Proof-of-concept for a Python interface written using Cython

This module is compatible with both Python 2 and Python 3. Unlike the existing
Python module, this module directly utilizes the Cantera C++ interface,
bypassing the "clib" compatibility layer, as well as all of the direct use of
the Python C API.

Currently, this contains just enough to instantiate a ThermoPhase object from an
XML input file.

include/cantera/base/ctml.h

@@ -790,6 +790,11 @@ std::string getChildValue(const Cantera::XML_Node& parent,
 void get_CTML_Tree(Cantera::XML_Node* node, const std::string file,
                    const int debug = 0);
 
+//! Read an ctml file from a file and fill up an XML tree.
+//!   @param file    Name of the file
+//!   @return        Root of the tree
+Cantera::XML_Node getCtmlTree(const std::string file);
+
 //! Convert a cti file into a ctml file
 /*!
  *

interfaces/cython/.gitignore

@@ -0,0 +1,3 @@
+cantera/*.cpp
+cantera/*.c
+setup.py

interfaces/cython/cantera/__init__.py

@@ -0,0 +1 @@
+from .solution import *

interfaces/cython/cantera/substance.pxd

@@ -0,0 +1,43 @@
+from libcpp.vector cimport vector
+from utils cimport *
+
+cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
+    cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
+        CxxThermoPhase()
+        double pressure() except +
+        void setMoleFractions(double*) except +
+        void getMassFractions(double*) except +
+        int nSpecies()
+        XML_Node& xml()
+
+
+cdef extern from "cantera/kinetics/Kinetics.h" namespace "Cantera":
+    cdef cppclass CxxKinetics "Cantera::Kinetics":
+        CxxKinetics()
+        int nReactions()
+
+
+cdef extern from "cantera/transport/TransportBase.h" namespace "Cantera":
+    cdef cppclass CxxTransport "Cantera::Transport":
+        CxxTransport(CxxThermoPhase*)
+        double viscosity() except +
+
+
+cdef extern from "cantera/thermo/ThermoFactory.h" namespace "Cantera":
+    cdef CxxThermoPhase* newPhase(string, string) except +
+    cdef CxxThermoPhase* newPhase(XML_Node&) except +
+
+
+cdef extern from "cantera/kinetics/KineticsFactory.h" namespace "Cantera":
+    cdef CxxKinetics* newKineticsMgr(XML_Node&, vector[CxxThermoPhase*]) except +
+
+
+cdef extern from "cantera/transport/TransportFactory.h" namespace "Cantera":
+    cdef CxxTransport* newDefaultTransportMgr(CxxThermoPhase*) except +
+    cdef CxxTransport* newTransportMgr(string, CxxThermoPhase*) except +
+
+
+cdef class _SolutionBase:
+    cdef CxxThermoPhase* thermo
+    cdef CxxKinetics* kinetics
+    cdef CxxTransport* transport

