[Python] Add ability to create ThermoPhase objects from Species

This makes it possible to create a phase without ever generating a CTI
or XML description. Does not yet work with phase types that require
additional parameters.

interfaces/cython/cantera/_cantera.pxd

@@ -84,6 +84,11 @@ cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
         cbool getElementPotentials(double*) except +
         void equilibrate(string, string, double, int, int, int, int) except +
 
+        # initialization
+        void addUndefinedElements() except +
+        cbool addSpecies(shared_ptr[CxxSpecies]) except +
+        void initThermo() except +
+
         # basic thermodynamic properties
         double temperature() except +
         double pressure() except +
@@ -387,9 +392,11 @@ cdef extern from "cantera/zeroD/ReactorNet.h":
 cdef extern from "cantera/thermo/ThermoFactory.h" namespace "Cantera":
     cdef CxxThermoPhase* newPhase(string, string) except +
     cdef CxxThermoPhase* newPhase(XML_Node&) except +
+    cdef CxxThermoPhase* newThermoPhase(string) except +
 
 cdef extern from "cantera/kinetics/KineticsFactory.h" namespace "Cantera":
     cdef CxxKinetics* newKineticsMgr(XML_Node&, vector[CxxThermoPhase*]) except +
+    cdef CxxKinetics* CxxNewKinetics "Cantera::newKineticsMgr" (string) except +
 
 cdef extern from "cantera/transport/TransportFactory.h" namespace "Cantera":
     cdef CxxTransport* newDefaultTransportMgr(CxxThermoPhase*) except +

interfaces/cython/cantera/base.pyx

@@ -1,6 +1,6 @@
 cdef class _SolutionBase:
     def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
-                  source=None, **kwargs):
+                  source=None, thermo=None, species=(), **kwargs):
         # Shallow copy of an existing Solution (for slicing support)
         cdef _SolutionBase other
         if origin is not None:
@@ -18,13 +18,31 @@ cdef class _SolutionBase:
             self._selected_species = other._selected_species.copy()
             return
 
-        # Instantiate a set of new Cantera C++ objects
+        if infile or source:
+            self._init_cti_xml(infile, phaseid, phases, source)
+        elif thermo and species:
+            self._init_parts(thermo, species)
+        else:
+            raise ValueError("Arguments are insufficient to define a phase")
+
+        # Initialization of transport is deferred to Transport.__init__
+        self.transport = NULL
+
+        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_cti_xml(self, infile, phaseid, phases, source):
+        """
+        Instantiate a set of new Cantera C++ objects from a CTI or XML
+        phase definition
+        """
         if infile:
             rootNode = CxxGetXmlFile(stringify(infile))
         elif source:
             rootNode = CxxGetXmlFromString(stringify(source))
-        else:
-            raise ValueError('No phase definition provided')
 
         # Get XML data
         cdef XML_Node* phaseNode
@@ -54,14 +72,21 @@ cdef class _SolutionBase:
         else:
             self.kinetics = NULL
 
-        # Initialization of transport is deferred to Transport.__init__
-        self.transport = NULL
+    def _init_parts(self, thermo, species):
+        """
+        Instantiate a set of new Cantera C++ objects based on a string defining
+        the model type and a list of Species objects.
+        """
+        self.thermo = newThermoPhase(stringify(thermo))
+        self.thermo.addUndefinedElements()
+        cdef Species S
+        for S in species:
+            self.thermo.addSpecies(S._species)
+        self.thermo.initThermo()
 
-        self._selected_species = np.ndarray(0, dtype=np.integer)
-
-    def __init__(self, *args, **kwargs):
-        if isinstance(self, Transport):
-            assert self.transport is not NULL
+        if isinstance(self, Kinetics):
+            # Not yet implemented
+            self.kinetics = CxxNewKinetics(stringify("none"))
 
     def __getitem__(self, selection):
         copy = self.__class__(origin=self)

interfaces/cython/cantera/test/test_thermo.py

@@ -620,6 +620,19 @@ ideal_gas(name='spam', elements='O H',
         gas = ct.Solution(source=xml_def)
         self.check(gas, 'spam', 350, 2e6, 2, 1)
 
+    def test_import_from_species(self):
+        gas1 = ct.Solution('h2o2.xml')
+        gas1.TPX = 350, 101325, 'H2:0.3, O2:0.7'
+        gas1.equilibrate('HP')
+
+        species = ct.Species.listFromFile('h2o2.xml')
+        gas2 = ct.ThermoPhase(thermo='IdealGas', species=species)
+        gas2.TPX = 350, 101325, 'H2:0.3, O2:0.7'
+        gas2.equilibrate('HP')
+        self.assertEqual(gas1.n_elements, gas2.n_elements)
+        self.assertEqual(gas1.species_names, gas2.species_names)
+        self.assertNear(gas1.T, gas2.T)
+        self.assertArrayNear(gas1.X, gas2.X)
 
     def test_checkReactionBalance(self):
         with self.assertRaises(Exception):