def setE0WithThermo(self):
"""
Helper method that sets species' E0 using the species' thermo data
"""
if self.getThermoData().E0 is not None:
self.conformer.E0 = self.getThermoData().E0
else:
if not self.thermo.Cp0 or not self.thermo.CpInf:
# set Cp0 and CpInf
from rmgpy.data.thermo import findCp0andCpInf
findCp0andCpInf(self, self.thermo)
self.conformer.E0 = self.getThermoData().toWilhoit().E0
def setE0WithThermo(self):
"""
Helper method that sets species' E0 using the species' thermo data
"""
if self.getThermoData().E0 is not None:
self.conformer.E0 = self.getThermoData().E0
else:
if not self.thermo.Cp0 or not self.thermo.CpInf:
# set Cp0 and CpInf
from rmgpy.data.thermo import findCp0andCpInf
findCp0andCpInf(self, self.thermo)
self.conformer.E0 = self.getThermoData().toWilhoit().E0
def run(inputFile, outputDir, original=None, maximumIsotopicAtoms = 1,
useOriginalReactions = False,
kineticIsotopeEffect = None):
"""
Accepts one input file with the RMG-Py model to generate.
Firstly, generates the RMG model for the first input file. Takes the core species of that mechanism
and generates all isotopomers of those core species. Next, generates all reactions between the
generated pool of isotopomers, and writes it to file.
"""
logging.info("isotope: Starting the RMG isotope generation method 'run'")
if not original:
logging.info("isotope: original model not found, generating new one in directory `rmg`")
logging.info("isotope: check `rmg/RMG.log` for the rest of the logging info.")
outputdirRMG = os.path.join(outputDir, 'rmg')
os.mkdir(outputdirRMG)
rmg = generate_RMG_model(inputFile, outputdirRMG)
else:
logging.info("isotope: original model being copied from previous RMG job in folder {}".format(original))
outputdirRMG = original
chemkinFile = os.path.join(outputdirRMG, 'chemkin', 'chem_annotated.inp')
dictFile = os.path.join(outputdirRMG, 'chemkin', 'species_dictionary.txt')
rmg = loadRMGJob(inputFile, chemkinFile, dictFile, generateImages=False, useChemkinNames=True)
logging.info("isotope: generating isotope model")
logging.info('Generating isotopomers for the core species in {}'.format(outputdirRMG))
isotopes = []
logging.info("isotope: adding all the new and old isotopomers")
for spc in rmg.reactionModel.core.species:
findCp0andCpInf(spc, spc.thermo)
isotopes.append([spc] + generate_isotopomers(spc, maximumIsotopicAtoms))
logging.info('isotope: number of isotopomers: {}'.format(sum([len(isotopomer) for isotopomer in isotopes if isotopomer])))
outputdirIso = os.path.join(outputDir, 'iso')
os.mkdir(outputdirIso)
logging.info('isotope: Generating RMG isotope model in {}'.format(outputdirIso))
generate_isotope_model(outputdirIso, rmg, isotopes, useOriginalReactions = useOriginalReactions, kineticIsotopeEffect = kineticIsotopeEffect)
def run(inputFile, outputDir, original=None, maximumIsotopicAtoms = 1,
useOriginalReactions = False,
kineticIsotopeEffect = None):
"""
Accepts one input file with the RMG-Py model to generate.
Firstly, generates the RMG model for the first input file. Takes the core species of that mechanism
and generates all isotopomers of those core species. Next, generates all reactions between the
generated pool of isotopomers, and writes it to file.
"""
logging.info("isotope: Starting the RMG isotope generation method 'run'")
if not original:
logging.info("isotope: original model not found, generating new one in directory `rmg`")
logging.info("isotope: check `rmg/RMG.log` for the rest of the logging info.")
