InterfaceKinetics rewite: added rmcVector and identifyMetalPhases routine.

added utility to clean tests. tests don't rerun when they should!

bin/clean_tests

@@ -0,0 +1,9 @@
+#!/bin/sh
+#
+#
+/bin/rm -rf build/test
+#
+#
+scons test-clean
+#
+#

include/cantera/kinetics/ElectrodeKinetics.h

@@ -51,10 +51,23 @@ public:
     //! Assignment operator
     ElectrodeKinetics& operator=(const ElectrodeKinetics& right);
 
+    //! Duplication function
+    /*!
+     *  @param tpVector Vector of %ThermoPhase pointers. These are shallow pointers to the
+     *                  %ThermoPhase objects that will comprise the phases for the new object.
+     * 
+     *   @return        Returns the duplicated object as the base class %Kinetics object.
+     */
     virtual Kinetics* duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const;
 
     virtual int type() const;
 
+    //!  Identify the metal phase and the electrons species
+    /*!
+     *   We fill in the internal variables, metalPhaseRS_ and kElectronRS_ here
+     */
+    void identifyMetalPhase();
+
 
 
 

include/cantera/kinetics/InterfaceKinetics.h

@@ -10,6 +10,7 @@
 
 #include "cantera/thermo/mix_defs.h"
 #include "Kinetics.h"
+#include "cantera/kinetics/RxnMolChange.h"
 
 #include "cantera/base/utilities.h"
 #include "RateCoeffMgr.h"
@@ -21,6 +22,7 @@ namespace Cantera
 // forward references
 class SurfPhase;
 class ImplicitSurfChem;
+class RxnMolChange;
 
 //!  A kinetics manager for heterogeneous reaction mechanisms. The
 //!  reactions are assumed to occur at a 2D interface between two 3D phases.
@@ -145,9 +147,17 @@ public:
         return m_prxn[k][i];
     }
 
-    virtual int reactionType(size_t i) const {
-        return m_index[i].first;
-    }
+    //!  return the reaction type of the reaction i
+    /*!
+     *    @param[in]   Reaction index
+     *
+     *    @return      Returns the reaction type of the reaction. 
+     */
+    virtual int reactionType(size_t i) const; 
+   //virtual int reactionType(size_t i) const {
+    //    return m_index[i].first;
+    //}
+
 
     virtual void getActivityConcentrations(doublereal* const conc);
 
@@ -484,7 +494,13 @@ protected:
      */
     vector_int reactionType_;
 
-    //! String expression for each rxn
+    //! Vector of additional information about each reaction
+    /*!
+     *  This vector contains information about the phase mole change for each reaction,
+     *  for example.
+     */
+    std::vector<RxnMolChange*> rmcVector;
+
     /*!
      * Vector of strings of length m_ii, the number of
      * reactions, containing the string expressions for each reaction

src/kinetics/ElectrodeKinetics.cpp

@@ -4,7 +4,6 @@
 
 #include "cantera/kinetics/ElectrodeKinetics.h"
 
-
 using namespace std;
 
