[Kinetics] Move common Kinetics features up to the base class

include/cantera/kinetics/AqueousKinetics.h

@@ -127,10 +127,6 @@ public:
         return getValue(m_index, i).first;
     }
 
-    virtual std::string reactionString(size_t i) const {
-        return m_rxneqn[i];
-    }
-
     virtual bool isReversible(size_t i) {
         if (std::find(m_revindex.begin(), m_revindex.end(), i)
                 < m_revindex.end()) {
@@ -159,13 +155,6 @@ public:
 
     void updateROP();
 
-    const std::vector<grouplist_t>& reactantGroups(size_t i) {
-        return m_rgroups[i];
-    }
-    const std::vector<grouplist_t>& productGroups(size_t i) {
-        return m_pgroups[i];
-    }
-
     /*!
      * Update temperature-dependent portions of reaction rates and
      * falloff functions.
@@ -214,8 +203,6 @@ protected:
     vector_fp  m_dn;
     std::vector<size_t> m_revindex;
 
-    std::vector<std::string> m_rxneqn;
-
     vector_fp m_conc;
     vector_fp m_grt;
 
@@ -243,9 +230,6 @@ private:
 
     void installReagents(const ReactionData& r);
 
-    void installGroups(size_t irxn, const std::vector<grouplist_t>& r,
-                       const std::vector<grouplist_t>& p);
-
     /**
      * Update the equilibrium constants in molar units.
      */

include/cantera/kinetics/GasKinetics.h

@@ -104,18 +104,6 @@ public:
         return getValue(m_index, i).first;
     }
 
-    virtual std::string reactionString(size_t i) const {
-        return m_rxneqn[i];
-    }
-
-    virtual std::string reactantString(size_t i) const {
-        return m_reactantStrings[i];
-    }
-
-    virtual std::string productString(size_t i) const {
-        return m_productStrings[i];
-    }
-
     virtual bool isReversible(size_t i) {
         if (std::find(m_revindex.begin(), m_revindex.end(), i)
                 < m_revindex.end()) {
@@ -141,13 +129,6 @@ public:
 
     void updateROP();
 
-    const std::vector<grouplist_t>& reactantGroups(size_t i) {
-        return m_rgroups[i];
-    }
-    const std::vector<grouplist_t>& productGroups(size_t i) {
-        return m_pgroups[i];
-    }
-
     //! Update temperature-dependent portions of reaction rates and falloff
     //! functions.
     virtual void update_rates_T();
@@ -186,9 +167,6 @@ protected:
     size_t m_nirrev;
     size_t m_nrev;
 
-    std::map<size_t, std::vector<grouplist_t> > m_rgroups;
-    std::map<size_t, std::vector<grouplist_t> > m_pgroups;
-
     std::vector<int>                         m_rxntype;
 
     std::vector<std::map<size_t, doublereal> > m_rrxn;
@@ -203,10 +181,6 @@ protected:
     vector_fp  m_dn;
     std::vector<size_t> m_revindex;
 
-    std::vector<std::string> m_rxneqn;
-    std::vector<std::string> m_reactantStrings;
-    std::vector<std::string> m_productStrings;
-
     //! @name Reaction rate data
     //!@{
     doublereal m_logp_ref;
@@ -244,10 +218,7 @@ private:
     void addPlogReaction(ReactionData& r);
     void addChebyshevReaction(ReactionData& r);
 
-    void installReagents(const ReactionData& r);
+    virtual void installReagents(const ReactionData& r);
-
-    void installGroups(size_t irxn, const std::vector<grouplist_t>& r,
-                       const std::vector<grouplist_t>& p);
 
     //! Update the equilibrium constants in molar units.
     void updateKc();

include/cantera/kinetics/InterfaceKinetics.h

@@ -219,10 +219,6 @@ public:
         }
     }
 
-    virtual std::string reactionString(size_t i) const {
-        return m_rxneqn[i];
-    }
-
     virtual void getFwdRateConstants(doublereal* kfwd);
     virtual void getRevRateConstants(doublereal* krev,
                                      bool doIrreversible = false);
@@ -531,13 +527,6 @@ public:
     std::vector<RxnMolChange*> rmcVector;
 
 protected:
-    /*!
-     * Vector of strings of length m_ii, the number of
-     * reactions, containing the string expressions for each reaction
-     * (e.g., reactants <=> product1 + product2)
-     */
-    std::vector<std::string> m_rxneqn;
-
     //! Array of concentrations for each species in the kinetics mechanism
     /*!
      * An array of generalized concentrations \f$ C_k \f$ that are defined

include/cantera/kinetics/Kinetics.h

@@ -700,18 +700,18 @@ public:
      *
      * @param i   reaction index
      */
-    virtual std::string reactionString(size_t i) const {
+    const std::string& reactionString(size_t i) const {
-        throw NotImplementedError("Kinetics::reactionStd::String");
+        return m_rxneqn[i];
     }
 
