From 4e997464576b5776b11e242526f9a20fc9984cf4 Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Sat, 15 Nov 2014 19:26:37 +0000
Subject: [PATCH] [Kinetics] Allow explicit specification of the sticking
 species

---
 include/cantera/kinetics/Reaction.h |  4 +++
 src/kinetics/InterfaceKinetics.cpp  | 48 ++++++++++++++++++-----------
 src/kinetics/Reaction.cpp           |  1 +
 3 files changed, 35 insertions(+), 18 deletions(-)

diff --git a/include/cantera/kinetics/Reaction.h b/include/cantera/kinetics/Reaction.h
index b9510c88b..11c48757b 100644
--- a/include/cantera/kinetics/Reaction.h
+++ b/include/cantera/kinetics/Reaction.h
@@ -198,6 +198,10 @@ public:
     // Set to true if `rate` is a parameterization of the sticking coefficient
     // rather than the forward rate constant
     bool is_sticking_coefficient;
+
+    // For reactions with multiple non-surface species, the sticking species
+    // needs to be explicitly identified.
+    std::string sticking_species;
 };
 
 
diff --git a/src/kinetics/InterfaceKinetics.cpp b/src/kinetics/InterfaceKinetics.cpp
index 5cca5e941..9b43b7d8f 100644
--- a/src/kinetics/InterfaceKinetics.cpp
+++ b/src/kinetics/InterfaceKinetics.cpp
@@ -915,37 +915,49 @@ void InterfaceKinetics::addReaction(shared_ptr<Reaction> r_base)
         }
 
         b_rate += 0.5;
+        std::string sticking_species = r.sticking_species;
+        if (sticking_species == "") {
+            // Identify the sticking species if not explicitly given
+            bool foundStick = false;
+            for (Composition::const_iterator iter = r.reactants.begin();
+                 iter != r.reactants.end();
+                 ++iter) {
+                size_t iPhase = speciesPhaseIndex(kineticsSpeciesIndex(iter->first));
+                if (iPhase != iInterface) {
+                    // Non-interface species. There should be exactly one of these
+                    if (foundStick) {
+                        throw CanteraError("InterfaceKinetics::addReaction",
+                            "Multiple non-interface species found"
+                            "in sticking reaction: '" + r.equation() + "'");
+                    }
+                    foundStick = true;
+                    sticking_species = iter->first;
+                }
+            }
+            if (!foundStick) {
+                throw CanteraError("InterfaceKinetics::addReaction",
+                    "No non-interface species found"
+                    "in sticking reaction: '" + r.equation() + "'");
+            }
+        }
 
-        // Identify the sticking species, and adjust the A-factor
-        bool foundStick = false;
+        // Adjust the A-factor
         for (Composition::const_iterator iter = r.reactants.begin();
              iter != r.reactants.end();
              ++iter) {
             size_t iPhase = speciesPhaseIndex(kineticsSpeciesIndex(iter->first));
             const ThermoPhase& p = thermo(iPhase);
             size_t k = p.speciesIndex(iter->first);
-            if (iPhase == iInterface) {
-                // Interface species. Convert from coverages used in the
+            if (iter->first == sticking_species) {
+                A_rate *= sqrt(GasConstant/(2*Pi*p.molecularWeight(k)));
+            } else {
+                // Non-sticking species. Convert from coverages used in the
                 // sticking probability expression to the concentration units
                 // used in the mass action rate expression
                 double order = getValue(r.orders, iter->first, iter->second);
                 A_rate /= pow(p.standardConcentration(k), order);
-            } else {
-                // Non-interface species. There should be exactly one of these
-                if (foundStick) {
-                    throw CanteraError("InterfaceKinetics::addReaction",
-                        "Multiple non-interface species found"
-                        "in sticking reaction: '" + r.equation() + "'");
-                }
-                foundStick = true;
-                A_rate *= sqrt(GasConstant/(2*Pi*p.molecularWeight(k)));
             }
         }
-        if (!foundStick) {
-            throw CanteraError("InterfaceKinetics::addReaction",
-                "No non-interface species found"
-                "in sticking reaction: '" + r.equation() + "'");
-        }
     }
     SurfaceArrhenius rate(A_rate, b_rate, r.rate.activationEnergy_R());
 
diff --git a/src/kinetics/Reaction.cpp b/src/kinetics/Reaction.cpp
index e98470a42..b94f9dc21 100644
--- a/src/kinetics/Reaction.cpp
+++ b/src/kinetics/Reaction.cpp
@@ -492,6 +492,7 @@ void setupInterfaceReaction(InterfaceReaction& R, const XML_Node& rxn_node)
     XML_Node& arr = rxn_node.child("rateCoeff").child("Arrhenius");
     if (lowercase(arr["type"]) == "stick") {
         R.is_sticking_coefficient = true;
+        R.sticking_species = arr["species"];
     }
     setupElementaryReaction(R, rxn_node);
 }