def saveChemkinFile(path, species, reactions, verbose=True):
from rmgpy.chemkin import writeKineticsEntry
s = 'REACTIONS KCAL/MOLE MOLES\n\n'
for rxn in reactions:
s += writeKineticsEntry(rxn, speciesList=species, verbose=verbose)
s += '\n'
s += 'END\n\n'
with open(path, 'w') as f:
f.write(s)
def saveChemkinFile(path, species, reactions, verbose = True):
from rmgpy.chemkin import writeKineticsEntry
s ='REACTIONS KCAL/MOLE MOLES\n\n'
for rxn in reactions:
s +=writeKineticsEntry(rxn, speciesList=species, verbose=verbose)
s +='\n'
s +='END\n\n'
with open(path, 'w') as f:
f.write(s)
def main(chemkin):
# Load Chemkin file
reactionModel = CoreEdgeReactionModel()
reactionModel.core.species, reactionModel.core.reactions = loadChemkinFile(
chemkin)
# Identify reactions to be removed
reactionList = reactionModel.core.reactions
duplicateReactionsToRemove = []
for index1 in range(len(reactionList)):
reaction1 = reactionList[index1]
for index2 in range(index1 + 1, len(reactionList)):
reaction2 = reactionList[index2]
# Check if the two reactions are identical
if (reaction1.reactants == reaction2.reactants
and reaction1.products == reaction2.products) or (
reaction1.reactants == reaction2.products
and reaction1.products == reaction2.reactants):
# Identify if exactly 1 of the reactions is a LibraryReaction
if isinstance(reaction1, LibraryReaction) != isinstance(
reaction2, LibraryReaction):
# Mark the non-LibraryReaction to be removed
if isinstance(reaction1, LibraryReaction):
duplicateReactionsToRemove.append(reaction2)
else:
duplicateReactionsToRemove.append(reaction1)
# Remove the identified reactions
for reaction in duplicateReactionsToRemove:
reactionList.remove(reaction)
# Write new Chemkin file
path = 'chem_annotated_new.inp'
speciesList = reactionModel.core.species + reactionModel.outputSpeciesList
rxnList = reactionModel.core.reactions + reactionModel.outputReactionList
with open(chemkin, 'rb') as old, open(path, 'wb') as new:
# Copy species and reactions blocks to new Chemkin file
line = old.readline()
while 'REACTIONS' not in line.upper():
new.write(line)
line = old.readline()
new.write('REACTIONS KCAL/MOLE MOLES\n\n')
rmgpy.chemkin.__chemkin_reaction_count = 0
for rxn in rxnList:
new.write(
writeKineticsEntry(rxn, speciesList=speciesList, verbose=True))
new.write('\n')
new.write('END\n\n')
print "New Chemkin file contains {0} reactions.".format(
rmgpy.chemkin.__chemkin_reaction_count)
def save(self, outputFile):
logging.info(
'Saving pressure dependence results for {0} network...'.format(
self.network.label))
f = open(outputFile, 'a')
f_chemkin = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'),
'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
printed_reactions = [] # list of rxns already printed
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
# make sure we aren't double counting any reactions
if not any([reaction.isIsomorphic(other_rxn,checkOnlyLabel=True) \
for other_rxn in printed_reactions]):
duplicate = False
# add reaction to printed reaction
printed_reactions.append(reaction)
else:
# comment out the extra reverse reaction
duplicate = True
# write chemkin output.
string = writeKineticsEntry(reaction,
speciesList=None,
verbose=False,
commented=duplicate)
f_chemkin.write('{0}\n'.format(string))
# write to 'output.py'
kdata = self.K[:, :, prod, reac].copy()
order = len(reaction.reactants)
kdata *= 1e6**(order - 1)
kunits = {
1: 's^-1',
2: 'cm^3/(mol*s)',
3: 'cm^6/(mol^2*s)'
}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P * 1e-5)
for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t, p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
pdep_function = '{0}\n\n'.format(prettify(string))
if duplicate:
# add comments to the start of the string
pdep_function = '# ' + pdep_function.replace(
'\n', '\n# ')
f.write(pdep_function)
f.close()
f_chemkin.close()
def save(self, outputFile):
logging.info('Saving pressure dependence results for {0} network...'.format(self.network.label))
f = open(outputFile, 'a')
f_chemkin = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
printed_reactions = [] # list of rxns already printed
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
# make sure we aren't double counting any reactions
if not any([reaction.isIsomorphic(other_rxn,checkOnlyLabel=True) \
for other_rxn in printed_reactions]):
duplicate = False
# add reaction to printed reaction
printed_reactions.append(reaction)
else:
# comment out the extra reverse reaction
duplicate = True
# write chemkin output.
string = writeKineticsEntry(reaction, speciesList=None, verbose=False, commented = duplicate)
f_chemkin.write('{0}\n'.format(string))
# write to 'output.py'
kdata = self.K[:,:,prod,reac].copy()
order = len(reaction.reactants)
kdata *= 1e6 ** (order-1)
kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P*1e-5) for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t,p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
pdep_function = '{0}\n\n'.format(prettify(string))
if duplicate:
# add comments to the start of the string
pdep_function = '# ' + pdep_function.replace('\n','\n# ')
f.write(pdep_function)
f.close()
f_chemkin.close()
def save(self, outputFile):
logging.info(
'Saving pressure dependence results for {0} network...'.format(
self.network.label))
f = open(outputFile, 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
kdata = self.K[:, :, prod, reac].copy()
order = len(reaction.reactants)
kdata *= 1e6**(order - 1)
kunits = {
1: 's^-1',
2: 'cm^3/(mol*s)',
3: 'cm^6/(mol^2*s)'
}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P * 1e-5)
for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t, p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
string = writeKineticsEntry(reaction,
speciesList=None,
verbose=False)
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
logging.info('Saving pressure dependence results for {0} network...'.format(self.network.label))
f = open(outputFile, 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
kdata = self.K[:,:,prod,reac].copy()
order = len(reaction.reactants)
kdata *= 1e6 ** (order-1)
kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P*1e-5) for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t,p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
string = writeKineticsEntry(reaction, speciesList=None, verbose=False)
f.write('{0}\n'.format(string))
f.close()
