Debug assistance in JDAS when excluding reactions from the ODE set.

This helped us figure out when PDep reactions are or are not excluded from the ODE solver
because they duplicate existing reactions.

Author: rwest

source/RMG/jing/rxnSys/JDAS.java

@@ -279,11 +279,25 @@ public void generatePDepReactionList(ReactionModel p_reactionModel,
             // check if this reaction is already in the list and also
             //  check if this reaction has a reverse reaction which is already present in the list.
             if (rxn.reactantEqualsProduct()) continue;
-			if (troeList.contains(rxn) || troeList.contains(reverse)) continue;
-			if (thirdBodyList.contains(rxn) || thirdBodyList.contains(reverse)) continue;
-			if (lindemannList.contains(rxn) || lindemannList.contains(reverse)) continue;
-			if (seedList.contains(rxn) || seedList.contains(reverse)) continue; // exclude rxns already in seed mechanism
-			
+			if (troeList.contains(rxn) || troeList.contains(reverse)) {
+				//Logger.debug(String.format("Excluding FAME-estimated PDep rate for %s from ODEs because its Troe rate is in a reaction library or seed mechanism.",rxn));
+				continue; // exclude rxns already in seed mechanism
+			}
+			else if (thirdBodyList.contains(rxn) || thirdBodyList.contains(reverse)) {
+				//Logger.debug(String.format("Excluding FAME-estimated PDep rate for %s from ODEs because its 3-body rate is in a reaction library or seed mechanism.",rxn));
+				continue; // exclude rxns already in seed mechanism
+			}
+			else if (lindemannList.contains(rxn) || lindemannList.contains(reverse)) {
+				//Logger.debug(String.format("Excluding FAME-estimated PDep rate for %s from ODEs because its Lindemann rate is in a reaction library or seed mechanism.",rxn));
+				continue; // exclude rxns already in seed mechanism
+			}
+			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
+			}
+			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));
+			}
             if (!pDepList.contains(rxn) && !pDepList.contains(reverse)) {
                 pDepList.add(rxn);
             } else if (pDepList.contains(rxn) && !pDepList.contains(reverse)) {