Doxygen update

Finished a draft of the File Tab within Doxygen. Each file now
has a link to the relevant modules and classes.

Cantera/cxx/include/equilibrium.h

@@ -1,7 +1,10 @@
 /**
  * @file equilibrium.h
- *
- * Header file providing support for chemical equilibrium calculations.
+ * cxx layer - Header file providing support for chemical equilibrium calculations
+ *    (see \ref equilfunctions)
+ */
+/*
+ * $Id$
  */
 #ifndef CT_EQUIL_INCL
 #define CT_EQUIL_INCL

Cantera/src/GeneralSpeciesThermo.cpp

@@ -1,8 +1,12 @@
 /**
  *  @file GeneralSpeciesThermo.cpp
- *
+ *  Declarations for a completely general species thermodynamic property
+ *  manager for a phase (see \ref spthermo and
+ * \link Cantera::GeneralSpeciesThermo GeneralSpeciesThermo\endlink).
+ */
+/*
+ * $Id$
  */
-                
 // Copyright 2001-2004  California Institute of Technology
                 
 #include "GeneralSpeciesThermo.h"

Cantera/src/GeneralSpeciesThermo.h

@@ -1,5 +1,10 @@
 /**
  * @file GeneralSpeciesThermo.h
+ *  Headers for a completely general species thermodynamic property
+ *  manager for a phase (see \ref spthermo and
+ * \link Cantera::GeneralSpeciesThermo GeneralSpeciesThermo\endlink).
+ *
+ *  Because it is general, it is slow.
  */
 
 /*

Cantera/src/IdealGasPhase.cpp

@@ -1,7 +1,12 @@
 /**
  *
  *  @file IdealGasPhase.cpp
+ *   ThermoPhase object for the ideal gas equation of
+ * state - workhorse for %Cantera (see \ref thermoprops 
+ * and class \link Cantera::IdealGasPhase IdealGasPhase\endlink).
  *
+ */
+/*
  * $Id$
  */
 

Cantera/src/IdealGasPhase.h

@@ -1,6 +1,9 @@
 /**
  *  @file IdealGasPhase.h 
- *   ThermoPhase object for the ideal gas equation of state.
+ *   ThermoPhase object for the ideal gas equation of
+ * state - workhorse for %Cantera (see \ref thermoprops 
+ * and class \link Cantera::IdealGasPhase IdealGasPhase\endlink).
+ * 
  */
 
 /*  $Author$

Cantera/src/Kinetics.cpp

@@ -1,6 +1,9 @@
 /**
  *  @file Kinetics.cpp
- *      Declarations for the base class for kinetics managers (see \ref kineticsmgr).
+ *      Declarations for the base class for kinetics 
+ *    managers (see \ref  kineticsmgr and class 
+ *  \link Cantera::Kinetics Kinetics\endlink).
+ *
  *      Kinetics managers calculate rates of progress of species due to homogeneous or heterogeneous kinetics.
  */
 

Cantera/src/Kinetics.h

@@ -1,7 +1,8 @@
 /**
  * @file Kinetics.h
  *  Base class for kinetics managers and also contains the kineticsmgr
- *  module documentation (see \ref  kineticsmgr).
+ *  module documentation (see \ref  kineticsmgr and class 
+ *  \link Cantera::Kinetics Kinetics\endlink).
  *
  *  $Author$
  *  $Date$

Cantera/src/Mu0Poly.cpp

@@ -1,8 +1,11 @@
 /**
  *  @file Mu0Poly.cpp
- *
- * Definitions for the Mu0Poly class.
- *
+ *  Definitions for a single-species standard state object derived
+ *  from \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType\endlink  based 
+ *  on a piecewise constant mu0 interpolation
+ *  (see \ref spthermo and class \link Cantera::Mu0Poly Mu0Poly\endlink).
+ */
+/*
  * $Author$
  * $Revision$
  * $Date$

Cantera/src/Mu0Poly.h

@@ -1,7 +1,9 @@
 /**
- *  @file Mu0Poly.h
- *  
- *  Declarations for piecewise constant mu0 interpolation.
+ *  @file Mu0Poly.h 
+ *  Header for a single-species standard state object derived
+ *  from \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType\endlink  based 
+ *  on a piecewise constant mu0 interpolation
+ *  (see \ref spthermo and class \link Cantera::Mu0Poly Mu0Poly\endlink).
  */
 
 /* $Author$

Cantera/src/NasaPoly1.h

@@ -1,10 +1,19 @@
-#ifndef CT_NASAPOLY1_H
-#define CT_NASAPOLY1_H
 
 /**
  *  @file NasaPoly1.h
+ *  Header for a single-species standard state object derived
+ *  from \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType\endlink  based 
+ *  on the NASA temperature polynomial form applied to one temperature region
+ *  (see \ref spthermo and class \link Cantera::NasaPoly1 NasaPoly1\endlink).
+ *
+ *  This parameterization has one NASA temperature region.
  */
 
+
+#ifndef CT_NASAPOLY1_H
+#define CT_NASAPOLY1_H
+
+
 /* $Author$
  * $Revision$
  * $Date$

Cantera/src/NasaPoly2.h

@@ -1,5 +1,9 @@
 /**
  *  @file NasaPoly2.h
+ *  Header for a single-species standard state object derived
+ *  from \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType\endlink  based 
+ *  on the NASA temperature polynomial form applied to two temperature regions
+ *  (see \ref spthermo and class \link Cantera::NasaPoly2 NasaPoly2\endlink).
  *
  *  Two zoned Nasa polynomial parameterization
  */

