Switched a call in MultiPhase to be public.

switched velocityBasis to a typedef. It seemed the better solution. Note the concept is still basically undeveloped.
Doxygen changes - supporting 1.6.2

Cantera/src/equil/MultiPhase.cpp

@@ -183,6 +183,7 @@ namespace Cantera {
     
     updateMoleFractions();
 
+    updatePhases();
   }
 
 

Cantera/src/equil/MultiPhase.h

@@ -549,8 +549,6 @@ namespace Cantera {
      */
     void uploadMoleFractionsFromPhases();
 
-  private:
-
     //! Set the states of the phase objects to the locally-stored
     //! state within this MultiPhase object.
     /*!
@@ -567,6 +565,7 @@ namespace Cantera {
      */
     void updatePhases() const;
 
+  private:
     //! Calculate the element abundance vector
     void calcElemAbundances() const;
 

Cantera/src/transport/LiquidTransport.cpp

@@ -189,7 +189,7 @@ namespace Cantera {
     int k;
     // constant substance attributes
     m_thermo = tr.thermo;
-    m_velocityBasis = tr.velocityBasis;
+    m_velocityBasis = tr.velocityBasis_;
     m_nsp   = m_thermo->nSpecies();
     m_tmin  = m_thermo->minTemp();
     m_tmax  = m_thermo->maxTemp();

Cantera/src/transport/TransportBase.h

@@ -57,17 +57,35 @@ namespace Cantera {
   // forward reference
   class XML_Writer;
 
-  /** The diffusion velocities can be referenced to a variety of things.
-   *  Most typical is to reference to the mass averaged velocity, but 
+  //! The diffusion fluxes must be referenced to a particular reference
+  //! fluid velocity.
+  /*!
+   * Most typical is to reference the diffusion fluxes to the mass averaged velocity, but 
    * referencing to the mole averaged velocity is suitable for some 
-   * liquid flows and referencing to a single species is suitable for 
-   * some solvent mixtures.  This enum should provide a means to identify 
-   * the reference velocity used for the transport model.
+   * liquid flows, and referencing to a single species is suitable for 
+   * solid phase transport within a lattice.  Currently, the identity of the reference
+   * velocity is coded into each transport object as a typedef named VelocityBasis, which
+   * is equated to an integer. Negative values of this variable refer to mass or mole-averaged
+   * velocities.  Zero or positive quantities refers to the reference
+   * velocity being referenced to a particular species. Below are the predefined constants
+   * for its value.
+   *
+   *  - VB_MASSAVG    Diffusion velocities are based on the mass averaged velocity
+   *  - VB_MOLEAVG    Diffusion velocities are based on the mole averaged velocities
+   *  - VB_SPECIES_0  Diffusion velocities are based on the relative motion wrt species 0
+   *  - VB_SPECIES_1  Diffusion velocities are based on the relative motion wrt species 1
+   *
    */
-  enum VelocityBasis { 
-    VB_MOLEAVG = -2,
-    VB_MASSAVG = -1
-  };
+  typedef int VelocityBasis;
+
+  //! Diffusion velocities are based on the mass averaged velocity
+  const VelocityBasis VB_MASSAVG = -1;
+  //! Diffusion velocities are based on the mole averaged velocities
+  const VelocityBasis VB_MOLEAVG = -2;
+  //! Diffusion velocities are based on the relative motion wrt species 0
+  const VelocityBasis VB_SPECIES_0 = 0;
+  //! Diffusion velocities are based on the relative motion wrt species 1
+  const VelocityBasis VB_SPECIES_1 = 1;
 
   //! Base class for transport property managers.
   /*!
@@ -106,6 +124,33 @@ namespace Cantera {
    *   also implicitly assumed that the underlying state within the ThermoPhase 
    *   object has not changed its values.
    *
+   *   
+   * <HR>
+   * <H2> Diffusion Fluxes and their Relationship to Reference Velocities </H2>
+   * <HR>
+   *
+   *  The diffusion fluxes must be referenced to a particular reference
+   *  fluid velocity.
+   *  Most typical is to reference the diffusion fluxes to the mass averaged velocity, but 
+   *  referencing to the mole averaged velocity is suitable for some 
+   *  liquid flows, and referencing to a single species is suitable for 
+   *  solid phase transport within a lattice.  Currently, the identity of the reference
+   *  velocity is coded into each transport object as a typedef named VelocityBasis, which
+   *  is equated to an integer. Negative values of this variable refer to mass or mole-averaged
+   *  velocities.  Zero or positive quantities refers to the reference
+   *  velocity being referenced to a particular species. Below are the predefined constants
+   *  for its value.
+   *
+   *  - VB_MASSAVG    Diffusion velocities are based on the mass averaged velocity
+   *  - VB_MOLEAVG    Diffusion velocities are based on the mole averaged velocities
+   *  - VB_SPECIES_0  Diffusion velocities are based on the relative motion wrt species 0
+   *  - VB_SPECIES_1  Diffusion velocities are based on the relative motion wrt species 1
+   *
+   *  All transport managers specify a default reference velocity in their default constructors.
+   *  All gas phase transport managers by default specify the mass-averaged velocity as their
+   *  reference velocities.
+   *
+   *
    *  @todo Provide a general mechanism to store the gradients of state variables
    *        within the system.
    *
@@ -587,7 +632,7 @@ namespace Cantera {
      *
      *   @param ivb   Species the velocity basis
      */
-    void setVelocityBasis(int  ivb) 
+    void setVelocityBasis(VelocityBasis ivb) 
     { 
       m_velocityBasis = ivb; 
     }
@@ -600,7 +645,7 @@ namespace Cantera {
      *
      *   @return   Returns the velocity basis
      */
-    int getVelocityBasis( ) const { 
+    VelocityBasis getVelocityBasis( ) const { 
       return m_velocityBasis; 
     }
 

