[Thermo] replace 'phase_id' by 'name'

* '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

include/cantera/base/Solution.h

@@ -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
 };
 
 }

interfaces/cython/cantera/_cantera.pxd

@@ -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

interfaces/cython/cantera/base.pyx

@@ -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
+        The name assigned to this object. The default value corresponds 
-        is based on the phase identifier in the CTI/XML/YAML input file;
+        to the CTI/XML/YAML input file phase entry.
-        a numbered suffix is added if needed to create a unique name.
         """
         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:
+        if name:
-            phaseNode = rootNode.findID(stringify(phase_id))
+            phaseNode = rootNode.findID(stringify(name))
         else:
             phaseNode = rootNode.findByName(stringify('phase'))
         if phaseNode is NULL:

interfaces/cython/cantera/ck2yaml.py

@@ -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=..."'

interfaces/cython/cantera/composite.py

@@ -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')
+        gas = ct.Solution('diamond.yaml', name='gas')
-        diamond = ct.Solution('diamond.yaml', phase_id='diamond')
+        diamond = ct.Solution('diamond.yaml', name='diamond')
 
-    The name of the `Solution` object needs to be unique and defaults to the
+    The name of the `Solution` object defaults to the *phase* specified in the 
-    *phase* specified in the input file. If another object using the same
+    input file. Once instatiated, a custom name can assigned via::
-    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.::
 
-        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')
+        gas = ct.Solution('diamond.yaml', name='gas')
-        diamond = ct.Solution('diamond.yaml', phase_id='diamond')
+        diamond = ct.Solution('diamond.yaml', name='diamond')
-        diamond_surf = ct.Interface('diamond.yaml', phase_id='diamond_100',
+        diamond_surf = ct.Interface('diamond.yaml', name='diamond_100',
                                     adjacent=[gas, diamond])
     """
     __slots__ = ('_phase_indices',)

interfaces/cython/cantera/kinetics.pyx

@@ -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):
+    def __init__(self, infile='', name='', adjacent=(), *args, **kwargs):
-        super().__init__(infile, phase_id, 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.")
 

interfaces/cython/cantera/test/test_convert.py

@@ -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')
+        ctiMetal, yamlMetal = self.checkConversion('sofc', name='metal')
-        ctiOxide, yamlOxide = self.checkConversion('sofc', phase_id='oxide_bulk')
+        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')
+        ctiGas, yamlGas = self.checkConversion('diamond', name='gas')
-        ctiSolid, yamlSolid = self.checkConversion('diamond', phase_id='diamond')
+        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')
+        ctiAnode, yamlAnode = self.checkConversion(name, name='anode')
-        ctiCathode, yamlCathode = self.checkConversion(name, phase_id='cathode')
+        ctiCathode, yamlCathode = self.checkConversion(name, name='cathode')
-        ctiMetal, yamlMetal = self.checkConversion(name, phase_id='electron')
+        ctiMetal, yamlMetal = self.checkConversion(name, name='electron')
-        ctiElyt, yamlElyt = self.checkConversion(name, phase_id='electrolyte')
+        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])
 

interfaces/cython/cantera/test/test_reactor.py

@@ -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')
 

interfaces/cython/cantera/test/test_thermo.py

@@ -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)

interfaces/cython/cantera/thermo.pyx

@@ -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)
+                          "Use 'name' attribute instead", DeprecationWarning)
-            return pystr(self.thermo.id())
+            return pystr(self.base.name())
         def __set__(self, id_):
             warnings.warn("To be removed after Cantera 2.5. "
-                          "Use 'phase' attribute instead", DeprecationWarning)
+                          "Use 'name' attribute instead", DeprecationWarning)
-            self.thermo.setID(stringify(id_))
+            self.base.setName(stringify(id_))
 
     property basis:
         """

src/base/Solution.cpp

@@ -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() :
+Solution::Solution() {}
-    m_name("<Solution_name>")
-{}
 
 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){
+void Solution::setName(const std::string& name) {
-    m_name = 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

src/thermo/Phase.cpp

@@ -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();
+    return m_name;
-    if (root) {
-        return root->name();
-    } else {
-        return m_name;
-    }
 }
 
 void Phase::setName(const std::string& name)
 {
-    auto root = m_root.lock();
+    m_name = name;
-    if (root) {
+    m_id = name;
-        root->setName(name);
-    } else {
-        m_name = name;
-    }
 }
 
 size_t Phase::nElements() const