From 0aa5723def8d9aff24f644785f385cd12c63b30f Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Fri, 16 Aug 2019 07:26:24 -0500
Subject: [PATCH 01/17] [Base] create SolutionBase object in C++

* Add Base.h/Base.cpp with definition of SolutionBase
* Link C++ object into Cython interface
* Add unique_name and type attributes to Cython _SolutionBase
---
 include/cantera/base/Base.h             | 72 +++++++++++++++++++++++++
 interfaces/cython/cantera/_cantera.pxd  | 14 +++++
 interfaces/cython/cantera/base.pyx      | 38 +++++++++++++
 interfaces/cython/cantera/composite.py  |  9 ++++
 interfaces/cython/cantera/kinetics.pyx  |  5 ++
 interfaces/cython/cantera/thermo.pyx    |  2 +
 interfaces/cython/cantera/transport.pyx |  4 ++
 src/base/Base.cpp                       | 38 +++++++++++++
 8 files changed, 182 insertions(+)
 create mode 100644 include/cantera/base/Base.h
 create mode 100644 src/base/Base.cpp

diff --git a/include/cantera/base/Base.h b/include/cantera/base/Base.h
new file mode 100644
index 00000000000..4c3acea5a14
--- /dev/null
+++ b/include/cantera/base/Base.h
@@ -0,0 +1,72 @@
+//! @file Base.h
+
+// 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.
+
+#ifndef CT_BASE_H
+#define CT_BASE_H
+
+#include "cantera/base/ctexceptions.h"
+
+namespace Cantera
+{
+
+class ThermoPhase;
+class Kinetics;
+class Transport;
+
+//! A container class holding managers for all pieces defining a phase
+class SolutionBase {
+public:
+    SolutionBase();
+    SolutionBase(const std::string& infile, const std::string& phasename);
+    ~SolutionBase() {}
+    SolutionBase(const SolutionBase&) = delete;
+    SolutionBase& operator=(const SolutionBase&) = delete;
+
+    //! String indicating the type of the SolutionBase object. Corresponds
+    //! to the type of phase originally instantiated
+    std::string type() const {
+        return m_type;
+    }
+
+    //! Set the type of this SolutionBase object
+    void setType(const std::string& type){
+        m_type = type;
+    }
+
+    //! Return the name of this SolutionBase object
+    std::string name() const {
+        return m_name;
+    }
+
+    //! Set the name of this SolutionBase object
+    void setName(const std::string& name){
+        m_name = name;
+    }
+
+    //! Generate self-documenting YAML string
+    virtual std::string toYAML() const {
+        throw NotImplementedError("SolutionBase::toYAML");
+    }
+
+    //! Set the ThermoPhase object
+    void setThermoPhase(shared_ptr<ThermoPhase> thermo);
+
+    //! Set the Kinetics object
+    void setKinetics(shared_ptr<Kinetics> kinetics);
+
+    //! Set the Transport object
+    void setTransport(shared_ptr<Transport> transport);
+
+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_type;  //! type of SolutionBase object
+    std::string m_name;  //! name of SolutionBase object
+};
+
+}
+#endif
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index a37104633f3..ff5ac7219f8 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -120,6 +120,19 @@ cdef extern from "cantera/thermo/Species.h" namespace "Cantera":
     cdef shared_ptr[CxxSpecies] CxxNewSpecies "newSpecies" (CxxAnyMap&) except +translate_exception
     cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (CxxAnyValue&) except +translate_exception
 
+
+cdef extern from "cantera/base/Base.h" namespace "Cantera":
+    cdef cppclass CxxSolutionBase "Cantera::SolutionBase":
+        CxxSolutionBase()
+        string type()
+        string setType(string)
+        string name()
+        void setName(string)
+        void setThermoPhase(shared_ptr[CxxThermoPhase])
+        void setKinetics(shared_ptr[CxxKinetics])
+        void setTransport(shared_ptr[CxxTransport])
+
+
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
     cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
         CxxThermoPhase()
@@ -928,6 +941,7 @@ cdef class GasTransportData:
     cdef _assign(self, shared_ptr[CxxTransportData] other)
 
 cdef class _SolutionBase:
+    cdef CxxSolutionBase* base
     cdef shared_ptr[CxxThermoPhase] _thermo
     cdef CxxThermoPhase* thermo
     cdef shared_ptr[CxxKinetics] _kinetics
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index f2284c1af9b..802b8c13f71 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -1,6 +1,10 @@
 # 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.
 
+from collections import defaultdict as _defaultdict
+
+_phase_counts = _defaultdict(int)
+
 cdef class _SolutionBase:
     def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
                   source=None, yaml=None, thermo=None, species=(),
@@ -10,6 +14,7 @@ cdef class _SolutionBase:
         if origin is not None:
             other = <_SolutionBase?>origin
 
+            self.base = other.base
             self.thermo = other.thermo
             self.kinetics = other.kinetics
             self.transport = other.transport
@@ -21,6 +26,9 @@ cdef class _SolutionBase:
             self._selected_species = other._selected_species.copy()
             return
 
+        # Assign type and unique_name during __init__
+        self.base = new CxxSolutionBase()
+
         if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
             self._init_yaml(infile, phaseid, phases, yaml)
         elif infile or source:
@@ -31,6 +39,8 @@ cdef class _SolutionBase:
             raise ValueError("Arguments are insufficient to define a phase")
 
         # Initialization of transport is deferred to Transport.__init__
+        self.base.setThermoPhase(self._thermo)
+        self.base.setKinetics(self._kinetics)
         self.transport = NULL
 
         self._selected_species = np.ndarray(0, dtype=np.integer)
@@ -39,6 +49,34 @@ cdef class _SolutionBase:
         if isinstance(self, Transport):
             assert self.transport is not NULL
 
+        base_type = kwargs.get('base_type', None)
+        if base_type:
+            self.base.setType(stringify(base_type))
+        else:
+            raise ValueError('Missing required keyword `base_type`.')
+
+        phasename = pystr(self.thermo.name())
+        name = kwargs.get('name', None)
+        if name is not None:
+            self.unique_name = name
+        else:
+            _phase_counts[phasename] += 1
+            n = _phase_counts[phasename]
+            self.unique_name = '{0}_{1}'.format(phasename, n)
+
+    property type:
+        """The type of the SolutionBase object."""
+        def __get__(self):
+            return pystr(self.base.type())
+
+    property unique_name:
+        """The unique name of the SolutionBase object."""
+        def __get__(self):
+            return pystr(self.base.name())
+
+        def __set__(self, name):
+            self.base.setName(stringify(name))
+
     def _init_yaml(self, infile, phaseid, phases, source):
         """
         Instantiate a set of new Cantera C++ objects from a YAML
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index 196dc48e798..22f5dee6d30 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -63,6 +63,9 @@ class Solution(ThermoPhase, Kinetics, Transport):
     """
     __slots__ = ()
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, base_type='Solution', **kwargs)
+
 
 class Interface(InterfacePhase, InterfaceKinetics):
     """
@@ -82,6 +85,9 @@ class Interface(InterfacePhase, InterfaceKinetics):
     """
     __slots__ = ('_phase_indices',)
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, base_type='Interface', **kwargs)
+
 
 class DustyGas(ThermoPhase, Kinetics, DustyGasTransport):
     """
@@ -93,6 +99,9 @@ class DustyGas(ThermoPhase, Kinetics, DustyGasTransport):
     """
     __slots__ = ()
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, base_type='DustyGas', **kwargs)
+
 
 class Quantity:
     """
diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index 44ae9281f01..89e7544c958 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/interfaces/cython/cantera/kinetics.pyx
@@ -26,6 +26,11 @@ cdef class Kinetics(_SolutionBase):
     a reaction mechanism.
     """
 
+    def __init__(self, *args, **kwargs):
+        base_type = kwargs.pop('base_type', 'Kinetics')
+        kwargs['base_type'] = base_type
+        super().__init__(*args, **kwargs)
+
     property n_total_species:
         """
         Total number of species in all phases participating in the kinetics
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 4980b69ecca..9ed8a479ea1 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -263,6 +263,8 @@ cdef class ThermoPhase(_SolutionBase):
 
     # The signature of this function causes warnings for Sphinx documentation
     def __init__(self, *args, **kwargs):
+        base_type = kwargs.pop('base_type', 'ThermoPhase')
+        kwargs['base_type'] = base_type
         super().__init__(*args, **kwargs)
         if 'source' not in kwargs:
             self.thermo_basis = mass_basis
diff --git a/interfaces/cython/cantera/transport.pyx b/interfaces/cython/cantera/transport.pyx
index b6235b7dee6..82fa37aca04 100644
--- a/interfaces/cython/cantera/transport.pyx
+++ b/interfaces/cython/cantera/transport.pyx
@@ -144,7 +144,11 @@ cdef class Transport(_SolutionBase):
                     model = 'None'
                 self.transport = newTransportMgr(stringify(model), self.thermo)
             self._transport.reset(self.transport)
+
+        base_type = kwargs.pop('base_type', 'Transport')
+        kwargs['base_type'] = base_type
         super().__init__(*args, **kwargs)
+        self.base.setTransport(self._transport)
 
     property transport_model:
         """
diff --git a/src/base/Base.cpp b/src/base/Base.cpp
new file mode 100644
index 00000000000..367b5659d41
--- /dev/null
+++ b/src/base/Base.cpp
@@ -0,0 +1,38 @@
+//! @file Base.cpp
+
+// 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.
+
+#include "cantera/base/Base.h"
+
+namespace Cantera
+{
+
+SolutionBase::SolutionBase() :
+    m_thermo(nullptr),
+    m_kinetics(nullptr),
+    m_transport(nullptr),
+    m_type("<SolutionBase_type>"),
+    m_name("<unique_name>")
+{}
+
+SolutionBase::SolutionBase(const std::string& infile,
+                           const std::string& phasename) :
+    SolutionBase()
+{
+    // this *may* be a spot to load all pieces of a phase
+    throw NotImplementedError("SolutionBase constructor from file");
+}
+
+void SolutionBase::setThermoPhase(shared_ptr<ThermoPhase> thermo) {
+    m_thermo = thermo;
+}
+
+void SolutionBase::setKinetics(shared_ptr<Kinetics> kinetics) {
+    m_kinetics = kinetics;
+}
+
+void SolutionBase::setTransport(shared_ptr<Transport> transport) {
+    m_transport = transport;
+}
+}

From bc04a967d29d22328f763036f786a827a1872cd6 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Fri, 16 Aug 2019 09:33:15 -0500
Subject: [PATCH 02/17] [Base] add unit test probing methods of C++
 SolutionBase

---
 interfaces/cython/cantera/test/test_thermo.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index 8ce4d846e6d..49ed49df609 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -12,6 +12,15 @@ class TestThermoPhase(utilities.CanteraTest):
     def setUp(self):
         self.phase = ct.Solution('h2o2.xml')
 
+    def test_cpp_attributes(self):
+        self.assertTrue(isinstance(self.phase.type, str))
+        self.assertTrue(self.phase.type=='Solution')
+        self.assertTrue(isinstance(self.phase.unique_name, str))
+        self.phase.unique_name = 'spam'
+        self.assertTrue(self.phase.unique_name=='spam')
+        with self.assertRaises(AttributeError):
+            self.phase.type = 'eggs'
+
     def test_phases(self):
         self.assertEqual(self.phase.n_phases, 1)
 

From 8036169772987d4022db3ad7e62e99708987094a Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Fri, 16 Aug 2019 10:42:30 -0500
Subject: [PATCH 03/17] [Base] link managers back to SolutionBase

---
 include/cantera/base/Base.h               |  7 ++++++-
 include/cantera/kinetics/Kinetics.h       | 10 ++++++++++
 include/cantera/thermo/ThermoPhase.h      | 10 ++++++++++
 include/cantera/transport/TransportBase.h | 10 ++++++++++
 interfaces/cython/cantera/_cantera.pxd    |  3 +++
 interfaces/cython/cantera/base.pyx        | 11 ++++++++---
 src/base/Base.cpp                         | 13 +++++++++++++
 7 files changed, 60 insertions(+), 4 deletions(-)

diff --git a/include/cantera/base/Base.h b/include/cantera/base/Base.h
index 4c3acea5a14..9c084642285 100644
--- a/include/cantera/base/Base.h
+++ b/include/cantera/base/Base.h
@@ -16,7 +16,8 @@ class Kinetics;
 class Transport;
 
 //! A container class holding managers for all pieces defining a phase
-class SolutionBase {
+class SolutionBase : public std::enable_shared_from_this<SolutionBase>
+{
 public:
     SolutionBase();
     SolutionBase(const std::string& infile, const std::string& phasename);
@@ -24,6 +25,10 @@ class SolutionBase {
     SolutionBase(const SolutionBase&) = delete;
     SolutionBase& operator=(const SolutionBase&) = delete;
 
+    static shared_ptr<SolutionBase> create() {
+        return shared_ptr<SolutionBase>( new SolutionBase );
+    }
+
     //! String indicating the type of the SolutionBase object. Corresponds
     //! to the type of phase originally instantiated
     std::string type() const {
diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
index 17b232d4b82..4cacaa8e49e 100644
--- a/include/cantera/kinetics/Kinetics.h
+++ b/include/cantera/kinetics/Kinetics.h
@@ -19,6 +19,8 @@
 namespace Cantera
 {
 
+class SolutionBase;
+
 /**
  * @defgroup chemkinetics Chemical Kinetics
  */
@@ -814,6 +816,11 @@ class Kinetics
     void selectPhase(const doublereal* data, const thermo_t* phase,
                      doublereal* phase_data);
 
+    //! Set root SolutionBase holding all phase information
+    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+        m_root = root;
+    }
+
 protected:
     //! Cache for saved calculations within each Kinetics object.
     ValueCache m_cache;
@@ -935,6 +942,9 @@ class Kinetics
 
     //! @see skipUndeclaredThirdBodies()
     bool m_skipUndeclaredThirdBodies;
+
+    //! reference to SolutionBase
+    std::weak_ptr<SolutionBase> m_root;
 };
 
 }
diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h
index fdac8cf29c9..2b21ce6e1d4 100644
--- a/include/cantera/thermo/ThermoPhase.h
+++ b/include/cantera/thermo/ThermoPhase.h
@@ -40,6 +40,8 @@ const int cSS_CONVENTION_VPSS = 1;
 const int cSS_CONVENTION_SLAVE = 2;
 //@}
 
+class SolutionBase;
+
 //! Base class for a phase with thermodynamic properties.
 /*!
  * Class ThermoPhase is the base class for the family of classes that represent
@@ -1616,6 +1618,11 @@ class ThermoPhase : public Phase
 
     //@}
 
+    //! Set root SolutionBase holding all phase information
+    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+        m_root = root;
+    }
+
 protected:
     //! Fills `names` and `data` with the column names and species thermo
     //! properties to be included in the output of the reportCSV method.
@@ -1660,6 +1667,9 @@ class ThermoPhase : public Phase
 
     //! last value of the temperature processed by reference state
     mutable doublereal m_tlast;
+
+    //! reference to SolutionBase
+    std::weak_ptr<SolutionBase> m_root;
 };
 
 //! typedef for the ThermoPhase class
diff --git a/include/cantera/transport/TransportBase.h b/include/cantera/transport/TransportBase.h
index 9447fd67703..171aff9f396 100644
--- a/include/cantera/transport/TransportBase.h
+++ b/include/cantera/transport/TransportBase.h
@@ -74,6 +74,8 @@ const VelocityBasis VB_SPECIES_2 = 2;
 const VelocityBasis VB_SPECIES_3 = 3;
 //@}
 
+class SolutionBase;
+
 //! Base class for transport property managers.
 /*!
  * All classes that compute transport properties for a single phase derive from
@@ -654,6 +656,11 @@ class Transport
      */
     virtual void setThermo(thermo_t& thermo);
 
+    //! Set root SolutionBase holding all phase information
+    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+        m_root = root;
+    }
+
 protected:
     //! Enable the transport object for use.
     /*!
@@ -680,6 +687,9 @@ class Transport
     //! Velocity basis from which diffusion velocities are computed.
     //! Defaults to the mass averaged basis = -2
     int m_velocityBasis;
+
+    //! reference to SolutionBase
+    std::weak_ptr<SolutionBase> m_root;
 };
 
 }
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index ff5ac7219f8..ff576b20efd 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -132,6 +132,8 @@ cdef extern from "cantera/base/Base.h" namespace "Cantera":
         void setKinetics(shared_ptr[CxxKinetics])
         void setTransport(shared_ptr[CxxTransport])
 
+    cdef shared_ptr[CxxSolutionBase] CxxNewSolutionBase "Cantera::SolutionBase::create" ()
+
 
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
     cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
@@ -942,6 +944,7 @@ cdef class GasTransportData:
 
 cdef class _SolutionBase:
     cdef CxxSolutionBase* base
+    cdef shared_ptr[CxxSolutionBase] _base
     cdef shared_ptr[CxxThermoPhase] _thermo
     cdef CxxThermoPhase* thermo
     cdef shared_ptr[CxxKinetics] _kinetics
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 802b8c13f71..4bb8dcb57ff 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -18,6 +18,7 @@ cdef class _SolutionBase:
             self.thermo = other.thermo
             self.kinetics = other.kinetics
             self.transport = other.transport
+            self._base = other._base
             self._thermo = other._thermo
             self._kinetics = other._kinetics
             self._transport = other._transport
@@ -26,9 +27,14 @@ cdef class _SolutionBase:
             self._selected_species = other._selected_species.copy()
             return
 
-        # Assign type and unique_name during __init__
-        self.base = new CxxSolutionBase()
+        # Assign base and set managers to NULL
+        self._base = CxxNewSolutionBase()
+        self.base = self._base.get()
+        self.thermo = NULL
+        self.kinetics = NULL
+        self.transport = NULL
 
+        # Parse inputs
         if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
             self._init_yaml(infile, phaseid, phases, yaml)
         elif infile or source:
@@ -41,7 +47,6 @@ cdef class _SolutionBase:
         # Initialization of transport is deferred to Transport.__init__
         self.base.setThermoPhase(self._thermo)
         self.base.setKinetics(self._kinetics)
-        self.transport = NULL
 
         self._selected_species = np.ndarray(0, dtype=np.integer)
 
diff --git a/src/base/Base.cpp b/src/base/Base.cpp
index 367b5659d41..82fe246e08d 100644
--- a/src/base/Base.cpp
+++ b/src/base/Base.cpp
@@ -4,6 +4,9 @@
 // at https://cantera.org/license.txt for license and copyright information.
 
