity(temperature)
P = Quantity(pressure)
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if len(termination) == 0:
raise InputError(
'No termination conditions specified for reaction system #{0}.'.
format(len(rmg.reactionSystems) + 2))
sensitiveSpecies = []
if sensitivity:
if isinstance(sensitivity, str): sensitivity = [sensitivity]
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
system = SimpleReactor(T, P, initialMoleFractions, termination,
sensitiveSpecies, sensitivityThreshold)
rmg.reactionSystems.append(system)
def simpleReactor(temperature,
pressure,
initialMoleFractions,
terminationConversion=None,
terminationTime=None,
sensitivity=None,
sensitivityThreshold=1e-3):
logging.debug('Found SimpleReactor reaction system')
for value in initialMoleFractions.values():
if value < 0:
raise InputError('Initial mole fractions cannot be negative.')
if sum(initialMoleFractions.values()) != 1:
logging.warning(
'Initial mole fractions do not sum to one; renormalizing.')
for spec in initialMoleFractions:
initialMoleFractions[spec] /= sum(initialMoleFractions.values())
T = Quantity(temperature)
P = Quantity(pressure)
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if len(termination) == 0:
raise InputError(
'No termination conditions specified for reaction system #{0}.'.
format(len(rmg.reactionSystems) + 2))
sensitiveSpecies = []
if sensitivity:
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
system = SimpleReactor(T, P, initialMoleFractions, termination,
sensitiveSpecies, sensitivityThreshold)
rmg.reactionSystems.append(system)
def saveForm(self, posted, form):
"""
Save form data into input.py file specified by the path.
"""
# Clean past history
self.rmg = RMG()
# Databases
#self.rmg.databaseDirectory = settings['database.directory']
self.rmg.thermoLibraries = []
if posted.thermo_libraries.all():
self.rmg.thermoLibraries = [
item.thermolib.encode()
for item in posted.thermo_libraries.all()
]
self.rmg.reactionLibraries = []
self.rmg.seedMechanisms = []
if posted.reaction_libraries.all():
for item in posted.reaction_libraries.all():
if not item.seedmech and not item.edge:
self.rmg.reactionLibraries.append(
(item.reactionlib.encode(), False))
elif not item.seedmech:
self.rmg.reactionLibraries.append(
(item.reactionlib.encode(), True))
else:
self.rmg.seedMechanisms.append(item.reactionlib.encode())
self.rmg.statmechLibraries = []
self.rmg.kineticsDepositories = 'default'
self.rmg.kineticsFamilies = 'default'
self.rmg.kineticsEstimator = 'rate rules'
# Species
self.rmg.initialSpecies = []
speciesDict = {}
initialMoleFractions = {}
self.rmg.reactionModel = CoreEdgeReactionModel()
for item in posted.reactor_species.all():
structure = Molecule().fromAdjacencyList(item.adjlist.encode())
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
structure,
label=item.name.encode(),
reactive=False if item.inert else True)
self.rmg.initialSpecies.append(spec)
speciesDict[item.name.encode()] = spec
initialMoleFractions[spec] = item.molefrac
# Reactor systems
self.rmg.reactionSystems = []
for item in posted.reactor_systems.all():
T = Quantity(item.temperature, item.temperature_units.encode())
P = Quantity(item.pressure, item.pressure_units.encode())
termination = []
if item.conversion:
termination.append(
TerminationConversion(speciesDict[item.species.encode()],
item.conversion))
termination.append(
TerminationTime(
Quantity(item.terminationtime, item.time_units.encode())))
# Sensitivity Analysis
sensitiveSpecies = []
if item.sensitivity:
if isinstance(item.sensitivity.encode(), str):
sensitivity = item.sensitivity.encode().split(',')
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec.strip()])
system = SimpleReactor(T, P, initialMoleFractions, termination,
sensitiveSpecies, item.sensitivityThreshold)
self.rmg.reactionSystems.append(system)
# Simulator tolerances
self.rmg.absoluteTolerance = form.cleaned_data['simulator_atol']
