Updated documentation for Phase/ThermoPhase class heirarchy

Removed some redundant documentation and fixed references to the no
longer existent Constituent and State classes.

doc/doxygen/phases.dox

@@ -1,87 +0,0 @@
-/**
- * @defgroup phases Models of Phases of Matter
- *
- *  These classes are used to represent the composition and state of a
- *  single phase of matter.
- *  Together these classes form the basis for describing the species and
- *  element compositions of a phase as well as the stoichiometry
- *  of each species, and for describing the current state of the
- *  phase. They do not in themselves contain Thermodynamic equation of
- *  state information. However, they do comprise all of the necessary
- *  background functionality to support thermodynamic calculations, and the
- *  class ThermoPhase inherits from the class Phase (see \ref thermoprops).
- *
- *  Class Elements manages the elements that are part of a
- *  chemistry specification for a phase.  This class may support calculations
- *  employing Multiple phases. In this case, a single Elements object may
- *  be shared by more than one Constituents class. Reactions between
- *  the phases may then be described using stoichiometry base on the
- *  same Elements class object.
- *
- *  The member functions of class %Elements return information about
- *  the elements described in a particular instantiation of the
- *  class.
- *
- *  Class %Constituents is designed to provide information
- *  about the elements and species in a phase - names, index
- *  numbers (location in arrays), atomic or molecular weights,
- *  etc. No computations are performed by the methods of this
- *  class. The set of elements must include all those that compose
- *  the species, but may include additional elements.
- *
- *  %Constituents contains a pointer to the Elements object, and
- *  it contains wrapper functions for all of the functionality
- *  of the %Elements object, i.e., atomic weights, number and identity
- *  of the elements. %Elements may be added to a phase by using
- *  the function Constituents::addUniqueElement(). The %Elements
- *  object may be shared amongst different Phases.
- *
- *  %Constituents also contains utilities retrieving the index of
- *  a species in the phase given its name, Constituents::speciesIndex().
- *
- *  Class State manages the independent variables of temperature,
- *  mass density, and species mass/mole fraction that define the
- *  thermodynamic state.
- *
- *  Class %State stores just enough information about a
- *  multicomponent solution to specify its intensive thermodynamic
- *  state.  It stores values for the temperature, mass density, and
- *  an array of species mass fractions. It also stores an array of
- *  species molecular weights, which are used to convert between
- *  mole and mass representations of the composition. These are the
- *  \e only properties of the species that class %State knows about.
- *
- *  Class %State is not usually used directly in application
- *  programs. Its primary use is as a base class for class
- *  Phase. Class %State has no virtual methods, and none of its
- *  methods are meant to be overloaded. However, this is one
- *  exception.  If the phase is incompressible, then the density
- *  must be replaced by the pressure as the independent variable. In
- *  this case, functions such as State::setMassFractions() within
- *  the class %State must actually now calculate the density (at
- *  constant <I>T</I> and <I>P</I>) instead of leaving it alone as
- *  befits an independent variable. Therefore, these types of
- *  functions are virtual functions and need to be overloaded for
- *  incompressible phases. Note, for nearly incompressible phases
- *  (or phases which utilize standard states based on a <I>T</I> and
- *  <I>P</I>) this change in independent variables may be
- *  advantageous as well, and these functions in %State need to
- *  overload as well so that the stored density within State
- *  doesn't become out of date.
- *
- *  Class Phase derives from both clases
- *  Constituents and State. In addition to the methods of those two
- *  classes, it implements methods that allow referencing a species
- *  by name. And, it contains a lot of utility functions that will
- *  set the %State of the phase in its entirety, by first setting
- *  the composition, then the temperature and then the density.
- *  An example of this is the function,
- *    Phase::setState_TRY(doublereal t, doublereal dens, const doublereal* y).
- *
- *  Class Phase contains method for saving and restoring the
- *  full internal states of each phase. These are called Phase::saveState()
- *  and Phase::restoreState(). These functions operate on a state
- *  vector, which is in general of length (2 + nSpecies()). The first
- *  two entries of the state vector is temperature and density.
- *
- */