 #include "cantera/base/Base.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/kinetics/Kinetics.h"
+#include "cantera/transport/TransportBase.h"
 
 namespace Cantera
 {
@@ -24,15 +27,25 @@ SolutionBase::SolutionBase(const std::string& infile,
     throw NotImplementedError("SolutionBase constructor from file");
 }
 
+
 void SolutionBase::setThermoPhase(shared_ptr<ThermoPhase> thermo) {
     m_thermo = thermo;
+    if (m_thermo) {
+        m_thermo->setRoot(shared_from_this());
+    }
 }
 
 void SolutionBase::setKinetics(shared_ptr<Kinetics> kinetics) {
     m_kinetics = kinetics;
+    if (m_kinetics) {
+        m_kinetics->setRoot(shared_from_this());
+    }
 }
 
 void SolutionBase::setTransport(shared_ptr<Transport> transport) {
     m_transport = transport;
+    if (m_transport) {
+        m_transport->setRoot(shared_from_this());
+    }
 }
 }

From bc6ff919148cdb194718ce0e5742dc85ff5db03a Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Fri, 16 Aug 2019 16:39:12 -0500
Subject: [PATCH 04/17] [Base] remove redundant unique_name attribute

* Resolve conflation of gas.ID and gas.name in unit tests
* Also fixes #691
---
 include/cantera/thermo/Phase.h                | 10 ++++++++++
 include/cantera/thermo/ThermoPhase.h          | 12 +----------
 interfaces/cython/cantera/_cantera.pxd        |  2 +-
 interfaces/cython/cantera/base.pyx            | 20 ++++++++++++-------
 .../cython/cantera/test/test_mixture.py       |  5 +++--
 interfaces/cython/cantera/test/test_thermo.py | 12 ++++-------
 interfaces/cython/cantera/thermo.pyx          | 11 ----------
 src/thermo/Phase.cpp                          | 15 ++++++++++++--
 src/thermo/ThermoFactory.cpp                  |  1 +
 9 files changed, 46 insertions(+), 42 deletions(-)

diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index a82e69d7842..289b3faba54 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -29,6 +29,8 @@ namespace Cantera
  * support thermodynamic calculations (see \ref thermoprops).
  */
 
+class SolutionBase;
+
 //! Class Phase is the base class for phases of matter, managing the species and
 //! elements in a phase, as well as the independent variables of temperature,
 //! mass density, species mass/mole fraction, and other generalized forces and
@@ -758,6 +760,11 @@ class Phase
         m_caseSensitiveSpecies = cflag;
     }
 
+    //! Set root SolutionBase holding all phase information
+    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+        m_root = root;
+    }
+
 protected:
     //! Cached for saved calculations within each ThermoPhase.
     /*!
@@ -870,6 +877,9 @@ class Phase
 
     //! Entropy at 298.15 K and 1 bar of stable state pure elements (J kmol-1)
     vector_fp m_entropy298;
+
+    //! reference to SolutionBase
+    std::weak_ptr<SolutionBase> m_root;
 };
 
 }
diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h
index 2b21ce6e1d4..a1b6da7a69d 100644
--- a/include/cantera/thermo/ThermoPhase.h
+++ b/include/cantera/thermo/ThermoPhase.h
@@ -6,7 +6,7 @@
  */
 
 // 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.
+// at http://www.cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_THERMOPHASE_H
 #define CT_THERMOPHASE_H
@@ -40,8 +40,6 @@ const int cSS_CONVENTION_VPSS = 1;
 const int cSS_CONVENTION_SLAVE = 2;
 //@}
 
-class SolutionBase;
-
 //! Base class for a phase with thermodynamic properties.
 /*!
  * Class ThermoPhase is the base class for the family of classes that represent
@@ -1618,11 +1616,6 @@ class ThermoPhase : public Phase
 
     //@}
 
-    //! Set root SolutionBase holding all phase information
-    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
-        m_root = root;
-    }
-
 protected:
     //! Fills `names` and `data` with the column names and species thermo
     //! properties to be included in the output of the reportCSV method.
@@ -1667,9 +1660,6 @@ class ThermoPhase : public Phase
 
     //! last value of the temperature processed by reference state
     mutable doublereal m_tlast;
-
-    //! reference to SolutionBase
-    std::weak_ptr<SolutionBase> m_root;
 };
 
 //! typedef for the ThermoPhase class
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index ff576b20efd..fa93cc36e46 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -943,8 +943,8 @@ cdef class GasTransportData:
     cdef _assign(self, shared_ptr[CxxTransportData] other)
 
 cdef class _SolutionBase:
-    cdef CxxSolutionBase* base
     cdef shared_ptr[CxxSolutionBase] _base
+    cdef CxxSolutionBase* base
     cdef shared_ptr[CxxThermoPhase] _thermo
     cdef CxxThermoPhase* thermo
     cdef shared_ptr[CxxKinetics] _kinetics
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 4bb8dcb57ff..7a271593895 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -60,22 +60,28 @@ cdef class _SolutionBase:
         else:
             raise ValueError('Missing required keyword `base_type`.')
 
-        phasename = pystr(self.thermo.name())
+        phase_name = pystr(self.thermo.id())
         name = kwargs.get('name', None)
         if name is not None:
-            self.unique_name = name
+            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[phasename] += 1
-            n = _phase_counts[phasename]
-            self.unique_name = '{0}_{1}'.format(phasename, n)
+            _phase_counts[phase_name] = 0
+            self.name = phase_name
 
     property type:
         """The type of the SolutionBase object."""
         def __get__(self):
             return pystr(self.base.type())
 
-    property unique_name:
-        """The unique name of the SolutionBase object."""
+    property name:
+        """
+        The name assigned to this SolutionBase object. The default is
+        taken from the CTI/XML/YAML input file.
+        """
         def __get__(self):
             return pystr(self.base.name())
 
diff --git a/interfaces/cython/cantera/test/test_mixture.py b/interfaces/cython/cantera/test/test_mixture.py
index 42f882bb404..b96107ee1f3 100644
--- a/interfaces/cython/cantera/test/test_mixture.py
+++ b/interfaces/cython/cantera/test/test_mixture.py
@@ -112,10 +112,11 @@ def test_charge(self):
 
     def test_phase_moles(self):
         M = self.mix.phase_moles()
+        name = self.phase2.name
         self.assertEqual(M[0], self.mix.phase_moles(0))
-        self.assertEqual(M[1], self.mix.phase_moles('air'))
+        self.assertEqual(M[1], self.mix.phase_moles(name))
 
-        self.mix.set_phase_moles('air', 4)
+        self.mix.set_phase_moles(name, 4)
         self.assertEqual(self.mix.phase_moles(1), 4)
 
     def test_species_moles(self):
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index 49ed49df609..e86752aa018 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -15,9 +15,9 @@ def setUp(self):
     def test_cpp_attributes(self):
         self.assertTrue(isinstance(self.phase.type, str))
         self.assertTrue(self.phase.type=='Solution')
-        self.assertTrue(isinstance(self.phase.unique_name, str))
-        self.phase.unique_name = 'spam'
-        self.assertTrue(self.phase.unique_name=='spam')
+        self.assertTrue(isinstance(self.phase.name, str))
+        self.phase.name = 'spam'
+        self.assertTrue(self.phase.name=='spam')
         with self.assertRaises(AttributeError):
             self.phase.type = 'eggs'
 
@@ -308,18 +308,14 @@ def test_default_report(self):
             self.assertNotIn(name, report)
 
     def test_name(self):
-        self.assertEqual(self.phase.name, 'ohmech')
-
         self.phase.name = 'something'
         self.assertEqual(self.phase.name, 'something')
         self.assertIn('something', self.phase.report())
 
     def test_ID(self):
         self.assertEqual(self.phase.ID, 'ohmech')
-
         self.phase.ID = 'something'
         self.assertEqual(self.phase.ID, 'something')
-        self.assertEqual(self.phase.name, 'ohmech')
 
     def test_badLength(self):
         X = np.zeros(5)
@@ -854,7 +850,7 @@ class ImportTest(utilities.CanteraTest):
     Test the various ways of creating a Solution object
     """
     def check(self, gas, name, T, P, nSpec, nElem):
-        self.assertEqual(gas.name, name)
+        self.assertEqual(gas.ID, name)
         self.assertNear(gas.T, T)
         self.assertNear(gas.P, P)
         self.assertEqual(gas.n_species, nSpec)
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 9ed8a479ea1..432cf1fc1be 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -284,16 +284,6 @@ cdef class ThermoPhase(_SolutionBase):
     def __call__(self, *args, **kwargs):
         print(self.report(*args, **kwargs))
 
-    property name:
-        """
-        The name assigned to this phase. The default is taken from the CTI/XML
-        input file.
-        """
-        def __get__(self):
-            return pystr(self.thermo.name())
-        def __set__(self, name):
-            self.thermo.setName(stringify(name))
-
     property ID:
         """
         The ID of the phase. The default is taken from the CTI/XML input file.
@@ -303,7 +293,6 @@ cdef class ThermoPhase(_SolutionBase):
         def __set__(self, id_):
             self.thermo.setID(stringify(id_))
 
-
     property basis:
         """
         Determines whether intensive thermodynamic properties are treated on a
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index 85798d5ec82..fc21d66ead5 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -10,6 +10,7 @@
 #include "cantera/base/utilities.h"
 #include "cantera/base/stringUtils.h"
 #include "cantera/base/ctml.h"
+#include "cantera/base/Base.h"
 #include "cantera/thermo/ThermoFactory.h"
 
 using namespace std;
@@ -78,12 +79,22 @@ void Phase::setID(const std::string& id_)
 
 std::string Phase::name() const
 {
-    return m_name;
+    if (m_root.expired()) {
+        return m_name;
+    } else {
+        auto root = m_root.lock();
+        return root->name();
+    }
 }
 
 void Phase::setName(const std::string& nm)
 {
-    m_name = nm;
+    if (m_root.expired()) {
+        m_name = nm;
+    } else {
+        auto root = m_root.lock();
+        root->setName(nm);
+    }
 }
 
 size_t Phase::nElements() const
diff --git a/src/thermo/ThermoFactory.cpp b/src/thermo/ThermoFactory.cpp
index 5d4c96f3396..e5a5da4941a 100644
--- a/src/thermo/ThermoFactory.cpp
+++ b/src/thermo/ThermoFactory.cpp
@@ -448,6 +448,7 @@ void addSpecies(ThermoPhase& thermo, const AnyValue& names, const AnyValue& spec
 void setupPhase(ThermoPhase& thermo, AnyMap& phaseNode, const AnyMap& rootNode)
 {
     thermo.setName(phaseNode["name"].asString());
+    thermo.setID(phaseNode["name"].asString());
     if (rootNode.hasKey("__file__")) {
         phaseNode["__file__"] = rootNode["__file__"];
     }

From 11681321b730bbe4d3c99cf09e235f20aa9c86e9 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Fri, 16 Aug 2019 19:43:40 -0500
Subject: [PATCH 05/17] [Base] associate phase ID with SolutionBase object

---
 include/cantera/base/Base.h            | 44 ++++++++++++++---------
 interfaces/cython/cantera/_cantera.pxd |  6 ++--
 interfaces/cython/cantera/base.pyx     | 17 +++++++--
 interfaces/cython/cantera/thermo.pyx   |  9 -----
 src/base/Base.cpp                      | 50 ++++++++++++++++++++++++--
 src/thermo/Phase.cpp                   | 17 ++-------
 6 files changed, 96 insertions(+), 47 deletions(-)

diff --git a/include/cantera/base/Base.h b/include/cantera/base/Base.h
index 9c084642285..a73c3511322 100644
--- a/include/cantera/base/Base.h
+++ b/include/cantera/base/Base.h
@@ -31,29 +31,42 @@ class SolutionBase : public std::enable_shared_from_this<SolutionBase>
 
     //! String indicating the type of the SolutionBase object. Corresponds
     //! to the type of phase originally instantiated
-    std::string type() const {
-        return m_type;
-    }
+    std::string type() const;
 
     //! Set the type of this SolutionBase object
-    void setType(const std::string& type){
-        m_type = type;
-    }
+    void setType(const std::string& type);
+
+    /*! Name and ID
+     * Class SolutionBase references two strings that identify a SolutionBase.
+     * The ID is the value of the ID attribute of the XML/YAML node that is used
+     * to initialize a phase when it is read. The name field is also initialized
+     * to the value of the ID attribute of the XML/YAML node.
+     *
+     * However, the name field may be changed to another value during the course
+     * of a calculation. For example, if a SolutionBase is located in two places,
+     * but has the same constitutive input, the IDs of the two SolutionBases
+     * will be the same, but the names of the two SOlutionBases  may be different.
+     *
+     * It is an error to have two phases in a single problem with the same name
+     * and ID (or the name from one phase being the same as the id of another
+     * SolutionBase). Thus, it is expected that there is a 1-1 correspondence
+     * between names and unique SolutionBase objects within a Cantera problem.
+     */
+
+    //! Return the string id for the SolutionBase.
+    std::string id() const;
+
+    //! Set the string id for the SolutionBase.
+    void setID(const std::string& id);
 
     //! Return the name of this SolutionBase object
-    std::string name() const {
-        return m_name;
-    }
+    std::string name() const;
 
     //! Set the name of this SolutionBase object
-    void setName(const std::string& name){
-        m_name = name;
-    }
+    void setName(const std::string& name);
 
     //! Generate self-documenting YAML string
-    virtual std::string toYAML() const {
-        throw NotImplementedError("SolutionBase::toYAML");
-    }
+    virtual std::string toYAML() const;
 
     //! Set the ThermoPhase object
     void setThermoPhase(shared_ptr<ThermoPhase> thermo);
@@ -70,7 +83,6 @@ class SolutionBase : public std::enable_shared_from_this<SolutionBase>
     shared_ptr<Transport> m_transport;  //! Transport manager
 
     std::string m_type;  //! type of SolutionBase object
-    std::string m_name;  //! name of SolutionBase object
 };
 
 }
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index fa93cc36e46..db4d7957e09 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -126,6 +126,8 @@ cdef extern from "cantera/base/Base.h" namespace "Cantera":
         CxxSolutionBase()
         string type()
         string setType(string)
+        string id()
+        void setID(string)
         string name()
         void setName(string)
         void setThermoPhase(shared_ptr[CxxThermoPhase])
@@ -142,10 +144,6 @@ cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
         # miscellaneous
         string type()
         string report(cbool, double) except +translate_exception
-        string name()
-        void setName(string)
-        string id()
-        void setID(string)
         double minTemp() except +translate_exception
         double maxTemp() except +translate_exception
         double refPressure() except +translate_exception
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 7a271593895..de5ef9cd961 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -60,7 +60,7 @@ cdef class _SolutionBase:
         else:
             raise ValueError('Missing required keyword `base_type`.')
 
