def loadRMGPyJob(inputFile, chemkinFile=None, speciesDict=None, generateImages=True):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
from rmgpy.rmg.main import RMG
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
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), 'chemkin', 'species_dictionary.txt')
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict)
# 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):
t.species = speciesDict[t.species]
reactionSystem.sensitiveSpecies = [speciesDict[spec] for spec in reactionSystem.sensitiveSpecies]
# Set reaction model to match model loaded from Chemkin file
rmg.reactionModel.core.species = speciesList
rmg.reactionModel.core.reactions = reactionList
# Generate species images
if generateImages:
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))
if not os.path.exists(path):
species.molecule[0].draw(str(path))
return rmg
def loadRMGPyJob(inputFile, chemkinFile, speciesDict=None):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
speciesList, reactionList = loadChemkinFile(chemkinFile,
speciesDict,
readComments=False)
assert speciesList, reactionList
# print 'labels from species in the chemkin file:'
# for spc in speciesList:
# print spc.label
# Map species in input file to corresponding species in Chemkin file
speciesDict = {}
assert rmg.initialSpecies
# print 'initial species: ', rmg.initialSpecies
#label of initial species must correspond to the label in the chemkin file WITHOUT parentheses.
#E.g.: "JP10" not "JP10(1)"
for spec0 in rmg.initialSpecies:
for species in speciesList:
if species.label == spec0.label:
speciesDict[spec0] = species
break
assert speciesDict
# 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):
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
# print 'core: ', speciesList
return rmg
def loadRMGPyJob(inputFile, chemkinFile, speciesDict=None):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict, readComments=False)
assert speciesList, reactionList
# print 'labels from species in the chemkin file:'
# for spc in speciesList:
# print spc.label
# Map species in input file to corresponding species in Chemkin file
speciesDict = {}
assert rmg.initialSpecies
# print 'initial species: ', rmg.initialSpecies
#label of initial species must correspond to the label in the chemkin file WITHOUT parentheses.
#E.g.: "JP10" not "JP10(1)"
for spec0 in rmg.initialSpecies:
for species in speciesList:
if species.label == spec0.label:
speciesDict[spec0] = species
break
assert speciesDict
# 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):
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
# print 'core: ', speciesList
return rmg
def loadRMGPyJob(inputFile, chemkinFile, speciesDict):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
import os.path
from rmgpy.chemkin import getSpeciesIdentifier, loadChemkinFile
from rmgpy.rmg.main import RMG
from rmgpy.solver.base import TerminationTime, TerminationConversion
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
speciesList, reactionList = loadChemkinFile(chemkinFile,
speciesDict,
readComments=False)
# Map species in input file to corresponding species in Chemkin file
speciesDict = {}
#label of initial species must correspond to the label in the chemkin file WITHOUT parentheses.
for spec0 in rmg.initialSpecies:
for species in speciesList:
if species.label == spec0.label:
speciesDict[spec0] = species
break
# 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):
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
return rmg
def loadRMGPyJob(inputFile, chemkinFile, speciesDict):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
import os.path
from rmgpy.chemkin import getSpeciesIdentifier, loadChemkinFile
from rmgpy.rmg.main import RMG
from rmgpy.solver.base import TerminationTime, TerminationConversion
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict, readComments=False)
# Map species in input file to corresponding species in Chemkin file
speciesDict = {}
#label of initial species must correspond to the label in the chemkin file WITHOUT parentheses.
for spec0 in rmg.initialSpecies:
for species in speciesList:
if species.label == spec0.label:
speciesDict[spec0] = species
break
# 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):
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
return rmg
def loadRMGPyJob(inputFile):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
chemkinFile = os.path.join(os.path.dirname(inputFile), 'chemkin', 'chem.inp')
speciesDict = os.path.join(os.path.dirname(inputFile), 'chemkin', 'species_dictionary.txt')
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict)
# 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):
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
return rmg
def loadRMGPyJob(inputFile,
chemkinFile=None,
speciesDict=None,
generateImages=True):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
# Load the specified RMG input file
rmg = RMG()
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
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), 'chemkin',
'species_dictionary.txt')
speciesList, reactionList = loadChemkinFile(chemkinFile, speciesDict)
# 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):
t.species = speciesDict[t.species]
reactionSystem.sensitiveSpecies = [
speciesDict[spec] for spec in reactionSystem.sensitiveSpecies
]
# Set reaction model to match model loaded from Chemkin file
rmg.reactionModel.core.species = speciesList
rmg.reactionModel.core.reactions = reactionList
# Generate species images
if generateImages:
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))
if not os.path.exists(path):
species.molecule[0].draw(str(path))
return rmg
def loadRMGPyJob(inputFile,
chemkinFile=None,
speciesDict=None,
generateImages=True,
useChemkinNames=False,
checkDuplicates=True):
"""
Load the results of an RMG-Py job generated from the given `inputFile`.
"""
from rmgpy.rmg.main import RMG
# Load the specified RMG input file
rmg = RMG(inputFile=inputFile)
rmg.loadInput(inputFile)
rmg.outputDirectory = os.path.abspath(os.path.dirname(inputFile))
# Load the final Chemkin model generated by RMG
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), 'chemkin',
'species_dictionary.txt')
speciesList, reactionList = loadChemkinFile(
chemkinFile,
speciesDict,
useChemkinNames=useChemkinNames,
checkDuplicates=checkDuplicates)
# 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:
if isinstance(reactionSystem, LiquidReactor):
# If there are constant species, map their input file names to
# corresponding species in Chemkin file
if reactionSystem.constSPCNames:
constSpeciesDict = {}
for spec0 in rmg.initialSpecies:
for constSpecLabel in reactionSystem.constSPCNames:
if spec0.label == constSpecLabel:
constSpeciesDict[constSpecLabel] = speciesDict[
spec0].label
break
reactionSystem.constSPCNames = [
constSpeciesDict[sname]
for sname in reactionSystem.constSPCNames
]
reactionSystem.initialConcentrations = dict([
(speciesDict[spec], conc) for spec, conc in
reactionSystem.initialConcentrations.iteritems()
])
else:
reactionSystem.initialMoleFractions = dict([
(speciesDict[spec], frac) for spec, frac in
reactionSystem.initialMoleFractions.iteritems()
])
for t in reactionSystem.termination:
if isinstance(t, TerminationConversion):
t.species = speciesDict[t.species]
if reactionSystem.sensitiveSpecies != ['all']:
reactionSystem.sensitiveSpecies = [
speciesDict[spec] for spec in reactionSystem.sensitiveSpecies
]
# Set reaction model to match model loaded from Chemkin file
rmg.reactionModel.core.species = speciesList
rmg.reactionModel.core.reactions = reactionList
# Generate species images
if generateImages:
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))
if not os.path.exists(path):
species.molecule[0].draw(str(path))
return rmg
