[Python] Add basic access to Species objects

interfaces/cython/cantera/_cantera.pxd

@@ -38,6 +38,21 @@ cdef extern from "cantera/cython/funcWrapper.h":
         CxxFunc1(callback_wrapper, void*)
         double eval(double) except +translate_exception
 
+cdef extern from "cantera/base/smart_ptr.h":
+    cppclass shared_ptr "Cantera::shared_ptr" [T]:
+        T* get()
+        void reset(T*)
+
+cdef extern from "cantera/thermo/Species.h":
+    cdef cppclass CxxSpecies "Cantera::Species":
+        CxxSpecies()
+        CxxSpecies(string, stdmap[string,double])
+
+        string name
+        stdmap[string,double] composition
+        double charge
+        double size
+
 
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
     cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
@@ -75,6 +90,8 @@ cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
 
         # species properties
         size_t nSpecies()
+        shared_ptr[CxxSpecies] species(string) except +
+        shared_ptr[CxxSpecies] species(size_t) except +
         size_t speciesIndex(string) except +
         string speciesName(size_t) except +
         double nAtoms(size_t, size_t) except +
@@ -588,6 +605,12 @@ ctypedef void (*transportMethod2d)(CxxTransport*, size_t, double*) except +
 ctypedef void (*kineticsMethod1d)(CxxKinetics*, double*) except +
 
 # classes
+cdef class Species:
+    cdef shared_ptr[CxxSpecies] _species
+    cdef CxxSpecies* species
+
+    cdef _assign(self, shared_ptr[CxxSpecies] other)
+
 cdef class _SolutionBase:
     cdef CxxThermoPhase* thermo
     cdef CxxKinetics* kinetics

interfaces/cython/cantera/test/test_thermo.py

@@ -624,3 +624,36 @@ ideal_gas(name='spam', elements='O H',
     def test_checkReactionBalance(self):
         with self.assertRaises(Exception):
             ct.Solution('../data/h2o2_unbalancedReaction.xml')
+
+
+class TestSpecies(utilities.CanteraTest):
+    def test_standalone(self):
+        s = ct.Species('CH4', {'C':1, 'H':4})
+
+        self.assertEqual(s.name, 'CH4')
+        c = s.composition
+        self.assertEqual(len(c), 2)
+        self.assertEqual(c['C'], 1)
+        self.assertEqual(c['H'], 4)
+
+    def test_defaults(self):
+        s = ct.Species('H2')
+        self.assertEqual(s.size, 0.0)
+        self.assertEqual(s.charge, 0.0)
+
+    def test_index_accessor(self):
+        gas = ct.Solution('h2o2.xml')
+
+        for k in range(gas.n_species):
+            s = gas.species(k)
+            self.assertEqual(s.name, gas.species_name(k))
+
+            for m,n in s.composition.items():
+                self.assertEqual(n, gas.n_atoms(k,m))
+
+    def test_name_accessor(self):
+        gas = ct.Solution('h2o2.xml')
+
+        for name in gas.species_names:
+            s = gas.species(name)
+            self.assertEqual(s.name, name)

interfaces/cython/cantera/thermo.pyx

@@ -13,6 +13,47 @@ cdef stdmap[string,double] comp_map(dict X) except *:
         m[stringify(species)] = value
     return m
 
+cdef comp_map_to_dict(stdmap[string,double] m):
+    return {pystr(species):value for species,value in m.items()}
+
+
+cdef class Species:
+    def __cinit__(self, *args, init=True, **kwargs):
+        if init:
+            self._species.reset(new CxxSpecies())
+            self.species = self._species.get()
+
+    def __init__(self, name=None, composition=None, charge=None, size=None,
+                 *args, init=True, **kwargs):
+        if not init:
+            return
+
+        if name is not None:
+            self.species.name = stringify(name)
+
+        if composition is not None:
+            self.species.composition = comp_map(composition)
+
+    cdef _assign(self, shared_ptr[CxxSpecies] other):
+        self._species = other
+        self.species = self._species.get()
+
+    property name:
+        def __get__(self):
+            return pystr(self.species.name)
+
+    property composition:
+        def __get__(self):
+            return comp_map_to_dict(self.species.composition)
+
+    property charge:
+        def __get__(self):
+            return self.species.charge
+
+    property size:
+        def __get__(self):
+            return self.species.size
+
 
 cdef class ThermoPhase(_SolutionBase):
     """
@@ -237,6 +278,16 @@ cdef class ThermoPhase(_SolutionBase):
 
         return index
 
+    def species(self, k):
+        s = Species(init=False)
+        if isinstance(k, (str, unicode)):
+            s._assign(self.thermo.species(stringify(k)))
+        elif isinstance(k, (int, float)):
+            s._assign(self.thermo.species(<int>k))
+        else:
+            raise TypeError("Argument must be a string or a number")
+        return s
+
     def n_atoms(self, species, element):
         """
         Number of atoms of element *element* in species *species*. The element

src/thermo/Species.cpp

@@ -9,8 +9,8 @@
 namespace Cantera {
 
 Species::Species()
-    : charge(std::numeric_limits<double>::quiet_NaN())
-    , size(std::numeric_limits<double>::quiet_NaN())
+    : charge(0.0)
+    , size(0.0)
 {
 }