[docs] Replace remaining Doxygen commands

include/cantera/base/Array.h

@@ -52,7 +52,7 @@ class Array2D
 
     //! Constructor.
     /*!
-     * Create an \c m by \c n array, and initialize all elements to \c v.
+     * Create an @c m by @c n array, and initialize all elements to @c v.
      *
      * @param m   Number of rows
      * @param n   Number of columns
@@ -62,8 +62,8 @@ class Array2D
 
     //! Constructor.
     /*!
-     * Create an \c m by \c n array, initialized with the contents of the array
-     * \c values.
+     * Create an @c m by @c n array, initialized with the contents of the array
+     * @c values.
      *
      * @param m   Number of rows
      * @param n   Number of columns

include/cantera/base/global.h

@@ -39,13 +39,13 @@ class AnyMap;
  * for input files along a path that includes platform-specific default
  * locations, and possibly user-specified locations:
  *
- *    - The current directory \c "." is always searched first. Then, on Windows, the
+ *    - The current directory @c "." is always searched first. Then, on Windows, the
  *      registry is checked to find the %Cantera installation directory, and the
- *      \c data subdirectory of the installation directory will be added to the search
+ *      @c data subdirectory of the installation directory will be added to the search
  *      path.
- *    - On any platform, if environment variable \c CANTERA_DATA is set to a directory
+ *    - On any platform, if environment variable @c CANTERA_DATA is set to a directory
  *      name or a list of directory names separated with the OS-dependent path
- *      separator (that is, \c ";" on Windows, \c ":" elsewhere), then these directories
+ *      separator (that is, @c ";" on Windows, @c ":" elsewhere), then these directories
  *      will be added to the search path.
  *    - Finally, the location where the data files were installed when %Cantera was
  *      built is added to the search path.
@@ -116,7 +116,7 @@ bool usingSharedLibrary();
 //! @{
 
 //! Returns the %Cantera version. This function is used to access the version from a
-//! library, rather than the \c CANTERA_VERSION macro that is available at compile time.
+//! library, rather than the @c CANTERA_VERSION macro that is available at compile time.
 //! @since New in %Cantera 3.0
 string version();
 
@@ -130,7 +130,7 @@ string gitCommit();
 //! preprocessor macro is defined.
 bool debugModeEnabled();
 
-//! Returns true if %Cantera was compiled with C++ \c HDF5 support.
+//! Returns true if %Cantera was compiled with C++ @c HDF5 support.
 //! @since New in %Cantera 3.0.
 bool usesHDF5();
 

include/cantera/base/utilities.h

@@ -29,7 +29,7 @@ namespace Cantera
 
 //! Templated Inner product of two vectors of length 4.
 /*!
- * If either \a x or \a y has length greater than 4, only the first 4 elements
+ * If either @e x or @e y has length greater than 4, only the first 4 elements
  * will be used.
  *
  * @param x   first reference to the templated class V
@@ -44,7 +44,7 @@ inline double dot4(const V& x, const V& y)
 
 //! Templated Inner product of two vectors of length 5
 /*!
- * If either \a x or \a y has length greater than 4, only the first 4 elements
+ * If either @e x or @e y has length greater than 4, only the first 4 elements
  * will be used.
  *
  * @param x   first reference to the templated class V

include/cantera/equil/MultiPhase.h

@@ -113,7 +113,7 @@ class MultiPhase
      */
     string elementName(size_t m) const;
 
-    //! Returns the index of the element with name \a name.
+    //! Returns the index of the element with name @e name.
     /*!
      * @param name   String name of the global element
      */
@@ -133,14 +133,14 @@ class MultiPhase
     //! which take an array pointer.
     void checkSpeciesArraySize(size_t kk) const;
 
-    //! Name of species with global index \a kGlob
+    //! Name of species with global index @e kGlob
     /*!
      * @param kGlob   global species index
      */
     string speciesName(const size_t kGlob) const;
 
