Merge pull request #740 from ReactionMechanismGenerator/verboseComments

Fix and re-add verbose comments back to RMG

Author: connie

rmgpy/data/kinetics/family.py

@@ -1037,13 +1037,13 @@ def getRootTemplate(self):
         else:
             return self.groups.top
 
-    def fillKineticsRulesByAveragingUp(self):
+    def fillKineticsRulesByAveragingUp(self, verbose=False):
         """
         Fill in gaps in the kinetics rate rules by averaging child nodes
         recursively starting from the top level root template.
         """
 
-        self.rules.fillRulesByAveragingUp(self.getRootTemplate(), {})
+        self.rules.fillRulesByAveragingUp(self.getRootTemplate(), {}, verbose)
 
 
 

rmgpy/data/kinetics/rules.py

@@ -440,9 +440,11 @@ def getAllRules(self, template):
 
         return entries
 
-    def fillRulesByAveragingUp(self, rootTemplate, alreadyDone):
+    def fillRulesByAveragingUp(self, rootTemplate, alreadyDone, verbose=False):
         """
         Fill in gaps in the kinetics rate rules by averaging child nodes.
+        If verbose is set to True, then exact sources of kinetics are saved in the kinetics comments
+        (warning: this uses up a lot of memory due to the extensively long comments)
         """
         rootLabel = ';'.join([g.label for g in rootTemplate])
 
@@ -472,7 +474,7 @@ def fillRulesByAveragingUp(self, rootTemplate, alreadyDone):
             if label in alreadyDone:
                 kinetics = alreadyDone[label]
             else:
-                kinetics = self.fillRulesByAveragingUp(template, alreadyDone)
+                kinetics = self.fillRulesByAveragingUp(template, alreadyDone, verbose)
 
             if kinetics is not None:
                 kineticsList.append([kinetics, template])
@@ -494,26 +496,27 @@ def fillRulesByAveragingUp(self, rootTemplate, alreadyDone):
             if len(kineticsList) > 1:
                 # We found one or more results! Let's average them together
                 kinetics = self.__getAverageKinetics([k for k, t in kineticsList])
-                kinetics.comment = 'Average of ({0})'.format(
-                     ' + '.join(';'.join(g.label for g in t) for k, t in kineticsList))
 
-                # For debug mode: uncomment the following kinetics commenting
-                # lines and use them instead of the lines above. Caution: large memory usage.
-
-                # kinetics.comment += 'Average of ({0})'.format(
-                #     ' + '.join(k.comment if k.comment != '' else ';'.join(g.label for g in t) for k, t in kineticsList))
+                if verbose:
+                    kinetics.comment = 'Average of ({0})'.format(
+                         ' + '.join(k.comment if k.comment != '' else ';'.join(g.label for g in t) for k, t in kineticsList))
+                
+                else:
+                    kinetics.comment = 'Average of ({0})'.format(
+                     ' + '.join(';'.join(g.label for g in t) for k, t in kineticsList))
 
             else:
                 k,t = kineticsList[0]
                 kinetics = deepcopy(k)
                 # Even though we are using just a single set of kinetics, it's still considered
                 # an average.  It just happens that the other distance 1 children had no data.
-                kinetics.comment = 'Average of ({0})'.format(';'.join(g.label for g in t))
 
-                # For debug mode: uncomment the following kinetics commenting
-                # lines and use them instead of the lines above. Caution: large memory usage.
+                if verbose:
+                    kinetics.comment = 'Average of ({0})'.format(k.comment if k.comment != '' else ';'.join(g.label for g in t))
+                else:
+                    kinetics.comment = 'Average of ({0})'.format(';'.join(g.label for g in t))
+                
 
-                # kinetics.comment += 'Average of ({0}).format(k.comment if k.comment != '' else ';'.join(g.label for g in t))
 
             entry = Entry(
                 index = 0,
@@ -633,6 +636,13 @@ def getTemplateLabel(template):
                 else:
                     # We found one or more results! Let's average them together
                     kinetics = self.__getAverageKinetics([k for k, t in kineticsList])
+                    # Unlike in the case of a single rule, the verbose comments for averaging are lost unless they are 
+                    # appended in the following lines.  Verbose comments are filtered out in 
+                    # rmgpy.rmg.model.CoreEdgeReactionModel.generateKinetics
+                    kinetics.comment = 'Average of ({0})'.format(
+                         ' + '.join(k.comment if k.comment != '' else ';'.join(g.label for g in t) for k, t in kineticsList))
+                    kinetics.comment +='\n'
+                    # Append standard portion of kinetics comments that appear in non-verbose mode.
                     kinetics.comment += 'Estimated using average of templates {0}'.format(
                         ' + '.join([getTemplateLabel(t) for k, t in kineticsList]),
                     )

rmgpy/rmg/main.py

@@ -322,7 +322,7 @@ def loadDatabase(self):
                 logging.info('Training set explicitly not added to rate rules in kinetics families...')
             logging.info('Filling in rate rules in kinetics families by averaging...')
             for family in self.database.kinetics.families.values():
-                family.fillKineticsRulesByAveragingUp()
+                family.fillKineticsRulesByAveragingUp(verbose=self.verboseComments)
 
     def initialize(self, **kwargs):
         """