-        phase_name = pystr(self.thermo.id())
+        phase_name = pystr(self.base.id())
         name = kwargs.get('name', None)
         if name is not None:
             self.name = name
@@ -73,10 +73,23 @@ cdef class _SolutionBase:
             self.name = phase_name
 
     property type:
-        """The type of the SolutionBase object."""
+        """
+        The type of the SolutionBase object. The type is set during object
+        instantiation and cannot be modified.
+        """
         def __get__(self):
             return pystr(self.base.type())
 
+    property ID:
+        """
+        The ID of the SolutionBase object. The default is taken from the
+        CTI/XML/YAML input file.
+        """
+        def __get__(self):
+            return pystr(self.base.id())
+        def __set__(self, id_):
+            self.base.setID(stringify(id_))
+
     property name:
         """
         The name assigned to this SolutionBase object. The default is
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 432cf1fc1be..09466dc4e37 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -284,15 +284,6 @@ cdef class ThermoPhase(_SolutionBase):
     def __call__(self, *args, **kwargs):
         print(self.report(*args, **kwargs))
 
-    property ID:
-        """
-        The ID of the phase. The default is taken from the CTI/XML input file.
-        """
-        def __get__(self):
-            return pystr(self.thermo.id())
-        def __set__(self, id_):
-            self.thermo.setID(stringify(id_))
-
     property basis:
         """
         Determines whether intensive thermodynamic properties are treated on a
diff --git a/src/base/Base.cpp b/src/base/Base.cpp
index 82fe246e08d..29043517e7d 100644
--- a/src/base/Base.cpp
+++ b/src/base/Base.cpp
@@ -15,8 +15,7 @@ SolutionBase::SolutionBase() :
     m_thermo(nullptr),
     m_kinetics(nullptr),
     m_transport(nullptr),
-    m_type("<SolutionBase_type>"),
-    m_name("<unique_name>")
+    m_type("<SolutionBase_type>")
 {}
 
 SolutionBase::SolutionBase(const std::string& infile,
@@ -27,6 +26,53 @@ SolutionBase::SolutionBase(const std::string& infile,
     throw NotImplementedError("SolutionBase constructor from file");
 }
 
+std::string SolutionBase::type() const {
+    return m_type;
+}
+
+void SolutionBase::setType(const std::string& type){
+    m_type = type;
+}
+
+std::string SolutionBase::id() const {
+    // currently managed by ThermoPhase
+    if (m_thermo) {
+        return m_thermo->id();
+    } else {
+        throw CanteraError("SolutionBase::id()", "Missing ThermoPhase.");
+    }
+}
+
+void SolutionBase::setID(const std::string& id) {
+    // currently managed by ThermoPhase
+    if (m_thermo) {
+        return m_thermo->setID(id);
+    } else {
+        throw CanteraError("SolutionBase::setID()", "Missing ThermoPhase.");
+    }
+}
+
+std::string SolutionBase::name() const {
+    // currently managed by ThermoPhase
+    if (m_thermo) {
+        return m_thermo->name();
+    } else {
+        throw CanteraError("SolutionBase::name()", "Missing ThermoPhase.");
+    }
+}
+
+void SolutionBase::setName(const std::string& name){
+    // currently managed by ThermoPhase
+    if (m_thermo) {
+        return m_thermo->setName(name);
+    } else {
+        throw CanteraError("SolutionBase::setName()", "Missing ThermoPhase.");
+    }
+}
+
+std::string SolutionBase::toYAML() const {
+    throw NotImplementedError("SolutionBase::toYAML");
+}
 
 void SolutionBase::setThermoPhase(shared_ptr<ThermoPhase> thermo) {
     m_thermo = thermo;
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index fc21d66ead5..c82b3e756b9 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -4,13 +4,12 @@
  */
 
 // 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.
+// at http://www.cantera.org/license.txt for license and copyright information.
 
 #include "cantera/thermo/Phase.h"
 #include "cantera/base/utilities.h"
 #include "cantera/base/stringUtils.h"
 #include "cantera/base/ctml.h"
-#include "cantera/base/Base.h"
 #include "cantera/thermo/ThermoFactory.h"
 
 using namespace std;
@@ -79,22 +78,12 @@ void Phase::setID(const std::string& id_)
 
 std::string Phase::name() const
 {
-    if (m_root.expired()) {
-        return m_name;
-    } else {
-        auto root = m_root.lock();
-        return root->name();
-    }
+    return m_name;
 }
 
 void Phase::setName(const std::string& nm)
 {
-    if (m_root.expired()) {
-        m_name = nm;
-    } else {
-        auto root = m_root.lock();
-        root->setName(nm);
-    }
+    m_name = nm;
 }
 
 size_t Phase::nElements() const

From 04dced2a0a01afe2c4924c72c7fd0cff96657fb5 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sat, 17 Aug 2019 08:16:57 -0500
Subject: [PATCH 06/17] [Base] break out thermo/kinetics manager types to
 Python

---
 interfaces/cython/cantera/base.pyx            | 15 +++++++++++++++
 interfaces/cython/cantera/kinetics.pyx        |  7 +++++++
 interfaces/cython/cantera/test/test_thermo.py | 11 ++++++++++-
 interfaces/cython/cantera/thermo.pyx          |  7 +++++++
 4 files changed, 39 insertions(+), 1 deletion(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index de5ef9cd961..7ef88c8d6bb 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -101,6 +101,21 @@ cdef class _SolutionBase:
         def __set__(self, name):
             self.base.setName(stringify(name))
 
+    property composite:
+        """
+        Returns tuple of thermo/kinetics/transport models associated with
+        this SolutionBase object.
+        """
+        def __get__(self):
+            thermo = None if self.thermo == NULL \
+                else pystr(self.thermo.type())
+            kinetics = None if self.kinetics == NULL \
+                else pystr(self.kinetics.kineticsType())
+            transport = None if self.transport == NULL \
+                else pystr(self.transport.transportType())
+
+            return thermo, kinetics, transport
+
     def _init_yaml(self, infile, phaseid, phases, source):
         """
         Instantiate a set of new Cantera C++ objects from a YAML
diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index 89e7544c958..f3c71bb8c2e 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/interfaces/cython/cantera/kinetics.pyx
@@ -31,6 +31,13 @@ cdef class Kinetics(_SolutionBase):
         kwargs['base_type'] = base_type
         super().__init__(*args, **kwargs)
 
+    property kinetics_model:
+        """
+        Return type of kinetics.
+        """
+        def __get__(self):
+            return pystr(self.kinetics.kineticsType())
+
     property n_total_species:
         """
         Total number of species in all phases participating in the kinetics
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index e86752aa018..c9a1ef54084 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -12,10 +12,19 @@ class TestThermoPhase(utilities.CanteraTest):
     def setUp(self):
         self.phase = ct.Solution('h2o2.xml')
 
-    def test_cpp_attributes(self):
+    def test_base_attributes(self):
         self.assertTrue(isinstance(self.phase.type, str))
         self.assertTrue(self.phase.type=='Solution')
         self.assertTrue(isinstance(self.phase.name, str))
+        self.assertTrue(isinstance(self.phase.thermo_model, str))
+        self.assertTrue(isinstance(self.phase.kinetics_model, str))
+        self.assertTrue(isinstance(self.phase.transport_model, str))
+        self.assertTrue(isinstance(self.phase.composite, tuple))
+        self.assertTrue(len(self.phase.composite)==3)
+        self.assertTrue(
+            self.phase.composite == (self.phase.thermo_model,
+                                     self.phase.kinetics_model,
+                                     self.phase.transport_model))
         self.phase.name = 'spam'
         self.assertTrue(self.phase.name=='spam')
         with self.assertRaises(AttributeError):
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 09466dc4e37..7777a808113 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -270,6 +270,13 @@ cdef class ThermoPhase(_SolutionBase):
             self.thermo_basis = mass_basis
         self._references = weakref.WeakKeyDictionary()
 
+    property thermo_model:
+        """
+        Return thermodynamic model describing phase.
+        """
+        def __get__(self):
+            return pystr(self.thermo.type())
+
     def report(self, show_thermo=True, float threshold=1e-14):
         """
         Generate a report describing the thermodynamic state of this phase. To

From b643a63a9d60c02ecf9638154a6995dd31469638 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sat, 17 Aug 2019 10:01:54 -0500
Subject: [PATCH 07/17] [Base] replace Solution property `ID` by `phase` in
 Python

* Clarifies the meaning of ID
* Creates a PEP8 compliant attribute that does not conflict with
a built-in function name that is also consistent with the YAML entry.
* Change associated member function names in C++ SolutionBase
* Deprecate `ID` in Python (to be removed after Cantera 2.5)
---
 include/cantera/base/Base.h                   | 26 ++++++++---------
 interfaces/cython/cantera/_cantera.pxd        |  4 +--
 interfaces/cython/cantera/base.pyx            | 27 ++++++++++++++++--
 .../cython/cantera/test/test_reactor.py       |  4 +--
 interfaces/cython/cantera/test/test_thermo.py | 28 +++++++++++++++----
 src/base/Base.cpp                             |  6 ++--
 6 files changed, 67 insertions(+), 28 deletions(-)

diff --git a/include/cantera/base/Base.h b/include/cantera/base/Base.h
index a73c3511322..a22e1580ed3 100644
--- a/include/cantera/base/Base.h
+++ b/include/cantera/base/Base.h
@@ -36,28 +36,28 @@ class SolutionBase : public std::enable_shared_from_this<SolutionBase>
     //! Set the type of this SolutionBase object
     void setType(const std::string& type);
 
-    /*! Name and ID
+    /*! Name and phase
      * Class SolutionBase references two strings that identify a SolutionBase.
-     * The ID is the value of the ID attribute of the XML/YAML node that is used
-     * to initialize a phase when it is read. The name field is also initialized
-     * to the value of the ID attribute of the XML/YAML node.
+     * The phase is the value of the phase name in YAML (or ID attribute
+     * of the XML node) that is used to initialize a phase when it is read.
+     * The name field is also initialized to the value of the phase name
+     * read from the XML/YAML node.
      *
      * However, the name field may be changed to another value during the course
      * of a calculation. For example, if a SolutionBase is located in two places,
-     * but has the same constitutive input, the IDs of the two SolutionBases
-     * will be the same, but the names of the two SOlutionBases  may be different.
+     * but has the same constitutive input, the phase of the two SolutionBases
+     * will be the same, but the names of the two SolutionBases need to differ.
      *
      * It is an error to have two phases in a single problem with the same name
-     * and ID (or the name from one phase being the same as the id of another
-     * SolutionBase). Thus, it is expected that there is a 1-1 correspondence
-     * between names and unique SolutionBase objects within a Cantera problem.
+     * attribute. Thus, it is expected that there is a 1-1 correspondence between
+     * names and unique SolutionBase objects within a Cantera problem.
      */
 
-    //! Return the string id for the SolutionBase.
-    std::string id() const;
+    //! Return the phase string of this SolutionBase.
+    std::string phase() const;
 
-    //! Set the string id for the SolutionBase.
-    void setID(const std::string& id);
+    //! Set the phase string of this SolutionBase.
+    void setPhase(const std::string& id);
 
     //! Return the name of this SolutionBase object
     std::string name() const;
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index db4d7957e09..94f232b8373 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -126,8 +126,8 @@ cdef extern from "cantera/base/Base.h" namespace "Cantera":
         CxxSolutionBase()
         string type()
         string setType(string)
-        string id()
-        void setID(string)
+        string phase()
+        void setPhase(string)
         string name()
         void setName(string)
         void setThermoPhase(shared_ptr[CxxThermoPhase])
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 7ef88c8d6bb..a5be061bfb5 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -60,7 +60,7 @@ cdef class _SolutionBase:
         else:
             raise ValueError('Missing required keyword `base_type`.')
 
-        phase_name = pystr(self.base.id())
+        phase_name = pystr(self.base.phase())
         name = kwargs.get('name', None)
         if name is not None:
             self.name = name
@@ -80,15 +80,36 @@ cdef class _SolutionBase:
         def __get__(self):
             return pystr(self.base.type())
 
+    property phase:
+        """
+        The ID of the SolutionBase object. The phase corresponds to the
+        CTI/XML/YAML input file entry.
+        """
+        def __get__(self):
+            return pystr(self.base.phase())
+        def __set__(self, phase_name):
+            # may consider removing/deprecating, but resetting of the phase name
+            # is required to associate surface kinetics (with phase name being 'gas')
+            self.base.setPhase(stringify(phase_name))
+
     property ID:
         """
         The ID of the SolutionBase object. The default is taken from the
         CTI/XML/YAML input file.
+
+        .. deprecated:: 2.5
+
+             To be deprecated with version 2.5, and removed thereafter.
+             Renamed to `phase`.
         """
         def __get__(self):
-            return pystr(self.base.id())
+            warnings.warn("To be removed after Cantera 2.5. "
+                          "Use `phase` attribute instead", DeprecationWarning)
+            return pystr(self.base.phase())
         def __set__(self, id_):
-            self.base.setID(stringify(id_))
+            warnings.warn("To be removed after Cantera 2.5. "
+                          "Use `phase` attribute instead", DeprecationWarning)
+            self.base.setPhase(stringify(id_))
 
     property name:
         """
diff --git a/interfaces/cython/cantera/test/test_reactor.py b/interfaces/cython/cantera/test/test_reactor.py
index 9e788cb5bb6..7d084bc7d05 100644
--- a/interfaces/cython/cantera/test/test_reactor.py
+++ b/interfaces/cython/cantera/test/test_reactor.py
@@ -929,9 +929,9 @@ def create_reactors(self, add_Q=False, add_mdot=False, add_surf=False):
         self.gas.TPX = 900, 25*ct.one_atm, 'CO:0.5, H2O:0.2'
 
         self.gas1 = ct.Solution('gri30.xml')
-        self.gas1.ID = 'gas'
+        self.gas1.phase = 'gas'
         self.gas2 = ct.Solution('gri30.xml')
-        self.gas2.ID = 'gas'
+        self.gas2.phase = 'gas'
         resGas = ct.Solution('gri30.xml')
         solid = ct.Solution('diamond.xml', 'diamond')
 
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index c9a1ef54084..cc57b712ee5 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -7,6 +7,8 @@
 import cantera as ct
 from . import utilities
 
+import warnings
+
 
 class TestThermoPhase(utilities.CanteraTest):
     def setUp(self):
@@ -321,10 +323,24 @@ def test_name(self):
         self.assertEqual(self.phase.name, 'something')
         self.assertIn('something', self.phase.report())
 
-    def test_ID(self):
-        self.assertEqual(self.phase.ID, 'ohmech')
-        self.phase.ID = 'something'
-        self.assertEqual(self.phase.ID, 'something')
+    def test_phase(self):
+        self.assertEqual(self.phase.phase, 'ohmech')
+        warnings.simplefilter("always")
+
+        with warnings.catch_warnings(record=True) as w:
+            self.assertEqual(self.phase.ID, '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))
+
+        with warnings.catch_warnings(record=True) as w:
+            self.phase.ID = 'something'
+            self.assertEqual(self.phase.phase, 'something')
+            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)
@@ -858,8 +874,8 @@ class ImportTest(utilities.CanteraTest):
     """
     Test the various ways of creating a Solution object
     """
-    def check(self, gas, name, T, P, nSpec, nElem):
-        self.assertEqual(gas.ID, name)
+    def check(self, gas, phase, T, P, nSpec, nElem):
+        self.assertEqual(gas.phase, phase)
         self.assertNear(gas.T, T)
         self.assertNear(gas.P, P)
         self.assertEqual(gas.n_species, nSpec)
diff --git a/src/base/Base.cpp b/src/base/Base.cpp
index 29043517e7d..258ee953e25 100644
--- a/src/base/Base.cpp
+++ b/src/base/Base.cpp
@@ -34,7 +34,7 @@ void SolutionBase::setType(const std::string& type){
     m_type = type;
 }
 