-    //! Returns the Number of atoms of global element \a mGlob in
-    //! global species \a kGlob.
+    //! Returns the Number of atoms of global element @e mGlob in
+    //! global species @e kGlob.
     /*!
      * @param kGlob   global species index
      * @param mGlob   global element index
@@ -151,7 +151,7 @@ class MultiPhase
     //! Returns the global Species mole fractions.
     /*!
      *   Write the array of species mole
-     *   fractions into array \c x. The mole fractions are
+     *   fractions into array @c x. The mole fractions are
      *   normalized to sum to one in each phase.
      *
      *    @param x  vector of mole fractions. Length = number of global species.
@@ -211,14 +211,14 @@ class MultiPhase
     //! which take an array pointer.
     void checkPhaseArraySize(size_t mm) const;
 
-    //! Returns the moles of global species \c k. units = kmol
+    //! Returns the moles of global species @c k. units = kmol
     /*!
      * @param kGlob   Global species index k
      */
     double speciesMoles(size_t kGlob) const;
 
-    //! Return the global index of the species belonging to phase number \c p
-    //! with local index \c k within the phase.
+    //! Return the global index of the species belonging to phase number @c p
+    //! with local index @c k within the phase.
     /*!
      * @param k local index of the species within the phase
      * @param p index of the phase
@@ -227,8 +227,8 @@ class MultiPhase
         return m_spstart[p] + k;
     }
 
-    //! Return the global index of the species belonging to phase name \c phaseName
-    //! with species name \c speciesName
+    //! Return the global index of the species belonging to phase name @c phaseName
+    //! with species name @c speciesName
     /*!
      * @param speciesName    Species Name
      * @param phaseName      Phase Name
@@ -257,23 +257,23 @@ class MultiPhase
     //! Total charge summed over all phases (Coulombs).
     double charge() const;
 
-    //! Charge (Coulombs) of phase with index \a p.
+    //! Charge (Coulombs) of phase with index @e p.
     /*!
      *  The net charge is computed as @f[ Q_p = N_p \sum_k F z_k X_k @f]
-     *  where the sum runs only over species in phase \a p.
+     *  where the sum runs only over species in phase @e p.
      *  @param p index of the phase for which the charge is desired.
      */
     double phaseCharge(size_t p) const;
 
-    //! Total moles of global element \a m, summed over all phases.
+    //! Total moles of global element @e m, summed over all phases.
     /*!
      * @param m   Index of the global element
      */
     double elementMoles(size_t m) const;
 
     //! Returns a vector of Chemical potentials.
     /*!
-     * Write into array \a mu the chemical potentials of all species
+     * Write into array @e mu the chemical potentials of all species
      * [J/kmol]. The chemical potentials are related to the activities by
      *
      * @f$
@@ -287,16 +287,16 @@ class MultiPhase
 
     //! Returns a vector of Valid chemical potentials.
     /*!
-     * Write into array \a mu the chemical potentials of all species with
+     * Write into array @e mu the chemical potentials of all species with
      * thermo data valid for the current temperature [J/kmol]. For other
-     * species, set the chemical potential to the value \a not_mu. If \a
+     * species, set the chemical potential to the value @e not_mu. If @e
      * standard is set to true, then the values returned are standard chemical
      * potentials.
      *
      * This method is designed for use in computing chemical equilibrium by
      * Gibbs minimization. For solution phases (more than one species), this
      * does the same thing as getChemPotentials. But for stoichiometric
-     * phases, this writes into array \a mu the user-specified value \a not_mu
+     * phases, this writes into array @e mu the user-specified value @e not_mu
      * instead of the chemical potential if the temperature is outside the
      * range for which the thermo data for the one species in the phase are
      * valid. The need for this arises since many condensed phases have thermo
@@ -307,7 +307,7 @@ class MultiPhase
      * result in spurious chemical potentials, and can lead to condensed
      * phases appearing when in fact they should be absent.
      *
-     * By setting \a not_mu to a large positive value, it is possible to force
+     * By setting @e not_mu to a large positive value, it is possible to force
      * routines which seek to minimize the Gibbs free energy of the mixture to
      * zero out any phases outside the temperature range for which their
      * thermo data are valid.
@@ -316,7 +316,7 @@ class MultiPhase
      *               for which the thermo data is not valid
      * @param mu    Vector of chemical potentials. length = Global species,
      *              units = J kmol-1
-     * @param standard  If this method is called with \a standard set to true,
+     * @param standard  If this method is called with @e standard set to true,
      *                  then the composition-independent standard chemical
      *                  potentials are returned instead of the composition-
      *                  dependent chemical potentials.
@@ -426,7 +426,7 @@ class MultiPhase
         return m_phase.size();
     }
 
