Create SolutionBase object in C++

include/cantera/base/Solution.h

@@ -0,0 +1,70 @@
+//! @file Solution.h
+
+// This file is part of Cantera. See License.txt in the top-level directory or
+// at https://cantera.org/license.txt for license and copyright information.
+
+#ifndef CT_SOLUTION_H
+#define CT_SOLUTION_H
+
+#include "cantera/base/ctexceptions.h"
+
+namespace Cantera
+{
+
+class ThermoPhase;
+class Kinetics;
+class Transport;
+
+//! A container class holding managers for all pieces defining a phase
+class Solution : public std::enable_shared_from_this<Solution>
+{
+private:
+    Solution();
+
+public:
+    ~Solution() {}
+    Solution(const Solution&) = delete;
+    Solution& operator=(const Solution&) = delete;
+
+    static shared_ptr<Solution> create() {
+        return shared_ptr<Solution>( new Solution );
+    }
+
+    //! Return the name of this Solution object
+    std::string name() const;
+
+    //! Set the name of this Solution object
+    void setName(const std::string& name);
+
+    //! Set the ThermoPhase object
+    void setThermoPhase(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 Kinetics object
+    Kinetics& kinetics() {
+        return *m_kinetics;
+    }
+
+    //! Accessor for the Transport object
+    Transport& transport() {
+        return *m_transport;
+    }
+
+protected:
+    shared_ptr<ThermoPhase> m_thermo;  //! ThermoPhase manager
+    shared_ptr<Kinetics> m_kinetics;  //! Kinetics manager
+    shared_ptr<Transport> m_transport;  //! Transport manager
+};
+
+}
+#endif

include/cantera/kinetics/Kinetics.h

@@ -19,6 +19,8 @@
 namespace Cantera
 {
 
+class Solution;
+
 /**
  * @defgroup chemkinetics Chemical Kinetics
  */
@@ -814,6 +816,11 @@ class Kinetics
     void selectPhase(const doublereal* data, const thermo_t* phase,
                      doublereal* phase_data);
 
+    //! Set root Solution holding all phase information
+    virtual void setRoot(std::shared_ptr<Solution> root) {
+        m_root = root;
+    }
+
 protected:
     //! Cache for saved calculations within each Kinetics object.
     ValueCache m_cache;
@@ -935,6 +942,9 @@ class Kinetics
 
     //! @see skipUndeclaredThirdBodies()
     bool m_skipUndeclaredThirdBodies;
+
+    //! reference to Solution
+    std::weak_ptr<Solution> m_root;
 };
 
 }

include/cantera/thermo/Phase.h

@@ -29,6 +29,8 @@ 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
@@ -758,6 +760,11 @@ class Phase
         m_caseSensitiveSpecies = cflag;
     }
 
+    //! Set root Solution holding all phase information
+    virtual void setRoot(std::shared_ptr<Solution> root) {
+        m_root = root;
+    }
+
 protected:
     //! Cached for saved calculations within each ThermoPhase.
     /*!
@@ -870,6 +877,9 @@ class Phase
 
     //! Entropy at 298.15 K and 1 bar of stable state pure elements (J kmol-1)
     vector_fp m_entropy298;
+
+    //! reference to Solution
+    std::weak_ptr<Solution> m_root;
 };
 
 }

include/cantera/transport/TransportBase.h

@@ -74,6 +74,8 @@ 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
@@ -654,6 +656,11 @@ class Transport
      */
     virtual void setThermo(thermo_t& thermo);
 
+    //! Set root Solution holding all phase information
+    virtual void setRoot(std::shared_ptr<Solution> root) {
+        m_root = root;
+    }
+
 protected:
     //! Enable the transport object for use.
     /*!
@@ -680,6 +687,9 @@ class Transport
     //! Velocity basis from which diffusion velocities are computed.
     //! Defaults to the mass averaged basis = -2
     int m_velocityBasis;
+
+    //! reference to Solution
+    std::weak_ptr<Solution> m_root;
 };
 
