Reorganize initial react step to react for each reaction system

This fixes a bug where no reactions are generated because the
react flags are reset after each reaction system. This also makes
the initial react stage more similar to how reactions are generated
in the main loop, where reacting is done for each reactor.

rmgpy/rmg/main.py

@@ -616,12 +616,15 @@ def execute(self, **kwargs):
         self.rmg_memories = []
 
         # Initiate first reaction discovery step after adding all core species
-        if self.filterReactions:
-            # Run the reaction system to update threshold and react flags
-            for index, reactionSystem in enumerate(self.reactionSystems):
-                self.rmg_memories.append(RMG_Memory(reactionSystem,self.balanceSpecies))
-                self.rmg_memories[index].generate_cond()
-                log_conditions(self.rmg_memories,index)
+        for index, reactionSystem in enumerate(self.reactionSystems):
+            # Initialize memory object to track conditions for ranged reactors
+            self.rmg_memories.append(RMG_Memory(reactionSystem, self.balanceSpecies))
+            self.rmg_memories[index].generate_cond()
+            log_conditions(self.rmg_memories, index)
+
+            # Update react flags
+            if self.filterReactions:
+                # Run the reaction system to update threshold and react flags
                 reactionSystem.initializeModel(
                     coreSpecies=self.reactionModel.core.species,
                     coreReactions=self.reactionModel.core.reactions,
@@ -639,23 +642,27 @@ def execute(self, **kwargs):
                     rxnSysBimolecularThreshold=reactionSystem.bimolecularThreshold,
                     rxnSysTrimolecularThreshold=reactionSystem.trimolecularThreshold,
                 )
-        else:
-            for index, reactionSystem in enumerate(self.reactionSystems):
-                self.rmg_memories.append(RMG_Memory(reactionSystem,self.balanceSpecies))
-                self.rmg_memories[index].generate_cond()
-                log_conditions(self.rmg_memories,index)
+            else:
+                # If we're not filtering reactions, then we only need to react
+                # the first reaction system since they share the same core
+                if index > 0:
+                    continue
+
+            # React core species to enlarge edge
+            self.reactionModel.enlarge(reactEdge=True,
+                unimolecularReact=self.unimolecularReact,
+                bimolecularReact=self.bimolecularReact,
+                trimolecularReact=self.trimolecularReact)
 
         if not np.isinf(self.modelSettingsList[0].toleranceThermoKeepSpeciesInEdge):
-            self.reactionModel.setThermodynamicFilteringParameters(self.Tmax,toleranceThermoKeepSpeciesInEdge=self.modelSettingsList[0].toleranceThermoKeepSpeciesInEdge,
-                                                              minCoreSizeForPrune=self.modelSettingsList[0].minCoreSizeForPrune, 
-                                                              maximumEdgeSpecies =self.modelSettingsList[0].maximumEdgeSpecies,
-                                                              reactionSystems=self.reactionSystems)
-
-        self.reactionModel.enlarge(reactEdge=True, 
-            unimolecularReact=self.unimolecularReact, 
-            bimolecularReact=self.bimolecularReact,
-            trimolecularReact=self.trimolecularReact)
-
+            self.reactionModel.setThermodynamicFilteringParameters(
+                self.Tmax,
+                toleranceThermoKeepSpeciesInEdge=self.modelSettingsList[0].toleranceThermoKeepSpeciesInEdge,
+                minCoreSizeForPrune=self.modelSettingsList[0].minCoreSizeForPrune,
+                maximumEdgeSpecies=self.modelSettingsList[0].maximumEdgeSpecies,
+                reactionSystems=self.reactionSystems
+            )
+
         if not np.isinf(self.modelSettingsList[0].toleranceThermoKeepSpeciesInEdge):
             self.reactionModel.thermoFilterDown(maximumEdgeSpecies=self.modelSettingsList[0].maximumEdgeSpecies)