Check is a Seed Mechanism exists before grabbing species/reactions

This commit adds if statements to three classes, checking whether a Seed
Mechanism exists before attempting to grab the species (reactions) stored
in the Seed.  Otherwise, NPE occurs when running RMG with no Seed Mechanisms.

Author: mrharper

source/RMG/jing/rxnSys/Chemkin.java

@@ -581,12 +581,15 @@ public static BufferedWriter writeChemkinPdepReactions(ReactionModel p_reactionM
       CoreEdgeReactionModel cerm = (CoreEdgeReactionModel)p_reactionModel;
 
 	  // First, get all the seed mechanism reactions into the seedList.
-	 for (Iterator iter = cerm.getSeedMechanism().getReactionSet().iterator(); iter.hasNext(); ) {
-		 Reaction r = (Reaction)iter.next();
-		 if (r.isForward()) {
-			 seedList.add(r);
-		 }
-	 }
+          // ... if a seed mechanism exists
+          if (cerm.getSeedMechanism() != null) {
+             for (Iterator iter = cerm.getSeedMechanism().getReactionSet().iterator(); iter.hasNext(); ) {
+                     Reaction r = (Reaction)iter.next();
+                     if (r.isForward()) {
+                             seedList.add(r);
+                     }
+             }
+          }
 
 	 // Then get troe, thirdbody, and Lindemann reactions (from primary reaction library) and add them to the pDepList
 	 // UNLESS they are already in the seed mechanism.

source/RMG/jing/rxnSys/CoreEdgeReactionModel.java

@@ -621,7 +621,8 @@ public LinkedHashSet getSpeciesSet() {
     public LinkedHashSet getCoreAndSeedSpeciesSet() {
 		LinkedHashSet speciesSet = new LinkedHashSet();
 		speciesSet.addAll(getCore().getSpeciesSet());
-		speciesSet.addAll(seed.getSpeciesSet());
+                if (seed != null)
+                    speciesSet.addAll(seed.getSpeciesSet());
 		return speciesSet;
     }
 

source/RMG/jing/rxnSys/JDAS.java

@@ -263,7 +263,9 @@ public void generatePDepReactionList(ReactionModel p_reactionModel,
             LinkedList nonPDepList, LinkedList pDepList) {
 
         CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
-		LinkedHashSet seedList = cerm.getSeedMechanism().getReactionSet();
+        LinkedHashSet seedList = new LinkedHashSet();
+        if (cerm.getSeedMechanism() != null)
+		seedList = cerm.getSeedMechanism().getReactionSet();
 
         for (Iterator iter = PDepNetwork.getCoreReactions(cerm).iterator(); iter.hasNext();) {
             PDepReaction rxn = (PDepReaction) iter.next();