Doxygen update

-- Worked on the file TAB descriptions
DebyeHuckel
   -- made a bunch of functions public again. They were mistakenly
      protected.

Cantera/src/ConstCpPoly.cpp

@@ -1,6 +1,10 @@
 /**
  *  @file ConstCpPoly.cpp
- *
+ * Declarations for the \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType \endlink object that
+ * employs a constant heat capacity assumption (see \ref spthermo and
+ * \link Cantera::ConstCpPoly ConstCpPoly \endlink).
+ */
+/*
  * $Author$
  * $Revision$
  * $Date$

Cantera/src/ConstCpPoly.h

@@ -1,14 +1,14 @@
 /**
  *  @file ConstCpPoly.h
- *
- * Declarations for the SpeciesThermoInterpType object that
- * employs a constant heat capacity assumption.
- *
+ * Headers for the \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType\endlink 
+ * object that employs a constant heat capacity assumption (see \ref spthermo and
+ * \link Cantera::ConstCpPoly ConstCpPoly\endlink).
+ */
+/*
  * $Author$
  * $Revision$
  * $Date$
  */
-
 // Copyright 2001  California Institute of Technology
 
 

Cantera/src/ConstDensityThermo.cpp

@@ -1,7 +1,13 @@
 /**
- *
  *  @file ConstDensityThermo.cpp
+ * Declarations for a Thermo manager for incompressible ThermoPhases 
+ * (see \ref thermoprops and \link Cantera::ConstDensityThermo ConstDensityThermo
+\endlink).
+ */
+/*
+ * $Id$
  *
+ *  Copyright 2002 California Institute of Technology
  */
 
 #ifdef WIN32

Cantera/src/ConstDensityThermo.h

@@ -1,10 +1,8 @@
 /**
- *
  *  @file ConstDensityThermo.h
- *
- *  Thermo manager for incompressible substances.
+ * Header for a Thermo manager for incompressible ThermoPhases 
+ * (see \ref thermoprops and \link Cantera::ConstDensityThermo ConstDensityThermo\endlink).
  */
-
 /*
  *  $Author$
  *  $Date$

Cantera/src/Constituents.cpp

@@ -1,6 +1,7 @@
 /**
  *  @file Constituents.cpp
- *  Implementation file for class Constituents
+ *  Header file  Class \link Cantera::Constituents Constitutents\endlink which 
+ *  manages a set of elements and species (see \ref phases).
  */
 
 /*  $Author$ 

Cantera/src/Constituents.h

@@ -1,7 +1,7 @@
-/*!
+/**
  * @file Constituents.h
- *
- *  Header file for class Constituents
+ *  Header file  Class \link Cantera::Constituents Constitutents\endlink which 
+ *  manages a set of elements and species (see \ref phases).
  */
 
 /*  $Author$ 
@@ -54,15 +54,18 @@ namespace Cantera {
     /******************************************************************/
 
 
-    /// Class %Constituents manages a set of elements and
-    /// species. 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. The species
-    /// all must belong to the same phase.
-
+    //! Class %Constituents manages a set of elements and  species.
+    /*!
+     * 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. The species
+     * all must belong to the same phase.
+     *
+     * @ingroup phases
+     */
     class Constituents {
 
     public:

Cantera/src/EdgePhase.h

@@ -1,7 +1,7 @@
 /**
- *
  *  @file EdgePhase.h
- *       Declarations for the EdgePhase thermodynamic object.
+ *       Declarations for the EdgePhase ThermoPhase object, which models the interface
+ *       between two surfaces (see \ref thermoprops and \link Cantera::EdgePhase EdgePhase\endlink).
  */
 
 /*  $Author$

Cantera/src/Elements.cpp

@@ -1,3 +1,12 @@
+/**
+ *  @file Elements.cpp
+ *  Declaration file for class, Elements, which contains the elements that
+ *  make up species (see \ref phases and \link Cantera::Elements Elements\endlink).
+ *
+ *  This file contains the definitions for functions in the class Elements.
+ *  It also contains a database of atomic weights.
+ */
+
 /****************************************************************************
  *  $RCSfile$
  *  $Author$
@@ -8,13 +17,6 @@
  ****************************************************************************/
 //  Copyright 2003  California Institute of Technology
 