 }

interfaces/cython/cantera/_cantera.pxd

@@ -120,17 +120,26 @@ cdef extern from "cantera/thermo/Species.h" namespace "Cantera":
     cdef shared_ptr[CxxSpecies] CxxNewSpecies "newSpecies" (CxxAnyMap&) except +translate_exception
     cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (CxxAnyValue&) except +translate_exception
 
+
+cdef extern from "cantera/base/Solution.h" namespace "Cantera":
+    cdef cppclass CxxSolution "Cantera::Solution":
+        CxxSolution()
+        string name()
+        void setName(string)
+        void setThermoPhase(shared_ptr[CxxThermoPhase])
+        void setKinetics(shared_ptr[CxxKinetics])
+        void setTransport(shared_ptr[CxxTransport])
+
+    cdef shared_ptr[CxxSolution] CxxNewSolution "Cantera::Solution::create" ()
+
+
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
     cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
         CxxThermoPhase()
 
         # miscellaneous
         string type()
         string report(cbool, double) except +translate_exception
-        string name()
-        void setName(string)
-        string id()
-        void setID(string)
         double minTemp() except +translate_exception
         double maxTemp() except +translate_exception
         double refPressure() except +translate_exception
@@ -928,6 +937,8 @@ cdef class GasTransportData:
     cdef _assign(self, shared_ptr[CxxTransportData] other)
 
 cdef class _SolutionBase:
+    cdef shared_ptr[CxxSolution] _base
+    cdef CxxSolution* base
     cdef shared_ptr[CxxThermoPhase] _thermo
     cdef CxxThermoPhase* thermo
     cdef shared_ptr[CxxKinetics] _kinetics

interfaces/cython/cantera/base.pyx

@@ -1,18 +1,40 @@
 # This file is part of Cantera. See License.txt in the top-level directory or
 # at https://cantera.org/license.txt for license and copyright information.
 
+from collections import defaultdict as _defaultdict
+
 cdef class _SolutionBase:
-    def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
+    def __cinit__(self, infile='', name='', adjacent=(), origin=None,
                   source=None, yaml=None, thermo=None, species=(),
                   kinetics=None, reactions=(), **kwargs):
+
+        if 'phaseid' in kwargs:
+            if name is not '':
+                raise AttributeError('duplicate specification of phase name')
+
+            warnings.warn("Keyword 'name' replaces 'phaseid'",
+                          FutureWarning)
+            name = kwargs['phaseid']
+
+        if 'phases' in kwargs:
+            if len(adjacent)>0:
+                raise AttributeError(
+                    'duplicate specification of adjacent phases')
+
+            warnings.warn("Keyword 'adjacent' replaces 'phases'",
+                          FutureWarning)
+            adjacent = kwargs['phases']
+
         # Shallow copy of an existing Solution (for slicing support)
         cdef _SolutionBase other
         if origin is not None:
             other = <_SolutionBase?>origin
 
+            self.base = other.base
             self.thermo = other.thermo
             self.kinetics = other.kinetics
             self.transport = other.transport
+            self._base = other._base
             self._thermo = other._thermo
             self._kinetics = other._kinetics
             self._transport = other._transport
@@ -21,25 +43,67 @@ cdef class _SolutionBase:
             self._selected_species = other._selected_species.copy()
             return
 
+        # Assign base and set managers to NULL
+        self._base = CxxNewSolution()
+        self.base = self._base.get()
+        self.thermo = NULL
+        self.kinetics = NULL
+        self.transport = NULL
+
+        # Parse inputs
         if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
-            self._init_yaml(infile, phaseid, phases, yaml)
+            self._init_yaml(infile, name, adjacent, yaml)
         elif infile or source:
-            self._init_cti_xml(infile, phaseid, phases, source)
+            self._init_cti_xml(infile, name, adjacent, source)
         elif thermo and species:
-            self._init_parts(thermo, species, kinetics, phases, reactions)
+            self._init_parts(thermo, species, kinetics, adjacent, reactions)
         else:
             raise ValueError("Arguments are insufficient to define a phase")
 