Cantera/src/NasaThermo.h

@@ -1,8 +1,9 @@
 /**
  * @file NasaThermo.h
- *    
- *   Definitions for the 2 regime 7 coefficient Nasa thermodynamic
- *   polynomials.
+ *   Header for the 2 regime 7 coefficient Nasa thermodynamic
+ *   polynomials for multiple species in a phase, derived from the
+ *   \link Cantera::SpeciesThermo SpeciesThermo\endlink base class (see \ref spthermo and
+ *   \link Cantera::NasaThermo NasaThermo\endlink).
  */
 
 /*

Cantera/src/Phase.cpp

@@ -1,5 +1,8 @@
 /**
  *  @file Phase.cpp
+ *   Definition file for class, Phase, which contains functions for setting the
+ *   state of a phase, and for referencing species by name
+ *   (see \ref phases and class \link Cantera::Phase Phase\endlink).
  */
 
 // Copyright 2001  California Institute of Technology

Cantera/src/Phase.h

@@ -1,13 +1,14 @@
 /**
  *  @file Phase.h
+ *   Header file for class, Phase, which contains functions for setting the
+ *   state of a phase, and for referencing species by name, and also contains text for the module phases
+ *   (see \ref phases and class \link Cantera::Phase Phase\endlink).
  */
-
 /*
  * $Author$
  * $Revision$
  * $Date$
  */
-
 // Copyright 2001  California Institute of Technology
 
 #ifndef CT_PHASE_H

Cantera/src/PureFluidPhase.cpp

@@ -1,4 +1,12 @@
-
+/**
+ *   @file PureFluidPhase.cpp
+ *   Definitions for a ThermoPhase object for a pure fluid phase consisting of gas, liquid, mixed-gas-liquid
+ *   and supercritical fluid (see \ref thermoprops 
+ *   and class \link Cantera::PureFluidPhase PureFluidPhase\endlink).
+ */
+/*
+ *  $Id$
+ */
 #include "xml.h"
 #include "PureFluidPhase.h"
 

Cantera/src/PureFluidPhase.h

@@ -1,10 +1,13 @@
 /**
  *  @file PureFluidPhase.h
- *
- * Declares class PureFluid.
+ *   Header for a ThermoPhase object for a pure fluid phase consisting of gas, liquid, mixed-gas-liquid
+ *   and supercrit fluid (see \ref thermoprops 
+ *   and class \link Cantera::PureFluidPhase PureFluidPhase\endlink).
+ * 
  *
  * This object is only available if the WITH_PURE_FLUIDS optional compile
  * capability has been turned on in Cantera's makefile system. 
+ * It inherits from ThermoPhase, but is built on top of the tpx package.
  */
 
 /*  $Author$

Cantera/src/ShomatePoly.h

@@ -1,8 +1,13 @@
 /**
  *  @file ShomatePoly.h
- *
+ *  Header for a single-species standard state object derived
+ *  from \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType\endlink  based 
+ *  on the Shomate temperature polynomial form applied to one temperature region
+ *  (see \ref spthermo and class \link Cantera::ShomatePoly ShomatePoly\endlink and
+ *   \link Cantera::ShomatePoly2 ShomatePoly2\endlink).
  *    Shomate polynomial expressions.
- *
+ */
+/*
  * $Author$
  * $Revision$
  * $Date$

Cantera/src/ShomateThermo.h

@@ -1,12 +1,13 @@
 /**
  * @file ShomateThermo.h
- * 
- * Definitions and declarations for a species property manager that
- * uses the Shomate polynomials.
- *
+ *   Header for the 2 regions Shomate polynomial
+ *   for multiple species in a phase, derived from the
+ *   \link Cantera::SpeciesThermo SpeciesThermo\endlink base class (see \ref spthermo and
+ *   \link Cantera::ShomateThermo ShomateThermo\endlink).
+ */
+/*
  * $Id$
  */
-
 // Copyright 2001  California Institute of Technology
 
 

Cantera/src/SimpleThermo.h

@@ -1,10 +1,12 @@
+/**
+ * @file SimpleThermo.h
+ *   Header for the SimpleThermo (constant heat capacity) species reference-state model
+ *   for multiple species in a phase, derived from the
+ *   \link Cantera::SpeciesThermo SpeciesThermo\endlink base class (see \ref spthermo and
+ *   \link Cantera::SimpleThermo SimpleThermo\endlink).
+ */
 /*
  * $Id$
- *
- * @file SimpleSpecies.h
- *
- *   Contains the definition and declarations for the SimpleSpecies 
- *   standard state species thermodynamic property manager for a phase.
  */
 
 #ifndef CT_SIMPLETHERMO_H
@@ -14,7 +16,7 @@
 
 namespace Cantera {
 
-  /**
+  /*!
    *  A constant-heat capacity species thermodynamic property manager class. 
    *  This makes the
    *  assumption that the heat capacity is a constant. Then, the following
@@ -22,13 +24,13 @@ namespace Cantera {
    *  functions for each species in the phase.
    *
    * \f[
-   * \frac{c_p(T)}{R} = Cp0\_R
+   *   \frac{c_p(T)}{R} = Cp0\_R
    * \f]
    * \f[
-   * \frac{h^0(T)}{RT} = \frac{1}{T} * (h0\_R + (T - T_0) * Cp0\_R)
+   *   \frac{h^0(T)}{RT} = \frac{1}{T} * (h0\_R + (T - T_0) * Cp0\_R)
    * \f]
    * \f[
-   * \frac{s^0(T)}{R} =  (s0\_R + (log(T) - log(T_0)) * Cp0\_R)
+   *   \frac{s^0(T)}{R} =  (s0\_R + (log(T) - log(T_0)) * Cp0\_R)
    * \f]
    *
    * This parameterization takes 4 input values. These are:

