[oneD] Enable Kinetics/Transport setters for smart pointers

include/cantera/oneD/Boundary1D.h

@@ -298,6 +298,9 @@ public:
     ReactingSurf1D();
     ReactingSurf1D(shared_ptr<Solution> solution, const std::string& id="");
 
+    virtual void setKinetics(shared_ptr<Kinetics> kin);
+
+    //! @deprecated  To be removed after Cantera 3.0; replaced by setKinetics
     void setKineticsMgr(InterfaceKinetics* kin);
 
     void enableCoverageEquations(bool docov) {

include/cantera/oneD/Domain1D.h

@@ -28,6 +28,8 @@ class MultiJac;
 class OneDim;
 class Refiner;
 class AnyMap;
+class Kinetics;
+class Transport;
 class Solution;
 class SolutionArray;
 
@@ -65,6 +67,24 @@ public:
         return (m_type >= cConnectorType);
     }
 
+    //! Set the solution manager.
+    //! @since  New in Cantera 3.0.
+    void setSolution(shared_ptr<Solution> sol) {
+        m_solution = sol;
+    }
+
+    //! Set the kinetics manager.
+    //! @since  New in Cantera 3.0.
+    virtual void setKinetics(shared_ptr<Kinetics> kin) {
+        throw NotImplementedError("Domain1D::setKinetics");
+    }
+
+    //! Set transport model to existing instance
+    //! @since  New in Cantera 3.0.
+    virtual void setTransport(shared_ptr<Transport> trans) {
+        throw NotImplementedError("Domain1D::setTransport");
+    }
+
     //! The container holding this domain.
     const OneDim& container() const {
         return *m_container;
@@ -398,12 +418,18 @@ public:
      */
     void linkLeft(Domain1D* left) {
         m_left = left;
+        if (!m_solution && left && left->solution()) {
+            m_solution = left->solution();
+        }
         locate();
     }
 
     //! Set the right neighbor to domain 'right.'
     void linkRight(Domain1D* right) {
         m_right = right;
+        if (!m_solution && right && right->solution()) {
+            m_solution = right->solution();
+        }
     }
 
     //! Append domain 'right' to this one, and update all links.

include/cantera/oneD/StFlow.h

@@ -52,9 +52,7 @@ public:
     StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1);
 
     //! Delegating constructor
-    StFlow(shared_ptr<ThermoPhase> th, size_t nsp = 1, size_t points = 1) :
-        StFlow(th.get(), nsp, points) {
-    }
+    StFlow(shared_ptr<ThermoPhase> th, size_t nsp = 1, size_t points = 1);
 
     //! Create a new flow domain.
     //! @param sol  Solution object used to evaluate all thermodynamic, kinetic, and
@@ -88,12 +86,16 @@ public:
      */
     void setThermo(IdealGasPhase& th);
 
-    //! Set the kinetics manager. The kinetics manager must
-    void setKinetics(Kinetics& kin) {
-        m_kin = &kin;
-    }
+    virtual void setKinetics(shared_ptr<Kinetics> kin);
+
+    //! Set the kinetics manager.
+    //! @deprecated  To be removed after Cantera 3.0; replaced by Domain1D::setKinetics
+    void setKinetics(Kinetics& kin);
+
+    virtual void setTransport(shared_ptr<Transport> trans);
 
     //! Set transport model to existing instance
+    //! @deprecated  To be removed after Cantera 3.0; replaced by Domain1D::setKinetics
     void setTransport(Transport& trans);
 
     //! Set the transport model

src/oneD/Boundary1D.cpp

@@ -644,8 +644,23 @@ ReactingSurf1D::ReactingSurf1D(shared_ptr<Solution> solution, const std::string&
     m_enabled = true;
 }
 