doc/doxygen/thermoprops.dox

@@ -243,21 +243,21 @@
  *        </TD>
  *      </TR>
  *      <TR>
- *        <TD> \link State::setConcentrations() setConcentrations()\endlink     </TD>
+ *        <TD> \link Phase::setConcentrations() setConcentrations()\endlink     </TD>
  *        <TD> Set the concentrations of all the species in the
  *                         phase. Note this implicitly specifies the pressure and
  *                         density of the phase. The temperature is assumed fixed.
  *        </TD>
  *      </TR>
  *      <TR>
- *        <TD> \link State::setDensity() setDensity()\endlink     </TD>
+ *        <TD> \link Phase::setDensity() setDensity()\endlink     </TD>
  *        <TD>  Set the total density of the phase. The temperature and
  *                         mole fractions are assumed fixed. Note this implicitly
  *                         sets the pressure of the phase.
  *        </TD>
  *      </TR>
  *      <TR>
- *        <TD> \link State::setTemperature() setTemperature()\endlink     </TD>
+ *        <TD> \link Phase::setTemperature() setTemperature()\endlink     </TD>
  *        <TD> Set the temperature of the phase. The density and
  *                         the mole fractions of the phase are fixed.
  *        </TD>

include/cantera/thermo/DebyeHuckel.h

@@ -100,7 +100,7 @@ class PDSS_Water;
  * of pressure. The standard state gibbs free energy is obtained
  * from the enthalpy and entropy functions.
  *
- * The vector Constituents::m_speciesSize[] is used to hold the
+ * The vector Phase::m_speciesSize[] is used to hold the
  * base values of species sizes. These are defined as the
  * molar volumes of species at infinite dilution at 300 K and 1 atm
  * of water. m_speciesSize are calculated during the initialization of the

include/cantera/thermo/HMWSoln.h

@@ -151,7 +151,7 @@ class PDSS_Water;
  * of pressure. The solute standard state gibbs free energy is obtained
  * from the enthalpy and entropy functions.
  *
- * The vector Constituents::m_speciesSize[] is used to hold the
+ * The vector Phase::m_speciesSize[] is used to hold the
  * base values of species sizes. These are defined as the
  * molar volumes of species at infinite dilution at 300 K and 1 atm
  * of water. m_speciesSize are calculated during the initialization of the

include/cantera/thermo/IdealGasPhase.h

@@ -31,10 +31,10 @@ namespace Cantera
  * The independent unknowns are density, mass fraction, and temperature.
  * the #setPressure() function will calculate the density consistent with
  * the current mass fraction vector and temperature and the desired pressure,
- * and then set the density in the derived State object.
+ * and then set the density.
  *
  * <HR>
- * <H2> Specification of Species Standard %State Properties </H2>
+ * <H2> Specification of Species Standard State Properties </H2>
  * <HR>
  *
  *  It is assumed that the reference state thermodynamics may be

include/cantera/thermo/Phase.h

@@ -15,6 +15,18 @@ namespace Cantera
 {
 class SpeciesThermo;
 
+/**
+ * @defgroup phases Models of Phases of Matter
+ *
+ * These classes are used to represent the composition and state of a single
+ * phase of matter. Together these classes form the basis for describing the
+ * species and element compositions of a phase as well as the stoichiometry
+ * of each species, and for describing the current state of the phase. They do
+ * not in themselves contain Thermodynamic equation of state information.
+ * However, they do comprise all of the necessary background functionality to
+ * support thermodynamic calculations (see \ref thermoprops).
+ */
+
 //!  Exception class to indicate a fixed set of elements.
 /*!
  *   This class is used to warn the user when the number of elements
@@ -31,6 +43,7 @@ public:
 
 //! Base class for phases of matter
 /*!
+ *
  * Class Phase manages the species and elements in a phase, as well as the
  * independent variables of temperature, mass density, and species mass/mole
  * fraction that define the thermodynamic state.