Cantera/src/SpeciesThermo.h

@@ -1,8 +1,8 @@
 /**
  *  @file SpeciesThermo.h
- *  Species thermodynamic property managers. In this file we describe
- *  the base class for the calculation of species thermodynamic
- *  property managers.
+ *  Virtual base class for the calculation of multiple-species thermodynamic
+ *  property managers and text for the spthermo module (see \ref spthermo 
+ *  and class \link Cantera::SpeciesThermo SpeciesThermo\endlink).
  *
  *  We also describe the doxygen module spthermo  (see \ref spthermo )
  */

Cantera/src/SpeciesThermoFactory.cpp

@@ -1,16 +1,19 @@
 /**
  *  @file SpeciesThermoFactory.cpp
+ *    Definitions for factory to build instances of classes that manage the
+ *    standard-state thermodynamic properties of a set of species 
+ *    (see \ref spthermo and class \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink);
+ */
+/*
+ * $Id$
  */
-
 // Copyright 2001  California Institute of Technology
 
-
 #ifdef WIN32
 #pragma warning(disable:4786)
 #endif
 
 
-
 #include "SpeciesThermoFactory.h"
 using namespace std;
 

Cantera/src/SpeciesThermoFactory.h

@@ -1,5 +1,8 @@
 /**
  *  @file SpeciesThermoFactory.h
+ *    Header for factory to build instances of classes that manage the
+ *    standard-state thermodynamic properties of a set of species 
+ *    (see \ref spthermo and class \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink);
  */
 
 /*

Cantera/src/SpeciesThermoMgr.h

@@ -1,9 +1,11 @@
 /**
  *  @file SpeciesThermoMgr.h
- *
  *  This file contains descriptions of templated subclasses of 
- *  the virtual base class, SpeciesThermo.
- *  These include  SpeciesThermoDuo and SpeciesThermo1.
+ *  the virtual base class, SpeciesThermo, which 
+ *  include  SpeciesThermoDuo and SpeciesThermo1
+ *  (see \ref spthermo and classes 
+ *   \link Cantera::SpeciesThermoDuo SpeciesThermoDuo\endlink and
+ *  \link Cantera::SpeciesThermo1 SpeciesThermo1\endlink)
  *
  * $Author$
  * $Revision$

Cantera/src/State.cpp

@@ -1,8 +1,10 @@
 /**
  *
  *  @file State.cpp
+ * Definitions for the class State, that manages the independent variables of temperature, mass density,
+ * and species mass/mole fraction that define the thermodynamic state (see \ref phases and
+ * class \link Cantera::State State\endlink).
  *
- *  This file implements class State.
  */
 
 /*

Cantera/src/State.h

@@ -1,8 +1,8 @@
 /**
- *
  *  @file State.h
- *
- *  This is the header file for class State.
+ * Header for the class State, that manages the independent variables of temperature, mass density,
+ * and species mass/mole fraction that define the thermodynamic state (see \ref phases and
+ * class \link Cantera::State State\endlink).
  */
 
 /*
@@ -15,7 +15,6 @@
  *
  */
 
-
 #ifndef CT_STATE2_H
 #define CT_STATE2_H
 
@@ -23,26 +22,29 @@
 
 namespace Cantera {
 
-    /**
-     * 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.
-     * For efficiency in mass/mole conversion, the vector of mass
-     * fractions divided by molecular weight \f$ Y_k/M_k \f$ is also
-     * stored.
-     *
-     * 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.
-     */
-
+    
+  //! 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.
+   * For efficiency in mass/mole conversion, the vector of mass
+   * fractions divided by molecular weight \f$ Y_k/M_k \f$ is also
+   * stored.
+   *
+   * 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.
+   *
+   * @ingroup phases
+   */
     class State {
 
     public:

Cantera/src/SurfPhase.cpp

@@ -1,6 +1,8 @@
 /**
  *  @file SurfPhase.cpp 
- *
+ *  Definitions for a simple thermoydnamics model of a surface phase derived from ThermoPhase, 
+ *  assuming an ideal solution model
+ *  (see \ref thermoprops and class \link Cantera::SurfPhase SurfPhase\endlink).
  */
 
 // Copyright 2002  California Institute of Technology

Cantera/src/SurfPhase.h

@@ -1,10 +1,8 @@
 /**
- *
  *  @file SurfPhase.h
- *
- *  Contains the declarations for the surface %ThermoPhase class,
- *  SurfPhase. 
- *
+ *  Header for a simple thermoydnamics model of a surface phase derived from ThermoPhase, 
+ *  assuming an ideal solution model
+ *  (see \ref thermoprops and class \link Cantera::SurfPhase SurfPhase\endlink).
  */
 
 /*  $Author$

Cantera/src/ThermoFactory.cpp

@@ -1,8 +1,9 @@
 /**
  *  @file ThermoFactory.cpp
+ *     Definitions for the factory class that can create known %ThermoPhase objects
+ *     (see \ref thermoprops and class \link Cantera::ThermoFactory ThermoFactory\endlink).
  *
- *  Definition of the %ThermoPhase factory base class.
- *  All known ThermoPhases to Cantera should be listed here.
+ 
  */
 
 /*

Cantera/src/ThermoFactory.h

@@ -1,8 +1,8 @@
 /**
  *  @file ThermoFactory.h
+ *     Headers for the factory class that can create known %ThermoPhase objects
+ *     (see \ref thermoprops and class \link Cantera::ThermoFactory ThermoFactory\endlink).
  *
- *         This file contains the definition for the factory
- *         class that can create know %ThermoPhase objects.
  */
 
 /*

Cantera/src/ThermoPhase.cpp

@@ -1,6 +1,8 @@
 /**
- *
  *  @file ThermoPhase.cpp
+ * Definition file for class ThermoPhase, the base class for phases with
+ * thermodynamic properties
+ * (see class \link Cantera::ThermoPhase ThermoPhase\endlink).
  */
 
