def loadChemkinFile(path, dictionaryPath=None):
"""
Load a Chemkin input file to `path` on disk, returning lists of the species
and reactions in the Chemkin file.
"""
speciesList = []; speciesDict = {}
reactionList = []
# If the dictionary path is given, the read it and generate Molecule objects
# You need to append an additional adjacency list for nonreactive species, such
# as N2, or else the species objects will not store any structures for the final
# HTML output.
if dictionaryPath:
with open(dictionaryPath, 'r') as f:
adjlist = ''
for line in f:
if line.strip() == '' and adjlist.strip() != '':
# Finish this adjacency list
species = Species().fromAdjacencyList(adjlist)
species.generateResonanceIsomers()
speciesDict[species.label] = species
adjlist = ''
else:
if "InChI" in line:
line = line.split()[0] + '\n'
if '//' in line:
index = line.index('//')
line = line[0:index]
adjlist += line
def removeCommentFromLine(line):
if '!' in line:
index = line.index('!')
comment = line[index+1:-1]
line = line[0:index] + '\n'
return line, comment
else:
comment = ''
return line, comment
def checkDuplicateKinetics(reaction, kinetics,comments,dupReactionList,reactionList):
if 'DUP' in kinetics:
kinetics = kinetics.replace('\nDUP','')
reaction = readKineticsEntry(kinetics,speciesDict,energyUnits,moleculeUnits)
reaction.kinetics.comment = comments
if dupReactionList:
if not reaction.hasTemplate(dupReactionList[-1].reactants,dupReactionList[-1].products):
# It's not the same kind of duplicate reaction
oldReactionKinetics = MultiKinetics()
for item in dupReactionList:
oldReactionKinetics.kineticsList.append(item.kinetics)
oldReaction = dupReactionList[0]
oldReaction.kinetics = oldReactionKinetics
reactionList.append(oldReaction)
dupReactionList = []
dupReactionList.append(reaction)
kinetics = ''
comments = ''
return reaction, kinetics, comments, dupReactionList, reactionList
else:
# No more duplicate reactions
if dupReactionList:
# add previous reaction if they were duplicate reactions
oldReactionKinetics = MultiKinetics()
for item in dupReactionList:
oldReactionKinetics.kineticsList.append(item.kinetics)
oldReaction = dupReactionList[0]
oldReaction.kinetics = oldReactionKinetics
reactionList.append(oldReaction)
dupReactionList = []
# add this new, nonduplicate reaction
reaction = readKineticsEntry(kinetics,speciesDict,energyUnits,moleculeUnits)
reaction.kinetics.comment = comments
reactionList.append(reaction)
kinetics = ''
comments = ''
return reaction, kinetics, comments, dupReactionList, reactionList
with open(path, 'r') as f:
line = f.readline()
while line != '':
line = removeCommentFromLine(line)[0]
line = line.strip()
tokens = line.split()
if 'SPECIES' in line:
# List of species identifiers
index = tokens.index('SPECIES')
tokens = tokens[index+1:]
while 'END' not in tokens:
line = f.readline()
line = removeCommentFromLine(line)[0]
line = line.strip()
tokens.extend(line.split())
for token in tokens:
if token == 'END':
break
if token in speciesDict:
species = speciesDict[token]
else:
species = Species(label=token)
speciesDict[token] = species
speciesList.append(species)
# Also always add in a few bath gases (since RMG-Java does)
for label, smiles in [('Ar','[Ar]'), ('He','[He]'), ('Ne','[Ne]'), ('N2','N#N')]:
molecule = Molecule().fromSMILES(smiles)
for species in speciesList:
if species.label == label:
if len(species.molecule) == 0:
species.molecule = [molecule]
break
if species.isIsomorphic(molecule):
break
else:
species = Species(label=label, molecule=[molecule])
speciesList.append(species)
speciesDict[label] = species
elif 'THERM' in line:
# List of thermodynamics (hopefully one per species!)
line = f.readline()
thermo = ''
while line != '' and 'END' not in line:
line = removeCommentFromLine(line)[0]
if len(line) >= 80:
if line[79] in ['1', '2', '3', '4']:
thermo += line
if line[79] == '4':
label, thermo = readThermoEntry(thermo)
try:
speciesDict[label].thermo = thermo
except KeyError:
if label in ['Ar', 'N2', 'He', 'Ne']:
pass
else:
logging.warning('Skipping unexpected species "{0}" while reading thermodynamics entry.'.format(label))
thermo = ''
line = f.readline()
elif 'REACTIONS' in line:
# Reactions section
energyUnits = 'CAL/MOL'
moleculeUnits = 'MOLES'
try:
energyUnits = tokens[1]
moleculeUnits = tokens[2]
except IndexError:
pass
kineticsList = []
commentsList = []
kinetics = ''
comments = ''
line = f.readline()
while line != '' and 'END' not in line:
lineStartsWithComment = line.startswith('!')
