Doxygen cleanup

doc/doxygen/thermoprops.dox

@@ -362,19 +362,19 @@
  * activity coefficients:
  *
  * @f[
- *  \mu_k =  \mu_k^\triangle(T,P) + R T ln(a_k^{\triangle}) =
- *            \mu_k^\triangle(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
+ *  \mu_k =  \mu_k^\triangle(T,P) + R T \ln(a_k^{\triangle}) =
+ *            \mu_k^\triangle(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
  * @f]
  *
  * And, the solvent employs the following convention
  * @f[
- *    \mu_o = \mu^o_o(T,P) + RT ln(a_o)
+ *    \mu_o = \mu^o_o(T,P) + RT \ln(a_o)
  * @f]
  *
  * where @f$ a_o @f$ is often redefined in terms of the osmotic coefficient @f$ \phi @f$.
  *
  *   @f[
- *       \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
+ *       \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
  *   @f]
  *
  *  %ThermoPhase classes which employ the molality based convention are all derived

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.
@@ -100,7 +100,7 @@ void appdelete();
 //! @copydoc Application::thread_complete
 void thread_complete();
 
-//! @defgroup globalSettings  Global %Cantera Settings
+//! @defgroup globalSettings  Global Cantera Settings
 //! @brief Functions for accessing global %Cantera settings.
 //! @ingroup globalData
 
@@ -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

@@ -252,7 +252,7 @@ class vcs_VolPhase
     /**
      * This is essentially a scatter operation.
      *
-     * @param LnAcJac_VCS Jacobian parameter
+     * @param LnACJac_VCS Jacobian parameter
      *     The Jacobians are actually d( lnActCoeff) / d (MolNumber);
      *     dLnActCoeffdMolNumber(k,j)
      *
@@ -261,7 +261,7 @@ class vcs_VolPhase
      */
     void sendToVCS_LnActCoeffJac(Array2D& LnACJac_VCS);
 
-    //! Set the pointer for Cantera's ThermoPhase parameter
+    //! Set the pointer for %Cantera's ThermoPhase parameter
     /*!
      * When we first initialize the ThermoPhase object, we read the state of the
      * ThermoPhase into vcs_VolPhase object.
@@ -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/equil/vcs_solve.h

@@ -820,7 +820,7 @@ class VCS_SOLVE
      * We are checking the equation:
      *
      *         sum_u = sum_j_comp [ sigma_i_j * u_j ]
-     *               = u_i_O + log((AC_i * W_i)/m_tPhaseMoles_old)
+     *               = u_i_O + \ln((AC_i * W_i)/m_tPhaseMoles_old)
      *
      * by first evaluating:
      *

include/cantera/kinetics/BlowersMaselRate.h

@@ -43,12 +43,12 @@ struct BlowersMaselData : public ReactionData
  * The Blowers Masel approximation @cite blowers2004 adjusts the activation energy
  * based on enthalpy change of a reaction:
  *
- *   \f{eqnarray*}{
- *        E_a &=& 0\; \text{if }\Delta H < -4E_0 \\
- *        E_a &=& \Delta H\; \text{if }\Delta H > 4E_0 \\
+ *   @f{eqnarray*}{
+ *        E_a &=& 0\; &\text{if }\Delta H < -4E_0 \\
+ *        E_a &=& \Delta H\; &\text{if }\Delta H > 4E_0 \\
  *        E_a &=& \frac{(w + \Delta H / 2)(V_P - 2w +
- *               \Delta H)^2}{(V_P^2 - 4w^2 + (\Delta H)^2)}\; \text{Otherwise}
- *   \f}
+ *               \Delta H)^2}{(V_P^2 - 4w^2 + (\Delta H)^2)}\; &\text{otherwise}
+ *   @f}
  * where
  *   @f[
  *        V_P = \frac{2w (w + E_0)}{w - E_0},

include/cantera/kinetics/Falloff.h

@@ -395,7 +395,7 @@ class TroeRate final : public FalloffRate
  *  where
  *  @f[ P_r = \frac{k_0 [M]}{k_{\infty}} @f]
  *
- *  @f[ F = {\left( a \; exp(\frac{-b}{T}) + exp(\frac{-T}{c})\right)}^n
+ *  @f[ F = {\left( a \; \exp(\frac{-b}{T}) + \exp(\frac{-T}{c})\right)}^n
  *              \;  d \; T^e @f]
  *      where
  *  @f[ n = \frac{1.0}{1.0 + (\log_{10} P_r)^2} @f]

include/cantera/kinetics/Kinetics.h

@@ -60,7 +60,7 @@ class AnyMap;
 //! quantities internally, and re-evaluate them only when the temperature has
 //! actually changed. Or a manager designed for use with reaction mechanisms
 //! with a few repeated activation energies might precompute the terms @f$
-//! exp(-E/RT) @f$, instead of evaluating the exponential repeatedly for each
+//! \exp(-E/RT) @f$, instead of evaluating the exponential repeatedly for each
 //! reaction. There are many other possible 'management styles', each of which
 //! might be better suited to some reaction mechanisms than others.
 //!
@@ -401,7 +401,7 @@ class Kinetics
      *  total number of reactions.
      *
      * @f[
-     *       Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ]
+     *       Kc_i = \exp [ \Delta G_{ss,i} ] \prod(Cs_k) \exp(\sum_k \nu_{k,i} F \phi_n)
      * @f]
      *
      * @param kc   Output vector containing the equilibrium constants.
@@ -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.