 /*

Cantera/src/ThermoPhase.h

@@ -1,8 +1,8 @@
 /**
  *  @file ThermoPhase.h
- *
- * Header file for class ThermoPhase.
- * Also contains the text for the Module thermoprops.
+ * Header file for class ThermoPhase, the base class for phases with
+ * thermodynamic properties, and the text for the Module thermoprops
+ * (see \ref thermoprops and class \link Cantera::ThermoPhase ThermoPhase\endlink).
  */
 
 /*
@@ -33,7 +33,6 @@ namespace Cantera {
   //@}
   class XML_Node;
 
-
   /**
    * @defgroup thermoprops Thermodynamic Properties
    *

Cantera/src/global.h

@@ -1,14 +1,16 @@
 /**
  * @file global.h
+ * This file contains definitions for utility functions and text for modules,
+ * inputfiles, logs, textlogs, HTML_logs (see \ref inputfiles, \ref logs, \ref textlogs and \ref HTML_logs).
  *
- * This file contains definitions for utility functions. These functions store 
+ * These functions store 
  * some parameters in  global storage that are accessible at all times
  * from the calling application.
  * Contains module definitions for
- *       inputfiles
- *       logs
- *       textlogs
- *       HTML_logs
+ *     -  inputfiles  (see \ref inputfiles)
+ *     -  logs        (see \ref logs)
+ *     -  textlogs    (see \ref textlogs)
+ *     -  HTML_logs   (see \ref HTML_logs)
  */
 
 /* $Author$

Cantera/src/logger.h

@@ -1,12 +1,16 @@
-/// @file logger.h
-/// Class Logger
-///
+/**
+ * @file logger.h
+ * Header for Base class for 'loggers' that write text messages to log files
+ * (see \ref textlogs and class \link Cantera::Logger Logger\endlink).
+ */
+/*
+ * $Id$
+ */
 
 #ifndef CT_LOGGER_H
 #define CT_LOGGER_H
 
 #include <iostream>
-//using namespace std;
 
 namespace Cantera {
 

Cantera/src/misc.cpp

@@ -1,12 +1,15 @@
 /**
  *  @file misc.cpp
- *
  * This file contains a miscellaneous collection of global data
- * functions.
+ * functions and text for the globalData module (see \ref globalData), the
+ * logs module (see \ref logs), and the HTML_logs module (see \ref HTML_logs).
  *
  * These modules are defined here:
- *      globalData
- *
+ *      globalData 
+ *      logs
+ *      HTML_logs
+ */
+/*
  *  $Id$
  */
 

Cantera/src/thermo/DebyeHuckel.cpp

@@ -1,8 +1,8 @@
 /**
  *  @file DebyeHuckel.cpp
- *    Declarations for the %DebyeHuckel ThermoPhase object, which modules dilute
+ *    Declarations for the %DebyeHuckel ThermoPhase object, which models dilute
  *    electrolyte solutions
- *    (see \link Cantera::DebyeHuckel DebyeHuckel \endlink).
+ *    (see \ref thermoprops and \link Cantera::DebyeHuckel DebyeHuckel \endlink).
  *
  * Class %DebyeHuckel represents a dilute liquid electrolyte phase which
  * obeys the Debye Huckel formulation for nonideality.

Cantera/src/thermo/DebyeHuckel.h

@@ -1,8 +1,8 @@
 /**
  *  @file DebyeHuckel.h
- *    Headers for the %DebyeHuckel ThermoPhase object, which modules dilute
+ *    Headers for the %DebyeHuckel ThermoPhase object, which models dilute
  *    electrolyte solutions
- *    (see \link Cantera::DebyeHuckel DebyeHuckel \endlink) .
+ *    (see \ref thermoprops and \link Cantera::DebyeHuckel DebyeHuckel \endlink) .
  *
  * Class %DebyeHuckel represents a dilute liquid electrolyte phase which
  * obeys the Debye Huckel formulation for nonideality.

Cantera/src/thermo/IdealMolalSoln.cpp

@@ -1,6 +1,17 @@
 /**
  *
  *  @file IdealMolalSoln.cpp
+ *   ThermoPhase object for the ideal molal equation of
+ * state (see \ref thermoprops 
+ * and class \link Cantera::IdealMolalSoln IdealMolalSoln\endlink).
+ *
+ * Definition file for a derived class of ThermoPhase that handles
+ * variable pressure standard state methods for calculating
+ * thermodynamic properties that are further based upon 
+ * activities on the molality scale. The Ideal molal
+ * solution assumes that all molality-based activity
+ * coefficients are equal to one. This turns out, actually, to be
+ * highly nonlinear when the solvent densities get low.
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of 

Cantera/src/thermo/IdealMolalSoln.h

@@ -1,12 +1,17 @@
 /**
  *  @file IdealMolalSoln.h
+ *   ThermoPhase object for the ideal molal equation of
+ * state (see \ref thermoprops 
+ * and class \link Cantera::IdealMolalSoln IdealMolalSoln\endlink).
  *
  * Header file for a derived class of ThermoPhase that handles
  * variable pressure standard state methods for calculating
  * thermodynamic properties that are further based upon 
  * activities on the molality scale. The Ideal molal
  * solution assumes that all molality-based activity
- * coefficients are equal to one.
+ * coefficients are equal to one. This turns out to be highly
+ * nonlinear in the limit of the solvent mole fraction going
+ * to zero.
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of 
@@ -27,7 +32,8 @@
 namespace Cantera {
 