self.rmg.relativeTolerance = form.cleaned_data['simulator_rtol']
self.rmg.sensitivityAbsoluteTolerance = form.cleaned_data[
'simulator_sens_atol']
self.rmg.sensitivityRelativeTolerance = form.cleaned_data[
'simulator_sens_rtol']
self.rmg.fluxToleranceKeepInEdge = form.cleaned_data[
'toleranceKeepInEdge']
self.rmg.fluxToleranceMoveToCore = form.cleaned_data[
'toleranceMoveToCore']
self.rmg.fluxToleranceInterrupt = form.cleaned_data[
'toleranceInterruptSimulation']
self.rmg.maximumEdgeSpecies = form.cleaned_data['maximumEdgeSpecies']
self.rmg.minCoreSizeForPrune = form.cleaned_data['minCoreSizeForPrune']
self.rmg.minSpeciesExistIterationsForPrune = form.cleaned_data[
'minSpeciesExistIterationsForPrune']
self.rmg.filterReactions = form.cleaned_data['filterReactions']
# Pressure Dependence
pdep = form.cleaned_data['pdep'].encode()
if pdep != 'off':
self.rmg.pressureDependence = PressureDependenceJob(network=None)
self.rmg.pressureDependence.method = pdep
# Process interpolation model
if form.cleaned_data['interpolation'].encode() == 'chebyshev':
self.rmg.pressureDependence.interpolationModel = (
form.cleaned_data['interpolation'].encode(),
form.cleaned_data['temp_basis'],
form.cleaned_data['p_basis'])
else:
self.rmg.pressureDependence.interpolationModel = (
form.cleaned_data['interpolation'].encode(), )
# Temperature and pressure range
self.rmg.pressureDependence.Tmin = Quantity(
form.cleaned_data['temp_low'],
form.cleaned_data['temprange_units'].encode())
self.rmg.pressureDependence.Tmax = Quantity(
form.cleaned_data['temp_high'],
form.cleaned_data['temprange_units'].encode())
self.rmg.pressureDependence.Tcount = form.cleaned_data[
'temp_interp']
self.rmg.pressureDependence.generateTemperatureList()
self.rmg.pressureDependence.Pmin = Quantity(
form.cleaned_data['p_low'],
form.cleaned_data['prange_units'].encode())
self.rmg.pressureDependence.Pmax = Quantity(
form.cleaned_data['p_high'],
form.cleaned_data['prange_units'].encode())
self.rmg.pressureDependence.Pcount = form.cleaned_data['p_interp']
self.rmg.pressureDependence.generatePressureList()
# Process grain size and count
self.rmg.pressureDependence.grainSize = Quantity(
form.cleaned_data['maximumGrainSize'],
form.cleaned_data['grainsize_units'].encode())
self.rmg.pressureDependence.grainCount = form.cleaned_data[
'minimumNumberOfGrains']
self.rmg.pressureDependence.maximumAtoms = form.cleaned_data[
'maximumAtoms']
# Additional Options
self.rmg.units = 'si'
self.rmg.saveRestartPeriod = Quantity(
form.cleaned_data['saveRestartPeriod'],
form.cleaned_data['saveRestartPeriodUnits'].encode(
)) if form.cleaned_data['saveRestartPeriod'] else None
self.rmg.generateOutputHTML = form.cleaned_data['generateOutputHTML']
self.rmg.generatePlots = form.cleaned_data['generatePlots']
self.rmg.saveSimulationProfiles = form.cleaned_data[
'saveSimulationProfiles']
self.rmg.saveEdgeSpecies = form.cleaned_data['saveEdgeSpecies']
self.rmg.verboseComments = form.cleaned_data['verboseComments']
# Species Constraints
speciesConstraints = form.cleaned_data['speciesConstraints']
if speciesConstraints == 'on':
allowed = []
if form.cleaned_data['allowed_inputSpecies']:
allowed.append('input species')
if form.cleaned_data['allowed_seedMechanisms']:
allowed.append('seed mechanisms')
if form.cleaned_data['allowed_reactionLibraries']:
allowed.append('reaction libraries')
self.rmg.speciesConstraints['allowed'] = allowed
self.rmg.speciesConstraints[
'maximumCarbonAtoms'] = form.cleaned_data['maximumCarbonAtoms']
self.rmg.speciesConstraints[
'maximumOxygenAtoms'] = form.cleaned_data['maximumOxygenAtoms']
self.rmg.speciesConstraints[
'maximumNitrogenAtoms'] = form.cleaned_data[
'maximumNitrogenAtoms']
self.rmg.speciesConstraints[
'maximumSiliconAtoms'] = form.cleaned_data[
'maximumSiliconAtoms']
self.rmg.speciesConstraints[
'maximumSulfurAtoms'] = form.cleaned_data['maximumSulfurAtoms']
self.rmg.speciesConstraints[
