allow cantera output to use RMG names

Added an option to 'toCantera' methods in Species and Reaction
to allow for the name of the species/reaction to be the RMG name
instead of the chemkin name. The default behavior is still the same.

This is one step in addressing issue #1065.

rmgpy/reaction.py

@@ -192,10 +192,13 @@ def toChemkin(self, speciesList=None, kinetics=True):
  else:
  return rmgpy.chemkin.writeReactionString(self)
 
- def toCantera(self, speciesList=None):
+ def toCantera(self, speciesList=None, useChemkinIdentifier = True):
  """
  Converts the RMG Reaction object to a Cantera Reaction object
  with the appropriate reaction class.
+
+ If useChemkinIdentifier is set to False, the species label is used
+ instead. Be sure that species' labels are unique when setting it False.
  """
  from rmgpy.kinetics import Arrhenius, ArrheniusEP, MultiArrhenius, PDepArrhenius, MultiPDepArrhenius, Chebyshev, ThirdBody, Lindemann, Troe
 
@@ -208,14 +211,20 @@ def toCantera(self, speciesList=None):
  # for initializing the cantera reaction object
  ctReactants = {}
  for reactant in self.reactants:
- reactantName = reactant.toChemkin() # Use the chemkin name for the species
+ if useChemkinIdentifier:
+ reactantName = reactant.toChemkin()
+ else:
+ reactantName = reactant.label
  if reactantName in ctReactants:
  ctReactants[reactantName] += 1
  else:
  ctReactants[reactantName] = 1
  ctProducts = {}
  for product in self.products:
- productName = product.toChemkin() # Use the chemkin name for the species
+ if useChemkinIdentifier:
+ productName = product.toChemkin()
+ else:
+ productName = product.label
  if productName in ctProducts:
  ctProducts[productName] += 1
  else:

rmgpy/species.py

@@ -257,10 +257,13 @@ def toChemkin(self):
  from rmgpy.chemkin import getSpeciesIdentifier
  return getSpeciesIdentifier(self)
 
- def toCantera(self):
+ def toCantera(self, useChemkinIdentifier = True):
  """
  Converts the RMG Species object to a Cantera Species object
  with the appropriate thermo data.
+
+ If useChemkinIdentifier is set to False, the species label is used
+ instead. Be sure that species' labels are unique when setting it False.
  """
  import cantera as ct
 
@@ -273,8 +276,10 @@ def toCantera(self):
  elementDict[symbol] = 1
  else:
  elementDict[symbol] += 1
-
- ctSpecies = ct.Species(self.toChemkin(), elementDict)
+ if useChemkinIdentifier:
+ ctSpecies = ct.Species(self.toChemkin(), elementDict)
+ else:
+ ctSpecies = ct.Species(self.label, elementDict)
  if self.thermo:
  try:
  ctSpecies.thermo = self.thermo.toCantera()