-std::string SolutionBase::id() const {
+std::string SolutionBase::phase() const {
     // currently managed by ThermoPhase
     if (m_thermo) {
         return m_thermo->id();
@@ -43,8 +43,10 @@ std::string SolutionBase::id() const {
     }
 }
 
-void SolutionBase::setID(const std::string& id) {
+void SolutionBase::setPhase(const std::string& id) {
     // currently managed by ThermoPhase
+    // note: may consider removing (but needed for association of surface
+    // kinetics which require the phase name "gas")
     if (m_thermo) {
         return m_thermo->setID(id);
     } else {

From 93d9bd6350fb29d2255c554ba35a27cac2f5acf8 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sat, 17 Aug 2019 11:54:57 -0500
Subject: [PATCH 08/17] [Base] clarify keyword arguments of _SolutionBase
 initializers

* Replace `phaseid` by `phase`
* Replace `phases` by `adjacent`
* Add deprecation warnings and update unit tests
---
 interfaces/cython/cantera/base.pyx            | 59 +++++++++++++------
 .../cython/cantera/test/test_convert.py       | 36 +++++------
 .../cython/cantera/test/test_kinetics.py      |  4 +-
 interfaces/cython/cantera/test/test_thermo.py |  7 +++
 4 files changed, 67 insertions(+), 39 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index a5be061bfb5..fd08b7d7d2e 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -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:
diff --git a/interfaces/cython/cantera/test/test_convert.py b/interfaces/cython/cantera/test/test_convert.py
index 1d464023232..726f547c2b2 100644
--- a/interfaces/cython/cantera/test/test_convert.py
+++ b/interfaces/cython/cantera/test/test_convert.py
@@ -571,8 +571,8 @@ def setUpClass(cls):
 
     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 @@ def test_ptcombust(self):
                          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 @@ def test_sofc(self):
         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 @@ def test_liquidvapor(self):
                          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 @@ def test_Redlich_Kwong_ndodecane(self):
     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 @@ def test_lithium_ion_battery(self):
         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])
 
diff --git a/interfaces/cython/cantera/test/test_kinetics.py b/interfaces/cython/cantera/test/test_kinetics.py
index 46385664584..58d0637eda3 100644
--- a/interfaces/cython/cantera/test/test_kinetics.py
+++ b/interfaces/cython/cantera/test/test_kinetics.py
@@ -185,7 +185,7 @@ def test_surface(self):
 
         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 @@ def test_interface(self):
         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'
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index cc57b712ee5..a9479cfa5ed 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -342,6 +342,13 @@ def test_phase(self):
             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'):

From ee484eef53fae1348a14d7705429fbc4afccaa3c Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sat, 17 Aug 2019 12:52:28 -0500
Subject: [PATCH 09/17] [Base] update docstrings for Solution and Interface
 objects

* Reflects changes to `phase` and `adjacent` keyword
---
 interfaces/cython/cantera/composite.py | 30 +++++++++++++++++---------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index 22f5dee6d30..917418c55f7 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -25,11 +25,20 @@ class Solution(ThermoPhase, Kinetics, Transport):
 
         gas = ct.Solution('gri30.cti')
 
-    If an input file defines multiple phases, the phase *name* (in CTI) or *id*
-    (in XML) can be used to specify the desired phase::
+    If an input file defines multiple phases, the phase *name* (in CTI), *id*
+    (in XML) or *phases* entry (in YAML) can be used to specify the desired
+    phase via the ``phase`` keyword argument of the constructor::
 
-        gas = ct.Solution('diamond.cti', 'gas')
-        diamond = ct.Solution('diamond.cti', 'diamond')
+        gas = ct.Solution('diamond.cti', phase='gas')
+        diamond = ct.Solution('diamond.cti', phase='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.::
+
+        gas = ct.Solution('gri30.cti', 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
@@ -57,7 +66,8 @@ class Solution(ThermoPhase, Kinetics, Transport):
             ideal_gas(name='gas', elements='O H Ar',
                       species='gri30: all',
                       reactions='gri30: all',
-                      options=['skip_undeclared_elements', 'skip_undeclared_species', 'skip_undeclared_third_bodies'],
+                      options=['skip_undeclared_elements', 'skip_undeclared_species', 
+                               'skip_undeclared_third_bodies'],
                       initial_state=state(temperature=300, pressure=101325))'''
         gas = ct.Solution(source=cti_def)
     """
@@ -77,11 +87,12 @@ class Interface(InterfacePhase, InterfaceKinetics):
 
     To construct an `Interface` object, adjacent bulk phases which participate
     in reactions need to be created and then passed in as a list in the
-    ``phases`` argument to the constructor::
+    ``adjacent`` argument to the constructor::
 
-        gas = ct.Solution('diamond.cti', 'gas')
-        diamond = ct.Solution('diamond.cti', 'diamond')
-        diamond_surf = ct.Interface('diamond.cti', 'diamond_100', [gas, diamond])
+        gas = ct.Solution('diamond.cti', phase='gas')
+        diamond = ct.Solution('diamond.cti', phase='diamond')
+        diamond_surf = ct.Interface('diamond.cti', phase='diamond_100',
+                                    adjacent=[gas, diamond])
     """
     __slots__ = ('_phase_indices',)
 
@@ -95,7 +106,6 @@ class DustyGas(ThermoPhase, Kinetics, DustyGasTransport):
 
     The only transport properties computed are the multicomponent diffusion
     coefficients. The model does not compute viscosity or thermal conductivity.
-
     """
     __slots__ = ()
 

From ec6f5e021a728db0d50102a7147fc027a5c19e04 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sun, 18 Aug 2019 05:43:19 -0500
Subject: [PATCH 10/17] [Base] use FutureWarning for deprecated keywords

---
 interfaces/cython/cantera/base.pyx            | 10 ++++----
 interfaces/cython/cantera/composite.py        | 24 +++++++++----------
 interfaces/cython/cantera/test/test_thermo.py |  4 ++--
 3 files changed, 18 insertions(+), 20 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index fd08b7d7d2e..290898bcca5 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -14,9 +14,8 @@ cdef class _SolutionBase:
             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)
+            warnings.warn("Keyword `phase` replaces `phaseid`",
+                          FutureWarning)
             phase = kwargs['phaseid']
 
         if 'phases' in kwargs:
@@ -24,9 +23,8 @@ cdef class _SolutionBase:
                 raise AttributeError(
                     'duplicate specification of adjacent phases')
 
-            warnings.warn("To be removed after Cantera 2.5. "
-                          "Keyword `phases` is replaced by `adjacent`",
-                          DeprecationWarning)
+            warnings.warn("Keyword `adjacent` replaces `phases`",
+                          FutureWarning)
             adjacent = kwargs['phases']
 
         # Shallow copy of an existing Solution (for slicing support)
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index 917418c55f7..77fb69f555a 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -23,14 +23,14 @@ class Solution(ThermoPhase, Kinetics, Transport):
     The most common way to instantiate `Solution` objects is by using a phase
     definition, species and reactions defined in an input file::
 
-        gas = ct.Solution('gri30.cti')
+        gas = ct.Solution('gri30.yaml')
 
-    If an input file defines multiple phases, the phase *name* (in CTI), *id*
-    (in XML) or *phases* entry (in YAML) can be used to specify the desired
+    If an input file defines multiple phases, the *phases* entry (in YAML),
+    *name* (in CTI), or *id* (in XML) can be used to specify the desired
     phase via the ``phase`` keyword argument of the constructor::
 
-        gas = ct.Solution('diamond.cti', phase='gas')
-        diamond = ct.Solution('diamond.cti', phase='diamond')
+        gas = ct.Solution('diamond.yaml', phase='gas')
+        diamond = ct.Solution('diamond.yaml', phase='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 
@@ -38,14 +38,14 @@ class Solution(ThermoPhase, Kinetics, Transport):
     by a suffix. A custom name can be set via the ``name`` keyword argument of
     the constructor, i.e.::
 
-        gas = ct.Solution('gri30.cti', name='my_custom_name')
+        gas = ct.Solution('gri30.yaml', 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
     directly in Python::
 
-        spec = ct.Species.listFromFile('gri30.cti')
-        rxns = ct.Reaction.listFromFile('gri30.cti')
+        spec = ct.Species.listFromFile('gri30.yaml')
+        rxns = ct.Reaction.listFromFile('gri30.yaml')
         gas = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
                           species=spec, reactions=rxns)
 
@@ -89,9 +89,9 @@ 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.cti', phase='gas')
-        diamond = ct.Solution('diamond.cti', phase='diamond')
-        diamond_surf = ct.Interface('diamond.cti', phase='diamond_100',
+        gas = ct.Solution('diamond.yaml', phase='gas')
+        diamond = ct.Solution('diamond.yaml', phase='diamond')
+        diamond_surf = ct.Interface('diamond.yaml', phase='diamond_100',
                                     adjacent=[gas, diamond])
     """
     __slots__ = ('_phase_indices',)
@@ -316,7 +316,7 @@ class SolutionArray:
     with shapes described in the same way as Numpy arrays. All of the states
     can be set in a single call::
 
-        >>> gas = ct.Solution('gri30.cti')
+        >>> gas = ct.Solution('gri30.yaml')
         >>> states = ct.SolutionArray(gas, (6, 10))
         >>> T = np.linspace(300, 1000, 10) # row vector
         >>> P = ct.one_atm * np.linspace(0.1, 5.0, 6)[:,np.newaxis] # column vector
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index a9479cfa5ed..5c3e783e194 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -345,8 +345,8 @@ def test_phase(self):
         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. "
+            self.assertTrue(issubclass(w[-1].category, FutureWarning))
+            self.assertTrue("Keyword `phase` replaces `phaseid`"
                             in str(w[-1].message))
 
     def test_badLength(self):

From cf29e6b27be0c227bf209951d911db796af38889 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sun, 29 Sep 2019 08:43:54 -0500
Subject: [PATCH 11/17] [Base] rename Base.h/.cpp to SolutionBase.h/.cpp

---
 .../cantera/base/{Base.h => SolutionBase.h}   | 21 ++++++++++++++++---
 include/cantera/thermo/ThermoPhase.h          |  2 +-
 interfaces/cython/cantera/_cantera.pxd        |  2 +-
 src/base/{Base.cpp => SolutionBase.cpp}       |  4 ++--
 src/thermo/Phase.cpp                          |  2 +-
 5 files changed, 23 insertions(+), 8 deletions(-)
 rename include/cantera/base/{Base.h => SolutionBase.h} (87%)
 rename src/base/{Base.cpp => SolutionBase.cpp} (97%)

diff --git a/include/cantera/base/Base.h b/include/cantera/base/SolutionBase.h
similarity index 87%
rename from include/cantera/base/Base.h
rename to include/cantera/base/SolutionBase.h
index a22e1580ed3..ea5ee8bb217 100644
--- a/include/cantera/base/Base.h
+++ b/include/cantera/base/SolutionBase.h
@@ -1,10 +1,10 @@
-//! @file Base.h
+//! @file SolutionBase.h
 
 // 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.
 
-#ifndef CT_BASE_H
-#define CT_BASE_H
+#ifndef CT_SOLUTIONBASE_H
+#define CT_SOLUTIONBASE_H
 
 #include "cantera/base/ctexceptions.h"
 
@@ -77,6 +77,21 @@ class SolutionBase : public std::enable_shared_from_this<SolutionBase>
     //! Set the Transport object
     void setTransport(shared_ptr<Transport> transport);
 
+    //! Accessor for the ThermoPhase object
+    shared_ptr<ThermoPhase> thermo() {
+        return m_thermo;
+    }
+
+    //! Accessor for the Kinetics object
+    shared_ptr<Kinetics> kinetics() {
+        return m_kinetics;
+    }
+
+    //! Accessor for the Transport object
+    shared_ptr<Transport> transport() {
+        return m_transport;
+    }
+
 protected:
     shared_ptr<ThermoPhase> m_thermo;  //! ThermoPhase manager
     shared_ptr<Kinetics> m_kinetics;  //! Kinetics manager
diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h
index a1b6da7a69d..fdac8cf29c9 100644
--- a/include/cantera/thermo/ThermoPhase.h
+++ b/include/cantera/thermo/ThermoPhase.h
@@ -6,7 +6,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_THERMOPHASE_H
 #define CT_THERMOPHASE_H
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 94f232b8373..7c4a4c253b8 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -121,7 +121,7 @@ cdef extern from "cantera/thermo/Species.h" namespace "Cantera":
     cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (CxxAnyValue&) except +translate_exception
 
 
-cdef extern from "cantera/base/Base.h" namespace "Cantera":
+cdef extern from "cantera/base/SolutionBase.h" namespace "Cantera":
     cdef cppclass CxxSolutionBase "Cantera::SolutionBase":
         CxxSolutionBase()
         string type()
diff --git a/src/base/Base.cpp b/src/base/SolutionBase.cpp
similarity index 97%
rename from src/base/Base.cpp
rename to src/base/SolutionBase.cpp
index 258ee953e25..dd9e8db6cca 100644
--- a/src/base/Base.cpp
+++ b/src/base/SolutionBase.cpp
@@ -1,9 +1,9 @@
-//! @file Base.cpp
+//! @file SolutionBase.cpp
 
 // 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.
 
-#include "cantera/base/Base.h"
+#include "cantera/base/SolutionBase.h"
 #include "cantera/thermo/ThermoPhase.h"
 #include "cantera/kinetics/Kinetics.h"
 #include "cantera/transport/TransportBase.h"
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index c82b3e756b9..85798d5ec82 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #include "cantera/thermo/Phase.h"
 #include "cantera/base/utilities.h"

From 5932a2403de5e14e8150105019fb0ff74eb11db6 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Tue, 1 Oct 2019 13:49:03 -0500
Subject: [PATCH 12/17] [Input] rename --id to --phase in ck2yaml options

The option --phase is consistent with the resulting yaml entry in 'phases'.
The --id option is still supported, with a warning being issued.
---
 include/cantera/base/SolutionBase.h    | 12 ++++++------
 interfaces/cython/cantera/ck2yaml.py   | 19 +++++++++++++------
 interfaces/cython/cantera/composite.py | 14 ++++++++++----
 3 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/include/cantera/base/SolutionBase.h b/include/cantera/base/SolutionBase.h
index ea5ee8bb217..cec66ffb135 100644
--- a/include/cantera/base/SolutionBase.h
+++ b/include/cantera/base/SolutionBase.h
@@ -78,18 +78,18 @@ class SolutionBase : public std::enable_shared_from_this<SolutionBase>
     void setTransport(shared_ptr<Transport> transport);
 
     //! Accessor for the ThermoPhase object
-    shared_ptr<ThermoPhase> thermo() {
-        return m_thermo;
+    ThermoPhase& thermo() {
+        return *m_thermo;
     }
 
     //! Accessor for the Kinetics object
-    shared_ptr<Kinetics> kinetics() {
-        return m_kinetics;
+    Kinetics& kinetics() {
+        return *m_kinetics;
     }
 
     //! Accessor for the Transport object
-    shared_ptr<Transport> transport() {
-        return m_transport;
+    Transport& transport() {
+        return *m_transport;
     }
 
 protected:
diff --git a/interfaces/cython/cantera/ck2yaml.py b/interfaces/cython/cantera/ck2yaml.py
index 43bef62a1f3..c935822fbce 100644
--- a/interfaces/cython/cantera/ck2yaml.py
+++ b/interfaces/cython/cantera/ck2yaml.py
@@ -12,7 +12,7 @@
             [--thermo=<filename>]
             [--transport=<filename>]
             [--surface=<filename>]
-            [--id=<phase-id>]
+            [--phase=<phasename>]
             [--output=<filename>]
             [--permissive]
             [-d | --debug]
@@ -32,7 +32,8 @@
 'surface'.
 