   /**  \addtogroup thermoprops */
-  /* @{ */
+  /* @{ 
+   */
  
 
   /**

Cantera/src/thermo/IdealSolidSolnPhase.cpp

@@ -1,8 +1,8 @@
 /**
  *  @file IdealSolidSolnPhase.cpp
- *      Code for the class IdealSolidSolnPhase,
- *      which implements an ideal solid solution model
- *      with incompressible thermodynamics.
+ *      Implementation file for an ideal solid solution model
+ *      with incompressible thermodynamics (see \ref thermoprops and
+ *      \link Cantera::IdealSolidSolnPhase IdealSolidSolnPhase\endlink).
  */
 /*
  * $Id$

Cantera/src/thermo/IdealSolidSolnPhase.h

@@ -1,15 +1,12 @@
 /**
  * @file IdealSolidSolnPhase.h
- *      Header file for the class IdealSolidSolnPhase  
- *      This class implements an ideal solid solution model
- *      with incompressible thermodynamics. 
+ *      Header file for an ideal solid solution model
+ *      with incompressible thermodynamics (see \ref thermoprops and
+ *      \link Cantera::IdealSolidSolnPhase IdealSolidSolnPhase\endlink).
  *
  *      This class inherits from the Cantera class ThermoPhase
  *      and implements an ideal solid solution model with incompressible
  *      thermodynamics.
- *
- *      The concept of a monomer unit is mapped onto a condensed
- *      phase species.
  */
 
 /* 

Cantera/src/thermo/MolalityVPSSTP.cpp

@@ -1,6 +1,15 @@
 /**
- *
  *  @file MolalityVPSSTP.cpp
+ *   Definitions for intermediate ThermoPhase object for phases which
+ *   employ molality based activity coefficient formulations
+ *  (see \ref thermoprops 
+ * and class \link Cantera::MolalityVPSSTP MolalityVPSSTP\endlink).
+ *
+ * Header file for a derived class of ThermoPhase that handles
+ * variable pressure standard state methods for calculating
+ * thermodynamic properties that are further based upon activities
+ * based on the molality scale.  These include most of the methods for
+ * calculating liquid electrolyte thermodynamics.
  */
 /*
  * Copywrite (2005) Sandia Corporation. Under the terms of 

Cantera/src/thermo/MolalityVPSSTP.h

@@ -1,5 +1,9 @@
 /**
  *  @file MolalityVPSSTP.h
+ *   Header for intermediate ThermoPhase object for phases which
+ *   employ molality based activity coefficient formulations
+ *  (see \ref thermoprops 
+ * and class \link Cantera::MolalityVPSSTP MolalityVPSSTP\endlink).
  *
  * Header file for a derived class of ThermoPhase that handles
  * variable pressure standard state methods for calculating

Cantera/src/thermo/SingleSpeciesTP.cpp

@@ -1,5 +1,8 @@
 /**
  *  @file SingleSpeciesTP.cpp
+ *  Definitions for the %SingleSpeciesTP class, which is a filter class for %ThermoPhase,
+ *  that eases the construction of single species phases 
+ *  ( see \ref thermoprops and class \link Cantera::SingleSpeciesTP SingleSpeciesTP\endlink).
  */
 
 /*

Cantera/src/thermo/SingleSpeciesTP.h

@@ -1,10 +1,10 @@
 /**
  *  @file SingleSpeciesTP.h
- *
- * Header file for class SingleSpeciesTP
+ *  Header for the %SingleSpeciesTP class, which is a filter class for %ThermoPhase,
+ *  that eases the construction of single species phases 
+ *  ( see \ref thermoprops and class \link Cantera::SingleSpeciesTP SingleSpeciesTP\endlink).
  *
  */
-
 /*
  * Copywrite (2005) Sandia Corporation. Under the terms of
  * Contract DE-AC04-94AL85000 with Sandia Corporation, the

Cantera/src/thermo/StoichSubstanceSSTP.cpp

@@ -1,7 +1,8 @@
 /**
- *
  *  @file StoichSubstanceSSTP.cpp
- *
+ *   Definition file for the StoichSubstanceSSTP class, which represents a fixed-composition
+ * incompressible substance (see \ref thermoprops and 
+ * class \link Cantera::StoichSubstanceSSTP StoichSubstanceSSTP\endlink)
  */
 
 /*

Cantera/src/thermo/StoichSubstanceSSTP.h

@@ -1,8 +1,8 @@
 /**
- *
  *  @file StoichSubstanceSSTP.h
- * 
- * Header file for the StoichSubstanceSSTP class
+ * Header file for the StoichSubstanceSSTP class, which represents a fixed-composition
+ * incompressible substance (see \ref thermoprops and 
+ * class \link Cantera::StoichSubstanceSSTP StoichSubstanceSSTP\endlink)
  */
 
 /*
@@ -26,11 +26,9 @@
 
 namespace Cantera {
 
-  /**
-   * @ingroup thermoprops
-   *
-   * Class %StoichSubstanceSSTP represents a stoichiometric (fixed composition) 
-   * incompressible substance.
+   //!  Class %StoichSubstanceSSTP represents a stoichiometric (fixed composition) 
+   //!  incompressible substance.
+   /*!
    * This class internally changes the independent degree of freedom from
    * density to pressure. This is necessary because the phase is incompressible.
    * It uses a constant volume approximation.
@@ -163,6 +161,7 @@ namespace Cantera {
    *  The model attribute, "StoichSubstanceSSTP", on the thermo element identifies the phase as being
    * a StoichSubstanceSSTP object.
    *
+   * @ingroup thermoprops
    */
   class StoichSubstanceSSTP : public SingleSpeciesTP {
 

