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[Thermo] replace 'phase_id' by 'name'

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* 'name' corresponds to the YAML entry
* rename Solution keyword 'phaseid' to 'name' (instead of 'phase_id')
* rename ck2yaml argument '--id' to '--name' (instead of '--phase-id')
* ensure that C++ Phase::m_id is always the same as Phase::m_name
This commit is contained in:
Ingmar Schoegl 2019-10-09 19:01:43 -05:00 • committed by Ray Speth
parent 5928d63746
commit 6e5d45273a
12 changed files with 83 additions and 107 deletions
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2
include/cantera/base/Solution.h
View file

@ -64,8 +64,6 @@ protected:
shared_ptr<ThermoPhase> m_thermo; //! ThermoPhase manager
shared_ptr<Kinetics> m_kinetics; //! Kinetics manager
shared_ptr<Transport> m_transport; //! Transport manager
std::string m_name; //! name of Solution object
};
}

2
interfaces/cython/cantera/_cantera.pxd
View file

@ -140,8 +140,6 @@ cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
# miscellaneous
string type()
string report(cbool, double) except +translate_exception
string id()
void setID(string)
double minTemp() except +translate_exception
double maxTemp() except +translate_exception
double refPressure() except +translate_exception

36
interfaces/cython/cantera/base.pyx
View file

@ -3,20 +3,18 @@
from collections import defaultdict as _defaultdict
_phase_counts = _defaultdict(int)
cdef class _SolutionBase:
def __cinit__(self, infile='', phase_id='', adjacent=(), origin=None,
def __cinit__(self, infile='', name='', adjacent=(), origin=None,
source=None, yaml=None, thermo=None, species=(),
kinetics=None, reactions=(), **kwargs):
if 'phaseid' in kwargs:
if phase_id is not '':
if name is not '':
raise AttributeError('duplicate specification of phase name')
warnings.warn("Keyword 'phase_id' replaces 'phaseid'",
warnings.warn("Keyword 'name' replaces 'phaseid'",
FutureWarning)
phase_id = kwargs['phaseid']
name = kwargs['phaseid']
if 'phases' in kwargs:
if len(adjacent)>0:
@ -54,9 +52,9 @@ cdef class _SolutionBase:
# Parse inputs
if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
self._init_yaml(infile, phase_id, adjacent, yaml)
self._init_yaml(infile, name, adjacent, yaml)
elif infile or source:
self._init_cti_xml(infile, phase_id, adjacent, source)
self._init_cti_xml(infile, name, adjacent, source)
elif thermo and species:
self._init_parts(thermo, species, kinetics, adjacent, reactions)
else:
@ -72,23 +70,17 @@ cdef class _SolutionBase:
if isinstance(self, Transport):
assert self.transport is not NULL
phase_name = pystr(self.thermo.id())
phase_name = pystr(self.base.name())
name = kwargs.get('name')
if name is not None:
self.name = name
elif phase_name in _phase_counts:
_phase_counts[phase_name] += 1
n = _phase_counts[phase_name]
self.name = '{0}_{1}'.format(phase_name, n)
else:
_phase_counts[phase_name] = 0
self.name = phase_name
property name:
"""
The name assigned to this SolutionBase object. The default value
is based on the phase identifier in the CTI/XML/YAML input file;
a numbered suffix is added if needed to create a unique name.
The name assigned to this object. The default value corresponds
to the CTI/XML/YAML input file phase entry.
"""
def __get__(self):
return pystr(self.base.name())
@ -111,7 +103,7 @@ cdef class _SolutionBase:
return thermo, kinetics, transport
def _init_yaml(self, infile, phase_id, adjacent, source):
def _init_yaml(self, infile, name, adjacent, source):
"""
Instantiate a set of new Cantera C++ objects from a YAML
phase definition
@ -123,7 +115,7 @@ cdef class _SolutionBase:
root = AnyMapFromYamlString(stringify(source))
phaseNode = root[stringify("phases")].getMapWhere(stringify("name"),
stringify(phase_id))
stringify(name))
# Thermo
if isinstance(self, ThermoPhase):
@ -146,7 +138,7 @@ cdef class _SolutionBase:
else:
self.kinetics = NULL
def _init_cti_xml(self, infile, phase_id, adjacent, source):
def _init_cti_xml(self, infile, name, adjacent, source):
"""
Instantiate a set of new Cantera C++ objects from a CTI or XML
phase definition
@ -158,8 +150,8 @@ cdef class _SolutionBase:
# Get XML data
cdef XML_Node* phaseNode
if phase_id:
phaseNode = rootNode.findID(stringify(phase_id))
if name:
phaseNode = rootNode.findID(stringify(name))
else:
phaseNode = rootNode.findByName(stringify('phase'))
if phaseNode is NULL:

10
interfaces/cython/cantera/ck2yaml.py
View file

@ -12,7 +12,7 @@ Usage:
[--thermo=<filename>]
[--transport=<filename>]
[--surface=<filename>]
[--phase-id=<phase-id>]
[--name=<name>]
[--output=<filename>]
[--permissive]
[-d | --debug]
@ -32,7 +32,7 @@ specified as 'input' and the surface phase input file should be specified as
'surface'.
The '--permissive' option allows certain recoverable parsing errors (e.g.
duplicate transport data) to be ignored. The '--phase-id=<phase-id>' option
duplicate transport data) to be ignored. The '--name=<name>' option
is used to override default phase names (i.e. 'gas').
"""
@ -2025,7 +2025,7 @@ def convert_mech(input_file, thermo_file=None, transport_file=None, surface_file
def main(argv):
longOptions = ['input=', 'thermo=', 'transport=', 'surface=', 'phase-id=',
longOptions = ['input=', 'thermo=', 'transport=', 'surface=', 'name=',
'output=', 'permissive', 'help', 'debug', 'quiet',
'no-validate', 'id=']
@ -2059,9 +2059,9 @@ def main(argv):
if '--id' in options:
phase_name = options.get('--id', 'gas')
logging.warning("\nFutureWarning: "
"option '--id=...' is superseded by '--phase-id=...'")
"option '--id=...' is superseded by '--name=...'")
else:
phase_name = options.get('--phase-id', 'gas')
phase_name = options.get('--name', 'gas')
if not input_file and not thermo_file:
print('At least one of the arguments "--input=..." or "--thermo=..."'

23
interfaces/cython/cantera/composite.py
View file

@ -33,19 +33,16 @@ class Solution(ThermoPhase, Kinetics, Transport):
If an input file defines multiple phases, the corresponding key in the
*phases* map (in YAML), *name* (in CTI), or *id* (in XML) can be used
to specify the desired phase via the ``phase_id`` keyword argument of
to specify the desired phase via the ``name`` keyword argument of
the constructor::
gas = ct.Solution('diamond.yaml', phase_id='gas')
diamond = ct.Solution('diamond.yaml', phase_id='diamond')
gas = ct.Solution('diamond.yaml', name='gas')
diamond = ct.Solution('diamond.yaml', name='diamond')
The name of the `Solution` object needs to be unique and defaults to the
*phase* specified in the input file. If another object using the same
constituting information already exists, the name is automatically appended
by a suffix. A custom name can be set via the ``name`` keyword argument of
the constructor, i.e.::
The name of the `Solution` object defaults to the *phase* specified in the
input file. Once instatiated, a custom name can assigned via::
gas = ct.Solution('gri30.yaml', name='my_custom_name')
gas.name = 'my_custom_name'
`Solution` objects can also be constructed using `Species` and `Reaction`
objects which can themselves either be imported from input files or defined
@ -54,7 +51,7 @@ class Solution(ThermoPhase, Kinetics, Transport):
spec = ct.Species.listFromFile('gri30.yaml')
rxns = ct.Reaction.listFromFile('gri30.yaml')
gas = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
species=spec, reactions=rxns)
species=spec, reactions=rxns, name='my_custom_name')
where the ``thermo`` and ``kinetics`` keyword arguments are strings
specifying the thermodynamic and kinetics model, respectively, and
@ -99,9 +96,9 @@ class Interface(InterfacePhase, InterfaceKinetics):
in reactions need to be created and then passed in as a list in the
``adjacent`` argument to the constructor::
gas = ct.Solution('diamond.yaml', phase_id='gas')
diamond = ct.Solution('diamond.yaml', phase_id='diamond')
diamond_surf = ct.Interface('diamond.yaml', phase_id='diamond_100',
gas = ct.Solution('diamond.yaml', name='gas')
diamond = ct.Solution('diamond.yaml', name='diamond')
diamond_surf = ct.Interface('diamond.yaml', name='diamond_100',
adjacent=[gas, diamond])
"""
__slots__ = ('_phase_indices',)

4
interfaces/cython/cantera/kinetics.pyx
View file

@ -371,8 +371,8 @@ cdef class InterfaceKinetics(Kinetics):
A kinetics manager for heterogeneous reaction mechanisms. The
reactions are assumed to occur at an interface between bulk phases.
"""
def __init__(self, infile='', phase_id='', adjacent=(), *args, **kwargs):
super().__init__(infile, phase_id, adjacent, *args, **kwargs)
def __init__(self, infile='', name='', adjacent=(), *args, **kwargs):
super().__init__(infile, name, adjacent, *args, **kwargs)
if pystr(self.kinetics.kineticsType()) not in ("Surf", "Edge"):
raise TypeError("Underlying Kinetics class is not of the correct type.")