     //! Returns a string containing the reactants side of the reaction equation.
-    virtual std::string reactantString(size_t i) const {
+    const std::string& reactantString(size_t i) const {
-        throw NotImplementedError("Kinetics::reactionString");
+        return m_reactantStrings[i];
     }
 
     //! Returns a string containing the products side of the reaction equation.
-    virtual std::string productString(size_t i) const {
+    const std::string& productString(size_t i) const {
-        throw NotImplementedError("Kinetics::productString");
+        return m_productStrings[i];
     }
 
     /**
@@ -785,22 +785,29 @@ public:
     virtual void finalize();
 
     /**
-     * Add a single reaction to the mechanism. This routine
+     * Add a single reaction to the mechanism. This routine 
-     * must be called after init() and before finalize().
+     * must be called after init() and before finalize(). Derived classes
+     * should call the base class method in addition to handling their
+     * own specialized behavior.
      *
      * @param r      Reference to the ReactionData object for the reaction
      *               to be added.
      */
-    virtual void addReaction(ReactionData& r) {
+    virtual void addReaction(ReactionData& r);
-        throw NotImplementedError("Kinetics::addReaction");
+
+    virtual void installReagents(const ReactionData& r) {
+        throw NotImplementedError("Kinetics::installReagents");
     }
 
+    virtual void installGroups(size_t irxn, const std::vector<grouplist_t>& r,
+                               const std::vector<grouplist_t>& p);
+
     virtual const std::vector<grouplist_t>& reactantGroups(size_t i) {
-        return m_dummygroups;
+        return m_rgroups[i];
     }
 
     virtual const std::vector<grouplist_t>& productGroups(size_t i) {
-        return m_dummygroups;
+        return m_pgroups[i];
     }
 
     //@}
@@ -949,9 +956,18 @@ protected:
     //! number of spatial dimensions of lowest-dimensional phase.
     size_t m_mindim;
 
+    //! Representation of each reaction equation
+    std::vector<std::string> m_rxneqn;
+
+    //! Representation of the reactant side of each reaction equation
+    std::vector<std::string> m_reactantStrings;
+
+    //! Representation of the product side of each reaction equation
+    std::vector<std::string> m_productStrings;
+
 private:
-    //! Vector of group lists
+    std::map<size_t, std::vector<grouplist_t> > m_rgroups;
-    std::vector<grouplist_t> m_dummygroups;
+    std::map<size_t, std::vector<grouplist_t> > m_pgroups;
 };
 
 }

src/kinetics/AqueousKinetics.cpp

@@ -63,14 +63,11 @@ AqueousKinetics& AqueousKinetics::operator=(const AqueousKinetics& right)
     m_fwdOrder = right.m_fwdOrder;
     m_nirrev = right.m_nirrev;
     m_nrev = right.m_nrev;
-    m_rgroups = right.m_rgroups;
-    m_pgroups = right.m_pgroups;
     m_rxntype = right.m_rxntype;
     m_rrxn = right.m_rrxn;
     m_prxn = right.m_prxn;
     m_dn = right.m_dn;
     m_revindex = right.m_revindex;
-    m_rxneqn = right.m_rxneqn;
 
     m_ropf = right.m_ropf;
     m_ropr = right.m_ropr;
@@ -356,12 +353,7 @@ void AqueousKinetics::addReaction(ReactionData& r)
     if (r.reactionType == ELEMENTARY_RXN) {
         addElementaryReaction(r);
     }
-
+    Kinetics::addReaction(r);
-    // operations common to all reaction types
-    installReagents(r);
-    installGroups(reactionNumber(), r.rgroups, r.pgroups);
-    incrementRxnCount();
-    m_rxneqn.push_back(r.equation);
 }
 
 void AqueousKinetics::addElementaryReaction(ReactionData& r)
@@ -442,17 +434,6 @@ void AqueousKinetics::installReagents(const ReactionData& r)
     }
 }
 
-void AqueousKinetics::installGroups(size_t irxn,
-                                    const vector<grouplist_t>& r,
-                                    const vector<grouplist_t>& p)
-{
-    if (!r.empty()) {
-        writelog("installing groups for reaction "+int2str(reactionNumber()));
-        m_rgroups[reactionNumber()] = r;
-        m_pgroups[reactionNumber()] = p;
-    }
-}
-
 void AqueousKinetics::init()
 {
     m_kk = thermo().nSpecies();

src/kinetics/GasKinetics.cpp

@@ -74,16 +74,11 @@ GasKinetics& GasKinetics::operator=(const GasKinetics& right)
     m_fwdOrder = right.m_fwdOrder;
     m_nirrev = right.m_nirrev;
     m_nrev = right.m_nrev;
-    m_rgroups = right.m_rgroups;
-    m_pgroups = right.m_pgroups;
     m_rxntype = right.m_rxntype;
     m_rrxn = right.m_rrxn;
     m_prxn = right.m_prxn;
     m_dn = right.m_dn;
     m_revindex = right.m_revindex;
-    m_rxneqn = right.m_rxneqn;
-    m_reactantStrings = right.m_reactantStrings;
-    m_productStrings = right.m_productStrings;
 
     m_logp_ref = right.m_logp_ref;
     m_logc_ref  = right.m_logc_ref;
@@ -498,12 +493,7 @@ void GasKinetics::addReaction(ReactionData& r)
     }
 
