Replace convenience classes by C++ Solution object

include/cantera/Edge.h

@@ -6,6 +6,8 @@
 #ifndef CXX_EDGE
 #define CXX_EDGE
 
+#pragma message("warning: Edge.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/ThermoFactory.h"
 #include "kinetics/importKinetics.h"
 #include "kinetics/EdgeKinetics.h"
@@ -15,13 +17,20 @@ namespace Cantera
 {
 
 //! Convenience class which inherits from both EdgePhase and EdgeKinetics
+/*!
+ * @deprecated To be removed after Cantera 2.5.0.
+ *             Replaceable with Solution and/or EdgePhase/EdgeKinetics.
+ */
 class Edge :
     public EdgePhase, public EdgeKinetics
 {
 public:
     Edge(const std::string& infile, std::string id, std::vector<ThermoPhase*> phases)
         : m_ok(false), m_r(0)
     {
+        warn_deprecated("class Metal",
+            "To be removed after Cantera 2.5.0. "
+            "Replaceable with Solution and/or EdgePhase/EdgeKinetics.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";

include/cantera/IdealGasMix.h

@@ -6,6 +6,8 @@
 #ifndef CXX_IDEALGASMIX
 #define CXX_IDEALGASMIX
 
+#pragma message("warning: IdealGasMix.h is deprecated and will be removed after Cantera 2.5.")
+
 #include "thermo/IdealGasPhase.h"
 #include "kinetics/GasKinetics.h"
 #include "kinetics/importKinetics.h"
@@ -15,6 +17,10 @@ namespace Cantera
 {
 
 //! Convenience class which inherits from both IdealGasPhase and GasKinetics
+/*!
+ * @deprecated To be removed after Cantera 2.5.
+ *             Replaceable with Solution and/or IdealGasPhase/GasKinetics.
+ */
 class IdealGasMix :
     public IdealGasPhase,
     public GasKinetics
@@ -25,6 +31,9 @@ class IdealGasMix :
     IdealGasMix(const std::string& infile, std::string id_="") :
         m_ok(false), m_r(0)
     {
+        warn_deprecated("class IdealGasMix",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or IdealGasPhase/GasKinetics.");
         m_r = get_XML_File(infile);
         m_id = id_;
         if (id_ == "-") {
@@ -38,12 +47,18 @@ class IdealGasMix :
 
     IdealGasMix(XML_Node& root,
                 std::string id_) : m_ok(false), m_r(&root), m_id(id_) {
+        warn_deprecated("class IdealGasMix",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or IdealGasPhase/GasKinetics.");
         m_ok = buildSolutionFromXML(root, id_, "phase", this, this);
     }
 
     IdealGasMix(const IdealGasMix& other) : m_ok(false),
         m_r(other.m_r),
         m_id(other.m_id) {
+        warn_deprecated("class IdealGasMix",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or IdealGasPhase/GasKinetics.");
         m_ok = buildSolutionFromXML(*m_r, m_id, "phase", this, this);
     }
 

include/cantera/IncompressibleSolid.h

@@ -6,26 +6,35 @@
 #ifndef CXX_INCOMPRESSIBLE
 #define CXX_INCOMPRESSIBLE
 
+#pragma message("warning: IncompressibleSolid.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/ConstDensityThermo.h"
 #include "kinetics/importKinetics.h"
 
 namespace Cantera
 {
 
 //! Wrapper for ConstDensityThermo with constructor from file
+/*!
+ * @deprecated To be removed after Cantera 2.5.0.
+ *             Replaceable with Solution and/or LatticePhase/IdealSolidSolnPhase.
+ */
 class IncompressibleSolid : public ConstDensityThermo
 {
 public:
     IncompressibleSolid(const std::string& infile,
                         std::string id="") : m_ok(false), m_r(0)
     {
+        warn_deprecated("class IncompressibleSolid",
+            "To be removed after Cantera 2.5.0. "
+            "Replaceable with Solution and/or LatticePhase/IdealSolidSolnPhase.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
         }
         m_ok = buildSolutionFromXML(*m_r, id, "phase", this, 0);
         if (!m_ok) throw CanteraError("IncompressibleSolid",
-                                          "buildSolutionFromXML returned false");
+                                      "buildSolutionFromXML returned false");
     }
 