'maximumHeavyAtoms'] = form.cleaned_data['maximumHeavyAtoms']
self.rmg.speciesConstraints[
'maximumRadicalElectrons'] = form.cleaned_data[
'maximumRadicalElectrons']
self.rmg.speciesConstraints['allowSingletO2'] = form.cleaned_data[
'allowSingletO2']
# Quantum Calculations
quantumCalc = form.cleaned_data['quantumCalc']
if quantumCalc == 'on':
from rmgpy.qm.main import QMCalculator
self.rmg.quantumMechanics = QMCalculator(
software=form.cleaned_data['software'].encode(),
method=form.cleaned_data['method'].encode(),
fileStore=form.cleaned_data['fileStore'].encode(),
scratchDirectory=form.cleaned_data['scratchDirectory'].encode(
),
onlyCyclics=form.cleaned_data['onlyCyclics'],
maxRadicalNumber=form.cleaned_data['maxRadicalNumber'],
)
# Save the input.py file
self.rmg.saveInput(self.savepath)
def liquidReactor(temperature,
initialConcentrations,
terminationConversion=None,
nSimsTerm = 4,
terminationTime=None,
terminationRateRatio=None,
sensitivity=None,
sensitivityThreshold=1e-3,
sensitivityTemperature=None,
sensitivityConcentrations=None,
constantSpecies=None):
logging.debug('Found LiquidReactor reaction system')
if not isinstance(temperature,list):
T = Quantity(temperature)
else:
if len(temperature) != 2:
raise InputError('Temperature and pressure ranges can either be in the form of (number,units) or a list with 2 entries of the same format')
T = [Quantity(t) for t in temperature]
for spec,conc in initialConcentrations.iteritems():
if not isinstance(conc,list):
concentration = Quantity(conc)
# check the dimensions are ok
# convert to mol/m^3 (or something numerically nice? or must it be SI)
initialConcentrations[spec] = concentration.value_si
else:
if len(conc) != 2:
raise InputError("Concentration values must either be in the form of (number,units) or a list with 2 entries of the same format")
initialConcentrations[spec] = [Quantity(conc[0]),Quantity(conc[1])]
if not isinstance(temperature,list) and all([not isinstance(x,list) for x in initialConcentrations.itervalues()]):
nSimsTerm=1
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if terminationRateRatio is not None:
termination.append(TerminationRateRatio(terminationRateRatio))
if len(termination) == 0:
raise InputError('No termination conditions specified for reaction system #{0}.'.format(len(rmg.reactionSystems)+2))
sensitiveSpecies = []
if sensitivity:
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
##chatelak: check the constant species exist
if constantSpecies is not None:
logging.debug(' Generation with constant species:')
for constantSpecie in constantSpecies:
logging.debug(" {0}".format(constantSpecie))
if not speciesDict.has_key(constantSpecie):
raise InputError('Species {0} not found in the input file'.format(constantSpecie))
if not isinstance(T,list):
sensitivityTemperature = T
if not any([isinstance(x,list) for x in initialConcentrations.itervalues()]):
sensitivityConcentrations = initialConcentrations
if sensitivityConcentrations is None or sensitivityTemperature is None:
sensConditions = None
else:
sensConditions = sensitivityConcentrations
sensConditions['T'] = Quantity(sensitivityTemperature).value_si
system = LiquidReactor(T, initialConcentrations, nSimsTerm, termination, sensitiveSpecies, sensitivityThreshold, sensConditions, constantSpecies)
rmg.reactionSystems.append(system)
def simpleReactor(temperature,
pressure,
initialMoleFractions,
nSimsTerm=6,
terminationConversion=None,
terminationTime=None,
terminationRateRatio=None,
balanceSpecies=None,
sensitivity=None,
sensitivityThreshold=1e-3,
sensitivityTemperature=None,
sensitivityPressure=None,
sensitivityMoleFractions=None,
):
logging.debug('Found SimpleReactor reaction system')
for key,value in initialMoleFractions.iteritems():
if not isinstance(value,list):
initialMoleFractions[key] = float(value)
if value < 0:
raise InputError('Initial mole fractions cannot be negative.')