-    //! Return true is species \a kGlob is a species in a multicomponent
+    //! Return true is species @e kGlob is a species in a multicomponent
     //! solution phase.
     /*!
      * @param kGlob   index of the global species
@@ -506,7 +506,7 @@ class MultiPhase
      */
     void getElemAbundances(double* elemAbundances) const;
 
-    //! Return true if the phase \a p has valid thermo data for the current
+    //! Return true if the phase @e p has valid thermo data for the current
     //! temperature.
     /*!
      * @param p  Index of the phase.

include/cantera/equil/MultiPhaseEquil.h

@@ -96,7 +96,7 @@ class MultiPhaseEquil
     //! The component species are taken to be the first M species in array
     //! 'species' that have linearly-independent compositions.
     //!
-    //! @param order On entry, vector \a order should contain species index
+    //! @param order On entry, vector @e order should contain species index
     //!     numbers in the order of decreasing desirability as a component.
     //!     For example, if it is desired to choose the components from among
     //!     the major species, this array might list species index numbers in

include/cantera/equil/vcs_VolPhase.h

@@ -423,13 +423,13 @@ class vcs_VolPhase
     //! Returns the number of element constraints
     size_t nElemConstraints() const;
 
-    //! Name of the element constraint with index \c e.
+    //! Name of the element constraint with index @c e.
     /*!
      * @param e Element index.
      */
     string elementName(const size_t e) const;
 
-    //! Type of the element constraint with index \c e.
+    //! Type of the element constraint with index @c e.
     /*!
      * @param e Element index.
      */

include/cantera/kinetics/Kinetics.h

@@ -419,7 +419,7 @@ class Kinetics
      * @f]
      * For example, if this method is called with the array of standard-state
      * molar Gibbs free energies for the species, then the values returned in
-     * array \c deltaProperty would be the standard-state Gibbs free energies of
+     * array @c deltaProperty would be the standard-state Gibbs free energies of
      * reaction for each reaction.
      *
      * @param property Input vector of property value. Length: #m_kk.

include/cantera/kinetics/ReactionPath.h

@@ -84,7 +84,7 @@ class Path
     typedef map<size_t, double> rxn_path_map;
 
     /**
-     *  Constructor. Construct a one-way path from \c begin to \c end.
+     *  Constructor. Construct a one-way path from @c begin to @c end.
      */
     Path(SpeciesNode* begin, SpeciesNode* end);
 
@@ -114,7 +114,7 @@ class Path
     }
 
     /**
-     *  If \c n is one of the nodes this path connects, then
+     *  If @c n is one of the nodes this path connects, then
      *  the other node is returned. Otherwise zero is returned.
      */
     SpeciesNode* otherNode(SpeciesNode* n) {
@@ -171,12 +171,12 @@ class ReactionPathDiagram
         return m_flxmax;
     }
 
-    //! The net flow from node \c k1 to node \c k2
+    //! The net flow from node @c k1 to node @c k2
     double netFlow(size_t k1, size_t k2) {
         return flow(k1, k2) - flow(k2, k1);
     }
 
-    //! The one-way flow from node \c k1 to node \c k2
+    //! The one-way flow from node @c k1 to node @c k2
     double flow(size_t k1, size_t k2) {
         return (m_paths[k1][k2] ? m_paths[k1][k2]->flow() : 0.0);
     }
@@ -190,7 +190,7 @@ class ReactionPathDiagram
 