interfaces/cython/cantera/substance.pyx

@@ -0,0 +1,84 @@
+import numpy as np
+cimport numpy as np
+
+from cython.operator cimport dereference as deref
+
+from utils cimport *
+
+cdef class _SolutionBase:
+    def __cinit__(self, infile, phaseid=''):
+        rootNode = getCtmlTree(stringify(infile))
+
+        # Get XML data
+        cdef XML_Node* phaseNode
+        if phaseid:
+            phaseNode = rootNode.findID(stringify(phaseid))
+        else:
+            phaseNode = rootNode.findByName(stringify('phase'))
+        if phaseNode is NULL:
+            raise ValueError("Couldn't read phase node from XML file")
+
+        # Thermo
+        if isinstance(self, ThermoPhase):
+            self.thermo = newPhase(deref(phaseNode))
+        else:
+            self.thermo = NULL
+
+        # Kinetics
+        cdef vector[CxxThermoPhase*] v
+
+        if isinstance(self, Kinetics):
+            v.push_back(self.thermo)
+            self.kinetics = newKineticsMgr(deref(phaseNode), v)
+        else:
+            self.kinetics = NULL
+
+        # Transport
+        if isinstance(self, Transport):
+            self.transport = newDefaultTransportMgr(self.thermo)
+        else:
+            self.transport = NULL
+
+    def __dealloc__(self):
+        del self.thermo
+        del self.kinetics
+        del self.transport
+
+
+cdef class ThermoPhase(_SolutionBase):
+    property nSpecies:
+        def __get__(self):
+            return self.thermo.nSpecies()
+
+    property pressure:
+        def __get__(self):
+            return self.thermo.pressure()
+
+    def setMoleFractions(self, X):
+        if len(X) != self.nSpecies:
+            raise ValueError("Mole fraction array has incorrect length")
+        cdef np.ndarray[np.double_t, ndim=1] X_c = np.ascontiguousarray(X, dtype=np.double)
+        self.thermo.setMoleFractions(&X_c[0])
+
+    property massFractions:
+        def __get__(self):
+            cdef np.ndarray[np.double_t, ndim=1] X_c = np.empty(self.nSpecies)
+            self.thermo.getMassFractions(&X_c[0])
+            return X_c
+
+
+cdef class Kinetics(_SolutionBase):
+    property nReactions:
+        def __get__(self):
+            return self.kinetics.nReactions()
+
+
+cdef class Transport(_SolutionBase):
+    property viscosity:
+        def __get__(self):
+            return self.transport.viscosity()
+
+
+class Solution(ThermoPhase, Kinetics, Transport):
+    def __init__(self, *args, **kwars):
+        pass

interfaces/cython/cantera/utils.pxd

@@ -0,0 +1,14 @@
+from libcpp.string cimport string
+
+cdef extern from "cantera/base/xml.h" namespace "Cantera":
+    cdef cppclass XML_Node:
+        XML_Node* findByName(string)
+        XML_Node* findID(string)
+        int nChildren()
+
+
+cdef extern from "cantera/base/ctml.h" namespace "ctml":
+    XML_Node getCtmlTree(string) except +
+
+
+cdef string stringify(x)

interfaces/cython/cantera/utils.pyx

@@ -0,0 +1,7 @@
+from utils cimport *
+
+cdef string stringify(x):
+    """ Converts Python strings to std::string. """
+    # This method works with both Python 2.x and 3.x.
+    tmp = bytes(x.encode())
+    return string(tmp)

interfaces/cython/setup.py.in

@@ -0,0 +1,37 @@
+import os
+from distutils.core import setup, Extension
+from distutils.sysconfig import get_config_var
+from Cython.Distutils import build_ext
+
+dataFiles = ['_cantera%s' % get_config_var('SO')]
+if os.name == 'nt':
+    dataFiles.append('cantera_shared.dll')
+else:
+    dataFiles.append('libcantera_shared.so')
+
+canteraExtensions = []
+
+def addExtension(name):
+    canteraExtensions.append(Extension("cantera.%s" % name,
+                                       ["cantera/%s.pyx" % name],
+                                       include_dirs=[".", "../../include"],
+                                       language="c++",
+                                       libraries=['cantera_shared','sundials_cvodes','sundials_idas','sundials_nvecserial','lapack','blas'],
+                                       library_dirs=['../../build/lib'],
+                                       extra_link_args=['-Wl,-rpath=$ORIGIN']))
+
+addExtension('solution')
+addExtension('utils')
+
+setup(name="Cantera",
+      version="2.1a1",
+      description="The Cantera Python Interface",
+      long_description="""
+              """,
+      author="Raymond Speth",
+      author_email="speth@mit.edu",
+      url="http://code.google.com/p/cantera",
+      packages = ["cantera"],
+      cmdclass = {'build_ext': build_ext},
+      ext_modules = canteraExtensions,
+      package_data = {'cantera': dataFiles})

src/base/ct2ctml.cpp

@@ -279,4 +279,12 @@ void get_CTML_Tree(Cantera::XML_Node* rootPtr, const std::string file, const int
     rootPtr->build(fin);
     fin.close();
 }
+
+Cantera::XML_Node getCtmlTree(const std::string file)
+{
+    Cantera::XML_Node root;
+    get_CTML_Tree(&root, file);
+    return root;
+}
+
 }