Doxygen update

Cantera/src/kinetics/FalloffFactory.cpp

@@ -18,7 +18,7 @@
 #include "FalloffFactory.h"
 #include "ctexceptions.h"
 
-#include <math.h>
+#include <cmath>
 
 namespace Cantera {
 

Cantera/src/kinetics/FalloffFactory.h

@@ -5,16 +5,13 @@
  *  (see \ref falloffGroup and class \link Cantera::Falloff Falloff\endlink).
  */
 
-
 /*
- *  $Author$
  *  $Date$
  *  $Revision$
  */
 
 // Copyright 2001  California Institute of Technology
 
-
 #ifndef CT_NEWFALLOFF_H
 #define CT_NEWFALLOFF_H
 
@@ -28,6 +25,15 @@
 
 namespace Cantera {
 
+  /**
+   *     @defgroup falloffGroup  Falloff Parameterizations
+   *    This section describes the parameterizations used 
+   *    to describe the fall-off in reaction rate constants
+   *    due to intermolecular energy transfer.
+   *
+   *    @ingroup chemkinetics
+   */
+
   /**
    * Base class for falloff function calculators. Each instance of a
    * subclass of Falloff computes one falloff function.

Cantera/src/kinetics/GasKinetics.h

@@ -75,7 +75,6 @@ namespace Cantera {
      * expressions for low-density gases.
      * @ingroup kinetics
      */
-
     class GasKinetics : public Kinetics {
 
     public:

Cantera/src/kinetics/Group.cpp

@@ -18,9 +18,10 @@
 #pragma warning(disable:4503)
 #endif
 
-#include <algorithm>
 #include "Group.h"
-#include <math.h>
+
+#include <algorithm>
+#include <cmath>
 
 namespace Cantera {
      

Cantera/src/thermo/HMWSoln.h

@@ -208,7 +208,7 @@ namespace Cantera {
    * \f$ m_k \f$ is the molality of the kth species. \f$ z_k \f$ is the charge
    * of the kth species. Note, the ionic strength is a defined units quantity.
    * The molality has defined units of gmol kg-1, and therefore the ionic
-   * strength has units of sqrt( gmol kg-1).
+   * strength has units of sqrt( gmol kg<SUP>-1</SUP>).
    *
    * In some instances, from some authors, a different 
    * formulation is used for the ionic strength in the equations below. The different
@@ -550,6 +550,8 @@ namespace Cantera {
    *
    *  It can be shown that the expression 
    *
+   *
+   *
    *  \f[
    *     B^{\phi}_{ca} = \beta^{(0)}_{ca} + \beta^{(1)}_{ca} \exp{(- \alpha^{(1)}_{ca} \sqrt{I})} 
    *             + \beta^{(2)}_{ca} \exp{(- \alpha^{(2)}_{ca} \sqrt{I} )} 
@@ -2203,15 +2205,12 @@ namespace Cantera {
     void getUnscaledMolalityActivityCoefficients(doublereal *acMolality) const;
 
   private:
-    //! Apply the current phScale to a set of activity Coefficients or activities
+
+    //! Apply the current phScale to a set of activity Coefficients
     /*!
      *  See the Eq3/6 Manual for a thorough discussion.
      *
-     * @param acMolality input/Output vector containing the molality based 
-     *                   activity coefficients. length: m_kk.
      */
-    // void applyphScale(doublereal *acMolality) const;
-
     void s_updateScaling_pHScaling() const;
 
