Doxygen changes.

Cantera/src/thermo/IdealMolalSoln.cpp

@@ -35,9 +35,10 @@
 
 namespace Cantera {
 
-
+  //!  Small value to be used in cutoff expressions with logs
   static double xxSmall = 1.0E-150;
-  /**
+
+  /*
    * Default constructor
    */
   IdealMolalSoln::IdealMolalSoln() :

Cantera/src/thermo/SpeciesThermoFactory.cpp

@@ -456,6 +456,11 @@ namespace Cantera {
 
 #endif
 
+  //!   Look up the elemental reference state entropies
+  /*!
+   *  @param elemName String name of the element
+   *  @param th_ptr   Pointer to the thermophase.
+   */
   static doublereal LookupGe(const std::string& elemName, ThermoPhase *th_ptr) {
 #ifdef OLDWAY
     int num = sizeof(geDataTable) / sizeof(struct GeData);
@@ -483,6 +488,13 @@ namespace Cantera {
 #endif
   }
 
+  //! Convert delta G formulation
+  /*!
+   *  Calculates the sum of the elemental reference state entropies
+   *
+   *  @param   k               species index
+   *  @param   th_ptr          Pointer to the ThermoPhase
+   */
  static doublereal convertDGFormation(int k, ThermoPhase *th_ptr) {
     /*
      * Ok let's get the element compositions and conversion factors.
@@ -505,7 +517,15 @@ namespace Cantera {
   }
 
 
-
+  //!  Install a NASA96 polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance.
+  /*!
+   * This is called by method installThermoForSpecies if a MinEQ3node block is found in the XML input.
+   *
+   *  @param speciesName        String name of the species
+   *  @param sp                 SpeciesThermo object that will receive the nasa polynomial object
+   *  @param k                  Species index within the phase
+   *  @param MinEQ3node         Ptr to the first XML_Node for the first MinEQ3 parameterization
+   */
   static void installMinEQ3asShomateThermoFromXML(std::string speciesName, 
 						  ThermoPhase *th_ptr,
 						  SpeciesThermo& sp, int k, 

Cantera/src/thermo/ThermoFactory.cpp

@@ -297,7 +297,21 @@ namespace Cantera {
       return (ThermoPhase *) 0;
   }
 
-
+  //====================================================================================================================
+  //!  Gather a vector of pointers to XML_Nodes for a phase
+  /*!
+   *
+   *   @param spDataNodeList         Output vector of pointer to XML_Nodes which contain the species XML_Nodes for the
+   *                                 species in the current phase.         
+   *   @param spNamesList            Output Vector of strings, which contain the names of the species in the phase
+   *   @param spRuleList             Output Vector of ints, which contain the value of sprule for each species in the phase
+   *   @param spArray_names          Vector of pointers to the XML_Nodes which contains the names of the 
+   *                                 species in the phase
+   *
+   *   @param spArray_dbases         Input vector of pointers to species data bases.
+   *                                 We search each data base for the required species names
+   *   @param  sprule                Input vector of sprule values
+   */
   static void formSpeciesXMLNodeList(std::vector<XML_Node *> &spDataNodeList,
 				     std::vector<std::string> &spNamesList,
 				     std::vector<int> &spRuleList,
@@ -318,7 +332,7 @@ namespace Cantera {
       // Get the top XML for the database
       const XML_Node *db = spArray_dbases[jsp];
 
-      // Get the array of species name strings and the count them
+      // Get the array of species name strings and then count them
       std::vector<std::string> spnames;
       getStringArray(speciesArray, spnames);
       int nsp = static_cast<int>(spnames.size());
@@ -408,7 +422,7 @@ namespace Cantera {
       }
     }
   }
-        
+  //====================================================================================================================
   /*
    * Import a phase specification.
    *   Here we read an XML description of the phase.

Cantera/src/thermo/VPSSMgrFactory.cpp

@@ -75,7 +75,7 @@ namespace Cantera {
    *  @param has_simple_constVol       Boolean indicating that one species has a simple ideal solution standard state
    *  @param has_water                 Boolean indicating that one species has a water standard state
    *  @param has_tpx                   Boolean indicating that one species has a tpx standard state
-   *  @param has_htpx                  Boolean indicating that one species has a htpx standard state
+   *  @param has_hptx                  Boolean indicating that one species has a htpx standard state
    *  @param has_other                 Boolean indicating that one species has different standard state than the ones listed above
    * 
    * @todo Make sure that spDadta_node is species Data XML node by checking 

Cantera/src/thermo/WaterPropsIAPWS.cpp

@@ -33,13 +33,13 @@ const doublereal Rho_c = 322.;
 //! Molecular Weight of water that is consistent with the paper (kg kmol-1)
 static const doublereal M_water = 18.015268; 
 
+//! Gas constant that is quoted in the paper
 /*
  * Note, this is the Rgas value quoted in the paper. For consistency
  * we have to use that value and not the updated value
  *
  * The Ratio of R/M = 0.46151805 kJ kg-1 K-1 , which is Eqn. (6.3) in the paper.
  */
-//static const doublereal Rgas = 8.314472E3;   // Joules kmol-1 K-1
 static const doublereal Rgas = 8.314371E3;   // Joules kmol-1 K-1
 //@{
 #ifndef MAX