Cantera/src/thermo/VPStandardStateTP.cpp

@@ -1,6 +1,9 @@
 /**
- *
  *  @file VPStandardStateTP.cpp
+ * Definition file for a derived class of ThermoPhase that handles
+ * variable pressure standard state methods for calculating
+ * thermodynamic properties (see \ref thermoprops and
+ * class \link Cantera::VPStandardStateTP VPStandardStateTP\endlink).
  */
 /*
  * Copywrite (2005) Sandia Corporation. Under the terms of 

Cantera/src/thermo/VPStandardStateTP.h

@@ -1,9 +1,11 @@
 /**
  *  @file VPStandardStateTP.h
- *
  * Header file for a derived class of ThermoPhase that handles
  * variable pressure standard state methods for calculating
- * thermodynamic properties. These include most of the
+ * thermodynamic properties (see \ref thermoprops and
+ * class \link Cantera::VPStandardStateTP VPStandardStateTP\endlink).
+ *
+ * These include most of the
  * methods for calculating liquid electrolyte thermodynamics.
  */
 /*

Cantera/src/thermo/WaterPropsIAPWS.cpp

@@ -1,6 +1,8 @@
-/*
- * @file WaterPropsIAPWS
- *
+/**
+ * @file WaterPropsIAPWS.cpp
+ * Definitions for a class for calculating the equation of state of water
+ * from the IAPWS 1995 Formulation based on the steam tables thermodynamic
+ * basis (See class \link WaterPropsIAPWS WaterPropsIAPWS\endlink).
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of

Cantera/src/thermo/WaterPropsIAPWS.h

@@ -1,6 +1,8 @@
 /**
  * @file WaterPropsIAPWS.h
- * Definitions for a class for calculating the equation of state of water. 
+ * Headers for a class for calculating the equation of state of water
+ * from the IAPWS 1995 Formulation based on the steam tables thermodynamic
+ * basis (See class \link WaterPropsIAPWS WaterPropsIAPWS\endlink).
  */
 /*
  * Copywrite (2005) Sandia Corporation. Under the terms of

Cantera/src/thermo/WaterPropsIAPWSphi.cpp

@@ -1,6 +1,7 @@
 /**
  * @file WaterPropsIAPWSphi.cpp
- *
+ *  Definitions for Lowest level of the classes which support a real water model
+ *  (see class #WaterPropsIAPWS and class  #WaterPropsIAPWSphi).
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of

Cantera/src/thermo/WaterPropsIAPWSphi.h

@@ -1,6 +1,8 @@
 /**
  * @file WaterPropsIAPWSphi.h
- *   Lowest level of the classes which support a real water model.
+ *  Header for Lowest level of the classes which support a real water model
+ *  (see class #WaterPropsIAPWS and class  #WaterPropsIAPWSphi).
+ *
  *   This class calculates dimensionless quantitites.
  */
 /*

Cantera/src/thermo/WaterSSTP.cpp

@@ -1,7 +1,7 @@
 /**
  *  @file WaterSSTP.cpp
- *   Declarations for the object WaterSSTP, which creates a
- *   single species %ThermoPhase object for real liquid water.
+ * Definitions for a %ThermoPhase class consisting of  pure water (see \ref thermoprops
+ * and class \link Cantera::WaterSSTP WaterSSTP\endlink).
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of

Cantera/src/thermo/WaterSSTP.h

@@ -1,7 +1,7 @@
 /**
  *  @file WaterSSTP.h
- * Declares a %ThermoPhase class consisting of 
- * pure water.
+ * Declares a %ThermoPhase class consisting of  pure water (see \ref thermoprops
+ * and class \link Cantera::WaterSSTP WaterSSTP\endlink).
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of

Cantera/src/units.h

@@ -1,8 +1,15 @@
 /**
  * @file units.h
+ * Header for units conversion utilities, which are used to translate
+ * user input from input files (See \ref inputfiles and 
+ * class \link Cantera::Unit Unit\endlink).
  *
- * Unit conversions. This header is included only by file misc.cpp.
+ * This header is included only by file misc.cpp.
  */
+/*
+ * $Id$
+ */
+//    Copyright 2002 California Institute of Technology
 
 #ifndef CT_UNITS_H
 #define CT_UNITS_H
@@ -12,194 +19,199 @@
 
 namespace Cantera {
 
-    class Unit {
-    public:
+  //! Unit conversion utility
+  /*!
+   *
+   * @ingroup inputfiles 
+   */
+  class Unit {
+  public:
 
-      //! Initialize the static Unit class.
-        static Unit* units() {
-            if (!s_u) s_u = new Unit;
-            return s_u;
-        }
+    //! Initialize the static Unit class.
+    static Unit* units() {
+      if (!s_u) s_u = new Unit;
+      return s_u;
+    }
 
