Resolved a few Doxygen warnings

include/cantera/kinetics/ReactionStoichMgr.h

@@ -36,11 +36,11 @@ class ReactionData;
  * - \f$ N_r \f$
  *     Integer reactant stoichiometric coefficient matrix. The (k,i)
  *     element of this matrix is the stoichiometric coefficient of
- *     species \i k as a reactant in reaction \i i.
+ *     species \e k as a reactant in reaction \e i.
  * - \f$ N_p \f$
  *     Integer product stoichiometric coefficient matrix. The (k,i)
  *     element of this matrix is the stoichiometric coefficient of
- *     species \i k as a product in reaction \i i.
+ *     species \e k as a product in reaction \e i.
  * - \f$ Q_{\rm fwd} \f$
  *     Vector of length I of forward rates of progress.
  * - \f$ Q_{\rm rev} \f$
@@ -100,15 +100,7 @@ public:
     /**
      * Add a reaction with specified, possibly non-integral, reaction orders.
      * @param rxn Reaction number
-     * @param reactants vector of integer reactant indices
-     * @param products vector of integer product indices
-     * @param reversible true if the reaction is reversible, false otherwise.
-     * If the reaction is reversible, its reverse rate will be computed from
-     * the reaction stoichiometry.
-     * @param fwdOrder reaction orders for the reactants. This vector must
-     * be the same length as 'reactants,' and the reaction orders are for the
-     * species with index in the corresponding location in 'reactants.'
-     *
+     * @param r Data structure containing reactant and product vectors, etc.
      */
     virtual void add(size_t rxn, const ReactionData& r);
 

include/cantera/numerics/Integrator.h

@@ -69,7 +69,7 @@ public:
     //!  Set error tolerances.
     /*!
      * @param reltol scalar relative tolerance
-     * @param number of equations
+     * @param n      Number of equations
      * @param abstol array of N absolute tolerance values
      */
     virtual void setTolerances(doublereal reltol, size_t n,

include/cantera/oneD/StFlow.h

@@ -56,7 +56,7 @@ public:
     //--------------------------------
 
     /// Constructor. Create a new flow domain.
-    /// @param gas Object representing the gas phase. This object
+    /// @param ph Object representing the gas phase. This object
     /// will be used to evaluate all thermodynamic, kinetic, and transport
     /// properties.
     /// @param nsp Number of species.

include/cantera/spectra/LineBroadener.h

@@ -1,5 +1,5 @@
 /**
- * @file LinerBoadener.h
+ * @file LineBroadener.h
  * Header file for class LineBroadener
  * @ingroup spectroscopy
  */

include/cantera/thermo/Phase.h

@@ -485,7 +485,7 @@ public:
     //! of the phase. We hold the temperature constant during this operation.
     //! Therefore, we have possibly changed the pressure of the phase by
     //! calling this routine.
-    //!     @param conc[in] Array of concentrations in dimensional units. For
+    //!     @param[in] conc Array of concentrations in dimensional units. For
     //! bulk phases c[k] is the concentration of the kth species in kmol/m3.
     //! For surface phases, c[k] is the concentration in kmol/m2. The length of
     //!  the vector is the numberof species in the phase.
@@ -563,14 +563,14 @@ public:
     //! @name Mean Properties
     //!@{
 
-    //! Evaluate the mole-fraction-weighted mean of an array \ref Q.
+    //! Evaluate the mole-fraction-weighted mean of an array Q.
     //! \f[ \sum_k X_k Q_k. \f]
     //! Q should contain pure-species molar property values.
     //!     @param[in] Q Array of length m_kk that is to be averaged.
     //!     @return mole-fraction-weighted mean of Q
     doublereal mean_X(const doublereal* const Q) const;
 
-    //! Evaluate the mass-fraction-weighted mean of an array \ref Q.
+    //! Evaluate the mass-fraction-weighted mean of an array Q.
     //! \f[ \sum_k Y_k Q_k \f]
     //!     @param[in] Q  Array of species property values in mass units.
     //!     @return The mass-fraction-weighted mean of Q.

src/equil/MultiPhaseEquil.cpp

@@ -920,7 +920,6 @@ double MultiPhaseEquil::phaseMoles(index_t iph) const
     return m_mix->phaseMoles(iph);
 }
 
-#include <cstdio>
 void MultiPhaseEquil::reportCSV(const std::string& reportFile)
 {
     size_t k;

src/equil/vcs_DoubleStarStar.cpp

@@ -1,5 +1,5 @@
 /**
- *  @file DoubleStarStar.cpp
+ *  @file vcs_DoubleStarStar.cpp
  *
  *  Header file for class DoubleStarStar
  */

src/equil/vcs_DoubleStarStar.h

@@ -1,5 +1,5 @@
 /**
- *  @file  DoubleStarStar.h
+ *  @file  vcs_DoubleStarStar.h
  *
  *  Header file for class DoubleStarStar
  */

src/equil/vcs_IntStarStar.cpp

@@ -1,5 +1,5 @@
 /**
- *  @file IntStarStar.cpp
+ *  @file vcs_IntStarStar.cpp
  *
  *  Header file for class IntStarStar
  */

src/equil/vcs_IntStarStar.h

@@ -1,5 +1,5 @@
 /**
- *  @file  IntStarStar.h
+ *  @file  vcs_IntStarStar.h
  *
  *  Header file for class IntStarStar
  */

src/equil/vcs_rearrange.cpp

@@ -1,5 +1,5 @@
 /**
- * @file vcs_rearrange.c
+ * @file vcs_rearrange.cpp
  *    implementation file for rearranging species.
  */
 /*

src/numerics/CVodesIntegrator.h

@@ -1,5 +1,5 @@
 /**
- *  @file CVodesWrapper.h
+ *  @file CVodesIntegrator.h
  */
 // Copyright 2005  California Institute of Technology
 

src/thermo/Elements.cpp

@@ -1,10 +1,6 @@
 /**
  *  @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.
+ *  This file contains a database of atomic weights.
  */
 //  Copyright 2003  California Institute of Technology
 
@@ -22,8 +18,7 @@ namespace Cantera
  *  Values are taken from the 1989 Standard Atomic Weights, CRC
  *
  *  awTable[] is a static function with scope limited to this file.
- *  It can only be referenced via the static Elements class function,
- *  LookupWtElements().
+ *  It can only be referenced via the LookupWtElements() function.
  *
  *  units = kg / kg-mol (or equivalently gm / gm-mol)
  *