[Kinetics] Refactor handling of sticking reactions

include/cantera/kinetics/InterfaceKinetics.h

@@ -377,10 +377,11 @@ class InterfaceKinetics : public Kinetics
 protected:
     //! Build a SurfaceArrhenius object from a Reaction, taking into account
     //! the possible sticking coefficient form and coverage dependencies
-    //! @param i  Reaction number. Set to npos if this reaction is replacing
-    //!           an existing rate constant.
+    //! @param i  Reaction number
     //! @param r  Reaction object containing rate coefficient parameters
-    SurfaceArrhenius buildSurfaceArrhenius(size_t i, InterfaceReaction& r);
+    //! @param replace  True if replacing an existing reaction
+    SurfaceArrhenius buildSurfaceArrhenius(size_t i, InterfaceReaction& r,
+                                           bool replace);
 
     //! Temporary work vector of length m_kk
     vector_fp m_grt;
@@ -669,12 +670,17 @@ class InterfaceKinetics : public Kinetics
      */
     std::vector<std::vector<bool> > m_rxnPhaseIsProduct;
 
-    //! Pairs of (reaction index, total order) for sticking reactions, which are
-    //! needed to compute the dependency of the rate constant on the site
-    //! density.
-    std::vector<std::pair<size_t, double> > m_sticking_orders;
+    //! Values used for converting sticking coefficients into rate constants
+    struct StickData {
+        size_t index; //!< index of the sticking reaction in the full reaction list
+        double order; //!< exponent applied to site density term
+        double multiplier; //!< multiplicative factor in rate expression
+    };
 
-    void applyStickingCorrection(double* kf);
+    //! Data for sticking reactions
+    std::vector<StickData> m_stickingData;
+
+    void applyStickingCorrection(double T, double* kf);
 
     int m_ioFlag;
 

src/kinetics/InterfaceKinetics.cpp

@@ -139,7 +139,7 @@ void InterfaceKinetics::_update_rates_T()
 
         //  Calculate the forward rate constant by calling m_rates and store it in m_rfn[]
         m_rates.update(T, m_logtemp, m_rfn.data());
-        applyStickingCorrection(m_rfn.data());
+        applyStickingCorrection(T, m_rfn.data());
 
         // If we need to do conversions between exchange current density
         // formulation and regular formulation (either way) do it here.
@@ -633,7 +633,7 @@ bool InterfaceKinetics::addReaction(shared_ptr<Reaction> r_base)
     }
 
     InterfaceReaction& r = dynamic_cast<InterfaceReaction&>(*r_base);
-    SurfaceArrhenius rate = buildSurfaceArrhenius(i, r);
+    SurfaceArrhenius rate = buildSurfaceArrhenius(i, r, false);
     m_rates.install(i, rate);
 
     // Turn on the global flag indicating surface coverage dependence
@@ -717,7 +717,7 @@ void InterfaceKinetics::modifyReaction(size_t i, shared_ptr<Reaction> r_base)
 {
     Kinetics::modifyReaction(i, r_base);
     InterfaceReaction& r = dynamic_cast<InterfaceReaction&>(*r_base);
-    SurfaceArrhenius rate = buildSurfaceArrhenius(npos, r);
+    SurfaceArrhenius rate = buildSurfaceArrhenius(i, r, true);
     m_rates.replace(i, rate);
 
     // Invalidate cached data
@@ -726,11 +726,8 @@ void InterfaceKinetics::modifyReaction(size_t i, shared_ptr<Reaction> r_base)
 }
 
 SurfaceArrhenius InterfaceKinetics::buildSurfaceArrhenius(
-    size_t i, InterfaceReaction& r)
+    size_t i, InterfaceReaction& r, bool replace)
 {
-    double A_rate = r.rate.preExponentialFactor();
-    double b_rate = r.rate.temperatureExponent();
-
     if (r.is_sticking_coefficient) {
         // Identify the interface phase
         size_t iInterface = npos;
@@ -742,7 +739,6 @@ SurfaceArrhenius InterfaceKinetics::buildSurfaceArrhenius(
             }
         }
 
