[Kinetics] Add functions for creating Reaction objects from CTI/XML

include/cantera/kinetics/Reaction.h

@@ -255,6 +255,27 @@ public:
 
 //! Create a new Reaction object for the reaction defined in `rxn_node`
 shared_ptr<Reaction> newReaction(const XML_Node& rxn_node);
+
+//! Create Reaction objects for all <reaction> nodes in an XML document.
+//!
+//! The `<reaction>` nodes are assumed to be children of the `<reactionData>`
+//! node in an XML document with a `<ctml>` root node, as in the case of XML
+//! files produced by conversion from CTI files.
+//!
+//! This function can be used in combination with get_XML_File() and
+//! get_XML_from_string() to get Reaction objects from either a file or a
+//! string, respectively, where the string or file is formatted as either CTI
+//! or XML.
+//!
+//! If Reaction objects are being created from a CTI definition that does not
+//! contain corresponding phase definitions, then one of the following must be
+//! true, or the resulting rate constants will be incorrect:
+//!
+//!   - The rate constants are expressed in (kmol, meter, second) units
+//!   - A `units` directive is included **and** all reactions take place in
+//!     bulk (e.g. gas) phases
+std::vector<shared_ptr<Reaction> > getReactions(const XML_Node& node);
+
 }
 
 #endif

interfaces/cython/cantera/_cantera.pxd

@@ -192,6 +192,9 @@ cdef extern from "cantera/thermo/SurfPhase.h":
 
 
 cdef extern from "cantera/kinetics/Reaction.h" namespace "Cantera":
+    cdef shared_ptr[CxxReaction] CxxNewReaction "newReaction" (XML_Node&)
+    cdef vector[shared_ptr[CxxReaction]] CxxGetReactions "getReactions" (XML_Node&)
+
     cdef cppclass CxxArrhenius "Cantera::Arrhenius":
         CxxArrhenius()
         CxxArrhenius(double, double, double)

interfaces/cython/cantera/reaction.pyx

@@ -22,6 +22,61 @@ cdef class Reaction:
         self._reaction = other
         self.reaction = self._reaction.get()
 
+    @staticmethod
+    def fromCti(text):
+        """
+        Create a Reaction object from its CTI string representation.
+        """
+        cxx_reactions = CxxGetReactions(deref(CxxGetXmlFromString(stringify(text))))
+        assert cxx_reactions.size() == 1, cxx_reactions.size()
+        return wrapReaction(cxx_reactions[0])
+
+    @staticmethod
+    def fromXml(text):
+        """
+        Create a Reaction object from its XML string representation.
+        """
+        cxx_reaction = CxxNewReaction(deref(CxxGetXmlFromString(stringify(text))))
+        return wrapReaction(cxx_reaction)
+
+    @staticmethod
+    def listFromFile(filename):
+        """
+        Create a list of Reaction objects from all of the reactions defined in a
+        CTI or XML file.
+
+        Directories on Cantera's input file path will be searched for the
+        specified file.
+
+        In the case of an XML file, the <reactions> nodes are assumed to be
+        children of the <reactionsData> node in a document with a <ctml> root
+        node, as in the XML files produced by conversion from CTI files.
+        """
+        cxx_reactions = CxxGetReactions(deref(CxxGetXmlFile(stringify(filename))))
+        return [wrapReaction(r) for r in cxx_reactions]
+
+    @staticmethod
+    def listFromXml(text):
+        """
+        Create a list of Reaction objects from all the reaction defined in an
+        XML string. The <reaction> nodes are assumed to be children of the
+        <reactionData> node in a document with a <ctml> root node, as in the XML
+        files produced by conversion from CTI files.
+        """
+        cxx_reactions = CxxGetReactions(deref(CxxGetXmlFromString(stringify(text))))
+        return [wrapReaction(r) for r in cxx_reactions]
+
+    @staticmethod
+    def listFromCti(text):
+        """
+        Create a list of Species objects from all the species defined in a CTI
+        string.
+        """
+        # Currently identical to listFromXml since get_XML_from_string is able
+        # to distinguish between CTI and XML.
+        cxx_reactions = CxxGetReactions(deref(CxxGetXmlFromString(stringify(text))))
+        return [wrapReaction(r) for r in cxx_reactions]
+
     property reactant_string:
         def __get__(self):
             return pystr(self.reaction.reactantString())