     //!  Apply the current phScale to a set of derivatives of the activity Coefficients
@@ -2792,8 +2791,32 @@ namespace Cantera {
      * neutral species interacting with itself.
      */
     mutable vector_fp  m_Mu_nnn;
+
+    //! Mu coefficient temperature derivative for the self-ternary neutral coefficient
+    /*!
+     * Array of 2D data used in the Pitzer/HMW formulation.
+     * Mu_nnn_L[i] represents the Mu coefficient temperature derivative for the
+     * nnn interaction. This is a general interaction representing
+     * neutral species interacting with itself.
+     */
     mutable vector_fp  m_Mu_nnn_L;
+
+    //! Mu coefficient 2nd temperature derivative for the self-ternary neutral coefficient
+    /*!
+     * Array of 2D data used in the Pitzer/HMW formulation.
+     * Mu_nnn_L[i] represents the Mu coefficient 2nd temperature derivative for the
+     * nnn interaction. This is a general interaction representing
+     * neutral species interacting with itself.
+     */
     mutable vector_fp  m_Mu_nnn_LL;
+
+    //! Mu coefficient pressure derivative for the self-ternary neutral coefficient
+    /*!
+     * Array of 2D data used in the Pitzer/HMW formulation.
+     * Mu_nnn_L[i] represents the Mu coefficient pressure derivative for the
+     * nnn interaction. This is a general interaction representing
+     * neutral species interacting with itself.
+     */
     mutable vector_fp  m_Mu_nnn_P;
 
     //! Array of coefficients form_Mu_nnn term

Cantera/src/thermo/IdealMolalSoln.cpp

@@ -28,9 +28,11 @@
 #include "ThermoFactory.h"
 #include <cmath>
 
+//@{
 #ifndef MAX
 #define MAX(x,y)    (( (x) > (y) ) ? (x) : (y))
 #endif
+//@}
 
 namespace Cantera {
 

Cantera/src/thermo/IdealMolalSoln.h

@@ -988,7 +988,7 @@ namespace Cantera {
 
     //! Internal error message
     /*!
-     * param msg message to be printed
+     *  @param          msg message to be printed
      */
     doublereal err(std::string msg) const;
 

Cantera/src/thermo/MolalityVPSSTP.h

@@ -242,12 +242,13 @@ namespace Cantera {
      */
     virtual int eosType() const;
 
-
     //! Set the pH scale, which determines the scale for single-ion activity 
     //! coefficients.
     /*!
      *  Single ion activity coefficients are not unique in terms of the
-     *  representing actual measureable quantities. 
+     *  representing actual measureable quantities.
+     *
+     * @param pHscaleType  Integer representing the pHscale 
      */
     void setpHScale(const int pHscaleType);
 
@@ -256,6 +257,8 @@ namespace Cantera {
     /*!
      *  Single ion activity coefficients are not unique in terms of the
      *  representing actual measureable quantities. 
+     *
+     * @return Return the pHscale type
      */
     int pHScale() const;
 

Cantera/src/thermo/SpeciesThermoFactory.cpp

@@ -4,9 +4,11 @@
  *    standard-state thermodynamic properties of a set of species 
  *    (see \ref spthermo and class \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink);
  */
-/*
+/* 
- * $Id$
+ * $Revision$
+ * $Date$
  */
+
 // Copyright 2001  California Institute of Technology
 
 #ifdef WIN32
@@ -442,7 +444,7 @@ namespace Cantera {
 
 #endif
 
-  doublereal LookupGe(const std::string& elemName, ThermoPhase *th_ptr) {
+  static doublereal LookupGe(const std::string& elemName, ThermoPhase *th_ptr) {
 #ifdef OLDWAY
     int num = sizeof(geDataTable) / sizeof(struct GeData);
     string s3 = elemName.substr(0,3);
@@ -469,7 +471,7 @@ namespace Cantera {
 #endif
   }
 
- doublereal convertDGFormation(int k, ThermoPhase *th_ptr) {
+ static doublereal convertDGFormation(int k, ThermoPhase *th_ptr) {
     /*
      * Ok let's get the element compositions and conversion factors.
      */
@@ -487,16 +489,6 @@ namespace Cantera {
 	totalSum += na * ge;
       }
     }
-    // Add in the charge
-    // if (m_charge_j != 0.0) {
-    // ename = "H";
-      // ge = LookupGe(ename);
-    // totalSum -= m_charge_j * ge;
-    //}
-    // Ok, now do the calculation. Convert to joules kmol-1
-    //doublereal dg = m_deltaG_formation_tr_pr * 4.184 * 1.0E3;
-    //! Store the result into an internal variable.
-    // doublereal Mu0_tr_pr = dg + totalSum;
     return totalSum;
   }