[Kinetics] Used shared pointers in Kinetics::addPhase

include/cantera/base/Solution.h

@@ -49,9 +49,9 @@ class Solution : public std::enable_shared_from_this<Solution>
     virtual void setTransport(shared_ptr<Transport> transport);
 
     //! Set the Transport object by name
-    //! @param model  name of transport model
+    //! @param model  name of transport model; if omitted, the default model is used
     //! @since New in Cantera 3.0
-    void setTransportModel(const std::string& model);
+    void setTransportModel(const std::string& model="");
 
     //! Accessor for the ThermoPhase pointer
     shared_ptr<ThermoPhase> thermo() {

include/cantera/kinetics/InterfaceKinetics.h

@@ -142,6 +142,9 @@ class InterfaceKinetics : public Kinetics
      *
      * @param thermo    Reference to the ThermoPhase to be added.
      */
+    virtual void addPhase(shared_ptr<ThermoPhase> thermo);
+
+    //! @see InterfaceKinetics::addPhase(shared_ptr<ThermoPhase>)
     virtual void addPhase(ThermoPhase& thermo);
 
     virtual void init();

include/cantera/kinetics/Kinetics.h

@@ -219,6 +219,12 @@ class Kinetics
         return m_rxnphase;
     }
 
+    /**
+     * Return pointer to phase where the reactions occur.
+     * @since New in Cantera 3.0
+     */
+    shared_ptr<ThermoPhase> reactionPhase() const;
+
     /**
      * This method returns a reference to the nth ThermoPhase object defined
      * in this kinetics mechanism. It is typically used so that member
@@ -1098,7 +1104,13 @@ class Kinetics
      *    kinetics manager object as the value.
      *
      * @param thermo    Reference to the ThermoPhase to be added.
+     * @since Changed in Cantera 3.0. Replaces version using reference.
      */
+    virtual void addPhase(shared_ptr<ThermoPhase> thermo);
+
+    //! @see Kinetics::addPhase(shared_ptr<ThermoPhase>)
+    //! @deprecated To be removed after Cantera 3.0. Replaced by version using shared
+    //!     pointer.
     virtual void addPhase(ThermoPhase& thermo);
 
     /**
@@ -1320,6 +1332,10 @@ class Kinetics
      */
     std::vector<ThermoPhase*> m_thermo;
 
+    //! vector of shared pointers, @see m_thermo
+    //! @todo replace m_thermo with shared version after Cantera 3.0
+    vector<shared_ptr<ThermoPhase>> m_sharedThermo;
+
     /**
      * m_start is a vector of integers specifying the beginning position for the
      * species vector for the n'th phase in the kinetics class.

src/kinetics/InterfaceKinetics.cpp

@@ -487,6 +487,13 @@ void InterfaceKinetics::setIOFlag(int ioFlag)
     }
 }
 
+void InterfaceKinetics::addPhase(shared_ptr<ThermoPhase> thermo)
+{
+    Kinetics::addPhase(thermo);
+    m_phaseExists.push_back(true);
+    m_phaseIsStable.push_back(true);
+}
+
 void InterfaceKinetics::addPhase(ThermoPhase& thermo)
 {
     Kinetics::addPhase(thermo);

src/kinetics/Kinetics.cpp

@@ -93,6 +93,16 @@ size_t Kinetics::surfacePhaseIndex() const
     return m_surfphase;
 }
 
+shared_ptr<ThermoPhase> Kinetics::reactionPhase() const
+{
+    if (!m_sharedThermo.size()) {
+        // @todo remove after Cantera 3.0
+        throw CanteraError("Kinetics::reactionPhase",
+            "Cannot access phases that were not added using smart pointers.");
+    }
+    return m_sharedThermo[m_rxnphase];
+}
+
 void Kinetics::checkSpeciesIndex(size_t k) const
 {
     if (k >= m_kk) {
@@ -561,8 +571,30 @@ Eigen::SparseMatrix<double> Kinetics::netProductionRates_ddX()
     return m_stoichMatrix * netRatesOfProgress_ddX();
 }
 
+void Kinetics::addPhase(shared_ptr<ThermoPhase> thermo)
+{
+    // the phase with lowest dimensionality is assumed to be the
+    // phase/interface at which reactions take place
+    if (thermo->nDim() <= m_mindim) {
+        m_mindim = thermo->nDim();
+        m_rxnphase = nPhases();
+    }
+
+    // there should only be one surface phase
+    if (thermo->type() == kineticsType()) {
+        m_surfphase = nPhases();
+    }
+    m_thermo.push_back(thermo.get());
+    m_sharedThermo.push_back(thermo);
+    m_phaseindex[m_thermo.back()->name()] = nPhases();
+    resizeSpecies();
+}
+
 void Kinetics::addPhase(ThermoPhase& thermo)
 {
+    warn_deprecated("Kinetics::addPhase",
+        "To be removed after Cantera 3.0. Use version with shared pointer instead.");
+
     // the phase with lowest dimensionality is assumed to be the
     // phase/interface at which reactions take place
     if (thermo.nDim() <= m_mindim) {

src/kinetics/KineticsFactory.cpp

@@ -89,7 +89,7 @@ shared_ptr<Kinetics> newKinetics(const vector<shared_ptr<ThermoPhase>>& phases,
 
     shared_ptr<Kinetics> kin(KineticsFactory::factory()->newKinetics(kinType));
     for (auto& phase : phases) {
-        kin->addPhase(*phase);
+        kin->addPhase(phase);
     }
     kin->init();
     addReactions(*kin, phaseNode, rootNode);