interfaces/cython/cantera/test/test_kinetics.py

@@ -510,3 +510,52 @@ class TestDuplicateReactions(utilities.CanteraTest):
     def test_declared_duplicate(self):
         gas = ct.Solution(self.infile, 'I')
         self.assertEqual(gas.n_reactions, 2)
+
+
+class TestReaction(utilities.CanteraTest):
+    @classmethod
+    def setUpClass(cls):
+        cls.gas = ct.Solution('h2o2.xml')
+
+    def test_fromCti(self):
+        r = ct.Reaction.fromCti('''three_body_reaction('2 O + M <=> O2 + M',
+            [1.200000e+11, -1.0, 0.0], efficiencies='AR:0.83 H2:2.4 H2O:15.4')''')
+
+        self.assertTrue(isinstance(r, ct.ThirdBodyReaction))
+        self.assertEqual(r.reactants['O'], 2)
+        self.assertEqual(r.products['O2'], 1)
+        self.assertEqual(r.efficiencies['H2O'], 15.4)
+        self.assertEqual(r.rate.temperature_exponent, -1.0)
+
+    def test_fromXml(self):
+        import xml.etree.ElementTree as ET
+        root = ET.parse('../../build/data/h2o2.xml').getroot()
+        rxn_node = root.find('.//reaction[@id="0001"]')
+        r = ct.Reaction.fromXml(ET.tostring(rxn_node))
+
+        self.assertTrue(isinstance(r, ct.ThirdBodyReaction))
+        self.assertEqual(r.reactants['O'], 2)
+        self.assertEqual(r.products['O2'], 1)
+        self.assertEqual(r.efficiencies['H2O'], 15.4)
+        self.assertEqual(r.rate.temperature_exponent, -1.0)
+
+    def test_listFromFile(self):
+        R = ct.Reaction.listFromFile('h2o2.xml')
+        eq1 = [r.equation for r in R]
+        eq2 = [self.gas.reaction(i).equation
+               for i in range(self.gas.n_reactions)]
+        self.assertEqual(eq1, eq2)
+
+    def test_listFromCti(self):
+        R = ct.Reaction.listFromCti(open('../../build/data/h2o2.cti').read())
+        eq1 = [r.equation for r in R]
+        eq2 = [self.gas.reaction(i).equation
+               for i in range(self.gas.n_reactions)]
+        self.assertEqual(eq1, eq2)
+
+    def test_listFromXml(self):
+        R = ct.Reaction.listFromCti(open('../../build/data/h2o2.xml').read())
+        eq1 = [r.equation for r in R]
+        eq2 = [self.gas.reaction(i).equation
+               for i in range(self.gas.n_reactions)]
+        self.assertEqual(eq1, eq2)

src/kinetics/Reaction.cpp

@@ -673,4 +673,19 @@ shared_ptr<Reaction> newReaction(const XML_Node& rxn_node)
     }
 }
 
+std::vector<shared_ptr<Reaction> > getReactions(const XML_Node& node)
+{
+    std::vector<shared_ptr<Reaction> > all_reactions;
+    std::vector<XML_Node*> reaction_nodes =
+        node.child("reactionData").getChildren("reaction");
+
+    for (std::vector<XML_Node*>::iterator iter = reaction_nodes.begin();
+         iter != reaction_nodes.end();
+         ++iter)
+    {
+        all_reactions.push_back(newReaction(**iter));
+    }
+    return all_reactions;
+}
+
 }