 The '--permissive' option allows certain recoverable parsing errors (e.g.
-duplicate transport data) to be ignored.
+duplicate transport data) to be ignored. The '--phase=<phasename>' option
+is used to override default phase names (i.e. 'gas').
 """
 
 from collections import defaultdict, OrderedDict
@@ -1797,7 +1798,7 @@ def parse_transport_data(self, lines, filename, line_offset):
             if speciesName in self.species_dict:
                 if len(data) != 7:
                     raise InputError('Unable to parse line {} of {}:\n"""\n{}"""\n'
-                        '6 transport parameters expected, but found {}.', 
+                        '6 transport parameters expected, but found {}.',
                             line_offset + i, filename, original_line, len(data)-1)
 
                 if self.species_dict[speciesName].transport is None:
@@ -2024,9 +2025,9 @@ def convert_mech(input_file, thermo_file=None, transport_file=None, surface_file
 
 def main(argv):
 
-    longOptions = ['input=', 'thermo=', 'transport=', 'surface=', 'id=',
+    longOptions = ['input=', 'thermo=', 'transport=', 'surface=', 'phase=',
                    'output=', 'permissive', 'help', 'debug', 'quiet',
-                   'no-validate']
+                   'no-validate', 'id=']
 
     try:
         optlist, args = getopt.getopt(argv, 'dh', longOptions)
@@ -2054,7 +2055,13 @@ def main(argv):
     quiet = '--quiet' in options
     transport_file = options.get('--transport')
     surface_file = options.get('--surface')
-    phase_name = options.get('--id', 'gas')
+
+    if '--id' in options:
+        phase_name = options.get('--id', 'gas')
+        logging.warning("\nFutureWarning: "
+                        "option '--id=...' is superseded by '--phase=...'")
+    else:
+        phase_name = options.get('--phase', 'gas')
 
     if not input_file and not thermo_file:
         print('At least one of the arguments "--input=..." or "--thermo=..."'
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index 77fb69f555a..9cc5898e3c7 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -32,9 +32,9 @@ class Solution(ThermoPhase, Kinetics, Transport):
         gas = ct.Solution('diamond.yaml', phase='gas')
         diamond = ct.Solution('diamond.yaml', phase='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 
+    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.::
 
@@ -54,6 +54,12 @@ class Solution(ThermoPhase, Kinetics, Transport):
     ``species`` and ``reactions`` keyword arguments are lists of `Species` and
     `Reaction` objects, respectively.
 
+    Types of underlying models that form the composite `Solution` object are
+    queried using the ``thermo_model``, ``kinetics_model`` and
+    ``transport_model`` attributes; further, the ``composite`` attribute is a
+    shorthand returning a tuple containing the types of the three contitutive
+    models.
+
     For non-trivial uses cases of this functionality, see the examples
     `extract_submechanism.py <https://cantera.org/examples/python/extract_submechanism.py.html>`_
     and `mechanism_reduction.py <https://cantera.org/examples/python/mechanism_reduction.py.html>`_.
@@ -66,7 +72,7 @@ class Solution(ThermoPhase, Kinetics, Transport):
             ideal_gas(name='gas', elements='O H Ar',
                       species='gri30: all',
                       reactions='gri30: all',
-                      options=['skip_undeclared_elements', 'skip_undeclared_species', 
+                      options=['skip_undeclared_elements', 'skip_undeclared_species',
                                'skip_undeclared_third_bodies'],
                       initial_state=state(temperature=300, pressure=101325))'''
         gas = ct.Solution(source=cti_def)

From 02175a3b17bc92b155976215c5132ac45e77abdd Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Tue, 8 Oct 2019 15:00:07 -0500
Subject: [PATCH 13/17] [Thermo] address discussion and review comments

* rename C++ object to 'Solution' (from 'SolutionBase')
* remove 'phaseID' from 'Solution' ('id' remains assigned to 'Phase')
* remove 'type' from C++ object (no polymorphism anticipated)
* assign 'name' to 'Solution' (link back from 'Phase' until deprecated)
* clarify 'phase' as 'phase_id' in Python interface
* address various feedback in review comments
---
 include/cantera/base/Solution.h               |  72 ++++++++++++
 include/cantera/base/SolutionBase.h           | 104 ------------------
 include/cantera/kinetics/Kinetics.h           |  10 +-
 include/cantera/thermo/Phase.h                |  10 +-
 include/cantera/transport/TransportBase.h     |  10 +-
 interfaces/cython/cantera/_cantera.pxd        |  18 ++-
 interfaces/cython/cantera/base.pyx            |  98 +++++------------
 interfaces/cython/cantera/ck2yaml.py          |  10 +-
 interfaces/cython/cantera/composite.py        |  26 ++---
 interfaces/cython/cantera/kinetics.pyx        |  11 +-
 .../cython/cantera/test/test_convert.py       |  32 +++---
 .../cython/cantera/test/test_reactor.py       |   4 +-
 interfaces/cython/cantera/test/test_thermo.py |  50 ++++-----
 interfaces/cython/cantera/thermo.pyx          |  33 +++++-
 src/base/Solution.cpp                         |  46 ++++++++
 src/base/SolutionBase.cpp                     |  99 -----------------
 src/thermo/Phase.cpp                          |  17 ++-
 17 files changed, 272 insertions(+), 378 deletions(-)
 create mode 100644 include/cantera/base/Solution.h
 delete mode 100644 include/cantera/base/SolutionBase.h
 create mode 100644 src/base/Solution.cpp
 delete mode 100644 src/base/SolutionBase.cpp

diff --git a/include/cantera/base/Solution.h b/include/cantera/base/Solution.h
new file mode 100644
index 00000000000..37141cc4dc9
--- /dev/null
+++ b/include/cantera/base/Solution.h
@@ -0,0 +1,72 @@
+//! @file Solution.h
+
+// 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.
+
+#ifndef CT_SOLUTION_H
+#define CT_SOLUTION_H
+
+#include "cantera/base/ctexceptions.h"
+
+namespace Cantera
+{
+
+class ThermoPhase;
+class Kinetics;
+class Transport;
+
+//! A container class holding managers for all pieces defining a phase
+class Solution : public std::enable_shared_from_this<Solution>
+{
+private:
+    Solution();
+
+public:
+    ~Solution() {}
+    Solution(const Solution&) = delete;
+    Solution& operator=(const Solution&) = delete;
+
+    static shared_ptr<Solution> create() {
+        return shared_ptr<Solution>( new Solution );
+    }
+
+    //! Return the name of this Solution object
+    std::string name() const;
+
+    //! Set the name of this Solution object
+    void setName(const std::string& name);
+
+    //! Set the ThermoPhase object
+    void setThermoPhase(shared_ptr<ThermoPhase> thermo);
+
+    //! Set the Kinetics object
+    void setKinetics(shared_ptr<Kinetics> kinetics);
+
+    //! Set the Transport object
+    void setTransport(shared_ptr<Transport> transport);
+
+    //! Accessor for the ThermoPhase object
+    ThermoPhase& thermo() {
+        return *m_thermo;
+    }
+
+    //! Accessor for the Kinetics object
+    Kinetics& kinetics() {
+        return *m_kinetics;
+    }
+
+    //! Accessor for the Transport object
+    Transport& transport() {
+        return *m_transport;
+    }
+
+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
+};
+
+}
+#endif
diff --git a/include/cantera/base/SolutionBase.h b/include/cantera/base/SolutionBase.h
deleted file mode 100644
index cec66ffb135..00000000000
--- a/include/cantera/base/SolutionBase.h
+++ /dev/null
@@ -1,104 +0,0 @@
-//! @file SolutionBase.h
-
-// 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.
-
-#ifndef CT_SOLUTIONBASE_H
-#define CT_SOLUTIONBASE_H
-
-#include "cantera/base/ctexceptions.h"
-
-namespace Cantera
-{
-
-class ThermoPhase;
-class Kinetics;
-class Transport;
-
-//! A container class holding managers for all pieces defining a phase
-class SolutionBase : public std::enable_shared_from_this<SolutionBase>
-{
-public:
-    SolutionBase();
-    SolutionBase(const std::string& infile, const std::string& phasename);
-    ~SolutionBase() {}
-    SolutionBase(const SolutionBase&) = delete;
-    SolutionBase& operator=(const SolutionBase&) = delete;
-
-    static shared_ptr<SolutionBase> create() {
-        return shared_ptr<SolutionBase>( new SolutionBase );
-    }
-
-    //! String indicating the type of the SolutionBase object. Corresponds
-    //! to the type of phase originally instantiated
-    std::string type() const;
-
-    //! Set the type of this SolutionBase object
-    void setType(const std::string& type);
-
-    /*! Name and phase
-     * Class SolutionBase references two strings that identify a SolutionBase.
-     * The phase is the value of the phase name in YAML (or ID attribute
-     * of the XML node) that is used to initialize a phase when it is read.
-     * The name field is also initialized to the value of the phase name
-     * read from the XML/YAML node.
-     *
-     * However, the name field may be changed to another value during the course
-     * of a calculation. For example, if a SolutionBase is located in two places,
-     * but has the same constitutive input, the phase of the two SolutionBases
-     * will be the same, but the names of the two SolutionBases need to differ.
-     *
-     * It is an error to have two phases in a single problem with the same name
-     * attribute. Thus, it is expected that there is a 1-1 correspondence between
-     * names and unique SolutionBase objects within a Cantera problem.
-     */
-
-    //! Return the phase string of this SolutionBase.
-    std::string phase() const;
-
-    //! Set the phase string of this SolutionBase.
-    void setPhase(const std::string& id);
-
-    //! Return the name of this SolutionBase object
-    std::string name() const;
-
-    //! Set the name of this SolutionBase object
-    void setName(const std::string& name);
-
-    //! Generate self-documenting YAML string
-    virtual std::string toYAML() const;
-
-    //! Set the ThermoPhase object
-    void setThermoPhase(shared_ptr<ThermoPhase> thermo);
-
-    //! Set the Kinetics object
-    void setKinetics(shared_ptr<Kinetics> kinetics);
-
-    //! Set the Transport object
-    void setTransport(shared_ptr<Transport> transport);
-
-    //! Accessor for the ThermoPhase object
-    ThermoPhase& thermo() {
-        return *m_thermo;
-    }
-
-    //! Accessor for the Kinetics object
-    Kinetics& kinetics() {
-        return *m_kinetics;
-    }
-
-    //! Accessor for the Transport object
-    Transport& transport() {
-        return *m_transport;
-    }
-
-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_type;  //! type of SolutionBase object
-};
-
-}
-#endif
diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
index 4cacaa8e49e..57b2853954f 100644
--- a/include/cantera/kinetics/Kinetics.h
+++ b/include/cantera/kinetics/Kinetics.h
@@ -19,7 +19,7 @@
 namespace Cantera
 {
 
-class SolutionBase;
+class Solution;
 
 /**
  * @defgroup chemkinetics Chemical Kinetics
@@ -816,8 +816,8 @@ class Kinetics
     void selectPhase(const doublereal* data, const thermo_t* phase,
                      doublereal* phase_data);
 
-    //! Set root SolutionBase holding all phase information
-    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+    //! Set root Solution holding all phase information
+    virtual void setRoot(std::shared_ptr<Solution> root) {
         m_root = root;
     }
 
@@ -943,8 +943,8 @@ class Kinetics
     //! @see skipUndeclaredThirdBodies()
     bool m_skipUndeclaredThirdBodies;
 
-    //! reference to SolutionBase
-    std::weak_ptr<SolutionBase> m_root;
+    //! reference to Solution
+    std::weak_ptr<Solution> m_root;
 };
 
 }
diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index 289b3faba54..0dc75d7f4c8 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -29,7 +29,7 @@ namespace Cantera
  * support thermodynamic calculations (see \ref thermoprops).
  */
 
-class SolutionBase;
+class Solution;
 
 //! Class Phase is the base class for phases of matter, managing the species and
 //! elements in a phase, as well as the independent variables of temperature,
@@ -760,8 +760,8 @@ class Phase
         m_caseSensitiveSpecies = cflag;
     }
 
-    //! Set root SolutionBase holding all phase information
-    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+    //! Set root Solution holding all phase information
+    virtual void setRoot(std::shared_ptr<Solution> root) {
         m_root = root;
     }
 
@@ -878,8 +878,8 @@ class Phase
     //! Entropy at 298.15 K and 1 bar of stable state pure elements (J kmol-1)
     vector_fp m_entropy298;
 
-    //! reference to SolutionBase
-    std::weak_ptr<SolutionBase> m_root;
+    //! reference to Solution
+    std::weak_ptr<Solution> m_root;
 };
 
 }
diff --git a/include/cantera/transport/TransportBase.h b/include/cantera/transport/TransportBase.h
index 171aff9f396..664d47d2a4d 100644
--- a/include/cantera/transport/TransportBase.h
+++ b/include/cantera/transport/TransportBase.h
@@ -74,7 +74,7 @@ const VelocityBasis VB_SPECIES_2 = 2;
 const VelocityBasis VB_SPECIES_3 = 3;
 //@}
 
-class SolutionBase;
+class Solution;
 
 //! Base class for transport property managers.
 /*!
@@ -656,8 +656,8 @@ class Transport
      */
     virtual void setThermo(thermo_t& thermo);
 
-    //! Set root SolutionBase holding all phase information
-    virtual void setRoot(std::shared_ptr<SolutionBase> root) {
+    //! Set root Solution holding all phase information
+    virtual void setRoot(std::shared_ptr<Solution> root) {
         m_root = root;
     }
 
@@ -688,8 +688,8 @@ class Transport
     //! Defaults to the mass averaged basis = -2
     int m_velocityBasis;
 
-    //! reference to SolutionBase
-    std::weak_ptr<SolutionBase> m_root;
+    //! reference to Solution
+    std::weak_ptr<Solution> m_root;
 };
 
 }
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 7c4a4c253b8..827b4acf240 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -121,20 +121,16 @@ cdef extern from "cantera/thermo/Species.h" namespace "Cantera":
     cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (CxxAnyValue&) except +translate_exception
 
 
-cdef extern from "cantera/base/SolutionBase.h" namespace "Cantera":
-    cdef cppclass CxxSolutionBase "Cantera::SolutionBase":
-        CxxSolutionBase()
-        string type()
-        string setType(string)
-        string phase()
-        void setPhase(string)
+cdef extern from "cantera/base/Solution.h" namespace "Cantera":
+    cdef cppclass CxxSolution "Cantera::Solution":
+        CxxSolution()
         string name()
         void setName(string)
         void setThermoPhase(shared_ptr[CxxThermoPhase])
         void setKinetics(shared_ptr[CxxKinetics])
         void setTransport(shared_ptr[CxxTransport])
 
-    cdef shared_ptr[CxxSolutionBase] CxxNewSolutionBase "Cantera::SolutionBase::create" ()
+    cdef shared_ptr[CxxSolution] CxxNewSolution "Cantera::Solution::create" ()
 
 
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
@@ -144,6 +140,8 @@ 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
@@ -941,8 +939,8 @@ cdef class GasTransportData:
     cdef _assign(self, shared_ptr[CxxTransportData] other)
 
 cdef class _SolutionBase:
-    cdef shared_ptr[CxxSolutionBase] _base
-    cdef CxxSolutionBase* base
+    cdef shared_ptr[CxxSolution] _base
+    cdef CxxSolution* base
     cdef shared_ptr[CxxThermoPhase] _thermo
     cdef CxxThermoPhase* thermo
     cdef shared_ptr[CxxKinetics] _kinetics
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 290898bcca5..76db56e5153 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -6,24 +6,24 @@ from collections import defaultdict as _defaultdict
 _phase_counts = _defaultdict(int)
 
 cdef class _SolutionBase:
-    def __cinit__(self, infile='', phase='', adjacent=(), origin=None,
+    def __cinit__(self, infile='', phase_id='', adjacent=(), origin=None,
                   source=None, yaml=None, thermo=None, species=(),
                   kinetics=None, reactions=(), **kwargs):
 
         if 'phaseid' in kwargs:
-            if phase is not '':
+            if phase_id is not '':
                 raise AttributeError('duplicate specification of phase name')
 
-            warnings.warn("Keyword `phase` replaces `phaseid`",
+            warnings.warn("Keyword 'phase_id' replaces 'phaseid'",
                           FutureWarning)
-            phase = kwargs['phaseid']
+            phase_id = kwargs['phaseid']
 
         if 'phases' in kwargs:
             if len(adjacent)>0:
                 raise AttributeError(
                     'duplicate specification of adjacent phases')
 
-            warnings.warn("Keyword `adjacent` replaces `phases`",
+            warnings.warn("Keyword 'adjacent' replaces 'phases'",
                           FutureWarning)
             adjacent = kwargs['phases']
 
@@ -46,7 +46,7 @@ cdef class _SolutionBase:
             return
 
         # Assign base and set managers to NULL
-        self._base = CxxNewSolutionBase()
+        self._base = CxxNewSolution()
         self.base = self._base.get()
         self.thermo = NULL
         self.kinetics = NULL
@@ -54,9 +54,9 @@ cdef class _SolutionBase:
 
