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[Base] clarify keyword arguments of _SolutionBase initializers

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* Replace `phaseid` by `phase`
* Replace `phases` by `adjacent`
* Add deprecation warnings and update unit tests
This commit is contained in:
Ingmar Schoegl 2019-08-17 11:54:57 -05:00 • committed by Ray Speth
parent dbac2fc79c
commit d8e09a9550
4 changed files with 67 additions and 39 deletions
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59
interfaces/cython/cantera/base.pyx
View file

@ -6,9 +6,29 @@ from collections import defaultdict as _defaultdict
_phase_counts = _defaultdict(int)
cdef class _SolutionBase:
def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
def __cinit__(self, infile='', phase='', adjacent=(), origin=None,
source=None, yaml=None, thermo=None, species=(),
kinetics=None, reactions=(), **kwargs):
if 'phaseid' in kwargs:
if phase is not '':
raise AttributeError('duplicate specification of phase name')
warnings.warn("To be removed after Cantera 2.5. "
"Keyword `phaseid` is replaced by `phase`",
DeprecationWarning)
phase = kwargs['phaseid']
if 'phases' in kwargs:
if len(adjacent)>0:
raise AttributeError(
'duplicate specification of adjacent phases')
warnings.warn("To be removed after Cantera 2.5. "
"Keyword `phases` is replaced by `adjacent`",
DeprecationWarning)
adjacent = kwargs['phases']
# Shallow copy of an existing Solution (for slicing support)
cdef _SolutionBase other
if origin is not None:
@ -36,11 +56,11 @@ cdef class _SolutionBase:
# Parse inputs
if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
self._init_yaml(infile, phaseid, phases, yaml)
self._init_yaml(infile, phase, adjacent, yaml)
elif infile or source:
self._init_cti_xml(infile, phaseid, phases, source)
self._init_cti_xml(infile, phase, adjacent, source)
elif thermo and species:
self._init_parts(thermo, species, kinetics, phases, reactions)
self._init_parts(thermo, species, kinetics, adjacent, reactions)
else:
raise ValueError("Arguments are insufficient to define a phase")
@ -137,7 +157,7 @@ cdef class _SolutionBase:
return thermo, kinetics, transport
def _init_yaml(self, infile, phaseid, phases, source):
def _init_yaml(self, infile, phase, adjacent, source):
"""
Instantiate a set of new Cantera C++ objects from a YAML
phase definition
@ -149,7 +169,7 @@ cdef class _SolutionBase:
root = AnyMapFromYamlString(stringify(source))
phaseNode = root[stringify("phases")].getMapWhere(stringify("name"),
stringify(phaseid))
stringify(phase))
# Thermo
if isinstance(self, ThermoPhase):
@ -160,19 +180,19 @@ cdef class _SolutionBase:
# Kinetics
cdef vector[CxxThermoPhase*] v
cdef _SolutionBase phase
cdef _SolutionBase adj
if isinstance(self, Kinetics):
v.push_back(self.thermo)
for phase in phases:
for adj in adjacent:
# adjacent bulk phases for a surface phase
v.push_back(phase.thermo)
v.push_back(adj.thermo)
self._kinetics = newKinetics(v, phaseNode, root)
self.kinetics = self._kinetics.get()
else:
self.kinetics = NULL
def _init_cti_xml(self, infile, phaseid, phases, source):
def _init_cti_xml(self, infile, phase, adjacent, source):
"""
Instantiate a set of new Cantera C++ objects from a CTI or XML
phase definition
@ -184,8 +204,8 @@ cdef class _SolutionBase:
# Get XML data
cdef XML_Node* phaseNode
if phaseid:
phaseNode = rootNode.findID(stringify(phaseid))
if phase:
phaseNode = rootNode.findID(stringify(phase))
else:
phaseNode = rootNode.findByName(stringify('phase'))
if phaseNode is NULL:
@ -200,19 +220,19 @@ cdef class _SolutionBase:
# Kinetics
cdef vector[CxxThermoPhase*] v
cdef _SolutionBase phase
cdef _SolutionBase adj
if isinstance(self, Kinetics):
v.push_back(self.thermo)
for phase in phases:
for adj in adjacent:
# adjacent bulk phases for a surface phase
v.push_back(phase.thermo)
v.push_back(adj.thermo)
self.kinetics = newKineticsMgr(deref(phaseNode), v)
self._kinetics.reset(self.kinetics)
else:
self.kinetics = NULL
def _init_parts(self, thermo, species, kinetics, phases, reactions):
def _init_parts(self, thermo, species, kinetics, adjacent, reactions):
"""
Instantiate a set of new Cantera C++ objects based on a string defining
the model type and a list of Species objects.
@ -228,14 +248,15 @@ cdef class _SolutionBase:
if not kinetics:
kinetics = "none"
cdef ThermoPhase phase
cdef ThermoPhase adj
cdef Reaction reaction
if isinstance(self, Kinetics):
self.kinetics = CxxNewKinetics(stringify(kinetics))
self._kinetics.reset(self.kinetics)
self.kinetics.addPhase(deref(self.thermo))
for phase in phases:
self.kinetics.addPhase(deref(phase.thermo))
for adj in adjacent:
# adjacent bulk phases for a surface phase
self.kinetics.addPhase(deref(adj.thermo))
self.kinetics.init()
self.kinetics.skipUndeclaredThirdBodies(True)
for reaction in reactions:

36
interfaces/cython/cantera/test/test_convert.py
View file

@ -571,8 +571,8 @@ class cti2yamlTest(utilities.CanteraTest):
def checkConversion(self, basename, cls=ct.Solution, ctiphases=(),
yamlphases=(), **kwargs):
ctiPhase = cls(basename + '.cti', phases=ctiphases, **kwargs)
yamlPhase = cls(basename + '.yaml', phases=yamlphases, **kwargs)
ctiPhase = cls(basename + '.cti', adjacent=ctiphases, **kwargs)
yamlPhase = cls(basename + '.yaml', adjacent=yamlphases, **kwargs)
self.assertEqual(ctiPhase.element_names, yamlPhase.element_names)
self.assertEqual(ctiPhase.species_names, yamlPhase.species_names)
@ -660,7 +660,7 @@ class cti2yamlTest(utilities.CanteraTest):
Path(self.test_work_dir).joinpath('ptcombust.yaml'))
ctiGas, yamlGas = self.checkConversion('ptcombust')
ctiSurf, yamlSurf = self.checkConversion('ptcombust', ct.Interface,
phaseid='Pt_surf', ctiphases=[ctiGas], yamlphases=[yamlGas])
phase='Pt_surf', ctiphases=[ctiGas], yamlphases=[yamlGas])
self.checkKinetics(ctiGas, yamlGas, [500, 1200], [1e4, 3e5])
self.checkThermo(ctiSurf, yamlSurf, [400, 800, 1600])
@ -670,16 +670,16 @@ class cti2yamlTest(utilities.CanteraTest):
cti2yaml.convert(Path(self.cantera_data).joinpath('sofc.cti'),
Path(self.test_work_dir).joinpath('sofc.yaml'))
ctiGas, yamlGas = self.checkConversion('sofc')
ctiMetal, yamlMetal = self.checkConversion('sofc', phaseid='metal')
ctiOxide, yamlOxide = self.checkConversion('sofc', phaseid='oxide_bulk')
ctiMetal, yamlMetal = self.checkConversion('sofc', phase='metal')
ctiOxide, yamlOxide = self.checkConversion('sofc', phase='oxide_bulk')
ctiMSurf, yamlMSurf = self.checkConversion('sofc', ct.Interface,
phaseid='metal_surface', ctiphases=[ctiGas, ctiMetal],
phase='metal_surface', ctiphases=[ctiGas, ctiMetal],
yamlphases=[yamlGas, yamlMetal])
ctiOSurf, yamlOSurf = self.checkConversion('sofc', ct.Interface,
phaseid='oxide_surface', ctiphases=[ctiGas, ctiOxide],
phase='oxide_surface', ctiphases=[ctiGas, ctiOxide],
yamlphases=[yamlGas, yamlOxide])
cti_tpb, yaml_tpb = self.checkConversion('sofc', ct.Interface,
phaseid='tpb', ctiphases=[ctiMetal, ctiMSurf, ctiOSurf],
phase='tpb', ctiphases=[ctiMetal, ctiMSurf, ctiOSurf],
yamlphases=[yamlMetal, yamlMSurf, yamlOSurf])
self.checkThermo(ctiMSurf, yamlMSurf, [900, 1000, 1100])
@ -694,7 +694,7 @@ class cti2yamlTest(utilities.CanteraTest):
Path(self.test_work_dir).joinpath('liquidvapor.yaml'))
for name in ['water', 'nitrogen', 'methane', 'hydrogen', 'oxygen',
'hfc134a', 'carbondioxide', 'heptane']:
ctiPhase, yamlPhase = self.checkConversion('liquidvapor', phaseid=name)
ctiPhase, yamlPhase = self.checkConversion('liquidvapor', phase=name)
self.checkThermo(ctiPhase, yamlPhase,
[1.3 * ctiPhase.min_temp, 0.7 * ctiPhase.max_temp])
@ -717,10 +717,10 @@ class cti2yamlTest(utilities.CanteraTest):
def test_diamond(self):
cti2yaml.convert(Path(self.cantera_data).joinpath('diamond.cti'),
Path(self.test_work_dir).joinpath('diamond.yaml'))
ctiGas, yamlGas = self.checkConversion('diamond', phaseid='gas')
ctiSolid, yamlSolid = self.checkConversion('diamond', phaseid='diamond')
ctiGas, yamlGas = self.checkConversion('diamond', phase='gas')
ctiSolid, yamlSolid = self.checkConversion('diamond', phase='diamond')
ctiSurf, yamlSurf = self.checkConversion('diamond',
ct.Interface, phaseid='diamond_100', ctiphases=[ctiGas, ctiSolid],
ct.Interface, phase='diamond_100', ctiphases=[ctiGas, ctiSolid],
yamlphases=[yamlGas, yamlSolid])
self.checkThermo(ctiSolid, yamlSolid, [300, 500])
self.checkThermo(ctiSurf, yamlSurf, [330, 490])
@ -730,16 +730,16 @@ class cti2yamlTest(utilities.CanteraTest):
cti2yaml.convert(Path(self.cantera_data).joinpath('lithium_ion_battery.cti'),
Path(self.test_work_dir).joinpath('lithium_ion_battery.yaml'))
name = 'lithium_ion_battery'
ctiAnode, yamlAnode = self.checkConversion(name, phaseid='anode')
ctiCathode, yamlCathode = self.checkConversion(name, phaseid='cathode')
ctiMetal, yamlMetal = self.checkConversion(name, phaseid='electron')
ctiElyt, yamlElyt = self.checkConversion(name, phaseid='electrolyte')
ctiAnode, yamlAnode = self.checkConversion(name, phase='anode')
ctiCathode, yamlCathode = self.checkConversion(name, phase='cathode')
ctiMetal, yamlMetal = self.checkConversion(name, phase='electron')
ctiElyt, yamlElyt = self.checkConversion(name, phase='electrolyte')
ctiAnodeInt, yamlAnodeInt = self.checkConversion(name,
phaseid='edge_anode_electrolyte',
phase='edge_anode_electrolyte',
ctiphases=[ctiAnode, ctiMetal, ctiElyt],
yamlphases=[yamlAnode, yamlMetal, yamlElyt])
ctiCathodeInt, yamlCathodeInt = self.checkConversion(name,
phaseid='edge_cathode_electrolyte',
phase='edge_cathode_electrolyte',
ctiphases=[ctiCathode, ctiMetal, ctiElyt],
yamlphases=[yamlCathode, yamlMetal, yamlElyt])