     /**
      *  Export the reaction path diagram. This method writes to stream
-     *  \c s the commands for the 'dot' program in the \c GraphViz
+     *  @c s the commands for the 'dot' program in the @c GraphViz
      *  package from AT&T. (GraphViz may be downloaded from www.graphviz.org.)
      *
      *  To generate a postscript reaction path diagram from the output of this

include/cantera/kinetics/StoichManager.h

@@ -37,7 +37,7 @@ namespace Cantera
  * @f]
  *
  * where @f$ \nu^{(p)_{k,i}} @f$ is the product-side stoichiometric
- * coefficient of species \a k in reaction \a i. This could be done by
+ * coefficient of species @e k in reaction @e i. This could be done by
  * straightforward matrix multiplication, but would be inefficient, since most
  * of the matrix elements of @f$ \nu^{(p)}_{k,i} @f$ are zero. We could do
  * better by using sparse-matrix algorithms to compute this product.
@@ -563,7 +563,7 @@ inline static void _scale(InputIter begin, InputIter end,
  * @f]
  * To understand the operations performed by this class, let @f$ N_{k,i} @f$
  * denote the stoichiometric coefficient of species k on one side (reactant or
- * product) in reaction i. Then \b N is a sparse K by I matrix of stoichiometric
+ * product) in reaction i. Then @b N is a sparse K by I matrix of stoichiometric
  * coefficients.
  *
  * The following matrix operations may be carried out with a vector S of length
@@ -576,7 +576,7 @@ inline static void _scale(InputIter begin, InputIter end,
  *
  * The actual implementation, however, does not compute these quantities by
  * matrix multiplication. A faster algorithm is used that makes use of the fact
- * that the \b integer-valued N matrix is very sparse, and the non-zero terms
+ * that the @b integer-valued N matrix is very sparse, and the non-zero terms
  * are small positive integers.
  * @f[
  * S_k = R_{i1} + \dots + R_{iM}

include/cantera/numerics/BandMatrix.h

@@ -38,14 +38,14 @@ class BandMatrix : public GeneralMatrix
 public:
     //! Base Constructor
     /*!
-     * Create an \c 0 by \c 0 matrix, and initialize all elements to \c 0.
+     * Create an @c 0 by @c 0 matrix, and initialize all elements to @c 0.
      */
     BandMatrix();
     ~BandMatrix();
 
     //! Creates a banded matrix and sets all elements to zero
     /*!
-     * Create an \c n by \c n  banded matrix, and initialize all elements to \c v.
+     * Create an @c n by @c n  banded matrix, and initialize all elements to @c v.
      *
      * @param n   size of the square matrix
      * @param kl  band size on the lower portion of the matrix
@@ -131,7 +131,7 @@ class BandMatrix : public GeneralMatrix
     //! Return the number of rows of storage needed for the band storage
     size_t ldim() const;
 
-    //! Multiply A*b and write result to \c prod.
+    //! Multiply A*b and write result to @c prod.
     virtual void mult(const double* b, double* prod) const;
     virtual void leftMult(const double* const b, double* const prod) const;
 

include/cantera/numerics/DenseMatrix.h

@@ -59,7 +59,7 @@ class DenseMatrix : public Array2D
 
     //! Constructor.
     /*!
-     * Create an \c n by \c m matrix, and initialize all elements to \c v.
+     * Create an @c n by @c m matrix, and initialize all elements to @c v.
      *
      * @param n  New number of rows
      * @param m  New number of columns
@@ -93,7 +93,7 @@ class DenseMatrix : public Array2D
 
     virtual void mult(const double* b, double* prod) const;
 
-    //! Multiply A*B and write result to \c prod.
+    //! Multiply A*B and write result to @c prod.
     /*!
      * Take this matrix to be of size NxM.
      * @param[in]  b     DenseMatrix B of size MxP
@@ -188,7 +188,7 @@ int solve(DenseMatrix& A, double* b, size_t nrhs=1, size_t ldb=0);
  */
 int solve(DenseMatrix& A, DenseMatrix& b);
 
-//! Multiply \c A*b and return the result in \c prod. Uses BLAS routine DGEMV.
+//! Multiply @c A*b and return the result in @c prod. Uses BLAS routine DGEMV.
 /*!
  * @f[
  *     prod_i = sum^N_{j = 1}{A_{ij} b_j}
@@ -200,7 +200,7 @@ int solve(DenseMatrix& A, DenseMatrix& b);
  */
 void multiply(const DenseMatrix& A, const double* const b, double* const prod);
 
-//! Multiply \c A*b and add it to the result in \c prod. Uses BLAS routine DGEMV.
+//! Multiply @c A*b and add it to the result in @c prod. Uses BLAS routine DGEMV.
 /*!
  * @f[
  *     prod_i += sum^N_{j = 1}{A_{ij} b_j}