else:
if len(value) != 2:
raise InputError("Initial mole fraction values must either be a number or a list with 2 entries")
initialMoleFractions[key] = [float(value[0]),float(value[1])]
if value[0] < 0 or value[1] < 0:
raise InputError('Initial mole fractions cannot be negative.')
elif value[1] < value[0]:
raise InputError('Initial mole fraction range out of order: {0}'.format(key))
if not isinstance(temperature,list):
T = Quantity(temperature)
else:
if len(temperature) != 2:
raise InputError('Temperature and pressure ranges can either be in the form of (number,units) or a list with 2 entries of the same format')
T = [Quantity(t) for t in temperature]
if not isinstance(pressure,list):
P = Quantity(pressure)
else:
if len(pressure) != 2:
raise InputError('Temperature and pressure ranges can either be in the form of (number,units) or a list with 2 entries of the same format')
P = [Quantity(p) for p in pressure]
if not isinstance(temperature,list) and not isinstance(pressure,list) and all([not isinstance(x,list) for x in initialMoleFractions.values()]):
nSimsTerm=1
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if terminationRateRatio is not None:
termination.append(TerminationRateRatio(terminationRateRatio))
if len(termination) == 0:
raise InputError('No termination conditions specified for reaction system #{0}.'.format(len(rmg.reactionSystems)+2))
sensitiveSpecies = []
if sensitivity:
if isinstance(sensitivity, str): sensitivity = [sensitivity]
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
if not isinstance(T,list):
sensitivityTemperature = T
if not isinstance(P,list):
sensitivityPressure = P
if not any([isinstance(x,list) for x in initialMoleFractions.itervalues()]):
sensitivityMoleFractions = deepcopy(initialMoleFractions)
if sensitivityMoleFractions is None or sensitivityTemperature is None or sensitivityPressure is None:
sensConditions = None
else:
sensConditions = sensitivityMoleFractions
sensConditions['T'] = Quantity(sensitivityTemperature).value_si
sensConditions['P'] = Quantity(sensitivityPressure).value_si
system = SimpleReactor(T, P, initialMoleFractions, nSimsTerm, termination, sensitiveSpecies, sensitivityThreshold,sensConditions)
rmg.reactionSystems.append(system)
assert balanceSpecies is None or isinstance(balanceSpecies,str), 'balanceSpecies should be the string corresponding to a single species'
rmg.balanceSpecies = balanceSpecies
if balanceSpecies: #check that the balanceSpecies can't be taken to zero
total = 0.0
for key,item in initialMoleFractions.iteritems():
if key == balanceSpecies:
assert not isinstance(item,list), 'balanceSpecies must not have a defined range'
xbspcs = item
if isinstance(item,list):
total += item[1]-item[0]
if total > xbspcs:
raise ValueError('The sum of the differences in the ranged mole fractions is greater than the mole fraction of the balance species, this would require the balanceSpecies mole fraction to be negative in some cases which is not allowed, either reduce the maximum mole fractions or dont use balanceSpecies')
def saveForm(self, posted, form):
"""
Save form data into input.py file specified by the path.
