def getKinetics(self):
"""
Extracts the kinetic data from the chemkin file for plotting purposes.
"""
from rmgpy.chemkin import loadChemkinFile
from rmgpy.kinetics import ArrheniusEP, Chebyshev
from rmgpy.reaction import Reaction
from rmgpy.data.base import Entry
kineticsDataList = []
chemkinPath = self.path + "/chemkin/chem.inp"
dictionaryPath = self.path + "RMG_Dictionary.txt"
speciesList, reactionList = loadChemkinFile(chemkinPath, dictionaryPath)
for reaction in reactionList:
# If the kinetics are ArrheniusEP, replace them with Arrhenius
if isinstance(reaction.kinetics, ArrheniusEP):
reaction.kinetics = reaction.kinetics.toArrhenius(reaction.getEnthalpyOfReaction(298))
reactants = " + ".join([moleculeToInfo(reactant) for reactant in reaction.reactants])
arrow = "⇔" if reaction.reversible else "→"
products = " + ".join([moleculeToInfo(reactant) for reactant in reaction.products])
source = str(reaction).replace("<=>", "=")
href = reaction.getURL()
entry = Entry()
entry.result = reactionList.index(reaction) + 1
forwardKinetics = reaction.kinetics
forward = True
chemkin = reaction.toChemkin(speciesList)
reverseKinetics = reaction.generateReverseRateCoefficient()
reverseKinetics.comment = "Fitted reverse reaction. " + reaction.kinetics.comment
rev_reaction = Reaction(reactants=reaction.products, products=reaction.reactants, kinetics=reverseKinetics)
chemkin_rev = rev_reaction.toChemkin(speciesList)
kineticsDataList.append(
[
reactants,
arrow,
products,
entry,
forwardKinetics,
source,
href,
forward,
chemkin,
reverseKinetics,
chemkin_rev,
]
)
return kineticsDataList
def getKinetics(self):
"""
Extracts the kinetic data from the chemkin file for plotting purposes.
"""
from rmgpy.chemkin import loadChemkinFile
from rmgpy.kinetics import ArrheniusEP, Chebyshev
from rmgpy.reaction import Reaction
from rmgpy.data.base import Entry
kineticsDataList = []
chemkinPath= self.path + '/chemkin/chem.inp'
dictionaryPath = self.path + 'RMG_Dictionary.txt'
if self.Foreign:
readComments = False
else:
readComments = True
if os.path.exists(dictionaryPath):
speciesList, reactionList = loadChemkinFile(chemkinPath, dictionaryPath, readComments=readComments)
else:
speciesList, reactionList = loadChemkinFile(chemkinPath, readComments=readComments)
for reaction in reactionList:
# If the kinetics are ArrheniusEP, replace them with Arrhenius
if isinstance(reaction.kinetics, ArrheniusEP):
reaction.kinetics = reaction.kinetics.toArrhenius(reaction.getEnthalpyOfReaction(298))
if os.path.exists(dictionaryPath):
reactants = ' + '.join([moleculeToInfo(reactant) for reactant in reaction.reactants])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join([moleculeToInfo(product) for product in reaction.products])
href = reaction.getURL()
else:
reactants = ' + '.join([reactant.label for reactant in reaction.reactants])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join([product.label for product in reaction.products])
href = ''
source = str(reaction).replace('<=>','=')
entry = Entry()
entry.result = reactionList.index(reaction)+1
forwardKinetics = reaction.kinetics
forward = True
chemkin = reaction.toChemkin(speciesList)
reverseKinetics = reaction.generateReverseRateCoefficient()
reverseKinetics.comment = 'Fitted reverse reaction. ' + reaction.kinetics.comment
rev_reaction = Reaction(reactants = reaction.products, products = reaction.reactants, kinetics = reverseKinetics)
chemkin_rev = rev_reaction.toChemkin(speciesList)
kineticsDataList.append([reactants, arrow, products, entry, forwardKinetics, source, href, forward, chemkin, reverseKinetics, chemkin_rev])
return kineticsDataList
def getKinetics(self):
"""
Extracts the kinetic data from the chemkin file for plotting purposes.