-      //! Destroy the static Unit class
-      /*!
-       * Note this can't be done in a destructor.
-       */
-	static void deleteUnit() {
-	    if (s_u) {
-	      delete s_u;
-	      s_u = 0;
-	    }
+    //! Destroy the static Unit class
+    /*!
+     * Note this can't be done in a destructor.
+     */
+    static void deleteUnit() {
+      if (s_u) {
+	delete s_u;
+	s_u = 0;
+      }
+    }
+
+    //! Empty Destructor
+    virtual ~Unit() {}
+
+    /**
+     * Return the multiplier required to convert an activation
+     * energy to SI units.
+     * @param units activation energy units
+     */
+    doublereal actEnergyToSI(std::string units) {
+      if (m_act_u.find(units) != m_act_u.end()) {
+	return m_act_u[units];
+      }
+      else {
+	return toSI(units);
+      }
+    }
+
+    /**
+     * Return the multiplier required to convert a dimensional quantity 
+     * with units specified by string 'units' to SI units.
+     * The list of recognized units is storred as a stl map
+     *  <string, doublereal>called  m_u[] and m_act_u for activity
+     * coefficients. These maps are initialized with likely values.
+     *
+     * @param units String containing the units description
+     */
+    doublereal toSI(std::string units) {
+
+      // if dimensionless, return 1.0
+      if (units == "") return 1.0;
+
+      doublereal f = 1.0, fctr;
+      int tsize;
+      std::string u = units, tok, tsub;
+      std::string::size_type k;
+      char action = '-';
+
+      while (1 > 0) {
+
+	// get token consisting of all characters up to the next 
+	// dash, slash, or the end of the string
+	k = u.find_first_of("/-");
+	if (k != std::string::npos)
+	  tok = u.substr(0,k);
+	else
+	  tok = u;
+	tsize = static_cast<int>(tok.size());
+	if (tsize == 0) 
+	  fctr = 1.0;
+	else if (tok[tsize - 1] == '2') {
+	  tsub = tok.substr(0,tsize-1);
+	  fctr = m_u[tsub];
+	  fctr *= fctr;
+	}
+	else if (tok[tsize - 1] == '3') {
+	  tsub = tok.substr(0,tsize-1);
+	  fctr = m_u[tsub];
+	  fctr *= fctr*fctr;
+	}
+	else if (tok[tsize - 1] == '4') {
+	  tsub = tok.substr(0,tsize-1);
+	  fctr = m_u[tsub];
+	  fctr *= fctr*fctr*fctr;
+	}
+	else if (tok[tsize - 1] == '5') {
+	  tsub = tok.substr(0,tsize-1);
+	  fctr = m_u[tsub];
+	  fctr *= fctr*fctr*fctr*fctr;
+	}
+	else if (tok[tsize - 1] == '6') {
+	  tsub = tok.substr(0,tsize-1);
+	  fctr = m_u[tsub];
+	  fctr *= fctr*fctr*fctr*fctr*fctr;
+	}
+	else {
+	  tsub = tok;
+	  fctr = m_u[tok];
 	}
 
-      //! Empty Destructor
-        virtual ~Unit() {}
+	// tok is not one of the entries in map m_u, then 
+	// m_u[tok] returns 0.0. Check for this.
+	if (fctr == 0) 
+	  throw CanteraError("toSI","unknown unit: "+tsub);
+	if (action == '-') f *= fctr;
+	else if (action == '/') f /= fctr;
+	if (k == std::string::npos) break;
+	action = u[k];
+	u = u.substr(k+1,u.size());
+      }
+      return f;
+    }
 
-        /**
-         * Return the multiplier required to convert an activation
-         * energy to SI units.
-         * @param units activation energy units
-         */
-        doublereal actEnergyToSI(std::string units) {
-            if (m_act_u.find(units) != m_act_u.end()) {
-                return m_act_u[units];
-            }
-            else {
-                return toSI(units);
-            }
-        }
+  private:
 
-        /**
-         * Return the multiplier required to convert a dimensional quantity 
-         * with units specified by string 'units' to SI units.
-         * The list of recognized units is storred as a stl map
-         *  <string, doublereal>called  m_u[] and m_act_u for activity
-         * coefficients. These maps are initialized with likely values.
-	 *
-	 * @param units String containing the units description
-         */
-        doublereal toSI(std::string units) {
+    /// pointer to the single instance of Unit
+    static Unit* s_u;
 
-            // if dimensionless, return 1.0
-            if (units == "") return 1.0;
+    //! Map between a string and a units double value
+    /*!
+     *  This map maps the dimension string to the units value adjustment. Example
+     *   -  m_u["m"]    = 1.0;
+     *   -  m_u["cm"]   = 0.01;
+     */
+    std::map<std::string, doublereal> m_u;
 
-            doublereal f = 1.0, fctr;
-            int tsize;
-            std::string u = units, tok, tsub;
-            std::string::size_type k;
-            char action = '-';
+    //! Map between a string and a units double value for activation energy units
+    /*!
+     *  This map maps the dimension string to the units value adjustment. Example
+     *   -    m_act_u["K"] =  GasConstant;
+     */
+    std::map<std::string, doublereal> m_act_u;
 
-            while (1 > 0) {
+    /*!
+     * Units class constructor, containing the default mappings between
+     * strings and units.
+     */
+    Unit(){
 
-                // get token consisting of all characters up to the next 
-                // dash, slash, or the end of the string
-                k = u.find_first_of("/-");
-                if (k != std::string::npos)
-                    tok = u.substr(0,k);
-                else
-                    tok = u;
-                tsize = static_cast<int>(tok.size());
-                if (tsize == 0) 
-                    fctr = 1.0;
-                else if (tok[tsize - 1] == '2') {
-                    tsub = tok.substr(0,tsize-1);
-                    fctr = m_u[tsub];
-                    fctr *= fctr;
-                }
-                else if (tok[tsize - 1] == '3') {
-                    tsub = tok.substr(0,tsize-1);
-                    fctr = m_u[tsub];
-                    fctr *= fctr*fctr;
-                }
-                else if (tok[tsize - 1] == '4') {
-                    tsub = tok.substr(0,tsize-1);
-                    fctr = m_u[tsub];
-                    fctr *= fctr*fctr*fctr;
-                }
-                else if (tok[tsize - 1] == '5') {
-                    tsub = tok.substr(0,tsize-1);
-                    fctr = m_u[tsub];
-                    fctr *= fctr*fctr*fctr*fctr;
-                }
-                else if (tok[tsize - 1] == '6') {
-                    tsub = tok.substr(0,tsize-1);
-                    fctr = m_u[tsub];
-                    fctr *= fctr*fctr*fctr*fctr*fctr;
-                }
-                else {
-                    tsub = tok;
-                    fctr = m_u[tok];
-                }
+      // length
+      m_u["m"]    = 1.0;
+      m_u["cm"]   = 0.01;
+      m_u["km"]   = 1.0e3;
+      m_u["mm"]   = 1.0e-3;
+      m_u["micron"]   = 1.0e-6;
+      m_u["nm"]   = 1.0e-9;
+      m_u["A"]   = 1.0e-10;
+      m_u["Angstrom"]   = 1.0e-10;
+      m_u["Angstroms"]   = 1.0e-10;
 