"""
# Clean past history
self.rmg = RMG()
# Databases
#self.rmg.databaseDirectory = settings['database.directory']
self.rmg.thermoLibraries = []
if posted.thermo_libraries.all():
self.rmg.thermoLibraries = [
item.thermolib.encode()
for item in posted.thermo_libraries.all()
]
self.rmg.reactionLibraries = []
self.rmg.seedMechanisms = []
if posted.reaction_libraries.all():
for item in posted.reaction_libraries.all():
if not item.seedmech and not item.edge:
self.rmg.reactionLibraries.append(
(item.reactionlib.encode(), False))
elif not item.seedmech:
self.rmg.reactionLibraries.append(
(item.reactionlib.encode(), True))
else:
self.rmg.seedMechanisms.append(item.reactionlib.encode())
self.rmg.statmechLibraries = []
self.rmg.kineticsDepositories = ['training']
self.rmg.kineticsFamilies = ['!Intra_Disproportionation']
self.rmg.kineticsEstimator = 'rate rules'
# Species
self.rmg.initialSpecies = []
speciesDict = {}
initialMoleFractions = {}
self.rmg.reactionModel = CoreEdgeReactionModel()
for item in posted.reactor_species.all():
structure = Molecule().fromAdjacencyList(item.adjlist.encode())
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
structure,
label=item.name.encode(),
reactive=False if item.inert else True)
self.rmg.initialSpecies.append(spec)
speciesDict[item.name.encode()] = spec
initialMoleFractions[spec] = item.molefrac
# Reactor systems
self.rmg.reactionSystems = []
for item in posted.reactor_systems.all():
T = Quantity(item.temperature, item.temperature_units.encode())
P = Quantity(item.pressure, item.pressure_units.encode())
termination = []
if item.conversion:
termination.append(
TerminationConversion(speciesDict[item.species.encode()],
item.conversion))
termination.append(
TerminationTime(
Quantity(item.terminationtime, item.time_units.encode())))
system = SimpleReactor(T, P, initialMoleFractions, termination)
self.rmg.reactionSystems.append(system)
# Simulator tolerances
self.rmg.absoluteTolerance = form.cleaned_data['simulator_atol']
self.rmg.relativeTolerance = form.cleaned_data['simulator_rtol']
self.rmg.fluxToleranceKeepInEdge = form.cleaned_data[
'toleranceKeepInEdge']
self.rmg.fluxToleranceMoveToCore = form.cleaned_data[
'toleranceMoveToCore']
self.rmg.fluxToleranceInterrupt = form.cleaned_data[
'toleranceInterruptSimulation']
self.rmg.maximumEdgeSpecies = form.cleaned_data['maximumEdgeSpecies']
# Pressure Dependence
pdep = form.cleaned_data['pdep'].encode()
if pdep != 'off':
self.rmg.pressureDependence = MEASURE()
self.rmg.pressureDependence.method = pdep
# Temperature and pressure range
interpolation = (form.cleaned_data['interpolation'].encode(),
form.cleaned_data['temp_basis'],
form.cleaned_data['p_basis'])
self.rmg.pressureDependence.Tmin = Quantity(
form.cleaned_data['temp_low'],
form.cleaned_data['temprange_units'].encode())
self.rmg.pressureDependence.Tmax = Quantity(
form.cleaned_data['temp_high'],
form.cleaned_data['temprange_units'].encode())
self.rmg.pressureDependence.Tcount = form.cleaned_data[
'temp_interp']
Tlist = getTemperaturesForModel(
interpolation, self.rmg.pressureDependence.Tmin.value,
self.rmg.pressureDependence.Tmax.value,
self.rmg.pressureDependence.Tcount)
self.rmg.pressureDependence.Tlist = Quantity(Tlist, "K")
self.rmg.pressureDependence.Pmin = Quantity(
form.cleaned_data['p_low'],
form.cleaned_data['prange_units'].encode())
self.rmg.pressureDependence.Pmax = Quantity(
form.cleaned_data['p_high'],
form.cleaned_data['prange_units'].encode())
self.rmg.pressureDependence.Pcount = form.cleaned_data['p_interp']
Plist = getPressuresForModel(
interpolation, self.rmg.pressureDependence.Pmin.value,
self.rmg.pressureDependence.Pmax.value,
self.rmg.pressureDependence.Pcount)
self.rmg.pressureDependence.Plist = Quantity(Plist, "Pa")
# Process grain size and count
self.rmg.pressureDependence.grainSize = Quantity(
form.cleaned_data['maximumGrainSize'],
form.cleaned_data['grainsize_units'].encode())
self.rmg.pressureDependence.grainCount = form.cleaned_data[
'minimumNumberOfGrains']
# Process interpolation model
self.rmg.pressureDependence.model = interpolation
# Additional Options
self.rmg.units = 'si'
self.rmg.saveRestartPeriod = Quantity(
form.cleaned_data['saveRestartPeriod'],
form.cleaned_data['saveRestartPeriodUnits'].encode(
)) if form.cleaned_data['saveRestartPeriod'] else None
self.rmg.drawMolecules = form.cleaned_data['drawMolecules']
self.rmg.generatePlots = form.cleaned_data['generatePlots']
self.rmg.saveConcentrationProfiles = form.cleaned_data[
'saveConcentrationProfiles']
# Save the input.py file
self.rmg.saveInput(self.savepath)
def surfaceReactor(temperature,
initialPressure,
initialGasMoleFractions,
initialSurfaceCoverages,
surfaceVolumeRatio,
nSims=4,
terminationConversion=None,
terminationTime=None,
terminationRateRatio=None,
sensitivity=None,
sensitivityThreshold=1e-3):
logging.debug('Found SurfaceReactor reaction system')
for value in initialGasMoleFractions.values():
if value < 0:
raise InputError('Initial mole fractions cannot be negative.')