-/**
- *  @file Elements.cpp
- *  Implementation file for the class Elements
- *
- *  This file contains the definitions for functions in the class Elements.
- *  It also contains a database of atomic weights.
- */
 
 #ifdef WIN32
 #pragma warning(disable:4786)

Cantera/src/Elements.h

@@ -6,8 +6,10 @@
  ***********************************************************************/
 //  Copyright 2001  California Institute of Technology
 
-/** @file Elements.h 
- *  Header file for class, Elements.
+/**
+ *  @file Elements.h 
+ *  Header file for class, Elements, which contains the elements that 
+ *  make up species (see \ref phases and \link Cantera::Elements Elements\endlink).
  *
  *  This file contains the declarations for the elements class.
  */
@@ -37,6 +39,8 @@ namespace Cantera {
      * 
      * The member functions return information about the elements described
      * in a particular instantiation of the class.
+     * 
+     * @ingroup phases
      */
     class Elements {
 

Cantera/src/Kinetics.cpp

@@ -1,6 +1,7 @@
 /**
  *  @file Kinetics.cpp
- *
+ *      Declarations for the base class for kinetics managers (see \ref kineticsmgr).
+ *      Kinetics managers calculate rates of progress of species due to homogeneous or heterogeneous kinetics.
  */
 
 // Copyright 2001-2004  California Institute of Technology            

Cantera/src/Kinetics.h

@@ -1,9 +1,7 @@
 /**
  * @file Kinetics.h
- *    
- *  Base class for kinetics managers
- *
- * Contains the kineticsmgr module documentation.
+ *  Base class for kinetics managers and also contains the kineticsmgr
+ *  module documentation (see \ref  kineticsmgr).
  *
  *  $Author$
  *  $Date$

Cantera/src/SpeciesThermoInterpType.h

@@ -1,6 +1,9 @@
 /**
  *  @file SpeciesThermoInterpType.h
- *
+ * Pure Virtual Base class for individual species reference state
+ * themodynamic managers (see \ref spthermo and class \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType \endlink).
+ */
+ /*
  * $Author$
  * $Revision$
  * $Date$

Cantera/src/ct_defs.h

@@ -1,10 +1,9 @@
 /**
- * 
  * @file ct_defs.h
- *
  * This file contains definitions of terms that are used in internal 
- * routines and are unlikely to need modifying. This file is included
- * into every file that is in the Cantera Namespace.
+ * routines and are unlikely to need modifying (text for module physConstants (see \ref physConstants) is found here). 
+ * This file is included
+ * in every file that is in the Cantera Namespace.
  *
  * All physical constants are storred here.
  * The module physConstants is defined here.

Cantera/src/ctexceptions.h

@@ -1,8 +1,8 @@
 /**
  * @file ctexceptions.h
- *
- *   This contains the definitions for the classes that are
- *   thrown when Cantera experiences an error condition.
+ *   Definitions for the classes that are
+ *   thrown when %Cantera experiences an error condition 
+ *   (also contains errorhandling module text - see \ref errorhandling).
  */
 
 /*

Cantera/src/importCTML.cpp

@@ -1,10 +1,12 @@
 /**
  *  @file importCTML.cpp
+ *     Declarations of global routines for the importing
+ *     of data from XML files (see \ref inputfiles).
  *
  *     This file contains routines which are global routines, i.e.,
  *     not part of any object. These routine take as input, ctml
- *     pointers to data, and pointers to Cantera objects. The purpose
- *     of these routines is to intialize the Cantera objects with data
+ *     pointers to data, and pointers to %Cantera objects. The purpose
+ *     of these routines is to intialize the %Cantera objects with data
  *     from the ctml tree structures.
  */
 