         # Parse inputs
         if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
-            self._init_yaml(infile, phase, adjacent, yaml)
+            self._init_yaml(infile, phase_id, adjacent, yaml)
         elif infile or source:
-            self._init_cti_xml(infile, phase, adjacent, source)
+            self._init_cti_xml(infile, phase_id, adjacent, source)
         elif thermo and species:
             self._init_parts(thermo, species, kinetics, adjacent, reactions)
         else:
@@ -72,14 +72,8 @@ cdef class _SolutionBase:
         if isinstance(self, Transport):
             assert self.transport is not NULL
 
-        base_type = kwargs.get('base_type', None)
-        if base_type:
-            self.base.setType(stringify(base_type))
-        else:
-            raise ValueError('Missing required keyword `base_type`.')
-
-        phase_name = pystr(self.base.phase())
-        name = kwargs.get('name', None)
+        phase_name = pystr(self.thermo.id())
+        name = kwargs.get('name')
         if name is not None:
             self.name = name
         elif phase_name in _phase_counts:
@@ -90,49 +84,11 @@ cdef class _SolutionBase:
             _phase_counts[phase_name] = 0
             self.name = phase_name
 
-    property type:
-        """
-        The type of the SolutionBase object. The type is set during object
-        instantiation and cannot be modified.
-        """
-        def __get__(self):
-            return pystr(self.base.type())
-
-    property phase:
-        """
-        The ID of the SolutionBase object. The phase corresponds to the
-        CTI/XML/YAML input file entry.
-        """
-        def __get__(self):
-            return pystr(self.base.phase())
-        def __set__(self, phase_name):
-            # may consider removing/deprecating, but resetting of the phase name
-            # is required to associate surface kinetics (with phase name being 'gas')
-            self.base.setPhase(stringify(phase_name))
-
-    property ID:
-        """
-        The ID of the SolutionBase object. The default is taken from the
-        CTI/XML/YAML input file.
-
-        .. deprecated:: 2.5
-
-             To be deprecated with version 2.5, and removed thereafter.
-             Renamed to `phase`.
-        """
-        def __get__(self):
-            warnings.warn("To be removed after Cantera 2.5. "
-                          "Use `phase` attribute instead", DeprecationWarning)
-            return pystr(self.base.phase())
-        def __set__(self, id_):
-            warnings.warn("To be removed after Cantera 2.5. "
-                          "Use `phase` attribute instead", DeprecationWarning)
-            self.base.setPhase(stringify(id_))
-
     property name:
         """
-        The name assigned to this SolutionBase object. The default is
-        taken from the CTI/XML/YAML input file.
+        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.
         """
         def __get__(self):
             return pystr(self.base.name())
@@ -155,7 +111,7 @@ cdef class _SolutionBase:
 
             return thermo, kinetics, transport
 
-    def _init_yaml(self, infile, phase, adjacent, source):
+    def _init_yaml(self, infile, phase_id, adjacent, source):
         """
         Instantiate a set of new Cantera C++ objects from a YAML
         phase definition
@@ -167,7 +123,7 @@ cdef class _SolutionBase:
             root = AnyMapFromYamlString(stringify(source))
 
         phaseNode = root[stringify("phases")].getMapWhere(stringify("name"),
-                                                          stringify(phase))
+                                                          stringify(phase_id))
 
         # Thermo
         if isinstance(self, ThermoPhase):
@@ -178,19 +134,19 @@ cdef class _SolutionBase:
 
         # Kinetics
         cdef vector[CxxThermoPhase*] v
-        cdef _SolutionBase adj
+        cdef _SolutionBase phase
 
         if isinstance(self, Kinetics):
             v.push_back(self.thermo)
-            for adj in adjacent:
+            for phase in adjacent:
                 # adjacent bulk phases for a surface phase
-                v.push_back(adj.thermo)
+                v.push_back(phase.thermo)
             self._kinetics = newKinetics(v, phaseNode, root)
             self.kinetics = self._kinetics.get()
         else:
             self.kinetics = NULL
 
-    def _init_cti_xml(self, infile, phase, adjacent, source):
+    def _init_cti_xml(self, infile, phase_id, adjacent, source):
         """
         Instantiate a set of new Cantera C++ objects from a CTI or XML
         phase definition
@@ -202,8 +158,8 @@ cdef class _SolutionBase:
 
         # Get XML data
         cdef XML_Node* phaseNode
-        if phase:
-            phaseNode = rootNode.findID(stringify(phase))
+        if phase_id:
+            phaseNode = rootNode.findID(stringify(phase_id))
         else:
             phaseNode = rootNode.findByName(stringify('phase'))
         if phaseNode is NULL:
@@ -218,13 +174,13 @@ cdef class _SolutionBase:
 
         # Kinetics
         cdef vector[CxxThermoPhase*] v
-        cdef _SolutionBase adj
+        cdef _SolutionBase phase
 
         if isinstance(self, Kinetics):
             v.push_back(self.thermo)
-            for adj in adjacent:
+            for phase in adjacent:
                 # adjacent bulk phases for a surface phase
-                v.push_back(adj.thermo)
+                v.push_back(phase.thermo)
             self.kinetics = newKineticsMgr(deref(phaseNode), v)
             self._kinetics.reset(self.kinetics)
         else:
@@ -246,15 +202,15 @@ cdef class _SolutionBase:
         if not kinetics:
             kinetics = "none"
 
-        cdef ThermoPhase adj
+        cdef ThermoPhase phase
         cdef Reaction reaction
         if isinstance(self, Kinetics):
             self.kinetics = CxxNewKinetics(stringify(kinetics))
             self._kinetics.reset(self.kinetics)
             self.kinetics.addPhase(deref(self.thermo))
-            for adj in adjacent:
+            for phase in adjacent:
                 # adjacent bulk phases for a surface phase
-                self.kinetics.addPhase(deref(adj.thermo))
+                self.kinetics.addPhase(deref(phase.thermo))
             self.kinetics.init()
             self.kinetics.skipUndeclaredThirdBodies(True)
             for reaction in reactions:
diff --git a/interfaces/cython/cantera/ck2yaml.py b/interfaces/cython/cantera/ck2yaml.py
index c935822fbce..1ffe5a3c729 100644
--- a/interfaces/cython/cantera/ck2yaml.py
+++ b/interfaces/cython/cantera/ck2yaml.py
@@ -12,7 +12,7 @@
             [--thermo=<filename>]
             [--transport=<filename>]
             [--surface=<filename>]
-            [--phase=<phasename>]
+            [--phase-id=<phase-id>]
             [--output=<filename>]
             [--permissive]
             [-d | --debug]
@@ -32,7 +32,7 @@
 'surface'.
 
 The '--permissive' option allows certain recoverable parsing errors (e.g.
-duplicate transport data) to be ignored. The '--phase=<phasename>' option
+duplicate transport data) to be ignored. The '--phase-id=<phase-id>' 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=',
+    longOptions = ['input=', 'thermo=', 'transport=', 'surface=', 'phase-id=',
                    '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=...'")
+                        "option '--id=...' is superseded by '--phase-id=...'")
     else:
-        phase_name = options.get('--phase', 'gas')
+        phase_name = options.get('--phase-id', 'gas')
 
     if not input_file and not thermo_file:
         print('At least one of the arguments "--input=..." or "--thermo=..."'
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index 9cc5898e3c7..fb9ae6b074a 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -25,12 +25,13 @@ class Solution(ThermoPhase, Kinetics, Transport):
 
         gas = ct.Solution('gri30.yaml')
 
-    If an input file defines multiple phases, the *phases* entry (in YAML),
-    *name* (in CTI), or *id* (in XML) can be used to specify the desired
-    phase via the ``phase`` keyword argument of the constructor::
+    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 
+    the constructor::
 
-        gas = ct.Solution('diamond.yaml', phase='gas')
-        diamond = ct.Solution('diamond.yaml', phase='diamond')
+        gas = ct.Solution('diamond.yaml', phase_id='gas')
+        diamond = ct.Solution('diamond.yaml', phase_id='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
@@ -79,9 +80,6 @@ class Solution(ThermoPhase, Kinetics, Transport):
     """
     __slots__ = ()
 
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, base_type='Solution', **kwargs)
-
 
 class Interface(InterfacePhase, InterfaceKinetics):
     """
@@ -95,16 +93,13 @@ 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='gas')
-        diamond = ct.Solution('diamond.yaml', phase='diamond')
-        diamond_surf = ct.Interface('diamond.yaml', phase='diamond_100',
+        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',
                                     adjacent=[gas, diamond])
     """
     __slots__ = ('_phase_indices',)
 
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, base_type='Interface', **kwargs)
-
 
 class DustyGas(ThermoPhase, Kinetics, DustyGasTransport):
     """
@@ -115,9 +110,6 @@ class DustyGas(ThermoPhase, Kinetics, DustyGasTransport):
     """
     __slots__ = ()
 
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, base_type='DustyGas', **kwargs)
-
 
 class Quantity:
     """
diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index f3c71bb8c2e..b16c9690af0 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/interfaces/cython/cantera/kinetics.pyx
@@ -26,11 +26,6 @@ cdef class Kinetics(_SolutionBase):
     a reaction mechanism.
     """
 
-    def __init__(self, *args, **kwargs):
-        base_type = kwargs.pop('base_type', 'Kinetics')
-        kwargs['base_type'] = base_type
-        super().__init__(*args, **kwargs)
-
     property kinetics_model:
         """
         Return type of kinetics.
@@ -376,13 +371,13 @@ 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='', phaseid='', phases=(), *args, **kwargs):
-        super().__init__(infile, phaseid, phases, *args, **kwargs)
+    def __init__(self, infile='', phase_id='', adjacent=(), *args, **kwargs):
+        super().__init__(infile, phase_id, adjacent, *args, **kwargs)
         if pystr(self.kinetics.kineticsType()) not in ("Surf", "Edge"):
             raise TypeError("Underlying Kinetics class is not of the correct type.")
 
         self._phase_indices = {}
-        for phase in [self] + list(phases):
+        for phase in [self] + list(adjacent):
             i = self.kinetics.phaseIndex(stringify(phase.name))
             self._phase_indices[phase] = i
             self._phase_indices[phase.name] = i
diff --git a/interfaces/cython/cantera/test/test_convert.py b/interfaces/cython/cantera/test/test_convert.py
index 726f547c2b2..d101ba38e64 100644
--- a/interfaces/cython/cantera/test/test_convert.py
+++ b/interfaces/cython/cantera/test/test_convert.py
@@ -660,7 +660,7 @@ def test_ptcombust(self):
                          Path(self.test_work_dir).joinpath('ptcombust.yaml'))
         ctiGas, yamlGas = self.checkConversion('ptcombust')
         ctiSurf, yamlSurf = self.checkConversion('ptcombust', ct.Interface,
-            phase='Pt_surf', ctiphases=[ctiGas], yamlphases=[yamlGas])
+            phase_id='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 @@ def test_sofc(self):
         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='metal')
-        ctiOxide, yamlOxide = self.checkConversion('sofc', phase='oxide_bulk')
+        ctiMetal, yamlMetal = self.checkConversion('sofc', phase_id='metal')
+        ctiOxide, yamlOxide = self.checkConversion('sofc', phase_id='oxide_bulk')
         ctiMSurf, yamlMSurf = self.checkConversion('sofc', ct.Interface,
-            phase='metal_surface', ctiphases=[ctiGas, ctiMetal],
+            phase_id='metal_surface', ctiphases=[ctiGas, ctiMetal],
             yamlphases=[yamlGas, yamlMetal])
         ctiOSurf, yamlOSurf = self.checkConversion('sofc', ct.Interface,
-            phase='oxide_surface', ctiphases=[ctiGas, ctiOxide],
+            phase_id='oxide_surface', ctiphases=[ctiGas, ctiOxide],
             yamlphases=[yamlGas, yamlOxide])
         cti_tpb, yaml_tpb = self.checkConversion('sofc', ct.Interface,
-            phase='tpb', ctiphases=[ctiMetal, ctiMSurf, ctiOSurf],
+            phase_id='tpb', ctiphases=[ctiMetal, ctiMSurf, ctiOSurf],
             yamlphases=[yamlMetal, yamlMSurf, yamlOSurf])
 
         self.checkThermo(ctiMSurf, yamlMSurf, [900, 1000, 1100])
@@ -694,7 +694,7 @@ def test_liquidvapor(self):
                          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=name)
+            ctiPhase, yamlPhase = self.checkConversion('liquidvapor', phase_id=name)
             self.checkThermo(ctiPhase, yamlPhase,
                              [1.3 * ctiPhase.min_temp, 0.7 * ctiPhase.max_temp])
 
@@ -717,10 +717,10 @@ def test_Redlich_Kwong_ndodecane(self):
     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='gas')
-        ctiSolid, yamlSolid = self.checkConversion('diamond', phase='diamond')
+        ctiGas, yamlGas = self.checkConversion('diamond', phase_id='gas')
+        ctiSolid, yamlSolid = self.checkConversion('diamond', phase_id='diamond')
         ctiSurf, yamlSurf = self.checkConversion('diamond',
-            ct.Interface, phase='diamond_100', ctiphases=[ctiGas, ctiSolid],
+            ct.Interface, phase_id='diamond_100', ctiphases=[ctiGas, ctiSolid],
             yamlphases=[yamlGas, yamlSolid])
         self.checkThermo(ctiSolid, yamlSolid, [300, 500])
         self.checkThermo(ctiSurf, yamlSurf, [330, 490])
@@ -730,16 +730,16 @@ def test_lithium_ion_battery(self):
         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='anode')
-        ctiCathode, yamlCathode = self.checkConversion(name, phase='cathode')
-        ctiMetal, yamlMetal = self.checkConversion(name, phase='electron')
-        ctiElyt, yamlElyt = self.checkConversion(name, phase='electrolyte')
+        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')
         ctiAnodeInt, yamlAnodeInt = self.checkConversion(name,
-            phase='edge_anode_electrolyte',
+            phase_id='edge_anode_electrolyte',
             ctiphases=[ctiAnode, ctiMetal, ctiElyt],
             yamlphases=[yamlAnode, yamlMetal, yamlElyt])
         ctiCathodeInt, yamlCathodeInt = self.checkConversion(name,
-            phase='edge_cathode_electrolyte',
+            phase_id='edge_cathode_electrolyte',
             ctiphases=[ctiCathode, ctiMetal, ctiElyt],
             yamlphases=[yamlCathode, yamlMetal, yamlElyt])
 
diff --git a/interfaces/cython/cantera/test/test_reactor.py b/interfaces/cython/cantera/test/test_reactor.py
index 7d084bc7d05..c8425d99047 100644
--- a/interfaces/cython/cantera/test/test_reactor.py
+++ b/interfaces/cython/cantera/test/test_reactor.py
@@ -929,9 +929,9 @@ def create_reactors(self, add_Q=False, add_mdot=False, add_surf=False):
         self.gas.TPX = 900, 25*ct.one_atm, 'CO:0.5, H2O:0.2'
 
         self.gas1 = ct.Solution('gri30.xml')
-        self.gas1.phase = 'gas'
+        self.gas1.phase_id = 'gas'
         self.gas2 = ct.Solution('gri30.xml')
-        self.gas2.phase = 'gas'
+        self.gas2.phase_id = 'gas'
         resGas = ct.Solution('gri30.xml')
         solid = ct.Solution('diamond.xml', 'diamond')
 
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index 5c3e783e194..c621c491bf4 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -15,20 +15,18 @@ def setUp(self):
         self.phase = ct.Solution('h2o2.xml')
 
     def test_base_attributes(self):
-        self.assertTrue(isinstance(self.phase.type, str))
-        self.assertTrue(self.phase.type=='Solution')
-        self.assertTrue(isinstance(self.phase.name, str))
-        self.assertTrue(isinstance(self.phase.thermo_model, str))
-        self.assertTrue(isinstance(self.phase.kinetics_model, str))
-        self.assertTrue(isinstance(self.phase.transport_model, str))
-        self.assertTrue(isinstance(self.phase.composite, tuple))
-        self.assertTrue(len(self.phase.composite)==3)
-        self.assertTrue(
-            self.phase.composite == (self.phase.thermo_model,
-                                     self.phase.kinetics_model,
-                                     self.phase.transport_model))
+        self.assertIsInstance(self.phase.name, str)
+        self.assertIsInstance(self.phase.thermo_model, str)
+        self.assertIsInstance(self.phase.kinetics_model, str)
+        self.assertIsInstance(self.phase.transport_model, str)
+        self.assertIsInstance(self.phase.composite, tuple)
+        self.assertEqual(len(self.phase.composite), 3)
+        self.assertEqual(self.phase.composite,
+                         (self.phase.thermo_model,
+                          self.phase.kinetics_model,
+                          self.phase.transport_model))
         self.phase.name = 'spam'
-        self.assertTrue(self.phase.name=='spam')
+        self.assertEqual(self.phase.name, 'spam')
         with self.assertRaises(AttributeError):
             self.phase.type = 'eggs'
 