-                // tok is not one of the entries in map m_u, then 
-                // m_u[tok] returns 0.0. Check for this.
-                if (fctr == 0) 
-                    throw CanteraError("toSI","unknown unit: "+tsub);
-                if (action == '-') f *= fctr;
-                else if (action == '/') f /= fctr;
-                if (k == std::string::npos) break;
-                action = u[k];
-                u = u.substr(k+1,u.size());
-            }
-            return f;
-        }
+      // energy
+      m_u["J"]        = 1.0;
+      m_u["kJ"]       = 1.0e3;
+      m_u["cal"]      = 4.184;
+      m_u["kcal"]     = 4184.0;
+      m_u["eV"]       = 1.60217733e-19;
 
-    private:
+      // quantity
+      m_u["mol"]      = 1.0e-3;
+      m_u["gmol"]     = 1.0e-3;
+      m_u["mole"]     = 1.0e-3;
+      m_u["kmol"]     = 1.0;
+      m_u["molec"]    = 1.0/Avogadro;
 
-        /// pointer to the single instance of Unit
-        static Unit* s_u;
+      // temperature
+      m_u["K"]        = 1.0;
+      m_u["C"]        = 1.0;
 
-      //! Map between a string and a units double value
-      /*!
-       *  This map maps the dimension string to the units value adjustment. Example
-       *   -  m_u["m"]    = 1.0;
-       *   -  m_u["cm"]   = 0.01;
-       */
-      std::map<std::string, doublereal> m_u;
+      // mass
+      m_u["g"]        = 1.0e-3;
+      m_u["kg"]       = 1.0;
 
-      //! Map between a string and a units double value for activation energy units
-      /*!
-       *  This map maps the dimension string to the units value adjustment. Example
-       *   -    m_act_u["K"] =  GasConstant;
-       */
-      std::map<std::string, doublereal> m_act_u;
+      // pressure
+      m_u["atm"]      = 1.01325e5;
+      m_u["bar"]      = 1.0e5;
+      m_u["Pa"]       = 1.0;
 
-      /*!
-       * Units class constructor, containing the default mappings between
-       * strings and units.
-       */
-        Unit(){
+      // time
+      m_u["s"]        = 1.0;
+      m_u["min"]      = 60.0;
+      m_u["hr"]       = 3600.0;
+      m_u["ms"]       = 0.001;
 
-            // length
-            m_u["m"]    = 1.0;
-            m_u["cm"]   = 0.01;
-            m_u["km"]   = 1.0e3;
-            m_u["mm"]   = 1.0e-3;
-            m_u["micron"]   = 1.0e-6;
-            m_u["nm"]   = 1.0e-9;
-            m_u["A"]   = 1.0e-10;
-            m_u["Angstrom"]   = 1.0e-10;
-            m_u["Angstroms"]   = 1.0e-10;
-
-            // energy
-            m_u["J"]        = 1.0;
-            m_u["kJ"]       = 1.0e3;
-            m_u["cal"]      = 4.184;
-            m_u["kcal"]     = 4184.0;
-            m_u["eV"]       = 1.60217733e-19;
-
-            // quantity
-            m_u["mol"]      = 1.0e-3;
-            m_u["gmol"]     = 1.0e-3;
-            m_u["mole"]     = 1.0e-3;
-            m_u["kmol"]     = 1.0;
-            m_u["molec"]    = 1.0/Avogadro;
-
-            // temperature
-            m_u["K"]        = 1.0;
-            m_u["C"]        = 1.0;
-
-            // mass
-            m_u["g"]        = 1.0e-3;
-            m_u["kg"]       = 1.0;
-
-            // pressure
-            m_u["atm"]      = 1.01325e5;
-            m_u["bar"]      = 1.0e5;
-            m_u["Pa"]       = 1.0;
-
-            // time
-            m_u["s"]        = 1.0;
-            m_u["min"]      = 60.0;
-            m_u["hr"]       = 3600.0;
-            m_u["ms"]       = 0.001;
-
-            m_act_u["eV"] = m_u["eV"]/m_u["molec"];
-            m_act_u["K"] =  GasConstant;
-            m_act_u["Kelvin"] =  GasConstant;
-            m_act_u["Dimensionless"] =  (GasConstant * 273.15);
-        }
-    };
+      m_act_u["eV"] = m_u["eV"]/m_u["molec"];
+      m_act_u["K"] =  GasConstant;
+      m_act_u["Kelvin"] =  GasConstant;
+      m_act_u["Dimensionless"] =  (GasConstant * 273.15);
+    }
+  };
 }
 
 #endif

Cantera/src/utilities.h

@@ -1,6 +1,7 @@
 /**
  *  @file utilities.h
- *
+ *  Various templated functions that carry out common vector
+ *  operations (see \ref globalUtilFuncs).
  */
 
 // Copyright 2001  California Institute of Technology

data/inputs/.cvsignore

@@ -1,3 +1,9 @@
 Makefile
 gri30.log
 ck2ctml.log
+ct2ctml.log
+diamond.xml
+liquidvapor.xml
+testdest.xml
+testdest2.xml
+

tools/bin/.cvsignore

@@ -0,0 +1 @@
+finish_install.py