totalInitialMoles = sum(initialGasMoleFractions.values())
if totalInitialMoles != 1:
logging.warning('Initial gas mole fractions do not sum to one; renormalizing.')
logging.debug('')
logging.debug('Original composition:')
for spec, molfrac in initialGasMoleFractions.iteritems():
logging.debug("{0} = {1}".format(spec, molfrac))
for spec in initialGasMoleFractions:
initialGasMoleFractions[spec] /= totalInitialMoles
logging.info('')
logging.debug('Normalized mole fractions:')
for spec, molfrac in initialGasMoleFractions.iteritems():
logging.debug("{0} = {1}".format(spec, molfrac))
if not isinstance(temperature, list):
T = Quantity(temperature)
else:
if len(temperature) != 2:
raise InputError('Temperature ranges can either be in the form '
'of (number,units) or a list with 2 entries of the same format')
T = [Quantity(t) for t in temperature]
if not isinstance(initialPressure, list):
initialP = Quantity(initialPressure)
else:
if len(initialPressure) != 2:
raise InputError('Initial pressure ranges can either be in the form '
'of (number,units) or a list with 2 entries of the same format')
initialP = [Quantity(p) for p in initialPressure]
if not isinstance(temperature, list) and not isinstance(initialPressure, list):
nSims = 1
if any([isinstance(x, list) for x in initialGasMoleFractions.values()]) or \
any([isinstance(x, list) for x in initialSurfaceCoverages.values()]):
raise NotImplementedError("Can't do ranges on species concentrations for surface reactors yet.")
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if terminationRateRatio is not None:
termination.append(TerminationRateRatio(terminationRateRatio))
if len(termination) == 0:
raise InputError('No termination conditions specified for reaction system #{0}.'.format(len(rmg.reactionSystems) + 2))
sensitiveSpecies = []
if sensitivity:
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
if not isinstance(T, list):
sensitivityTemperature = T
if not isinstance(initialPressure, list):
sensitivityPressure = initialPressure
sensConditions = None
if sensitivity:
raise NotImplementedError("Can't currently do sensitivity with surface reactors.")
"""
The problem is inside base.pyx it reads the dictionary 'sensConditions'
and guesses whether they're all concentrations (liquid reactor) or
mole fractions (simple reactor). In fact, some may be surface coverages.
"""
system = SurfaceReactor(T=T,
initialP=initialP,
initialGasMoleFractions=initialGasMoleFractions,
initialSurfaceCoverages=initialSurfaceCoverages,
surfaceVolumeRatio=surfaceVolumeRatio,
surfaceSiteDensity=rmg.surfaceSiteDensity,
nSims=nSims,
termination=termination,
sensitiveSpecies=sensitiveSpecies,
sensitivityThreshold=sensitivityThreshold,
sensConditions=sensConditions)
rmg.reactionSystems.append(system)
system.log_initial_conditions(number=len(rmg.reactionSystems))