     bool operator!() {

include/cantera/Interface.h

@@ -9,6 +9,8 @@
 #ifndef CXX_INTERFACE
 #define CXX_INTERFACE
 
+#pragma message("warning: Interface.h is deprecated and will be removed after Cantera 2.5.")
+
 #include "thermo.h"
 #include "kinetics.h"
 #include "cantera/thermo/SurfPhase.h"
@@ -22,6 +24,9 @@ namespace Cantera
  * and InterfaceKinetics. It therefore represents a surface phase, and also acts
  * as the kinetics manager to manage reactions occurring on the surface,
  * possibly involving species from other phases.
+ *
+ * @deprecated To be removed after Cantera 2.5.
+ *             Replaceable with Solution and/or SurfPhase/InterfaceKinetics.
  */
 class Interface :
     public SurfPhase,
@@ -42,6 +47,10 @@ class Interface :
               std::vector<ThermoPhase*> otherPhases) :
         m_ok(false),
         m_r(0) {
+        warn_deprecated("class Interface",
+            "To be removed after Cantera 2.5. "
+            "Replaceable with Solution and/or SurfPhase/InterfaceKinetics.");
+
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
@@ -79,11 +88,15 @@ class Interface :
 //! Import an instance of class Interface from a specification in an input file.
 /*!
  *  This is the preferred method to create an Interface instance.
+ *
+ * @deprecated To be removed after Cantera 2.5. Replaceable with Solution.
  */
 inline Interface* importInterface(const std::string& infile,
                                   const std::string& id,
                                   std::vector<ThermoPhase*> phases)
 {
+    warn_deprecated("importInterface", "To be removed after Cantera 2.5. "
+                    "Replaceable with Solution.");
     return new Interface(infile, id, phases);
 }
 

include/cantera/Metal.h

@@ -6,25 +6,34 @@
 #ifndef CXX_METAL
 #define CXX_METAL
 
+#pragma message("warning: Metal.h is deprecated and will be removed after Cantera 2.5.0.")
+
 #include "thermo/MetalPhase.h"
 #include "kinetics/importKinetics.h"
 
 namespace Cantera
 {
 
 //! Wrapper for MetalPhase with constructor from file
+/*!
+ * @deprecated To be removed after Cantera 2.5.0.
+ *             Replaceable with Solution and/or MetalPhase.
+ */
 class Metal : public MetalPhase
 {
 public:
     Metal(const std::string& infile, std::string id="") : m_ok(false), m_r(0)
     {
+        warn_deprecated("class Metal",
+            "To be removed after Cantera 2.5.0. "
+            "Replaceable with Solution and/or MetalPhase.");
         m_r = get_XML_File(infile);
         if (id == "-") {
             id = "";
         }
         m_ok = buildSolutionFromXML(*m_r, id, "phase", this, 0);
         if (!m_ok) throw CanteraError("Metal::Metal",
-                                          "buildSolutionFromXML returned false");
+                                      "buildSolutionFromXML returned false");
     }
 
     bool operator!() {

include/cantera/base/Solution.h

@@ -26,6 +26,7 @@ class Solution : public std::enable_shared_from_this<Solution>
     Solution(const Solution&) = delete;
     Solution& operator=(const Solution&) = delete;
 
+    //! Create an empty Solution object
     static shared_ptr<Solution> create() {
         return shared_ptr<Solution>( new Solution );
     }
@@ -37,27 +38,27 @@ class Solution : public std::enable_shared_from_this<Solution>
     void setName(const std::string& name);
 
     //! Set the ThermoPhase object
-    void setThermoPhase(shared_ptr<ThermoPhase> thermo);
+    void setThermo(shared_ptr<ThermoPhase> thermo);
 
     //! Set the Kinetics object
     void setKinetics(shared_ptr<Kinetics> kinetics);
 
     //! Set the Transport object
     void setTransport(shared_ptr<Transport> transport);
 
-    //! Accessor for the ThermoPhase object
-    ThermoPhase& thermo() {
-        return *m_thermo;
+    //! Accessor for the ThermoPhase pointer
+    shared_ptr<ThermoPhase> thermo() {
+        return m_thermo;
     }
 
-    //! Accessor for the Kinetics object
-    Kinetics& kinetics() {
-        return *m_kinetics;
+    //! Accessor for the Kinetics pointer
+    shared_ptr<Kinetics> kinetics() {
+        return m_kinetics;
     }
 
-    //! Accessor for the Transport object
-    Transport& transport() {
-        return *m_transport;
+    //! Accessor for the Transport pointer
+    shared_ptr<Transport> transport() {
+        return m_transport;
     }
 
 protected:
@@ -66,5 +67,22 @@ class Solution : public std::enable_shared_from_this<Solution>
     shared_ptr<Transport> m_transport;  //!< Transport manager
 };
 
