[Python] Add functions for creating Species objects from CTI/XML
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Ray Speth
parent
64c66437eb
commit
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5 changed files with 177 additions and 11 deletions
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@ -53,6 +53,17 @@ public:
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//! Create a new Species object from a 'species' XML_Node.
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shared_ptr<Species> newSpecies(const XML_Node& species_node);
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//! Generate Species objects for all <species> nodes in an XML document.
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//!
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//! The <species> nodes are assumed to be children of the <speciesData> node in
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//! an XML document with a <ctml> root node, as in the case of XML files
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//! produced by conversion from CTI files.
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//!
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//! This function can be used in combination with get_XML_File and
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//! get_XML_from_string to get Species objects from either a file or a string,
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//! respectively, where the string or file is formatted as either CTI or XML.
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std::vector<shared_ptr<Species> > getSpecies(const XML_Node& node);
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}
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#endif
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@ -53,7 +53,7 @@ cdef extern from "cantera/thermo/SpeciesThermoFactory.h":
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cdef CxxSpeciesThermo* CxxNewSpeciesThermo "Cantera::newSpeciesThermoInterpType"\
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(int, double, double, double, double*) except +
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cdef extern from "cantera/thermo/Species.h":
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cdef extern from "cantera/thermo/Species.h" namespace "Cantera":
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cdef cppclass CxxSpecies "Cantera::Species":
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CxxSpecies()
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CxxSpecies(string, stdmap[string,double])
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@ -64,6 +64,9 @@ cdef extern from "cantera/thermo/Species.h":
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double charge
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double size
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cdef shared_ptr[CxxSpecies] CxxNewSpecies "newSpecies" (XML_Node&)
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cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (XML_Node&)
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cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
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cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
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CxxThermoPhase()
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@ -627,6 +627,9 @@ ideal_gas(name='spam', elements='O H',
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class TestSpecies(utilities.CanteraTest):
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def setUp(self):
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self.gas = ct.Solution('h2o2.xml')
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def test_standalone(self):
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s = ct.Species('CH4', {'C':1, 'H':4})
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@ -642,22 +645,82 @@ class TestSpecies(utilities.CanteraTest):
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self.assertEqual(s.charge, 0.0)
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def test_index_accessor(self):
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gas = ct.Solution('h2o2.xml')
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for k in range(gas.n_species):
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s = gas.species(k)
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self.assertEqual(s.name, gas.species_name(k))
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for k in range(self.gas.n_species):
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s = self.gas.species(k)
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self.assertEqual(s.name, self.gas.species_name(k))
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for m,n in s.composition.items():
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self.assertEqual(n, gas.n_atoms(k,m))
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self.assertEqual(n, self.gas.n_atoms(k,m))
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def test_name_accessor(self):
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gas = ct.Solution('h2o2.xml')
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for name in gas.species_names:
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s = gas.species(name)
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for name in self.gas.species_names:
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s = self.gas.species(name)
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self.assertEqual(s.name, name)
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def test_fromCti(self):
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h2_cti = """
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species(
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name="H2",
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atoms="H:2",
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thermo=(
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NASA([200.00, 1000.00],
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[2.344331120E+00, 7.980520750E-03, -1.947815100E-05,
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2.015720940E-08, -7.376117610E-12, -9.179351730E+02,
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6.830102380E-01]),
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NASA([1000.00, 3500.00],
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[3.337279200E+00, -4.940247310E-05, 4.994567780E-07,
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-1.795663940E-10, 2.002553760E-14, -9.501589220E+02,
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-3.205023310E+00])
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),
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transport=gas_transport(geom="linear",
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diam=2.92,
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well_depth=38.00,
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polar=0.79,
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rot_relax=280.00),
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note = "TPIS78"
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)"""
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s1 = self.gas.species('H2')
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s2 = ct.Species.fromCti(h2_cti)
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self.assertEqual(s2.name, 'H2')
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self.assertEqual(s1.composition, s2.composition)
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self.assertEqual(s1.thermo.cp(350), s2.thermo.cp(350))
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def test_fromXml(self):
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import xml.etree.ElementTree as ET
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root = ET.parse('../../build/data/h2o2.xml').getroot()
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h2_node = root.find('.//species[@name="H2"]')
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h2_string = ET.tostring(h2_node)
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s1 = self.gas.species('H2')
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s2 = ct.Species.fromXml(h2_string)
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self.assertEqual(s2.name, 'H2')
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self.assertEqual(s1.composition, s2.composition)
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self.assertEqual(s1.thermo.cp(350), s2.thermo.cp(350))
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def test_listFromFile_cti(self):
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S = ct.Species.listFromFile('h2o2.cti')