4
interfaces/cython/cantera/test/test_kinetics.py
View file

@ -185,7 +185,7 @@ class KineticsFromReactions(utilities.CanteraTest):
surf2 = ct.Interface(thermo='Surface', kinetics='interface',
species=surf_species, reactions=reactions,
phases=[gas])
adjacent=[gas])
surf1.site_density = surf2.site_density = 5e-9
gas.TP = surf2.TP = surf1.TP = 900, 2*ct.one_atm
surf2.concentrations = surf1.concentrations
@ -1032,7 +1032,7 @@ class TestReaction(utilities.CanteraTest):
self.assertNear(r1.coverage_deps['H(S)'][2], -6e6)
surf2 = ct.Interface(thermo='Surface', species=surf_species,
kinetics='interface', reactions=[r1], phases=[gas])
kinetics='interface', reactions=[r1], adjacent=[gas])
surf2.site_density = surf1.site_density
surf1.coverages = surf2.coverages = 'PT(S):0.7, H(S):0.3'

7
interfaces/cython/cantera/test/test_thermo.py
View file

@ -343,6 +343,13 @@ class TestThermoPhase(utilities.CanteraTest):
self.assertTrue("To be removed after Cantera 2.5. "
in str(w[-1].message))
with warnings.catch_warnings(record=True) as w:
gas = ct.Solution('h2o2.cti', phaseid='ohmech')
self.assertTrue(len(w) == 1)
self.assertTrue(issubclass(w[-1].category, DeprecationWarning))
self.assertTrue("To be removed after Cantera 2.5. "
in str(w[-1].message))
def test_badLength(self):
X = np.zeros(5)
with self.assertRaisesRegex(ValueError, 'incorrect length'):