Checking against "pdep" reactions in ReactionLibrary reactions.txt file

This commit switches the general order of adding reactions to the ODE input
file and CHEMKIN chem.inp file from:
   * Seed
   * Reaction Library pdepreactions
   * RMG (fame) pdepreactions
   * RMG nonpdep reactions

to:
   * Seed
   * Reaction Library pdepreactions
   * RMG nonpdep reactions
   # RMG (fame) pdepreactions

Example: Suppose user started with H and O2 in the input file, and Glarborg/C3
reaction library.  RMG would find H+O2=O+OH in Glarborg/C3 library and would
make HO2 (H+O2) included, thereby finding the O+OH well, making
H+O2(+m)=O+OH(+m).  In the previous order, RMG would add the RMG pdepreactions
reaction to the list, and then add the Glarborg/C3 reaction to the list: this
would be an incorrect duplicate.

With the new order, RMG adds the Glarborg/C3 reaction, and then recognizes
the RMG (fame) pdepreaction to be a duplicate and will not add it to the ODE
or CHEMKIN list.

source/RMG/jing/rxnSys/Chemkin.java

@@ -603,6 +603,17 @@ public static BufferedWriter writeChemkinPdepReactions(ReactionModel p_reactionM
 		 }
 	 }
 
+      	 // Then add all non-pdep, non-seed, reactions to the nonPDepList
+      for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext(); ) {
+		  Reaction r = (Reaction)iter.next();
+		  if (!r.isForward()) continue;
+                  // Check the seedList against r and its reverse
+		  if (seedList.contains(r) || seedList.contains(r.getReverseReaction())) continue;
+		  if (r instanceof ThirdBodyReaction || r instanceof TROEReaction || r instanceof LindemannReaction) continue;
+		  // Made it through all the tests.
+		  nonPDepList.add(r);
+      }
+
 	 // Then get reactions from pressure-dependent networks and add them to pDepList
       for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
       	PDepNetwork pdn = (PDepNetwork)iter.next();
@@ -618,21 +629,13 @@ public static BufferedWriter writeChemkinPdepReactions(ReactionModel p_reactionM
       		if (rxn.reactantEqualsProduct()) continue;
 			if (pDepList.contains(rxn) || pDepList.contains(rxn.getReverseReaction())) continue;
 			if (seedList.contains(rxn) || seedList.contains(rxn.getReverseReaction())) continue;
+                        if (nonPDepList.contains(rxn) || nonPDepList.contains(rxn.getReverseReaction())) continue;
 
 			// Made it through all the tests.
 			pDepList.add(rxn);
       	}
       }
-	 // Then add all non-pdep, non-seed, reactions to the nonPDepList
-      for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext(); ) {
-		  Reaction r = (Reaction)iter.next();
-		  if (!r.isForward()) continue;
-		  if (seedList.contains(r)) continue;
-		  if (r instanceof ThirdBodyReaction || r instanceof TROEReaction || r instanceof LindemannReaction) continue;
-		  // Made it through all the tests.
-		  nonPDepList.add(r);
-      }
-
+
 	  // First report seed mechanism reactions
 	  for (Iterator iter = seedList.iterator(); iter.hasNext();){
 		  Reaction r = (Reaction)iter.next();

source/RMG/jing/rxnSys/JDAS.java

@@ -267,6 +267,13 @@ public void generatePDepReactionList(ReactionModel p_reactionModel,
         if (cerm.getSeedMechanism() != null)
 		seedList = cerm.getSeedMechanism().getReactionSet();
 
+        for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext();) {
+            Reaction r = (Reaction) iter.next();
+            if (r.isForward() && !(r instanceof ThirdBodyReaction) && !(r instanceof TROEReaction) && !(r instanceof LindemannReaction)) {
+                nonPDepList.add(r);
+            }
+        }
+
         for (Iterator iter = PDepNetwork.getCoreReactions(cerm).iterator(); iter.hasNext();) {
             PDepReaction rxn = (PDepReaction) iter.next();
             if (cerm.categorizeReaction(rxn) != 1) {
@@ -297,6 +304,17 @@ else if (seedList.contains(rxn) || seedList.contains(reverse)) {
 				//Logger.debug(String.format("Excluding FAME-estimated PDep rate for %s from ODEs because it's in the seed mechanism",rxn));
 				continue; // exclude rxns already in seed mechanism
 			}
+                        /*
+                         * This elseif statement exists to catch pressure-dependent reactions
+                         * that were supplied to a Reaction Library in the reactions.txt file
+                         * (e.g. the pdep kinetics were fit to a particular pressure, OR
+                         * H+O2=O+OH).  We want the Reaction Library's value to override
+                         * the FAME-estimated pdep kinetics.
+                         */
+                        else if (nonPDepList.contains(rxn) || nonPDepList.contains(reverse)) {
+                                //Logger.debug(String.format("Excluding FAME-estimated PDep rate for %s from ODEs because it's in the reaction mechanism",rxn));
+				continue; // exclude rxns already in mechanism
+                        }
 			else {
 				//Logger.debug(String.format("Including FAME-estimated PDep rate for  %s in ODEs because it's not in the seed mechanism, nor does it have a P-dep rate from a reaction library.",rxn));
 			}
@@ -313,12 +331,7 @@ else if (seedList.contains(rxn) || seedList.contains(reverse)) {
             }
         }
 
-        for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext();) {
-            Reaction r = (Reaction) iter.next();
-            if (r.isForward() && !(r instanceof ThirdBodyReaction) && !(r instanceof TROEReaction) && !(r instanceof LindemannReaction)) {
-                nonPDepList.add(r);
-            }
-        }
+
 
         duplicates.clear();