32
interfaces/cython/cantera/test/test_convert.py
View file

@ -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,
phase_id='Pt_surf', ctiphases=[ctiGas], yamlphases=[yamlGas])
name='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', phase_id='metal')
ctiOxide, yamlOxide = self.checkConversion('sofc', phase_id='oxide_bulk')
ctiMetal, yamlMetal = self.checkConversion('sofc', name='metal')
ctiOxide, yamlOxide = self.checkConversion('sofc', name='oxide_bulk')
ctiMSurf, yamlMSurf = self.checkConversion('sofc', ct.Interface,
phase_id='metal_surface', ctiphases=[ctiGas, ctiMetal],
name='metal_surface', ctiphases=[ctiGas, ctiMetal],
yamlphases=[yamlGas, yamlMetal])
ctiOSurf, yamlOSurf = self.checkConversion('sofc', ct.Interface,
phase_id='oxide_surface', ctiphases=[ctiGas, ctiOxide],
name='oxide_surface', ctiphases=[ctiGas, ctiOxide],
yamlphases=[yamlGas, yamlOxide])
cti_tpb, yaml_tpb = self.checkConversion('sofc', ct.Interface,
phase_id='tpb', ctiphases=[ctiMetal, ctiMSurf, ctiOSurf],
name='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', phase_id=name)
ctiPhase, yamlPhase = self.checkConversion('liquidvapor', name=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', phase_id='gas')
ctiSolid, yamlSolid = self.checkConversion('diamond', phase_id='diamond')
ctiGas, yamlGas = self.checkConversion('diamond', name='gas')
ctiSolid, yamlSolid = self.checkConversion('diamond', name='diamond')
ctiSurf, yamlSurf = self.checkConversion('diamond',
ct.Interface, phase_id='diamond_100', ctiphases=[ctiGas, ctiSolid],
ct.Interface, name='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, phase_id='anode')
ctiCathode, yamlCathode = self.checkConversion(name, phase_id='cathode')
ctiMetal, yamlMetal = self.checkConversion(name, phase_id='electron')
ctiElyt, yamlElyt = self.checkConversion(name, phase_id='electrolyte')
ctiAnode, yamlAnode = self.checkConversion(name, name='anode')
ctiCathode, yamlCathode = self.checkConversion(name, name='cathode')
ctiMetal, yamlMetal = self.checkConversion(name, name='electron')
ctiElyt, yamlElyt = self.checkConversion(name, name='electrolyte')
ctiAnodeInt, yamlAnodeInt = self.checkConversion(name,
phase_id='edge_anode_electrolyte',
name='edge_anode_electrolyte',
ctiphases=[ctiAnode, ctiMetal, ctiElyt],
yamlphases=[yamlAnode, yamlMetal, yamlElyt])
ctiCathodeInt, yamlCathodeInt = self.checkConversion(name,
phase_id='edge_cathode_electrolyte',
name='edge_cathode_electrolyte',
ctiphases=[ctiCathode, ctiMetal, ctiElyt],
yamlphases=[yamlCathode, yamlMetal, yamlElyt])

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

@ -929,9 +929,9 @@ class TestConstPressureReactor(utilities.CanteraTest):
self.gas.TPX = 900, 25*ct.one_atm, 'CO:0.5, H2O:0.2'
self.gas1 = ct.Solution('gri30.xml')
self.gas1.phase_id = 'gas'
self.gas1.name = 'gas'
self.gas2 = ct.Solution('gri30.xml')
self.gas2.phase_id = 'gas'
self.gas2.name = 'gas'
resGas = ct.Solution('gri30.xml')
solid = ct.Solution('diamond.xml', 'diamond')