+void ReactingSurf1D::setKinetics(shared_ptr<Kinetics> kin)
+{
+    m_solution = Solution::create();
+    m_solution->setThermo(kin->reactionPhase());
+    m_solution->setKinetics(kin);
+    m_solution->setTransportModel("none");
+    m_kin = dynamic_pointer_cast<InterfaceKinetics>(kin).get();
+    m_surfindex = kin->reactionPhaseIndex();
+    m_sphase = dynamic_pointer_cast<SurfPhase>(kin->reactionPhase()).get();
+    m_nsp = m_sphase->nSpecies();
+    m_enabled = true;
+}
+
 void ReactingSurf1D::setKineticsMgr(InterfaceKinetics* kin)
 {
+    warn_deprecated("ReactingSurf1D::setKineticsMgr",
+        "To be removed after Cantera 3.0. Replaced by Domain1D::setKinetics.");
     m_kin = kin;
     m_surfindex = kin->reactionPhaseIndex();
     m_sphase = (SurfPhase*)&kin->thermo(m_surfindex);

src/oneD/StFlow.cpp

@@ -108,6 +108,13 @@ StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) :
     m_kRadiating[1] = m_thermo->speciesIndex("H2O");
 }
 
+StFlow::StFlow(shared_ptr<ThermoPhase> th, size_t nsp, size_t points)
+    : StFlow(th.get(), nsp, points)
+{
+    m_solution = Solution::create();
+    m_solution->setThermo(th);
+}
+
 StFlow::StFlow(shared_ptr<Solution> sol, const std::string& id, size_t points)
     : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), points)
 {
@@ -141,6 +148,50 @@ void StFlow::setThermo(IdealGasPhase& th) {
     m_thermo = &th;
 }
 
+void StFlow::setKinetics(shared_ptr<Kinetics> kin)
+{
+    if (!m_solution) {
+        // @todo remove after Cantera 3.0
+        throw CanteraError("StFlow::setKinetics",
+            "Unable to update object that was not constructed from smart pointers.");
+    }
+    m_kin = kin.get();
+    m_solution->setKinetics(kin);
+}
+
+void StFlow::setKinetics(Kinetics& kin)
+{
+    // @todo: resolve crash for updated m_solution->registerChangedCallback
+    // warn_deprecated("StFlow::setKinetics",
+    //     "To be removed after Cantera 3.0. Replaced by Domain1D::setKinetics.");
+    m_kin = &kin;
+}
+
+void StFlow::setTransport(shared_ptr<Transport> trans)
+{
+    if (!m_solution) {
+        // @todo remove after Cantera 3.0
+        throw CanteraError("StFlow::setTransport",
+            "Unable to update object that was not constructed from smart pointers.");
+    }
+    if (!trans) {
+        throw CanteraError("StFlow::setTransport", "Unable to set empty transport.");
+    }
+    m_trans = trans.get();
+    if (m_trans->transportModel() == "None") {
+        throw CanteraError("StFlow::setTransport", "Invalid Transport model 'None'.");
+    }
+    m_do_multicomponent = (m_trans->transportModel() == "Multi" ||
+        m_trans->transportModel() == "CK_Multi");
+
+    m_diff.resize(m_nsp * m_points);
+    if (m_do_multicomponent) {
+        m_multidiff.resize(m_nsp * m_nsp*m_points);
+        m_dthermal.resize(m_nsp, m_points, 0.0);
+    }
+    m_solution->setTransport(trans);
+}
+
 void StFlow::resize(size_t ncomponents, size_t points)
 {
     Domain1D::resize(ncomponents, points);
@@ -193,6 +244,7 @@ void StFlow::resetBadValues(double* xg)
 void StFlow::setTransportModel(const std::string& trans)
 {
     if (!m_solution) {
+        // @todo remove after Cantera 3.0
         throw CanteraError("StFlow::setTransportModel",
             "Unable to set Transport manager by name as object was not initialized\n"
             "from a Solution manager: set Transport object directly instead.");
@@ -206,6 +258,9 @@ std::string StFlow::transportModel() const {
 
 void StFlow::setTransport(Transport& trans)
 {
+    // @todo: resolve crash for updated m_solution->registerChangedCallback
+    // warn_deprecated("StFlow::setTransport",
+    //     "To be removed after Cantera 3.0. Replaced by Domain1D::setTransport.");
     m_trans = &trans;
     if (m_trans->transportModel() == "None") {
         throw CanteraError("StFlow::setTransport",