def removeSpeciesFromEdge(self, spec):
"""
Remove species `spec` from the reaction model edge.
"""
# remove the species
self.edge.species.remove(spec)
# identify any reactions it's involved in
rxnList = []
for rxn in self.edge.reactions:
if spec in rxn.reactants or spec in rxn.products:
rxnList.append(rxn)
# remove those reactions
for rxn in rxnList:
self.edge.reactions.remove(rxn)
# Remove the species from any unirxn networks it is in
if settings.unimolecularReactionNetworks:
networksToDelete = []
for network in self.unirxnNetworks:
if spec in network.getSpeciesList():
# Delete all path reactions involving the species
rxnList = []
for rxn in network.pathReactions:
if spec in rxn.reactants or spec in rxn.products:
rxnList.append(rxn)
for rxn in rxnList:
network.pathReactions.remove(rxn)
# Delete all net reactions involving the species
rxnList = []
for rxn in network.netReactions:
if spec in rxn.reactants or spec in rxn.products:
rxnList.append(rxn)
for rxn in rxnList:
network.netReactions.remove(rxn)
# Delete all isomers involving the species
isomerList = []
for isomer in network.isomers:
if spec in isomer.species:
isomerList.append(isomer)
for isomer in isomerList:
network.isomers.remove(isomer)
# If no remaining reactions, delete the network (actually
# add to list of networks to be deleted in a subsequent
# step)
if len(network.pathReactions) == 0 and len(network.netReactions) == 0:
networksToDelete.append(network)
# Complete deletion of empty networks
for network in networksToDelete:
logging.debug('Deleting empty unirxn network %s' % network.id)
self.unirxnNetworks.remove(network)
# remove from the global list of species, to free memory
species.speciesList.remove(spec)
def updateUnimolecularReactionNetworks(self):
"""
Iterate through all of the currently-existing unimolecular reaction
networks, updating those that have been marked as invalid. In each update,
the phenomonological rate coefficients :math:`k(T,P)` are computed for
each net reaction in the network, and the resulting reactions added or
updated.
"""
from unirxn.network import Isomer, UnirxnNetworkException
from reaction import PDepReaction
from kinetics import ChebyshevKinetics, PDepArrheniusKinetics
count = sum([1 for network in self.unirxnNetworks if not network.valid])
logging.info('Updating %i modified unimolecular reaction networks...' % count)
for network in self.unirxnNetworks:
if not network.valid:
logging.verbose('Updating unimolecular reaction network %s' % network.id)
# Other inputs
method, Tlist, Plist, grainSize, numGrains, model = settings.unimolecularReactionNetworks
network.bathGas = [spec for spec in self.core.species if not spec.reactive][0]
network.bathGas.expDownParam = 4.86 * 4184
# Generate isomers
for reaction in network.pathReactions:
# Create isomer for the reactant
isomer = None
for isom in network.isomers:
if all([spec in isom.species for spec in reaction.reactants]):
isomer = isom
if isomer is None:
isomer = Isomer(reaction.reactants)
network.isomers.append(isomer)
reaction.reactant = isomer
# Create isomer for the product
isomer = None
for isom in network.isomers:
if all([spec in isom.species for spec in reaction.products]):
isomer = isom
if isomer is None:
isomer = Isomer(reaction.products)
network.isomers.append(isomer)
reaction.product = isomer
# Update list of explored isomers to include all species in core
for isom in network.isomers:
if isom.isUnimolecular():
spec = isom.species[0]
if spec not in network.explored:
if spec in self.core.species:
network.explored.append(spec)
# Remove any isomers that aren't found in any path reactions
# Ideally this block of code wouldn't be needed, but it's here
# just in case
isomerList = []
for isomer in network.isomers:
found = False
for reaction in network.pathReactions:
if reaction.reactant is isomer or reaction.product is isomer:
found = True
break
if not found:
isomerList.append(isomer)
if len(isomerList) > 0:
logging.debug('Removed %i isomer(s) from network %i.' % (len(isomerList), network.id))
for isomer in isomerList: network.isomers.remove(isomer)
# Sort isomers so that all unimolecular isomers come first
isomers = [isom for isom in network.isomers if isom.isUnimolecular()]
isomers.extend([isom for isom in network.isomers if isom.isMultimolecular()])
network.isomers = isomers
# Get list of species in network
speciesList = network.getSpeciesList()
# Calculate ground-state energy of all species in network
# For now we assume that this is equal to the enthalpy of formation
# of the species
for spec in speciesList:
spec.E0 = spec.getEnthalpy(T=298)
# Determine isomer ground-state energies
for isomer in network.isomers:
isomer.E0 = sum([spec.E0 for spec in isomer.species])
# Determine transition state ground-state energies of the reactions
for reaction in network.pathReactions:
E0 = sum([spec.E0 for spec in reaction.reactants])
reaction.E0 = E0 + reaction.kinetics[0].getActivationEnergy(reaction.getEnthalpyOfReaction(T=298))
# Shift network such that lowest-energy isomer has a ground state of 0.0
network.shiftToZeroEnergy()
# Determine energy grains
Elist = network.determineEnergyGrains(grainSize, numGrains, max(Tlist))
# Calculate density of states for all isomers in network
network.calculateDensitiesOfStates(Elist)
# Determine phenomenological rate coefficients
K = network.calculateRateCoefficients(Tlist, Plist, Elist, method)
# Generate PDepReaction objects
for i, product in enumerate(network.isomers):
for j, reactant in enumerate(network.isomers[0:i]):
if numpy.any(K[:,:,i,j]):
if not numpy.all(K[:,:,i,j]):
raise UnirxnNetworkException('Zero rate coefficient encountered while updating network %s.' % network)
# Find the path reaction
netReaction = None
for r in network.netReactions:
if r.hasTemplate(reactant.species, product.species):
netReaction = r
# If path reaction does not already exist, make a new one
if netReaction is None:
netReaction = PDepReaction(reactant.species, product.species, network, None)
network.netReactions.append(netReaction)
self.addReactionToEdge(netReaction)
# Set its kinetics using interpolation model
if model[0].lower() == 'chebyshev':
modelType, degreeT, degreeP = model
chebyshev = ChebyshevKinetics()
chebyshev.fitToData(Tlist, Plist, K[:,:,i,j], degreeT, degreeP)
netReaction.kinetics = chebyshev
elif model.lower() == 'pdeparrhenius':
pDepArrhenius = PDepArrheniusKinetics()
pDepArrhenius.fitToData(Tlist, Plist, K[:,:,i,j])
netReaction.kinetics = pDepArrhenius
else:
pass
# Update cantera if this is a core reaction
if netReaction in self.core.reactions:
netReaction.toCantera()
for spec in speciesList:
del spec.E0
for reaction in network.pathReactions:
del reaction.reactant
del reaction.product
del reaction.E0
network.valid = True
