def loadRMGJavaJob(inputFile, chemkinFile=None, speciesDict=None):
"""
Load the results of an RMG-Java job generated from the given `inputFile`.
"""
from rmgpy.molecule import Molecule
# Load the specified RMG-Java input file
# This implementation only gets the information needed to generate flux diagrams
rmg = RMG()
rmg.loadRMGJavaInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG-Java
if not chemkinFile:
chemkinFile = os.path.join(os.path.dirname(inputFile), 'chemkin',
'chem.inp')
if not speciesDict:
speciesDict = os.path.join(os.path.dirname(inputFile),
'RMG_Dictionary.txt')
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict)
# Bath gas species don't appear in RMG-Java species dictionary, so handle
# those as a special case
for species in speciesList:
if species.label == 'Ar':
species.molecule = [Molecule().fromSMILES('[Ar]')]
elif species.label == 'Ne':
species.molecule = [Molecule().fromSMILES('[Ne]')]
elif species.label == 'He':
species.molecule = [Molecule().fromSMILES('[He]')]
elif species.label == 'N2':
species.molecule = [Molecule().fromSMILES('N#N')]
# Map species in input file to corresponding species in Chemkin file
speciesDict = {}
for spec0 in rmg.initialSpecies:
for species in speciesList:
if species.isIsomorphic(spec0):
speciesDict[spec0] = species
break
# Generate flux pairs for each reaction if needed
for reaction in reactionList:
if not reaction.pairs: reaction.generatePairs()
# Replace species in input file with those in Chemkin file
for reactionSystem in rmg.reactionSystems:
reactionSystem.initialMoleFractions = dict([
(speciesDict[spec], frac)
for spec, frac in reactionSystem.initialMoleFractions.iteritems()
])
for t in reactionSystem.termination:
if isinstance(t, TerminationConversion):
if t.species not in speciesDict.values():
t.species = speciesDict[t.species]
# Set reaction model to match model loaded from Chemkin file
rmg.reactionModel.core.species = speciesList
rmg.reactionModel.core.reactions = reactionList
# RMG-Java doesn't generate species images, so draw them ourselves now
speciesPath = os.path.join(os.path.dirname(inputFile), 'species')
try:
os.mkdir(speciesPath)
except OSError:
pass
for species in speciesList:
path = os.path.join(speciesPath + '/{0!s}.png'.format(species))
species.molecule[0].draw(str(path))
return rmg
def loadRMGJavaJob(inputFile, chemkinFile=None, speciesDict=None):
"""
Load the results of an RMG-Java job generated from the given `inputFile`.
"""
from rmgpy.molecule import Molecule
# Load the specified RMG-Java input file
# This implementation only gets the information needed to generate flux diagrams
rmg = RMG()
rmg.loadRMGJavaInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG-Java
if not chemkinFile:
chemkinFile = os.path.join(os.path.dirname(inputFile), 'chemkin', 'chem.inp')
if not speciesDict:
speciesDict = os.path.join(os.path.dirname(inputFile), 'RMG_Dictionary.txt')
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict)
# Bath gas species don't appear in RMG-Java species dictionary, so handle
# those as a special case
for species in speciesList:
if species.label == 'Ar':
species.molecule = [Molecule().fromSMILES('[Ar]')]
elif species.label == 'Ne':
species.molecule = [Molecule().fromSMILES('[Ne]')]
elif species.label == 'He':
species.molecule = [Molecule().fromSMILES('[He]')]
elif species.label == 'N2':
species.molecule = [Molecule().fromSMILES('N#N')]
# Map species in input file to corresponding species in Chemkin file
speciesDict = {}
for spec0 in rmg.initialSpecies:
for species in speciesList:
if species.isIsomorphic(spec0):
speciesDict[spec0] = species
break
# Generate flux pairs for each reaction if needed
for reaction in reactionList:
if not reaction.pairs: reaction.generatePairs()
# Replace species in input file with those in Chemkin file
for reactionSystem in rmg.reactionSystems:
reactionSystem.initialMoleFractions = dict([(speciesDict[spec], frac) for spec, frac in reactionSystem.initialMoleFractions.iteritems()])
for t in reactionSystem.termination:
if isinstance(t, TerminationConversion):
if t.species not in speciesDict.values():
t.species = speciesDict[t.species]
# Set reaction model to match model loaded from Chemkin file
rmg.reactionModel.core.species = speciesList
rmg.reactionModel.core.reactions = reactionList
# RMG-Java doesn't generate species images, so draw them ourselves now
speciesPath = os.path.join(os.path.dirname(inputFile), 'species')
try:
os.mkdir(speciesPath)
except OSError:
pass
for species in speciesList:
path = os.path.join(speciesPath + '/{0!s}.png'.format(species))
species.molecule[0].draw(str(path))
return rmg