"""
from rmgpy.chemkin import loadChemkinFile
from rmgpy.kinetics import ArrheniusEP, Chebyshev
from rmgpy.reaction import Reaction
from rmgpy.data.base import Entry
kineticsDataList = []
chemkinPath= os.path.join(self.path, 'chemkin','chem.inp')
dictionaryPath = os.path.join(self.path, 'RMG_Dictionary.txt' )
if self.Foreign:
readComments = False
else:
readComments = True
if os.path.exists(dictionaryPath):
speciesList, reactionList = loadChemkinFile(chemkinPath, dictionaryPath, readComments=readComments)
else:
speciesList, reactionList = loadChemkinFile(chemkinPath, readComments=readComments)
for reaction in reactionList:
# If the kinetics are ArrheniusEP, replace them with Arrhenius
if isinstance(reaction.kinetics, ArrheniusEP):
reaction.kinetics = reaction.kinetics.toArrhenius(reaction.getEnthalpyOfReaction(298))
if os.path.exists(dictionaryPath):
reactants = ' + '.join([moleculeToInfo(reactant) for reactant in reaction.reactants])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join([moleculeToInfo(product) for product in reaction.products])
href = reaction.getURL()
else:
reactants = ' + '.join([reactant.label for reactant in reaction.reactants])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join([product.label for product in reaction.products])
href = ''
source = str(reaction).replace('<=>','=')
entry = Entry()
entry.result = reactionList.index(reaction)+1
forwardKinetics = reaction.kinetics
forward = True
chemkin = reaction.toChemkin(speciesList)
reverseKinetics = reaction.generateReverseRateCoefficient()
reverseKinetics.comment = 'Fitted reverse reaction. ' + reaction.kinetics.comment
rev_reaction = Reaction(reactants = reaction.products, products = reaction.reactants, kinetics = reverseKinetics)
chemkin_rev = rev_reaction.toChemkin(speciesList)
kineticsDataList.append([reactants, arrow, products, entry, forwardKinetics, source, href, forward, chemkin, reverseKinetics, chemkin_rev])
return kineticsDataList
def getKinetics(self):
"""
Extracts the kinetic data from the chemkin file for plotting purposes.
"""
from rmgpy.chemkin import load_chemkin_file
from rmgpy.kinetics import ArrheniusEP, ArrheniusBM
from rmgpy.reaction import Reaction
from rmgpy.data.base import Entry
kinetics_data_list = []
chem_file = os.path.join(self.path, 'chemkin', 'chem.inp')
dict_file = os.path.join(self.path, 'RMG_Dictionary.txt')
if self.foreign:
read_comments = False
else:
read_comments = True
if os.path.exists(dict_file):
spc_list, rxn_list = load_chemkin_file(chem_file,
dict_file,
read_comments=read_comments)
else:
spc_list, rxn_list = load_chemkin_file(chem_file,
read_comments=read_comments)
for reaction in rxn_list:
# If the kinetics are ArrheniusEP and ArrheniusBM, replace them with Arrhenius
if isinstance(reaction.kinetics, (ArrheniusEP, ArrheniusBM)):
reaction.kinetics = reaction.kinetics.to_arrhenius(
reaction.get_enthalpy_of_reaction(298))
if os.path.exists(dict_file):
reactants = ' + '.join([
moleculeToInfo(reactant) for reactant in reaction.reactants
])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join(
[moleculeToInfo(product) for product in reaction.products])
href = reaction.get_url()
else:
reactants = ' + '.join(
[reactant.label for reactant in reaction.reactants])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join(
[product.label for product in reaction.products])
href = ''
source = str(reaction).replace('<=>', '=')
entry = Entry()
entry.result = rxn_list.index(reaction) + 1
forward_kinetics = reaction.kinetics
forward = True
chemkin = reaction.to_chemkin(spc_list)
rev_kinetics = reaction.generate_reverse_rate_coefficient()
rev_kinetics.comment = 'Fitted reverse reaction. ' + reaction.kinetics.comment
rev_reaction = Reaction(reactants=reaction.products,
products=reaction.reactants,
kinetics=rev_kinetics)
chemkin_rev = rev_reaction.to_chemkin(spc_list)
kinetics_data_list.append([
reactants, arrow, products, entry, forward_kinetics, source,
href, forward, chemkin, rev_kinetics, chemkin_rev
])
return kinetics_data_list