         # Initialization of transport is deferred to Transport.__init__
-        self.transport = NULL
+        self.base.setThermoPhase(self._thermo)
+        self.base.setKinetics(self._kinetics)
 
         self._selected_species = np.ndarray(0, dtype=np.integer)
 
     def __init__(self, *args, **kwargs):
         if isinstance(self, Transport):
             assert self.transport is not NULL
 
-    def _init_yaml(self, infile, phaseid, phases, source):
+        phase_name = pystr(self.base.name())
+        name = kwargs.get('name')
+        if name is not None:
+            self.name = name
+        else:
+            self.name = phase_name
+
+    property name:
+        """
+        The name assigned to this object. The default value corresponds 
+        to the CTI/XML/YAML input file phase entry.
+        """
+        def __get__(self):
+            return pystr(self.base.name())
+
+        def __set__(self, name):
+            self.base.setName(stringify(name))
+
+    property composite:
+        """
+        Returns tuple of thermo/kinetics/transport models associated with
+        this SolutionBase object.
+        """
+        def __get__(self):
+            thermo = None if self.thermo == NULL \
+                else pystr(self.thermo.type())
+            kinetics = None if self.kinetics == NULL \
+                else pystr(self.kinetics.kineticsType())
+            transport = None if self.transport == NULL \
+                else pystr(self.transport.transportType())
+
+            return thermo, kinetics, transport
+
+    def _init_yaml(self, infile, name, adjacent, source):
         """
         Instantiate a set of new Cantera C++ objects from a YAML
         phase definition
@@ -51,7 +115,7 @@ cdef class _SolutionBase:
             root = AnyMapFromYamlString(stringify(source))
 
         phaseNode = root[stringify("phases")].getMapWhere(stringify("name"),
-                                                          stringify(phaseid))
+                                                          stringify(name))
 
         # Thermo
         if isinstance(self, ThermoPhase):
@@ -66,15 +130,15 @@ cdef class _SolutionBase:
 
         if isinstance(self, Kinetics):
             v.push_back(self.thermo)
-            for phase in phases:
+            for phase in adjacent:
                 # adjacent bulk phases for a surface phase
                 v.push_back(phase.thermo)
             self._kinetics = newKinetics(v, phaseNode, root)
             self.kinetics = self._kinetics.get()
         else:
             self.kinetics = NULL
 
-    def _init_cti_xml(self, infile, phaseid, phases, source):
+    def _init_cti_xml(self, infile, name, adjacent, source):
         """
         Instantiate a set of new Cantera C++ objects from a CTI or XML
         phase definition
@@ -86,8 +150,8 @@ cdef class _SolutionBase:
 
         # Get XML data
         cdef XML_Node* phaseNode
-        if phaseid:
-            phaseNode = rootNode.findID(stringify(phaseid))
+        if name:
+            phaseNode = rootNode.findID(stringify(name))
         else:
             phaseNode = rootNode.findByName(stringify('phase'))
         if phaseNode is NULL:
@@ -106,15 +170,15 @@ cdef class _SolutionBase:
 
         if isinstance(self, Kinetics):
             v.push_back(self.thermo)
-            for phase in phases:
+            for phase in adjacent:
                 # adjacent bulk phases for a surface phase
                 v.push_back(phase.thermo)
             self.kinetics = newKineticsMgr(deref(phaseNode), v)
             self._kinetics.reset(self.kinetics)
         else:
             self.kinetics = NULL
 
-    def _init_parts(self, thermo, species, kinetics, phases, reactions):
+    def _init_parts(self, thermo, species, kinetics, adjacent, reactions):
         """
         Instantiate a set of new Cantera C++ objects based on a string defining
         the model type and a list of Species objects.
@@ -136,7 +200,8 @@ cdef class _SolutionBase:
             self.kinetics = CxxNewKinetics(stringify(kinetics))
             self._kinetics.reset(self.kinetics)
             self.kinetics.addPhase(deref(self.thermo))
-            for phase in phases:
+            for phase in adjacent:
+                # adjacent bulk phases for a surface phase
                 self.kinetics.addPhase(deref(phase.thermo))
             self.kinetics.init()
             self.kinetics.skipUndeclaredThirdBodies(True)