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self.assertEqual({sp.name for sp in S},
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set(self.gas.species_names))
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def test_listFromFile_xml(self):
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S = ct.Species.listFromFile('h2o2.xml')
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self.assertEqual({sp.name for sp in S},
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set(self.gas.species_names))
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def test_listFromCti(self):
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S = ct.Species.listFromCti(open('../../build/data/h2o2.cti').read())
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self.assertEqual({sp.name for sp in S},
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set(self.gas.species_names))
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def test_listFromXml(self):
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S = ct.Species.listFromXml(open('../../build/data/h2o2.xml').read())
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self.assertEqual({sp.name for sp in S},
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set(self.gas.species_names))
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class TestSpeciesThermo(utilities.CanteraTest):
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def setUp(self):
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@ -36,6 +36,80 @@ cdef class Species:
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self._species = other
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self.species = self._species.get()
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@staticmethod
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def fromCti(text):
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"""
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Create a Species object from its CTI string representation.
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"""
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cxx_species = CxxGetSpecies(deref(CxxGetXmlFromString(stringify(text))))
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assert cxx_species.size() == 1, cxx_species.size()
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species = Species(init=False)
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species._assign(cxx_species[0])
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return species
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@staticmethod
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def fromXml(text):
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"""
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Create a Species object from its XML string representation.
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"""
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cxx_species = CxxNewSpecies(deref(CxxGetXmlFromString(stringify(text))))
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species = Species(init=False)
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species._assign(cxx_species)
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return species
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@staticmethod
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def listFromFile(filename):
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"""
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Create a list of Species objects from all of the species defined in a
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CTI or XML file.
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Directories on Cantera's input file path will be searched for the
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specified file.
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In the case of an XML file, the <species> nodes are assumed to be
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children of the <speciesData> node in a document with a <ctml> root
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node, as in the XML files produced by conversion from CTI files.
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"""
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cxx_species = CxxGetSpecies(deref(CxxGetXmlFile(stringify(filename))))
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species = []
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for a in cxx_species:
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b = Species(init=False)
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b._assign(a)
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species.append(b)
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return species
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@staticmethod
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def listFromXml(text):
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"""
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Create a list of Species objects from all the species defined in an
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XML string. The <species> nodes are assumed to be children of the
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<speciesData> node in a document with a <ctml> root node, as in the XML
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files produced by conversion from CTI files.
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"""
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cxx_species = CxxGetSpecies(deref(CxxGetXmlFromString(stringify(text))))
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species = []
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for a in cxx_species:
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b = Species(init=False)
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b._assign(a)
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species.append(b)
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return species
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@staticmethod
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def listFromCti(text):
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"""
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Create a list of Species objects from all the species defined in a CTI
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string.
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"""
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# Currently identical to listFromXml since get_XML_from_string is able
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# to distinguish between CTI and XML.
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cxx_species = CxxGetSpecies(deref(CxxGetXmlFromString(stringify(text))))
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species = []
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for a in cxx_species:
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b = Species(init=False)
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b._assign(a)
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species.append(b)
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return species
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property name:
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def __get__(self):
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return pystr(self.species.name)
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@ -82,4 +82,19 @@ shared_ptr<Species> newSpecies(const XML_Node& species_node)
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return s;
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}
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std::vector<shared_ptr<Species> > getSpecies(const XML_Node& node)
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{
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std::vector<shared_ptr<Species> > all_species;
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std::vector<XML_Node*> species_nodes =
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node.child("speciesData").getChildren("species");
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for (std::vector<XML_Node*>::iterator iter = species_nodes.begin();
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iter != species_nodes.end();
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++iter)
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{
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all_species.push_back(newSpecies(**iter));
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}
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return all_species;
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}
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}
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