Smart clib cabinets / add Solution to clib API

include/cantera/base/Interface.h

@@ -52,7 +52,7 @@ class Interface : public Solution
 
 //! Create and initialize a new Interface from an input file
 /*!
- * This constructor wraps newPhase() and newKinetics()
+ * This constructor wraps newThermo() and newKinetics()
  *
  * @param infile name of the input file
  * @param name   name of the surface phase in the file.
@@ -68,7 +68,7 @@ shared_ptr<Interface> newInterface(const std::string& infile,
 
 //! Create and initialize a new Interface from an input file
 /*!
- * This constructor wraps newPhase() and newKinetics()
+ * This constructor wraps newThermo() and newKinetics()
  *
  * @param infile name of the input file
  * @param name   name of the phase in the file. If this is the empty string, the first
@@ -82,7 +82,7 @@ shared_ptr<Interface> newInterface(const std::string& infile,
 
 //! Create and initialize a new Interface from AnyMap objects
 /*!
- * This constructor wraps newPhase() and newKinetics()
+ * This constructor wraps newThermo() and newKinetics()
  *
  * @param phaseNode the node containing the phase definition (that is, thermo model,
  *     list of species, and initial state)

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() {
@@ -148,7 +148,7 @@ class Solution : public std::enable_shared_from_this<Solution>
 
 //! Create and initialize a new Solution from an input file
 /*!
- * This constructor wraps newPhase(), newKinetics() and newTransportMgr() routines
+ * This constructor wraps newThermo(), newKinetics() and newTransport() routines
  * for initialization.
  *
  * @param infile name of the input file
@@ -166,8 +166,8 @@ shared_ptr<Solution> newSolution(const std::string& infile, const std::string& n
 
 //! Create and initialize a new Solution manager from an input file
 /*!
- * This constructor wraps newPhase(), newKinetics() and
- * newTransportMgr() routines for initialization.
+ * This constructor wraps newThermo(), newKinetics() and newTransport() routines
+ * for initialization.
  *
  * @param infile name of the input file
  * @param name   name of the phase in the file.
@@ -184,8 +184,8 @@ shared_ptr<Solution> newSolution(const std::string& infile,
 
 //! Create and initialize a new Solution manager from AnyMap objects
 /*!
- * This constructor wraps newPhase(), newKinetics() and
- * newTransportMgr() routines for initialization.
+ * This constructor wraps newThermo(), newKinetics() and newTransport() routines
+ * for initialization.
  *
  * @param phaseNode the node containing the phase definition (that is, thermo model,
  *     list of species, and initial state)

include/cantera/clib/ct.h

@@ -16,6 +16,21 @@ extern "C" {
 
     CANTERA_CAPI int ct_appdelete();
 
+    CANTERA_CAPI int soln_newSolution(const char* infile,
+                                      const char* name,
+                                      const char* transport);
+    CANTERA_CAPI int soln_newInterface(const char* infile,
+                                       const char* name,
+                                       int na,
+                                       const int* adjacent);
+    CANTERA_CAPI int soln_del(int n); //!< note that linked objects are deleted as well
+    CANTERA_CAPI int soln_name(int n, int buflen, char* buf);
+    CANTERA_CAPI int soln_thermo(int n);
+    CANTERA_CAPI int soln_kinetics(int n);
+    CANTERA_CAPI int soln_transport(int n);
+    CANTERA_CAPI size_t soln_nAdjacent(int n);
+    CANTERA_CAPI int soln_adjacent(int n, int a);
+
     CANTERA_CAPI int thermo_newFromFile(const char* filename, const char* phasename);
     CANTERA_CAPI int thermo_del(int n);
     CANTERA_CAPI size_t thermo_nElements(int n);
@@ -166,6 +181,7 @@ extern "C" {
     CANTERA_CAPI int ct_suppress_thermo_warnings(int suppress);
     CANTERA_CAPI int ct_use_legacy_rate_constants(int legacy);
     CANTERA_CAPI int ct_clearStorage();
+    CANTERA_CAPI int ct_resetStorage();
 
 #ifdef __cplusplus
 }

include/cantera/clib/ctreactor.h

@@ -21,6 +21,7 @@ extern "C" {
     CANTERA_CAPI int reactor_setEnergy(int i, int eflag);
     CANTERA_CAPI int reactor_setThermoMgr(int i, int n);
     CANTERA_CAPI int reactor_setKineticsMgr(int i, int n);
+    CANTERA_CAPI int reactor_insert(int i, int n);
     CANTERA_CAPI double reactor_mass(int i);
     CANTERA_CAPI double reactor_volume(int i);
     CANTERA_CAPI double reactor_density(int i);

include/cantera/kinetics/BulkKinetics.h

@@ -20,7 +20,10 @@ namespace Cantera
 class BulkKinetics : public Kinetics
 {
 public:
-    BulkKinetics(ThermoPhase* thermo = 0);
+    BulkKinetics();
+
+    //! @deprecated  To be removed after Cantera 3.0; code base only uses default.
+    BulkKinetics(ThermoPhase* thermo);
 