     // operations common to all reaction types
-    installReagents(r);
+    Kinetics::addReaction(r);
-    installGroups(reactionNumber(), r.rgroups, r.pgroups);
-    incrementRxnCount();
-    m_rxneqn.push_back(r.equation);
-    m_reactantStrings.push_back(r.reactantString);
-    m_productStrings.push_back(r.productString);
     m_rxntype.push_back(r.reactionType);
 }
 
@@ -657,16 +647,6 @@ void GasKinetics::installReagents(const ReactionData& r)
     }
 }
 
-void GasKinetics::installGroups(size_t irxn,
-                                const vector<grouplist_t>& r, const vector<grouplist_t>& p)
-{
-    if (!r.empty()) {
-        writelog("installing groups for reaction "+int2str(reactionNumber()));
-        m_rgroups[reactionNumber()] = r;
-        m_pgroups[reactionNumber()] = p;
-    }
-}
-
 void GasKinetics::init()
 {
     m_kk = thermo().nSpecies();

src/kinetics/InterfaceKinetics.cpp

@@ -129,7 +129,6 @@ InterfaceKinetics& InterfaceKinetics::operator=(const InterfaceKinetics& right)
     m_rrxn                 = right.m_rrxn;
     m_prxn                 = right.m_prxn;
     reactionType_          = right.reactionType_;
-    m_rxneqn               = right.m_rxneqn;
     m_conc                 = right.m_conc;
     m_actConc              = right.m_actConc;
     m_mu0                  = right.m_mu0;
@@ -888,25 +887,8 @@ void InterfaceKinetics::addReaction(ReactionData& r)
          */
         addElementaryReaction(r);
     }
-    /*
-     * Add the reactants and products for  m_ropnet;the current reaction
-     * to the various stoichiometric coefficient arrays.
-     */
-    installReagents(r);
-    /*
-     * Save the reaction and product groups, which are
-     * part of the ReactionData class, in this class.
-     * They aren't used for anything but reaction path
-     * analysis.
-     */
-    //installGroups(reactionNumber(), r.rgroups, r.pgroups);
-    /*
-     * Increase the internal number of reactions, m_ii, by one.
-     * increase the size of m_perturb by one as well.
-     */
-    incrementRxnCount();
 
-    m_rxneqn.push_back(r.equation);
+    Kinetics::addReaction(r);
 
     m_rxnPhaseIsReactant.push_back(std::vector<bool>(nPhases(), false));
     m_rxnPhaseIsProduct.push_back(std::vector<bool>(nPhases(), false));

src/kinetics/Kinetics.cpp

@@ -8,6 +8,7 @@
 // Copyright 2001-2004  California Institute of Technology
 
 #include "cantera/kinetics/Kinetics.h"
+#include "cantera/kinetics/ReactionData.h"
 #include "cantera/base/stringUtils.h"
 
 using namespace std;
@@ -25,8 +26,7 @@ Kinetics::Kinetics() :
     m_phaseindex(),
     m_surfphase(npos),
     m_rxnphase(npos),
-    m_mindim(4),
+    m_mindim(4)
-    m_dummygroups(0)
 {
 }
 
@@ -43,8 +43,7 @@ Kinetics::Kinetics(const Kinetics& right) :
     m_phaseindex(),
     m_surfphase(npos),
     m_rxnphase(npos),
-    m_mindim(4),
+    m_mindim(4)
-    m_dummygroups(0)
 {
     /*
      * Call the assignment operator
@@ -74,7 +73,11 @@ Kinetics& Kinetics::operator=(const Kinetics& right)
     m_surfphase         = right.m_surfphase;
     m_rxnphase          = right.m_rxnphase;
     m_mindim            = right.m_mindim;
-    m_dummygroups       = right.m_dummygroups;
+    m_rxneqn            = right.m_rxneqn;
+    m_reactantStrings   = right.m_reactantStrings;
+    m_productStrings    = right.m_productStrings;
+    m_rgroups = right.m_rgroups;
+    m_pgroups = right.m_pgroups;
 
     return *this;
 }
@@ -289,4 +292,23 @@ void Kinetics::finalize()
     }
 }
 
+void Kinetics::addReaction(ReactionData& r) {
+    installReagents(r);
+    installGroups(nReactions(), r.rgroups, r.pgroups);
+    incrementRxnCount();
+    m_rxneqn.push_back(r.equation);
+    m_reactantStrings.push_back(r.reactantString);
+    m_productStrings.push_back(r.productString);
+}
+
+void Kinetics::installGroups(size_t irxn, const vector<grouplist_t>& r,
+                             const vector<grouplist_t>& p)
+{
+    if (!r.empty()) {
+        writelog("installing groups for reaction "+int2str(irxn));
+        m_rgroups[irxn] = r;
+        m_pgroups[irxn] = p;
+    }
+}
+
 }