outputdirRMG = os.path.join(outputDir, 'rmg')
os.mkdir(outputdirRMG)
rmg = generate_RMG_model(inputFile, outputdirRMG)
else:
logging.info("isotope: original model being copied from previous RMG job in folder {}".format(original))
outputdirRMG = original
chemkinFile = os.path.join(outputdirRMG, 'chemkin', 'chem_annotated.inp')
dictFile = os.path.join(outputdirRMG, 'chemkin', 'species_dictionary.txt')
rmg = loadRMGJob(inputFile, chemkinFile, dictFile, generateImages=False, useChemkinNames=True)
logging.info("isotope: generating isotope model")
logging.info('Generating isotopomers for the core species in {}'.format(outputdirRMG))
isotopes = []
logging.info("isotope: adding all the new and old isotopomers")
for spc in rmg.reactionModel.core.species:
findCp0andCpInf(spc, spc.thermo)
isotopes.append([spc] + generate_isotopomers(spc, maximumIsotopicAtoms))
logging.info('isotope: number of isotopomers: {}'.format(sum([len(isotopomer) for isotopomer in isotopes if isotopomer])))
outputdirIso = os.path.join(outputDir, 'iso')
os.mkdir(outputdirIso)
logging.info('isotope: Generating RMG isotope model in {}'.format(outputdirIso))
generate_isotope_model(outputdirIso, rmg, isotopes, useOriginalReactions = useOriginalReactions, kineticIsotopeEffect = kineticIsotopeEffect)
def reconstructKineticsFromSource(self,
reaction,
source,
fixBarrierHeight=False,
forcePositiveBarrier=False):
"""
Reaction is the original reaction with original kinetics.
Note that for Library and PDep reactions this function does not do anything other than return the original kinetics...
You must enter source data in the appropriate format such as returned from returned from self.extractSourceFromComments,
self-constructed.
fixBarrierHeight and forcePositiveBarrier will change the kinetics based on the Reaction.fixBarrierHeight function.
Return Arrhenius form kinetics if the source is from training reaction or rate rules.
"""
from rmgpy.data.thermo import findCp0andCpInf
from rmgpy.thermo import Wilhoit
if 'Library' in source:
return reaction.kinetics
elif 'PDep' in source:
return reaction.kinetics
else:
rxnCopy = deepcopy(reaction)
if 'Training' in source:
trainingEntry = source['Training'][1]
reverse = source['Training'][2]
if reverse:
reverseKinetics = trainingEntry.data
rxnCopy.kinetics = reverseKinetics
forwardKinetics = rxnCopy.generateReverseRateCoefficient()
kinetics = forwardKinetics
else:
kinetics = trainingEntry.data
elif 'Rate Rules' in source:
sourceDict = source['Rate Rules'][1]
rules = sourceDict['rules']
training = sourceDict['training']
degeneracy = sourceDict['degeneracy']
logA = 0
n = 0
alpha = 0
E0 = 0
for ruleEntry, weight in rules:
logA += numpy.log10(ruleEntry.data.A.value_si) * weight
n += ruleEntry.data.n.value_si * weight
alpha += ruleEntry.data.alpha.value_si * weight
E0 += ruleEntry.data.E0.value_si * weight
for ruleEntry, trainingEntry, weight in training:
logA += numpy.log10(ruleEntry.data.A.value_si) * weight
n += ruleEntry.data.n.value_si * weight
alpha += ruleEntry.data.alpha.value_si * weight
E0 += ruleEntry.data.E0.value_si * weight
Aunits = ruleEntry.data.A.units
if Aunits == 'cm^3/(mol*s)' or Aunits == 'cm^3/(molecule*s)' or Aunits == 'm^3/(molecule*s)':
Aunits = 'm^3/(mol*s)'
elif Aunits == 'cm^6/(mol^2*s)' or Aunits == 'cm^6/(molecule^2*s)' or Aunits == 'm^6/(molecule^2*s)':
Aunits = 'm^6/(mol^2*s)'
elif Aunits == 's^-1' or Aunits == 'm^3/(mol*s)' or Aunits == 'm^6/(mol^2*s)':
pass
else:
raise Exception(
'Invalid units {0} for averaging kinetics.'.format(
Aunits))
kinetics = ArrheniusEP(
A=(degeneracy * 10**logA, Aunits),
n=n,
alpha=alpha,
E0=(E0 * 0.001, "kJ/mol"),
)
else:
raise Exception(
"Source data must be either 'Library', 'PDep','Training', or 'Rate Rules'."