8
interfaces/cython/cantera/test/test_thermo.py
View file

@ -323,7 +323,7 @@ class TestThermoPhase(utilities.CanteraTest):
self.assertIn('something', self.phase.report())
def test_phase(self):
self.assertEqual(self.phase.phase_id, 'ohmech')
self.assertEqual(self.phase.name, 'ohmech')
warnings.simplefilter("always")
with warnings.catch_warnings(record=True) as w:
@ -335,7 +335,7 @@ class TestThermoPhase(utilities.CanteraTest):
with warnings.catch_warnings(record=True) as w:
self.phase.ID = 'something'
self.assertEqual(self.phase.phase_id, 'something')
self.assertEqual(self.phase.name, 'something')
self.assertEqual(len(w), 1)
self.assertTrue(issubclass(w[-1].category, DeprecationWarning))
self.assertIn("To be removed after Cantera 2.5. ",
@ -345,7 +345,7 @@ class TestThermoPhase(utilities.CanteraTest):
gas = ct.Solution('h2o2.cti', phaseid='ohmech')
self.assertEqual(len(w), 1)
self.assertTrue(issubclass(w[-1].category, FutureWarning))
self.assertIn("Keyword 'phase_id' replaces 'phaseid'",
self.assertIn("Keyword 'name' replaces 'phaseid'",
str(w[-1].message))
def test_badLength(self):
@ -881,7 +881,7 @@ class ImportTest(utilities.CanteraTest):
Test the various ways of creating a Solution object
"""
def check(self, gas, phase, T, P, nSpec, nElem):
self.assertEqual(gas.phase_id, phase)
self.assertEqual(gas.name, phase)
self.assertNear(gas.T, T)
self.assertNear(gas.P, P)
self.assertEqual(gas.n_species, nSpec)

24
interfaces/cython/cantera/thermo.pyx
View file

@ -290,36 +290,24 @@ cdef class ThermoPhase(_SolutionBase):
def __call__(self, *args, **kwargs):
print(self.report(*args, **kwargs))
property phase_id:
"""
The identifier of the object. The default value corresponds to the
CTI/XML/YAML input file phase entry, and should remain unchanged.
"""
def __get__(self):
return pystr(self.thermo.id())
def __set__(self, phase_id):
# may consider removing/deprecating, but resetting of the phase name
# is required to associate surface kinetics (with phase name being 'gas')
self.thermo.setID(stringify(phase_id))
property ID:
"""
The identifier of the object. The default value corresponds to the
CTI/XML/YAML input file phase entry, and should remain unchanged.
CTI/XML/YAML input file phase entry.
.. deprecated:: 2.5
To be deprecated with version 2.5, and removed thereafter.
Renamed to `phase_ID`.
Usage merged with `name`.
"""
def __get__(self):
warnings.warn("To be removed after Cantera 2.5. "
"Use 'phase' attribute instead", DeprecationWarning)
return pystr(self.thermo.id())
"Use 'name' attribute instead", DeprecationWarning)
return pystr(self.base.name())
def __set__(self, id_):
warnings.warn("To be removed after Cantera 2.5. "
"Use 'phase' attribute instead", DeprecationWarning)
self.thermo.setID(stringify(id_))
"Use 'name' attribute instead", DeprecationWarning)
self.base.setName(stringify(id_))
property basis:
"""

28
src/base/Solution.cpp
View file

@ -1,4 +1,7 @@
//! @file Solution.cpp
/**
* @file Solution.cpp
* Definition file for class Solution.
*/
// This file is part of Cantera. See License.txt in the top-level directory or
// at https://cantera.org/license.txt for license and copyright information.
@ -11,16 +14,24 @@
namespace Cantera
{
Solution::Solution() :
m_name("<Solution_name>")
{}
Solution::Solution() {}
std::string Solution::name() const {
return m_name;
if (m_thermo) {
return m_thermo->name();
} else {
throw CanteraError("Solution::name()",
"Requires associated 'ThermoPhase'");
}
}
void Solution::setName(const std::string& name){
m_name = name;
void Solution::setName(const std::string& name) {
if (m_thermo) {
m_thermo->setName(name);
} else {
throw CanteraError("Solution::setName()",
"Requires associated 'ThermoPhase'");
}
}
void Solution::setThermoPhase(shared_ptr<ThermoPhase> thermo) {
@ -43,4 +54,5 @@ void Solution::setTransport(shared_ptr<Transport> transport) {
m_transport->setRoot(shared_from_this());
}
}
}
} // namespace Cantera

17
src/thermo/Phase.cpp
View file

@ -9,7 +9,6 @@
#include "cantera/thermo/Phase.h"
#include "cantera/base/utilities.h"
#include "cantera/base/stringUtils.h"
#include "cantera/base/Solution.h"
#include "cantera/base/ctml.h"
#include "cantera/thermo/ThermoFactory.h"
@ -75,26 +74,18 @@ std::string Phase::id() const
void Phase::setID(const std::string& id_)
{
m_id = id_;
m_name = id_;
}
std::string Phase::name() const
{
auto root = m_root.lock();
if (root) {
return root->name();
} else {
return m_name;
}
return m_name;
}
void Phase::setName(const std::string& name)
{
auto root = m_root.lock();
if (root) {
root->setName(name);
} else {
m_name = name;
}
m_name = name;
m_id = name;
}
size_t Phase::nElements() const