Cantera/src/importCTML.h

@@ -1,6 +1,15 @@
 /**
  *  @file importCTML.h
+ *   Definitions of global routines for the importing
+ *   of data from XML files (see \ref inputfiles).
  *
+ *     This file contains routines which are global routines, i.e.,
+ *     not part of any object. These routine take as input, ctml
+ *     pointers to data, and pointers to %Cantera objects. The purpose
+ *     of these routines is to intialize the %Cantera objects with data
+ *     from the ctml tree structures.
+ */
+/*
  * $Author$
  * $Revision$
  * $Date$
@@ -262,6 +271,8 @@ namespace Cantera {
    *   @param kin Kinetics object
    *   @param rdata  Object containing the information about one reaction
    *   @param errorTolerance double containing the error tolerance.
+   *
+   * @ingroup kineticsmgr
    */
   void checkRxnElementBalance(Kinetics& kin, 
 			      const ReactionData &rdata, 
@@ -280,6 +291,8 @@ namespace Cantera {
    *  @param negA    Boolean indicating whether negative A's are ok.
    *
    *   Trigger anexception for negative A unless specifically authorized.
+   *
+   * @ingroup kineticsmgr
    */
   void getRateCoefficient(const XML_Node& kf, kinetics_t& kin, 
 			  ReactionData& rdata, int negA);

Cantera/src/speciesThermoTypes.h

@@ -1,6 +1,9 @@
 /**
  *  @file speciesThermoTypes.h
- *
+ *       Contains const definitions for types of species 
+ *       reference-state thermodynamics managers (see \ref spthermo)
+ */
+/*
  * $Author$
  * $Revision$
  * $Date$

Cantera/src/thermo/DebyeHuckel.cpp

@@ -1,7 +1,11 @@
 /**
  *  @file DebyeHuckel.cpp
+ *    Declarations for the %DebyeHuckel ThermoPhase object, which modules dilute
+ *    electrolyte solutions
+ *    (see \link Cantera::DebyeHuckel DebyeHuckel \endlink).
  *
- * Definitions of the DebyeHuckel object.
+ * Class %DebyeHuckel represents a dilute liquid electrolyte phase which
+ * obeys the Debye Huckel formulation for nonideality.
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of 

Cantera/src/thermo/DebyeHuckel.h

@@ -1,7 +1,11 @@
 /**
  *  @file DebyeHuckel.h
+ *    Headers for the %DebyeHuckel ThermoPhase object, which modules dilute
+ *    electrolyte solutions
+ *    (see \link Cantera::DebyeHuckel DebyeHuckel \endlink) .
  *
- *    Declarations for the DebyeHuckel phase
+ * Class %DebyeHuckel represents a dilute liquid electrolyte phase which
+ * obeys the Debye Huckel formulation for nonideality.
  */
 /*
  * Copywrite (2006) Sandia Corporation. Under the terms of 
@@ -181,7 +185,8 @@ namespace Cantera {
    *  \f]
    *
    *  The specification of which species are weakly associated acids is made in the input file via the
-   *  <TT> stoichIsMods </TT> XML block, where the charge for k1 is also specified. An example is given below:
+   *  <TT> stoichIsMods </TT> XML block, where the charge for k1 is also specified. 
+   *  An example is given below:
    * 
    * @code
    *          <stoichIsMods>
@@ -702,7 +707,7 @@ namespace Cantera {
      */
     virtual doublereal cp_mole() const;
 
-    /// Molar heat capacity at constant volume. Units: J/kmol/K.
+    //! Molar heat capacity at constant volume. Units: J/kmol/K.
     /*
      *      (HKM -> Bump up to Parent object)
      */
@@ -1266,6 +1271,7 @@ namespace Cantera {
      * @param lambda_RT Input vector of dimensionless element potentials
      *                  The length is equal to nElements().
      */ 
+  public:
     virtual void setToEquilState(const doublereal* lambda_RT) {
       err("setToEquilState");
     }