+//! Create and initialize a new Solution manager from an input file
+/*!
+ * This constructor wraps newPhase(), newKinetics() and
+ * newTransportMgr() routines for initialization.
+ *
+ * @param infile name of the input file
+ * @param name   name of the phase in the file.
+ *               If this is blank, the first phase in the file is used.
+ * @param transport name of the transport model.
+ * @param adjacent vector containing adjacent solution objects.
+ * @returns an initialized Solution object.
+ */
+shared_ptr<Solution> newSolution(const std::string& infile,
+                                 const std::string& name="",
+                                 const std::string& transport="",
+                                 const std::vector<shared_ptr<Solution>>& adjacent={});
+
 }
 #endif

include/cantera/kinetics/InterfaceKinetics.h

@@ -678,6 +678,7 @@ class InterfaceKinetics : public Kinetics
     //! EdgeKinetics)
     size_t m_nDim;
 };
+
 }
 
 #endif

include/cantera/kinetics/Kinetics.h

@@ -19,8 +19,6 @@
 namespace Cantera
 {
 
-class Solution;
-
 /**
  * @defgroup chemkinetics Chemical Kinetics
  */

include/cantera/oneD/StFlow.h

@@ -45,7 +45,12 @@ class StFlow : public Domain1D
     //!     to evaluate all thermodynamic, kinetic, and transport properties.
     //! @param nsp Number of species.
     //! @param points Initial number of grid points
-    StFlow(IdealGasPhase* ph = 0, size_t nsp = 1, size_t points = 1);
+    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) {
+    }
 
     //! @name Problem Specification
     //! @{

include/cantera/thermo/IdealGasPhase.h

@@ -631,6 +631,7 @@ class IdealGasPhase: public ThermoPhase
      */
     void _updateThermo() const;
 };
+
 }
 
 #endif

include/cantera/thermo/Phase.h

@@ -10,6 +10,7 @@
 #define CT_PHASE_H
 
 #include "cantera/base/ctexceptions.h"
+#include "cantera/base/Solution.h"
 #include "cantera/thermo/Elements.h"
 #include "cantera/thermo/Species.h"
 #include "cantera/base/ValueCache.h"
@@ -29,8 +30,6 @@ namespace Cantera
  * support thermodynamic calculations (see \ref thermoprops).
  */
 
-class Solution;
-
 //! Class Phase is the base class for phases of matter, managing the species and
 //! elements in a phase, as well as the independent variables of temperature,
 //! mass density, species mass/mole fraction, and other generalized forces and

include/cantera/thermo/SurfPhase.h

@@ -447,6 +447,7 @@ class SurfPhase : public ThermoPhase
      */
     void _updateThermo(bool force=false) const;
 };
+
 }
 
 #endif

include/cantera/transport/TransportBase.h

@@ -74,8 +74,6 @@ const VelocityBasis VB_SPECIES_2 = 2;
 const VelocityBasis VB_SPECIES_3 = 3;
 //@}
 
-class Solution;
-
 //! Base class for transport property managers.
 /*!
  * All classes that compute transport properties for a single phase derive from

include/cantera/zeroD/Reactor.h

@@ -64,6 +64,11 @@ class Reactor : public ReactorBase
         setKineticsMgr(contents);
     }
 
+    void insert(shared_ptr<Solution> sol) {
+        setThermoMgr(*sol->thermo());
+        setKineticsMgr(*sol->kinetics());
+    }
+
     virtual void setKineticsMgr(Kinetics& kin);
 
     virtual void setChemistry(bool cflag = true) {

include/cantera/zeroD/Reservoir.h

@@ -35,6 +35,10 @@ class Reservoir : public ReactorBase
     void insert(ThermoPhase& contents) {
         setThermoMgr(contents);
     }
+
+    void insert(shared_ptr<Solution> sol) {
+        setThermoMgr(*sol->thermo());
+    }
 };
 
 }

interfaces/cython/cantera/_cantera.pxd

@@ -127,7 +127,7 @@ cdef extern from "cantera/base/Solution.h" namespace "Cantera":
         CxxSolution()
         string name()
         void setName(string)
-        void setThermoPhase(shared_ptr[CxxThermoPhase])
+        void setThermo(shared_ptr[CxxThermoPhase])
         void setKinetics(shared_ptr[CxxKinetics])
         void setTransport(shared_ptr[CxxTransport])
 

interfaces/cython/cantera/base.pyx

@@ -61,7 +61,7 @@ cdef class _SolutionBase:
             raise ValueError("Arguments are insufficient to define a phase")
 
         # Initialization of transport is deferred to Transport.__init__
-        self.base.setThermoPhase(self._thermo)
+        self.base.setThermo(self._thermo)
         self.base.setKinetics(self._kinetics)
 
         self._selected_species = np.ndarray(0, dtype=np.integer)