     virtual void resizeReactions();
 

include/cantera/kinetics/GasKinetics.h

@@ -28,10 +28,10 @@ class GasKinetics : public BulkKinetics
     //! @{
 
     //! Constructor.
-    /*!
-     *  @param thermo  Pointer to the gas ThermoPhase (optional)
-     */
-    GasKinetics(ThermoPhase* thermo = 0);
+    GasKinetics();
+
+    //! @deprecated  To be removed after Cantera 3.0; code base only uses default.
+    GasKinetics(ThermoPhase* thermo);
 
     virtual std::string kineticsType() const {
         return "Gas";

include/cantera/kinetics/InterfaceKinetics.h

@@ -56,15 +56,19 @@ class ImplicitSurfChem;
 class InterfaceKinetics : public Kinetics
 {
 public:
+    //! Constructor
+    InterfaceKinetics();
+
     //! Constructor
     /*!
-     * @param thermo The optional parameter may be used to initialize the object
+     * @param thermo The parameter may be used to initialize the object
      *               with one ThermoPhase object.
      *               HKM Note -> Since the interface kinetics object will
      *               probably require multiple ThermoPhase objects, this is
      *               probably not a good idea to have this parameter.
+     * @deprecated  To be removed after Cantera 3.0; code base only uses default.
      */
-    InterfaceKinetics(ThermoPhase* thermo = 0);
+    InterfaceKinetics(ThermoPhase* thermo);
 
     virtual ~InterfaceKinetics();
 
@@ -126,7 +130,7 @@ class InterfaceKinetics : public Kinetics
     //! @name Reaction Mechanism Construction
     //! @{
 
-    //!  Add a phase to the kinetics manager object.
+    //!  Add a thermo phase to the kinetics manager object.
     /*!
      * This must be done before the function init() is called or
      * before any reactions are input.
@@ -138,6 +142,9 @@ class InterfaceKinetics : public Kinetics
      *
      * @param thermo    Reference to the ThermoPhase to be added.
      */
+    virtual void addThermo(shared_ptr<ThermoPhase> thermo);
+
+    //! @see InterfaceKinetics::addThermo(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 New in Cantera 3.0. Replaces addPhase.
      */
+    virtual void addThermo(shared_ptr<ThermoPhase> thermo);
+
+    //! @see Kinetics::addThermo(shared_ptr<ThermoPhase>)
+    //! @deprecated To be removed after Cantera 3.0. Replaced by addThermo
+    //!     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.

include/cantera/kinetics/KineticsFactory.h

@@ -38,6 +38,7 @@ class KineticsFactory : public Factory<Kinetics>
 
 /**
  *  Create a new kinetics manager.
+ *  @deprecated  To be removed after Cantera 3.0; superseded by newKinetics.
  */
 Kinetics* newKineticsMgr(const string& model);
 
@@ -58,6 +59,13 @@ shared_ptr<Kinetics> newKinetics(const string& model);
  * @param rootNode   The root node of the file containing the phase definition,
  *     which will be treated as the default source for reactions
  */
+shared_ptr<Kinetics> newKinetics(const vector<shared_ptr<ThermoPhase>>& phases,
+                                 const AnyMap& phaseNode,
+                                 const AnyMap& rootNode=AnyMap());
+
+//! @copydoc KineticsFactory::newKinetics(const vector<shared_ptr<ThermoPhase>>&, const AnyMap&, const AnyMap&)
+//! @deprecated  To be removed after Cantera 3.0;
+//!     superseded by newKinetics() returning shared_ptr
 unique_ptr<Kinetics> newKinetics(const std::vector<ThermoPhase*>& phases,
                                  const AnyMap& phaseNode,
                                  const AnyMap& rootNode=AnyMap());
@@ -73,6 +81,13 @@ unique_ptr<Kinetics> newKinetics(const std::vector<ThermoPhase*>& phases,
  * @param phase_name  The name of the reacting phase in the input file (that is, the
  *     name of the first phase in the `phases` vector)
  */
+shared_ptr<Kinetics> newKinetics(const vector<shared_ptr<ThermoPhase>>& phases,
+                                 const string& filename,
+                                 const string& phase_name);
+
+//! @copydoc KineticsFactory::newKinetics(const vector<shared_ptr<ThermoPhase>>&, const string&, const string&)
+//! @deprecated  To be removed after Cantera 3.0;
+//!     superseded by newKinetics() returning shared_ptr
 unique_ptr<Kinetics> newKinetics(const std::vector<ThermoPhase*>& phases,
                                  const std::string& filename,
                                  const std::string& phase_name);

include/cantera/oneD/Boundary1D.h

@@ -298,6 +298,9 @@ class ReactingSurf1D : public Boundary1D
     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 @@ class Domain1D
         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 @@ class Domain1D
      */
     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 @@ class StFlow : public Domain1D
     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 @@ class StFlow : public Domain1D
      */
     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