Add and modify calls for generateTransportData()

- move call for seed species from initialize() to
addSeedMechanismToCore()
- call getTransportData() for reactions found in reaction libraries in
addReactionLibraryToEdge()

Author: bbuesser

rmgpy/rmg/main.py

@@ -335,9 +335,6 @@ def initialize(self, args):
             # DON'T generate any more reactions for the seed species at this time
             for seedMechanism in self.seedMechanisms:
                 self.reactionModel.addSeedMechanismToCore(seedMechanism, react=False)
-            
-            for spec in self.reactionModel.core.species:
-                spec.generateTransportData(self.database)
 
             # Reaction libraries: add species and reactions from reaction library to the edge so
             # that RMG can find them if their rates are large enough

rmgpy/rmg/model.py

@@ -1278,6 +1278,7 @@ def addSeedMechanismToCore(self, seedMechanism, react=False):
             r, isNew = self.makeNewReaction(rxn) # updates self.newSpeciesList and self.newReactionlist
         for spec in self.newSpeciesList:
             if spec.reactive: spec.generateThermoData(database, quantumMechanics=self.quantumMechanics)
+            spec.generateTransportData(database)
         for spec in self.newSpeciesList:
             self.addSpeciesToCore(spec)
 
@@ -1327,6 +1328,7 @@ def addReactionLibraryToEdge(self, reactionLibrary):
             if not isNew: logging.info("This library reaction was not new: {0}".format(rxn))
         for spec in self.newSpeciesList:
             if spec.reactive: spec.generateThermoData(database, quantumMechanics=self.quantumMechanics)
+            spec.generateTransportData(database)
         for spec in self.newSpeciesList:
             self.addSpeciesToEdge(spec)