)
# Convert ArrheniusEP to Arrhenius
if fixBarrierHeight:
for spc in rxnCopy.reactants + rxnCopy.products:
# Need wilhoit to do this
if not isinstance(spc.thermo, Wilhoit):
findCp0andCpInf(spc, spc.thermo)
wilhoit = spc.thermo.toWilhoit()
spc.thermo = wilhoit
rxnCopy.kinetics = kinetics
rxnCopy.fixBarrierHeight(forcePositive=forcePositiveBarrier)
return rxnCopy.kinetics
else:
H298 = rxnCopy.getEnthalpyOfReaction(298)
if isinstance(kinetics, ArrheniusEP):
kinetics = kinetics.toArrhenius(H298)
return kinetics
def reconstructKineticsFromSource(self, reaction, source, fixBarrierHeight=False, forcePositiveBarrier=False):
"""
Reaction is the original reaction with original kinetics.
Note that for Library and PDep reactions this function does not do anything other than return the original kinetics...
You must enter source data in the appropriate format such as returned from returned from self.extractSourceFromComments,
self-constructed.
fixBarrierHeight and forcePositiveBarrier will change the kinetics based on the Reaction.fixBarrierHeight function.
Return Arrhenius form kinetics if the source is from training reaction or rate rules.
"""
from rmgpy.data.thermo import findCp0andCpInf
from rmgpy.thermo import Wilhoit
if 'Library' in source:
return reaction.kinetics
elif 'PDep' in source:
return reaction.kinetics
else:
rxnCopy = deepcopy(reaction)
if 'Training' in source:
trainingEntry = source['Training'][1]
reverse = source['Training'][2]
if reverse:
reverseKinetics = trainingEntry.data
rxnCopy.kinetics = reverseKinetics
forwardKinetics = rxnCopy.generateReverseRateCoefficient()
kinetics = forwardKinetics
else:
kinetics = trainingEntry.data
elif 'Rate Rules' in source:
sourceDict = source['Rate Rules'][1]
rules = sourceDict['rules']
training = sourceDict['training']
degeneracy = sourceDict['degeneracy']
logA = 0
n = 0
alpha = 0
E0 = 0
for ruleEntry, weight in rules:
logA += numpy.log10(ruleEntry.data.A.value_si)*weight
n += ruleEntry.data.n.value_si*weight
alpha +=ruleEntry.data.alpha.value_si*weight
E0 +=ruleEntry.data.E0.value_si*weight
for ruleEntry, trainingEntry, weight in training:
logA += numpy.log10(ruleEntry.data.A.value_si)*weight
n += ruleEntry.data.n.value_si*weight
alpha +=ruleEntry.data.alpha.value_si*weight
E0 +=ruleEntry.data.E0.value_si*weight
Aunits = ruleEntry.data.A.units
if Aunits == 'cm^3/(mol*s)' or Aunits == 'cm^3/(molecule*s)' or Aunits == 'm^3/(molecule*s)':
Aunits = 'm^3/(mol*s)'
elif Aunits == 'cm^6/(mol^2*s)' or Aunits == 'cm^6/(molecule^2*s)' or Aunits == 'm^6/(molecule^2*s)':
Aunits = 'm^6/(mol^2*s)'
elif Aunits == 's^-1' or Aunits == 'm^3/(mol*s)' or Aunits == 'm^6/(mol^2*s)':
pass
else:
raise Exception('Invalid units {0} for averaging kinetics.'.format(Aunits))
kinetics = ArrheniusEP(
A = (degeneracy*10**logA, Aunits),
n = n,
alpha = alpha,
E0 = (E0*0.001,"kJ/mol"),
)
else:
raise Exception("Source data must be either 'Library', 'PDep','Training', or 'Rate Rules'.")
# Convert ArrheniusEP to Arrhenius
if fixBarrierHeight:
for spc in rxnCopy.reactants + rxnCopy.products:
# Need wilhoit to do this
if not isinstance(spc.thermo, Wilhoit):
findCp0andCpInf(spc, spc.thermo)
wilhoit = spc.thermo.toWilhoit()
spc.thermo = wilhoit
rxnCopy.kinetics = kinetics
rxnCopy.fixBarrierHeight(forcePositive=forcePositiveBarrier)
return rxnCopy.kinetics
else:
H298 = rxnCopy.getEnthalpyOfReaction(298)
if isinstance(kinetics, ArrheniusEP):
kinetics = kinetics.toArrhenius(H298)
return kinetics