Cantera/src/transport/TransportFactory.cpp

@@ -1111,15 +1111,15 @@ namespace Cantera {
 	 * <velocityBasis basis="mole"> <!-- mole averaged -->
 	 * <velocityBasis basis="H2O">  <!-- H2O solvent -->
 	 */
-	if ( tranTypeNode.hasChild("velocityBasis")) {
+	if (tranTypeNode.hasChild("velocityBasis")) {
 	  std::string velocityBasis = 
 	    tranTypeNode.child("velocityBasis").attrib("basis");
-	  if ( velocityBasis == "mass" ) 
-	    trParam.velocityBasis = VB_MASSAVG;
-	  else if ( velocityBasis == "mole" ) 
-	    trParam.velocityBasis = VB_MOLEAVG;
-	  else if ( trParam.thermo->speciesIndex( velocityBasis ) > 0 ) 
-	    trParam.velocityBasis = trParam.thermo->speciesIndex( velocityBasis ) ;
+	  if (velocityBasis == "mass") 
+	    trParam.velocityBasis_ = VB_MASSAVG;
+	  else if (velocityBasis == "mole") 
+	    trParam.velocityBasis_ = VB_MOLEAVG;
+	  else if (trParam.thermo->speciesIndex(velocityBasis) > 0) 
+	    trParam.velocityBasis_ = trParam.thermo->speciesIndex(velocityBasis) ;
 	  else {
 	    int linenum;
 	    throw TransportDBError( linenum, "Unknown attribute " + velocityBasis + " for <velocityBasis> node. ");

Cantera/src/transport/TransportParams.h

@@ -19,11 +19,12 @@ namespace Cantera {
 
   public:
 
+    //! Default Constructor
     TransportParams() : 
       nsp_(0),
       thermo(0),
       mw(0),
-      velocityBasis(VB_MASSAVG),
+      velocityBasis_(VB_MASSAVG),
       tmax(1000000.),
       tmin(10.),
       mode_(0),
@@ -32,6 +33,7 @@ namespace Cantera {
     {
     }
 
+    //! Destructor
     virtual ~TransportParams() 
     {
 #ifdef DEBUG_MODE
@@ -39,20 +41,37 @@ namespace Cantera {
 #endif
     }
 
+    //! Local storage of the number of species
     int nsp_;
-    //        phase_t* mix;
+
+    //!  Pointer to the ThermoPhase object
     thermo_t* thermo;
+
+    //! Local storage of the molecular weights of the species
+    /*!
+     *  Length is nsp_ and units are kg kmol-1.
+     */
     vector_fp        mw;
 
     //! A basis for the average velocity can be specified. 
-    //! Valid bases include "mole" "mass" and species names.
-    int velocityBasis;
+    /*!
+     *  Valid bases include "mole", "mass", and "species" names.
+     */
+    VelocityBasis velocityBasis_;
 
-    //minimum and maximum temperatures for parameter fits
+    //! Maximum temperatures for parameter fits
     doublereal tmax;
+
+    //! Minimum temperatures for parameter fits
     doublereal tmin;
+
+    //!  Mode parameter
     int mode_;
+
+    //! Pointer to the xml tree describing the implementation of transport for this object
     XML_Writer* xml;
+
+    //! Log level
     int log_level;
 
   };

docs/install_examples/linux_64_gcc424_dbg_python252_numpy

@@ -31,6 +31,9 @@ export WITH_ELECTROLYTES
 WITH_VCSNONIDEAL="y"
 export WITH_VCSNONIDEAL
 
+WITH_H298MODIFY_CAPABILITY="y"
+export WITH_H298MODIFY_CAPABILITY
+
 BUILD_MATLAB_TOOLBOX="y"
 export BUILD_MATLAB_TOOLBOX
 

docs/install_examples/linux_64_gcc424_opt_python252_numpy

@@ -29,6 +29,9 @@ export WITH_ELECTROLYTES
 WITH_VCSNONIDEAL="y"
 export WITH_VCSNONIDEAL
 
+WITH_H298MODIFY_CAPABILITY="y"
+export WITH_H298MODIFY_CAPABILITY
+
 BUILD_MATLAB_TOOLBOX="y"
 export BUILD_MATLAB_TOOLBOX