@@ -324,30 +322,30 @@ def test_name(self):
         self.assertIn('something', self.phase.report())
 
     def test_phase(self):
-        self.assertEqual(self.phase.phase, 'ohmech')
+        self.assertEqual(self.phase.phase_id, 'ohmech')
         warnings.simplefilter("always")
 
         with warnings.catch_warnings(record=True) as w:
             self.assertEqual(self.phase.ID, 'ohmech')
-            self.assertTrue(len(w) == 1)
+            self.assertEqual(len(w), 1)
             self.assertTrue(issubclass(w[-1].category, DeprecationWarning))
-            self.assertTrue("To be removed after Cantera 2.5. "
-                            in str(w[-1].message))
+            self.assertIn("To be removed after Cantera 2.5. ",
+                          str(w[-1].message))
 
         with warnings.catch_warnings(record=True) as w:
             self.phase.ID = 'something'
-            self.assertEqual(self.phase.phase, 'something')
-            self.assertTrue(len(w) == 1)
+            self.assertEqual(self.phase.phase_id, 'something')
+            self.assertEqual(len(w), 1)
             self.assertTrue(issubclass(w[-1].category, DeprecationWarning))
-            self.assertTrue("To be removed after Cantera 2.5. "
-                            in str(w[-1].message))
+            self.assertIn("To be removed after Cantera 2.5. ",
+                          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.assertEqual(len(w), 1)
             self.assertTrue(issubclass(w[-1].category, FutureWarning))
-            self.assertTrue("Keyword `phase` replaces `phaseid`"
-                            in str(w[-1].message))
+            self.assertIn("Keyword 'phase_id' replaces 'phaseid'",
+                          str(w[-1].message))
 
     def test_badLength(self):
         X = np.zeros(5)
@@ -882,7 +880,7 @@ 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, phase)
+        self.assertEqual(gas.phase_id, phase)
         self.assertNear(gas.T, T)
         self.assertNear(gas.P, P)
         self.assertEqual(gas.n_species, nSpec)
@@ -1171,7 +1169,7 @@ def test_invalid(self):
     def test_wrap(self):
         st = self.gas.species('H2O').thermo
 
-        self.assertTrue(isinstance(st, ct.NasaPoly2))
+        self.assertIsInstance(st, ct.NasaPoly2)
 
         for T in [300, 500, 900, 1200, 2000]:
             self.gas.TP = T, 101325
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 7777a808113..e71b12ed6dd 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -263,8 +263,6 @@ cdef class ThermoPhase(_SolutionBase):
 
     # The signature of this function causes warnings for Sphinx documentation
     def __init__(self, *args, **kwargs):
-        base_type = kwargs.pop('base_type', 'ThermoPhase')
-        kwargs['base_type'] = base_type
         super().__init__(*args, **kwargs)
         if 'source' not in kwargs:
             self.thermo_basis = mass_basis
@@ -291,6 +289,37 @@ 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.
+
+        .. deprecated:: 2.5
+
+             To be deprecated with version 2.5, and removed thereafter.
+             Renamed to `phase_ID`.
+        """
+        def __get__(self):
+            warnings.warn("To be removed after Cantera 2.5. "
+                          "Use 'phase' attribute instead", DeprecationWarning)
+            return pystr(self.thermo.id())
+        def __set__(self, id_):
+            warnings.warn("To be removed after Cantera 2.5. "
+                          "Use 'phase' attribute instead", DeprecationWarning)
+            self.thermo.setID(stringify(id_))
+
     property basis:
         """
         Determines whether intensive thermodynamic properties are treated on a
diff --git a/src/base/Solution.cpp b/src/base/Solution.cpp
new file mode 100644
index 00000000000..51099a18681
--- /dev/null
+++ b/src/base/Solution.cpp
@@ -0,0 +1,46 @@
+//! @file Solution.cpp
+
+// 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.
+
+#include "cantera/base/Solution.h"
+#include "cantera/thermo/ThermoPhase.h"
+#include "cantera/kinetics/Kinetics.h"
+#include "cantera/transport/TransportBase.h"
+
+namespace Cantera
+{
+
+Solution::Solution() :
+    m_name("<Solution_name>")
+{}
+
+std::string Solution::name() const {
+    return m_name;
+}
+
+void Solution::setName(const std::string& name){
+    m_name = name;
+}
+
+void Solution::setThermoPhase(shared_ptr<ThermoPhase> thermo) {
+    m_thermo = thermo;
+    if (m_thermo) {
+        m_thermo->setRoot(shared_from_this());
+    }
+}
+
+void Solution::setKinetics(shared_ptr<Kinetics> kinetics) {
+    m_kinetics = kinetics;
+    if (m_kinetics) {
+        m_kinetics->setRoot(shared_from_this());
+    }
+}
+
+void Solution::setTransport(shared_ptr<Transport> transport) {
+    m_transport = transport;
+    if (m_transport) {
+        m_transport->setRoot(shared_from_this());
+    }
+}
+}
diff --git a/src/base/SolutionBase.cpp b/src/base/SolutionBase.cpp
deleted file mode 100644
index dd9e8db6cca..00000000000
--- a/src/base/SolutionBase.cpp
+++ /dev/null
@@ -1,99 +0,0 @@
-//! @file SolutionBase.cpp
-
-// 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.
-
-#include "cantera/base/SolutionBase.h"
-#include "cantera/thermo/ThermoPhase.h"
-#include "cantera/kinetics/Kinetics.h"
-#include "cantera/transport/TransportBase.h"
-
-namespace Cantera
-{
-
-SolutionBase::SolutionBase() :
-    m_thermo(nullptr),
-    m_kinetics(nullptr),
-    m_transport(nullptr),
-    m_type("<SolutionBase_type>")
-{}
-
-SolutionBase::SolutionBase(const std::string& infile,
-                           const std::string& phasename) :
-    SolutionBase()
-{
-    // this *may* be a spot to load all pieces of a phase
-    throw NotImplementedError("SolutionBase constructor from file");
-}
-
-std::string SolutionBase::type() const {
-    return m_type;
-}
-
-void SolutionBase::setType(const std::string& type){
-    m_type = type;
-}
-
-std::string SolutionBase::phase() const {
-    // currently managed by ThermoPhase
-    if (m_thermo) {
-        return m_thermo->id();
-    } else {
-        throw CanteraError("SolutionBase::id()", "Missing ThermoPhase.");
-    }
-}
-
-void SolutionBase::setPhase(const std::string& id) {
-    // currently managed by ThermoPhase
-    // note: may consider removing (but needed for association of surface
-    // kinetics which require the phase name "gas")
-    if (m_thermo) {
-        return m_thermo->setID(id);
-    } else {
-        throw CanteraError("SolutionBase::setID()", "Missing ThermoPhase.");
-    }
-}
-
-std::string SolutionBase::name() const {
-    // currently managed by ThermoPhase
-    if (m_thermo) {
-        return m_thermo->name();
-    } else {
-        throw CanteraError("SolutionBase::name()", "Missing ThermoPhase.");
-    }
-}
-
-void SolutionBase::setName(const std::string& name){
-    // currently managed by ThermoPhase
-    if (m_thermo) {
-        return m_thermo->setName(name);
-    } else {
-        throw CanteraError("SolutionBase::setName()", "Missing ThermoPhase.");
-    }
-}
-
-std::string SolutionBase::toYAML() const {
-    throw NotImplementedError("SolutionBase::toYAML");
-}
-
-void SolutionBase::setThermoPhase(shared_ptr<ThermoPhase> thermo) {
-    m_thermo = thermo;
-    if (m_thermo) {
-        m_thermo->setRoot(shared_from_this());
-    }
-}
-
-void SolutionBase::setKinetics(shared_ptr<Kinetics> kinetics) {
-    m_kinetics = kinetics;
-    if (m_kinetics) {
-        m_kinetics->setRoot(shared_from_this());
-    }
-}
-
-void SolutionBase::setTransport(shared_ptr<Transport> transport) {
-    m_transport = transport;
-    if (m_transport) {
-        m_transport->setRoot(shared_from_this());
-    }
-}
-}
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index 85798d5ec82..202f33b43c2 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -9,6 +9,7 @@
 #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"
 
@@ -78,12 +79,22 @@ void Phase::setID(const std::string& id_)
 
 std::string Phase::name() const
 {
-    return m_name;
+    auto root = m_root.lock();
+    if (root) {
+        return root->name();
+    } else {
+        return m_name;
+    }
 }
 
-void Phase::setName(const std::string& nm)
+void Phase::setName(const std::string& name)
 {
-    m_name = nm;
+    auto root = m_root.lock();
+    if (root) {
+        root->setName(name);
+    } else {
+        m_name = name;
+    }
 }
 
 size_t Phase::nElements() const

From ce707142a17f8cd65e879578cc56af3b1c8cbf97 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Wed, 9 Oct 2019 19:01:43 -0500
Subject: [PATCH 14/17] [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               |  2 --
 interfaces/cython/cantera/_cantera.pxd        |  2 --
 interfaces/cython/cantera/base.pyx            | 36 ++++++++-----------
 interfaces/cython/cantera/ck2yaml.py          | 10 +++---
 interfaces/cython/cantera/composite.py        | 23 ++++++------
 interfaces/cython/cantera/kinetics.pyx        |  4 +--
 .../cython/cantera/test/test_convert.py       | 32 ++++++++---------
 .../cython/cantera/test/test_reactor.py       |  4 +--
 interfaces/cython/cantera/test/test_thermo.py |  8 ++---
 interfaces/cython/cantera/thermo.pyx          | 24 ++++---------
 src/base/Solution.cpp                         | 28 ++++++++++-----
 src/thermo/Phase.cpp                          | 17 +++------
 12 files changed, 83 insertions(+), 107 deletions(-)

diff --git a/include/cantera/base/Solution.h b/include/cantera/base/Solution.h
index 37141cc4dc9..50c8979e338 100644
--- a/include/cantera/base/Solution.h
+++ b/include/cantera/base/Solution.h
@@ -64,8 +64,6 @@ class Solution : public std::enable_shared_from_this<Solution>
     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
 };
 
 }
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 827b4acf240..02a1fb1213e 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/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
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 76db56e5153..3609ba25a77 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/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
-        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:
diff --git a/interfaces/cython/cantera/ck2yaml.py b/interfaces/cython/cantera/ck2yaml.py
index 1ffe5a3c729..39df856bfdc 100644
--- a/interfaces/cython/cantera/ck2yaml.py
+++ b/interfaces/cython/cantera/ck2yaml.py
@@ -12,7 +12,7 @@
             [--thermo=<filename>]
             [--transport=<filename>]
             [--surface=<filename>]
-            [--phase-id=<phase-id>]
+            [--name=<name>]
             [--output=<filename>]
             [--permissive]
             [-d | --debug]
@@ -32,7 +32,7 @@
 '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=..."'
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index fb9ae6b074a..ee5421be9c7 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -27,19 +27,16 @@ 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
@@ -48,7 +45,7 @@ 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
@@ -93,9 +90,9 @@ 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',)
diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index b16c9690af0..05ddf9fdffe 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/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):
-        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.")
 
diff --git a/interfaces/cython/cantera/test/test_convert.py b/interfaces/cython/cantera/test/test_convert.py
index d101ba38e64..0d5c7707e3c 100644
--- a/interfaces/cython/cantera/test/test_convert.py
+++ b/interfaces/cython/cantera/test/test_convert.py
@@ -660,7 +660,7 @@ def test_ptcombust(self):
                          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 @@ def test_sofc(self):
         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 @@ def test_liquidvapor(self):
                          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 @@ def test_Redlich_Kwong_ndodecane(self):
     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 @@ def test_lithium_ion_battery(self):
         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])
 
diff --git a/interfaces/cython/cantera/test/test_reactor.py b/interfaces/cython/cantera/test/test_reactor.py
index c8425d99047..71cc77634eb 100644
--- a/interfaces/cython/cantera/test/test_reactor.py
+++ b/interfaces/cython/cantera/test/test_reactor.py
@@ -929,9 +929,9 @@ def create_reactors(self, add_Q=False, add_mdot=False, add_surf=False):
         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')
 
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index c621c491bf4..ff20e3cdc83 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -322,7 +322,7 @@ def test_name(self):
         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:
@@ -334,7 +334,7 @@ def test_phase(self):
 
         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. ",
@@ -344,7 +344,7 @@ def test_phase(self):
             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):
@@ -880,7 +880,7 @@ 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)
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index e71b12ed6dd..3d6260dcff0 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -289,36 +289,24 @@ 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:
         """
diff --git a/src/base/Solution.cpp b/src/base/Solution.cpp
index 51099a18681..85e0f1877c9 100644
--- a/src/base/Solution.cpp
+++ b/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() :
-    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
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index 202f33b43c2..f1ef31a9a44 100644
--- a/src/thermo/Phase.cpp
+++ b/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();
-    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

From 891ce3e3302a78cec75bd47ca9e4a4fb5f4c1d2e Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Thu, 10 Oct 2019 06:37:19 -0500
Subject: [PATCH 15/17] [Thermo] deprecate Phase::id and Phase::setID

* Merge usage of 'id' and 'name' in the context of Phase objects
* Raise deprecation warnings for Phase::id and Phase::setID
---
 include/cantera/thermo/Phase.h                | 27 ++++++++++---------
 interfaces/cython/cantera/composite.py        |  5 ++--
 .../cython/cantera/test/test_mixture.py       |  5 ++--
 src/kinetics/Kinetics.cpp                     |  6 ++---
 src/kinetics/importKinetics.cpp               |  8 +++---
 src/thermo/FixedChemPotSSTP.cpp               |  1 -
 src/thermo/LatticeSolidPhase.cpp              |  2 +-
 src/thermo/Phase.cpp                          |  6 +++++
 src/thermo/PureFluidPhase.cpp                 |  2 +-
 src/thermo/ThermoFactory.cpp                  | 10 +++----
 10 files changed, 38 insertions(+), 34 deletions(-)

diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index 0dc75d7f4c8..5365a3b41ee 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -124,30 +124,31 @@ class Phase
      */
     void setXMLdata(XML_Node& xmlPhase);
 
-    /*! @name Name and ID
-     * Class Phase contains two strings that identify a phase. The ID is the
-     * value of the ID attribute of the XML phase node that is used to
-     * initialize a phase when it is read. The name field is also initialized
-     * to the value of the ID attribute of the XML phase node.
+    /*! @name Name
+     * Class Phase uses the string name to identify a phase. The name is the
+     * value of the corresponding key in the phase map (in YAML), name (in
+     * CTI), or id (in XML) that is used to initialize a phase when it is read.
      *
      * However, the name field may be changed to another value during the
-     * course of a calculation. For example, if a phase is located in two
-     * places, but has the same constitutive input, the IDs of the two phases
-     * will be the same, but the names of the two phases may be different.
-     *
-     * It is an error to have two phases in a single problem with the same name
-     * and ID (or the name from one phase being the same as the id of
-     * another phase). Thus, it is expected that there is a 1-1 correspondence
-     * between names and unique phases within a Cantera problem.
+     * course of a calculation. For example, if duplicates of a phase object
+     * are instantiated and used in multiple places (e.g. a ReactorNet), they
+     * will have the same constitutive input, i.e. the names of the phases will
+     * be the same. Note that this is not a problem for Cantera internally;
+     * however, a user may want to rename phase objects in order to clarify.
      */
     //!@{
 
     //! Return the string id for the phase.
+    /*!
+     * @deprecated To be removed after Cantera 2.5.
+     */
     std::string id() const;
 
     //! Set the string id for the phase.
     /*!
      *    @param id String id of the phase
+     *
+     * @deprecated To be removed after Cantera 2.5.
      */
     void setID(const std::string& id);
 
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index ee5421be9c7..dcae86607fe 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -33,8 +33,9 @@ class Solution(ThermoPhase, Kinetics, Transport):
         gas = ct.Solution('diamond.yaml', name='gas')
         diamond = ct.Solution('diamond.yaml', name='diamond')
 