 namespace Cantera
@@ -32,7 +31,7 @@ ElectrodeKinetics::ElectrodeKinetics(const ElectrodeKinetics& right) :
     /*
      * Call the assignment operator
      */
-    operator=(right);
+    ElectrodeKinetics::operator=(right);
 }
 //============================================================================================================================
 ElectrodeKinetics& ElectrodeKinetics::operator=(const ElectrodeKinetics& right)
@@ -66,9 +65,58 @@ Kinetics* ElectrodeKinetics::duplMyselfAsKinetics(const std::vector<thermo_t*> &
     return iK;
 }
 //============================================================================================================================
+//====================================================================================================================
+//  Identify the metal phase and the electrons species
+void ElectrodeKinetics::identifyMetalPhase()
+{
+    metalPhaseRS_ = npos;
+    kElectronRS_ = -1;
+    size_t np = nPhases();
+    //
+    // Identify the metal phase as the phase with the electron species (element index of 1 for element E
+    // Should probably also stipulate a charge of -1.
+    //
+    for (size_t iph = 0; iph < np; iph++) {
+        ThermoPhase* tp = m_thermo[iph];
+        size_t nSpecies = tp->nSpecies();
+        size_t nElements = tp->nElements();
+        size_t eElectron = tp->elementIndex("E");
+        if (eElectron != npos) {
+            for (size_t k = 0; k < nSpecies; k++) {
+                if (tp->nAtoms(k,eElectron) == 1) {
+                    int ifound = 1;
+                    for (size_t e = 0; e < nElements; e++) {
+                        if (tp->nAtoms(k,e) != 0.0) {
+                            if (e != eElectron) {
+                                ifound = 0;
+                            }
+                        }
+                    }
+                    if (ifound == 1) {
+                        metalPhaseRS_ = iph;
+                        kElectronRS_ = m_start[iph] + k;
+                    }
+                }
+            }
+        }
+       //
+       //  Identify the solution phase as a 3D phase, with nonzero phase charge change 
+       //  in at least one reaction
+       //
+       if (iph != metalPhaseRS_) {
+            for (size_t i = 0; i < m_ii; i++) {
+                RxnMolChange* rmc = rmcVector[i];
+                if (rmc->m_phaseChargeChange[iph] != 0) {
+                    if (rmc->m_phaseDims[iph] == 3) {
+                       solnPhaseRS_ = iph;
+                       break;
+                    }
+                }
+             }
+        }
 
-
-
+    }
+}
 
 //==================================================================================================================
 }

src/kinetics/InterfaceKinetics.cpp

@@ -57,6 +57,11 @@ InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) :
 InterfaceKinetics::~InterfaceKinetics()
 {
     delete m_integrator;
+
+    for (size_t i = 0; i < rmcVector.size(); i++) {
+        delete rmcVector[i];
+    }
+
 }
 //============================================================================================================================
 InterfaceKinetics::InterfaceKinetics(const InterfaceKinetics& right) :
@@ -160,6 +165,17 @@ InterfaceKinetics& InterfaceKinetics::operator=(const InterfaceKinetics& right)
     m_rxnPhaseIsProduct    = right.m_rxnPhaseIsProduct;
     m_ioFlag               = right.m_ioFlag;
 
+    for (size_t i = 0; i <  rmcVector.size(); i++) {
+        delete rmcVector[i];
+    }
+    rmcVector.resize(m_ii, 0);
+    for (size_t i = 0; i < m_ii; i++) {
+        if (right.rmcVector[i]) {
+            rmcVector[i] = new RxnMolChange(*(right.rmcVector[i]));
+        }
+    }
+
+
     return *this;
 }
 //============================================================================================================================
@@ -174,7 +190,7 @@ Kinetics* InterfaceKinetics::duplMyselfAsKinetics(const std::vector<thermo_t*> &
     iK->assignShallowPointers(tpVector);
     return iK;
 }
-
+//============================================================================================================================
 void InterfaceKinetics::setElectricPotential(int n, doublereal V)
 {
     thermo(n).setElectricPotential(V);
@@ -1287,6 +1303,11 @@ int InterfaceKinetics::phaseStability(const size_t iphase) const
     return m_phaseIsStable[iphase];
 }
 //==================================================================================================================
+int InterfaceKinetics::reactionType(size_t i) const 
+{
+      return reactionType_[i];
+}
+//==================================================================================================================
 void InterfaceKinetics::setPhaseStability(const size_t iphase, const int isStable)
 {
     if (iphase >= m_thermo.size()) {
@@ -1335,6 +1356,14 @@ void EdgeKinetics::finalize()
         m_rkcn.resize(1, 0.0);
     }
 
+    //
+    // Malloc and calculate all of the quantities that go into the extra description of reactions
+    //
+    rmcVector.resize(m_ii, 0);
+    for (size_t i = 0; i < m_ii; i++) {
+          rmcVector[i] = new RxnMolChange(this, i);
+    }
+
     m_finalized = true;
 }