-        b_rate += 0.5;
         std::string sticking_species = r.sticking_species;
         if (sticking_species == "") {
             // Identify the sticking species if not explicitly given
@@ -768,14 +764,15 @@ SurfaceArrhenius InterfaceKinetics::buildSurfaceArrhenius(
         }
 
         double surface_order = 0.0;
+        double multiplier = 1.0;
         // Adjust the A-factor
         for (const auto& sp : r.reactants) {
             size_t iPhase = speciesPhaseIndex(kineticsSpeciesIndex(sp.first));
             const ThermoPhase& p = thermo(iPhase);
             const ThermoPhase& surf = thermo(surfacePhaseIndex());
             size_t k = p.speciesIndex(sp.first);
             if (sp.first == sticking_species) {
-                A_rate *= sqrt(GasConstant/(2*Pi*p.molecularWeight(k)));
+                multiplier *= sqrt(GasConstant/(2*Pi*p.molecularWeight(k)));
             } else {
                 // Non-sticking species. Convert from coverages used in the
                 // sticking probability expression to the concentration units
@@ -785,19 +782,32 @@ SurfaceArrhenius InterfaceKinetics::buildSurfaceArrhenius(
                 // site density is known at this time.
                 double order = getValue(r.orders, sp.first, sp.second);
                 if (&p == &surf) {
-                    A_rate *= pow(p.size(k), order);
+                    multiplier *= pow(p.size(k), order);
                     surface_order += order;
                 } else {
-                    A_rate *= pow(p.standardConcentration(k), -order);
+                    multiplier *= pow(p.standardConcentration(k), -order);
                 }
             }
         }
-        if (i != npos) {
-            m_sticking_orders.emplace_back(i, surface_order);
+
+        if (!replace) {
+            m_stickingData.emplace_back(
+                StickData{i, surface_order, multiplier});
+        } else {
+            // Modifying an existing sticking reaction.
+            for (auto& item : m_stickingData) {
+                if (item.index == i) {
+                    item.order = surface_order;
+                    item.multiplier = multiplier;
+                    break;
+                }
+            }
         }
     }
 
-    SurfaceArrhenius rate(A_rate, b_rate, r.rate.activationEnergy_R());
+    SurfaceArrhenius rate(r.rate.preExponentialFactor(),
+                          r.rate.temperatureExponent(),
+                          r.rate.activationEnergy_R());
 
     // Set up coverage dependencies
     for (const auto& sp : r.coverage_deps) {
@@ -976,9 +986,9 @@ void InterfaceKinetics::determineFwdOrdersBV(ElectrochemicalReaction& r, vector_
     }
 }
 
-void InterfaceKinetics::applyStickingCorrection(double* kf)
+void InterfaceKinetics::applyStickingCorrection(double T, double* kf)
 {
-    if (m_sticking_orders.empty()) {
+    if (m_stickingData.empty()) {
         return;
     }
 
@@ -989,14 +999,15 @@ void InterfaceKinetics::applyStickingCorrection(double* kf)
     SurfPhase& surf = dynamic_cast<SurfPhase&>(thermo(reactionPhaseIndex()));
     double n0 = surf.siteDensity();
     if (!cached.validate(n0)) {
-        factors.resize(m_sticking_orders.size());
-        for (size_t n = 0; n < m_sticking_orders.size(); n++) {
-            factors[n] = pow(n0, -m_sticking_orders[n].second);
+        factors.resize(m_stickingData.size());
+        for (size_t n = 0; n < m_stickingData.size(); n++) {
+            factors[n] = pow(n0, -m_stickingData[n].order);
         }
     }
 
-    for (size_t n = 0; n < m_sticking_orders.size(); n++) {
-        kf[m_sticking_orders[n].first] *= factors[n];
+    for (size_t n = 0; n < m_stickingData.size(); n++) {
+        const StickData& item = m_stickingData[n];
+        kf[item.index] *= factors[n] * sqrt(T) * item.multiplier;
     }
 }