-    The name of the `Solution` object defaults to the *phase* specified in the 
-    input file. Once instatiated, a custom name can assigned via::
+    The name of the `Solution` object defaults to the *phase* identifier 
+    specified in the input file. Upon initialization of a 'Solution' object, 
+    a custom name can assigned via::
 
         gas.name = 'my_custom_name'
 
diff --git a/interfaces/cython/cantera/test/test_mixture.py b/interfaces/cython/cantera/test/test_mixture.py
index b96107ee1f3..42f882bb404 100644
--- a/interfaces/cython/cantera/test/test_mixture.py
+++ b/interfaces/cython/cantera/test/test_mixture.py
@@ -112,11 +112,10 @@ def test_charge(self):
 
     def test_phase_moles(self):
         M = self.mix.phase_moles()
-        name = self.phase2.name
         self.assertEqual(M[0], self.mix.phase_moles(0))
-        self.assertEqual(M[1], self.mix.phase_moles(name))
+        self.assertEqual(M[1], self.mix.phase_moles('air'))
 
-        self.mix.set_phase_moles(name, 4)
+        self.mix.set_phase_moles('air', 4)
         self.assertEqual(self.mix.phase_moles(1), 4)
 
     def test_species_moles(self):
diff --git a/src/kinetics/Kinetics.cpp b/src/kinetics/Kinetics.cpp
index 300110b57e8..570f592f980 100644
--- a/src/kinetics/Kinetics.cpp
+++ b/src/kinetics/Kinetics.cpp
@@ -306,7 +306,7 @@ size_t Kinetics::kineticsSpeciesIndex(const std::string& nm,
     }
 
     for (size_t n = 0; n < m_thermo.size(); n++) {
-        string id = thermo(n).id();
+        string id = thermo(n).name();
         if (ph == id) {
             size_t k = thermo(n).speciesIndex(nm);
             if (k == npos) {
@@ -451,7 +451,7 @@ void Kinetics::addPhase(thermo_t& thermo)
         m_rxnphase = nPhases();
     }
     m_thermo.push_back(&thermo);
-    m_phaseindex[m_thermo.back()->id()] = nPhases();
+    m_phaseindex[m_thermo.back()->name()] = nPhases();
     resizeSpecies();
 }
 
@@ -608,7 +608,7 @@ shared_ptr<Reaction> Kinetics::reaction(size_t i)
     checkReactionIndex(i);
     return m_reactions[i];
 }
-    
+
 shared_ptr<const Reaction> Kinetics::reaction(size_t i) const
 {
     checkReactionIndex(i);
diff --git a/src/kinetics/importKinetics.cpp b/src/kinetics/importKinetics.cpp
index 7d05355ff75..296eb6f35dc 100644
--- a/src/kinetics/importKinetics.cpp
+++ b/src/kinetics/importKinetics.cpp
@@ -168,7 +168,7 @@ bool importKinetics(const XML_Node& phase, std::vector<ThermoPhase*> th,
         // loop over the supplied 'ThermoPhase' objects representing
         // phases, to find an object with the same id.
         for (size_t m = 0; m < th.size(); m++) {
-            if (th[m]->id() == phase_id) {
+            if (th[m]->name() == phase_id) {
                 phase_ok = true;
                 // if no phase with this id has been added to
                 //the kinetics manager yet, then add this one
@@ -176,7 +176,7 @@ bool importKinetics(const XML_Node& phase, std::vector<ThermoPhase*> th,
                     k->addPhase(*th[m]);
                 }
             }
-            msg += " "+th[m]->id();
+            msg += " "+th[m]->name();
         }
         if (!phase_ok) {
             throw CanteraError("importKinetics",
@@ -254,7 +254,7 @@ bool checkElectrochemReaction(const XML_Node& p, Kinetics& kin, const XML_Node&
         size_t k = ph.speciesIndex(sp.first);
         double stoich = sp.second;
         for (size_t m = 0; m < phase_ids.size(); m++) {
-            if (phase_ids[m] == ph.id()) {
+            if (phase_ids[m] == ph.name()) {
                 e_counter[m] += stoich * ph.charge(k);
                 break;
             }
@@ -267,7 +267,7 @@ bool checkElectrochemReaction(const XML_Node& p, Kinetics& kin, const XML_Node&
         size_t k = ph.speciesIndex(sp.first);
         double stoich = sp.second;
         for (size_t m = 0; m < phase_ids.size(); m++) {
-            if (phase_ids[m] == ph.id()) {
+            if (phase_ids[m] == ph.name()) {
                 e_counter[m] -= stoich * ph.charge(k);
                 break;
             }
diff --git a/src/thermo/FixedChemPotSSTP.cpp b/src/thermo/FixedChemPotSSTP.cpp
index a94a0e10563..62105fdf902 100644
--- a/src/thermo/FixedChemPotSSTP.cpp
+++ b/src/thermo/FixedChemPotSSTP.cpp
@@ -40,7 +40,6 @@ FixedChemPotSSTP::FixedChemPotSSTP(const std::string& Ename, doublereal val) :
     chemPot_(0.0)
 {
     std::string pname = Ename + "Fixed";
-    setID(pname);
     setName(pname);
     setNDim(3);
     addElement(Ename);
diff --git a/src/thermo/LatticeSolidPhase.cpp b/src/thermo/LatticeSolidPhase.cpp
index 02293b85ba7..a3ce57767fc 100644
--- a/src/thermo/LatticeSolidPhase.cpp
+++ b/src/thermo/LatticeSolidPhase.cpp
@@ -347,7 +347,7 @@ void LatticeSolidPhase::setLatticeStoichiometry(const compositionMap& comp)
     }
     // Add in the lattice stoichiometry constraint
     for (size_t i = 1; i < m_lattice.size(); i++) {
-        string econ = fmt::format("LC_{}_{}", i, id());
+        string econ = fmt::format("LC_{}_{}", i, name());
         size_t m = addElement(econ, 0.0, 0, 0.0, CT_ELEM_TYPE_LATTICERATIO);
         size_t mm = nElements();
         for (size_t k = 0; k < m_lattice[0]->nSpecies(); k++) {
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index f1ef31a9a44..e662fbdedfe 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -68,11 +68,17 @@ void Phase::setXMLdata(XML_Node& xmlPhase)
 
 std::string Phase::id() const
 {
+    warn_deprecated("Phase::id",
+                    "To be removed after Cantera 2.5. "
+                    "Usage merged with 'Phase::name'");
     return m_id;
 }
 
 void Phase::setID(const std::string& id_)
 {
+    warn_deprecated("Phase::setID",
+                    "To be removed after Cantera 2.5. "
+                    "Usage merged with 'Phase::setName'");
     m_id = id_;
     m_name = id_;
 }
diff --git a/src/thermo/PureFluidPhase.cpp b/src/thermo/PureFluidPhase.cpp
index 2382ac51199..5b77323500a 100644
--- a/src/thermo/PureFluidPhase.cpp
+++ b/src/thermo/PureFluidPhase.cpp
@@ -64,7 +64,7 @@ void PureFluidPhase::initThermo()
     m_sub->setStdState(h0_RT*GasConstant*298.15/m_mw,
                        s_R*GasConstant/m_mw, T0, p);
     debuglog("PureFluidPhase::initThermo: initialized phase "
-             +id()+"\n", m_verbose);
+             +name()+"\n", m_verbose);
 }
 
 void PureFluidPhase::setParametersFromXML(const XML_Node& eosdata)
diff --git a/src/thermo/ThermoFactory.cpp b/src/thermo/ThermoFactory.cpp
index e5a5da4941a..b152c55570b 100644
--- a/src/thermo/ThermoFactory.cpp
+++ b/src/thermo/ThermoFactory.cpp
@@ -250,7 +250,6 @@ void importPhase(XML_Node& phase, ThermoPhase* th)
     th->setXMLdata(phase);
 
     // set the id attribute of the phase to the 'id' attribute in the XML tree.
-    th->setID(phase.id());
     th->setName(phase.id());
 
     // Number of spatial dimensions. Defaults to 3 (bulk phase)
@@ -258,7 +257,7 @@ void importPhase(XML_Node& phase, ThermoPhase* th)
         int idim = intValue(phase["dim"]);
         if (idim < 1 || idim > 3) {
             throw CanteraError("importPhase",
-                               "phase, " + th->id() +
+                               "phase, " + th->name() +
                                ", has unphysical number of dimensions: " + phase["dim"]);
         }
         th->setNDim(idim);
@@ -274,7 +273,7 @@ void importPhase(XML_Node& phase, ThermoPhase* th)
         th->setParametersFromXML(eos);
     } else {
         throw CanteraError("importPhase",
-                           " phase, " + th->id() +
+                           " phase, " + th->name() +
                            ", XML_Node does not have a \"thermo\" XML_Node");
     }
 
@@ -284,7 +283,7 @@ void importPhase(XML_Node& phase, ThermoPhase* th)
         vpss_ptr = dynamic_cast <VPStandardStateTP*>(th);
         if (vpss_ptr == 0) {
             throw CanteraError("importPhase",
-                               "phase, " + th->id() + ", was VPSS, but dynamic cast failed");
+                               "phase, " + th->name() + ", was VPSS, but dynamic cast failed");
         }
     }
 
@@ -300,7 +299,7 @@ void importPhase(XML_Node& phase, ThermoPhase* th)
     vector<XML_Node*> sparrays = phase.getChildren("speciesArray");
     if (ssConvention != cSS_CONVENTION_SLAVE && sparrays.empty()) {
         throw CanteraError("importPhase",
-                           "phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n"
+                           "phase, " + th->name() + ", has zero \"speciesArray\" XML nodes.\n"
                            + " There must be at least one speciesArray nodes "
                            "with one or more species");
     }
@@ -448,7 +447,6 @@ void addSpecies(ThermoPhase& thermo, const AnyValue& names, const AnyValue& spec
 void setupPhase(ThermoPhase& thermo, AnyMap& phaseNode, const AnyMap& rootNode)
 {
     thermo.setName(phaseNode["name"].asString());
-    thermo.setID(phaseNode["name"].asString());
     if (rootNode.hasKey("__file__")) {
         phaseNode["__file__"] = rootNode["__file__"];
     }

From 9696e55aa54ae2559accebd23b67d6e026066ee9 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sun, 6 Oct 2019 20:18:20 -0500
Subject: [PATCH 16/17] [Thermo] deprecate name/id support in
 Phase::speciesIndex

---
 include/cantera/thermo/Phase.h | 14 +++++---------
 src/thermo/Phase.cpp           |  5 +++++
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index 5365a3b41ee..86288ebfe2e 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -68,15 +68,11 @@ class Solution;
  * operate on a state vector, which is in general of length (2 + nSpecies()).
  * The first two entries of the state vector are temperature and density.
  *
- * A species name may be referred to via three methods:
- *
- *    -   "speciesName"
- *    -   "PhaseId:speciesName"
- *    -   "phaseName:speciesName"
- *    .
- *
- * The first two methods of naming may not yield a unique species within
- * complicated assemblies of %Cantera Phases.
+ * A species name is referred to via "speciesName", which is unique within a
+ * given phase. Note that within multiphase mixtures ("MultiPhase"), both a
+ * phase name/index as well as species name are required to access information
+ * about a species in a particular phase. For surfaces, the species names are
+ * unique among the phases.
  *
  * @todo
  *   - Make the concept of saving state vectors more general, so that it can
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index e662fbdedfe..3e827e980a4 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -214,6 +214,11 @@ size_t Phase::speciesIndex(const std::string& nameStr) const
         std::string pn;
         std::string sn = parseSpeciesName(nameStr, pn);
         if (pn == "" || pn == m_name || pn == m_id) {
+            warn_deprecated("Phase::speciesIndex()",
+                            "Retrieval of species indices via "
+                            "'PhaseId:speciesName' or 'phaseName:"
+                            "speciesName to be removed "
+                            "after Cantera 2.5.");
             it = m_speciesIndices.find(nameStr);
             if (it != m_speciesIndices.end()) {
                 return it->second;

From 6190b4fca1fa463101d37c0c6384e9dbe6d9761e Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Tue, 22 Oct 2019 13:44:50 -0500
Subject: [PATCH 17/17] [Thermo] address code review comments

---
 include/cantera/base/Solution.h         |  6 +++---
 include/cantera/thermo/Phase.h          |  4 ++--
 interfaces/cython/cantera/base.pyx      |  5 +----
 interfaces/cython/cantera/transport.pyx |  2 --
 src/thermo/Phase.cpp                    | 12 ++++--------
 5 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/include/cantera/base/Solution.h b/include/cantera/base/Solution.h
index 50c8979e338..bf886a95dc1 100644
--- a/include/cantera/base/Solution.h
+++ b/include/cantera/base/Solution.h
@@ -61,9 +61,9 @@ class Solution : public std::enable_shared_from_this<Solution>
     }
 
 protected:
-    shared_ptr<ThermoPhase> m_thermo;  //! ThermoPhase manager
-    shared_ptr<Kinetics> m_kinetics;  //! Kinetics manager
-    shared_ptr<Transport> m_transport;  //! Transport manager
+    shared_ptr<ThermoPhase> m_thermo;  //!< ThermoPhase manager
+    shared_ptr<Kinetics> m_kinetics;  //!< Kinetics manager
+    shared_ptr<Transport> m_transport;  //!< Transport manager
 };
 
 }
diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index 86288ebfe2e..48635dc4c00 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -68,8 +68,8 @@ class Solution;
  * operate on a state vector, which is in general of length (2 + nSpecies()).
  * The first two entries of the state vector are temperature and density.
  *
- * A species name is referred to via "speciesName", which is unique within a
- * given phase. Note that within multiphase mixtures ("MultiPhase"), both a
+ * A species name is referred to via speciesName(), which is unique within a
+ * given phase. Note that within multiphase mixtures (MultiPhase()), both a
  * phase name/index as well as species name are required to access information
  * about a species in a particular phase. For surfaces, the species names are
  * unique among the phases.
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 3609ba25a77..6444a4c56d2 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -70,16 +70,13 @@ cdef class _SolutionBase:
         if isinstance(self, Transport):
             assert self.transport is not NULL
 
-        phase_name = pystr(self.base.name())
         name = kwargs.get('name')
         if name is not None:
             self.name = name
-        else:
-            self.name = phase_name
 
     property name:
         """
-        The name assigned to this object. The default value corresponds 
+        The name assigned to this object. The default value corresponds
         to the CTI/XML/YAML input file phase entry.
         """
         def __get__(self):
diff --git a/interfaces/cython/cantera/transport.pyx b/interfaces/cython/cantera/transport.pyx
index 82fa37aca04..b9b0bb24e81 100644
--- a/interfaces/cython/cantera/transport.pyx
+++ b/interfaces/cython/cantera/transport.pyx
@@ -145,8 +145,6 @@ cdef class Transport(_SolutionBase):
                 self.transport = newTransportMgr(stringify(model), self.thermo)
             self._transport.reset(self.transport)
 
-        base_type = kwargs.pop('base_type', 'Transport')
-        kwargs['base_type'] = base_type
         super().__init__(*args, **kwargs)
         self.base.setTransport(self._transport)
 
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index 3e827e980a4..2c18552e387 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -69,16 +69,14 @@ void Phase::setXMLdata(XML_Node& xmlPhase)
 std::string Phase::id() const
 {
     warn_deprecated("Phase::id",
-                    "To be removed after Cantera 2.5. "
-                    "Usage merged with 'Phase::name'");
+        "To be removed after Cantera 2.5. Usage merged with 'Phase::name'");
     return m_id;
 }
 
 void Phase::setID(const std::string& id_)
 {
     warn_deprecated("Phase::setID",
-                    "To be removed after Cantera 2.5. "
-                    "Usage merged with 'Phase::setName'");
+        "To be removed after Cantera 2.5. Usage merged with 'Phase::setName'");
     m_id = id_;
     m_name = id_;
 }
@@ -215,10 +213,8 @@ size_t Phase::speciesIndex(const std::string& nameStr) const
         std::string sn = parseSpeciesName(nameStr, pn);
         if (pn == "" || pn == m_name || pn == m_id) {
             warn_deprecated("Phase::speciesIndex()",
-                            "Retrieval of species indices via "
-                            "'PhaseId:speciesName' or 'phaseName:"
-                            "speciesName to be removed "
-                            "after Cantera 2.5.");
+                "Retrieval of species indices via 'PhaseId:speciesName' or "
+                "'phaseName:speciesName' to be removed after Cantera 2.5.");
             it = m_speciesIndices.find(nameStr);
             if (it != m_speciesIndices.end()) {
                 return it->second;