line, comment = removeCommentFromLine(line)
line = line.strip(); comment = comment.strip()
if 'rev' in line or 'REV' in line:
# can no longer name reactants rev...
line = f.readline()
if '=' in line and not lineStartsWithComment:
# Finish previous record
kineticsList.append(kinetics)
commentsList.append(comments)
kinetics = ''
comments = ''
if line: kinetics += line + '\n'
if comment: comments += comment + '\n'
line = f.readline()
# Don't forget the last reaction!
if kinetics.strip() != '':
kineticsList.append(kinetics)
commentsList.append(comments)
if kineticsList[0] == '' and commentsList[-1] == '':
# True for Chemkin files generated from RMG-Py
kineticsList.pop(0)
commentsList.pop(-1)
elif kineticsList[0] == '' and commentsList[0] == '':
# True for Chemkin files generated from RMG-Java
kineticsList.pop(0)
commentsList.pop(0)
else:
# In reality, comments can occur anywhere in the Chemkin
# file (e.g. either or both of before and after the
# reaction equation)
# If we can't tell what semantics we are using, then just
# throw the comments away
# (This is better than failing to load the Chemkin file at
# all, which would likely occur otherwise)
if kineticsList[0] == '':
kineticsList.pop(0)
if len(kineticsList) != len(commentsList):
commentsList = ['' for kinetics in kineticsList]
for kinetics, comments in zip(kineticsList, commentsList):
reaction = readKineticsEntry(kinetics, speciesDict, energyUnits, moleculeUnits)
reaction = readReactionComments(reaction, comments)
reactionList.append(reaction)
line = f.readline()
# Check for marked (and unmarked!) duplicate reactions
# Combine marked duplicate reactions into a single reaction using MultiKinetics
# Raise exception for unmarked duplicate reactions
duplicateReactionsToRemove = []
duplicateReactionsToAdd = []
for index1 in range(len(reactionList)):
reaction1 = reactionList[index1]
if reaction1 in duplicateReactionsToRemove:
continue
for index2 in range(index1+1, len(reactionList)):
reaction2 = reactionList[index2]
if reaction1.reactants == reaction2.reactants and reaction1.products == reaction2.products:
if reaction1.duplicate and reaction2.duplicate:
if not isinstance(reaction1, LibraryReaction) or not isinstance(reaction2, LibraryReaction):
# Only make a MultiKinetics for library reactions, not template reactions
continue
for reaction in duplicateReactionsToAdd:
if reaction1.reactants == reaction.reactants and reaction1.products == reaction.products:
break
else:
assert reaction1.library.label == reaction2.library.label
reaction = LibraryReaction(
index = reaction1.index,
reactants = reaction1.reactants,
products = reaction1.products,
kinetics = MultiKinetics(),
library = reaction1.library,
duplicate = False,
)
duplicateReactionsToAdd.append(reaction)
reaction.kinetics.kineticsList.append(reaction1.kinetics)
duplicateReactionsToRemove.append(reaction1)
reaction.kinetics.kineticsList.append(reaction2.kinetics)
duplicateReactionsToRemove.append(reaction2)
elif reaction1.kinetics.isPressureDependent() == reaction2.kinetics.isPressureDependent():
# If both reactions are pressure-independent or both are pressure-dependent, then they need duplicate tags
# Chemkin treates pdep and non-pdep reactions as different, so those are okay
raise ChemkinError('Encountered unmarked duplicate reaction {0}.'.format(reaction1))
for reaction in duplicateReactionsToRemove:
reactionList.remove(reaction)
reactionList.extend(duplicateReactionsToAdd)
index = 0
for reaction in reactionList:
index += 1
reaction.index = index
return speciesList, reactionList
