Resolve some Doxygen warnings

doc/doxygen/Doxyfile

@@ -291,22 +291,6 @@ SUBGROUPING            = YES
 
 TYPEDEF_HIDES_STRUCT   = NO
 
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penality.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will rougly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols
-
-SYMBOL_CACHE_SIZE      = 0
-
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -658,7 +642,8 @@ EXCLUDE_SYMBOLS        = std::*
 
 EXAMPLE_PATH           = samples \
                          data/inputs \
-                         doc/doxygen
+                         doc/doxygen \
+                         doc/sphinx/cxx-guide
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp

include/cantera/base/ctexceptions.h

@@ -33,7 +33,7 @@ namespace Cantera
  *  Below is an example of how to catch errors that throw the CanteraError class.
  *  In general, all Cantera C++ programs will have this basic structure.
  *
- *  \include edemo.cpp
+ *  \include demo1a.cpp
  *
  *  The function showErrors() will print out the fatal error
  *  condition to standard output.
@@ -160,6 +160,7 @@ public:
      *
      * @param func String name for the function within which the error was
      *             generated.
+     * @param arrayName name of the corresponding array
      * @param m   This is the value of the out-of-bounds index.
      * @param mmax This is the maximum allowed value of the index. The
      *             minimum allowed value is assumed to be 0.

include/cantera/base/utilities.h

@@ -1,7 +1,7 @@
 /**
  *  @file utilities.h
  *  Various templated functions that carry out common vector
- *  operations (see \ref globalUtilFuncs).
+ *  operations (see \ref utils).
  */
 
 // Copyright 2001  California Institute of Technology

include/cantera/base/xml.h

@@ -407,7 +407,7 @@ public:
 
     //! Sets the name of the XML node
     /*!
-     * @param name The name of the XML node
+     * @param name_ The name of the XML node
      */
     void setName(const std::string& name_) {
         m_name = name_;

include/cantera/equil/ChemEquil.h

@@ -126,8 +126,13 @@ public:
      * ThermoPhase object. The properties must be already contained
      * within the current thermodynamic state of the system.
      *
+     * @param s phase object to be equilibrated
+     * @param XY property pair to hold constant
      * @param elMoles specified vector of element abundances.
-     *
+     * @param useThermoPhaseElementPotentials get the initial estimate for the
+     *     chemical potentials from the ThermoPhase object (true) or create
+     *     our own estimate (false)
+     * @param loglvel Specify amount of debug logging (0 to disable)
      * @return Successful returns are indicated by a return value of 0.
      *     Unsuccessful returns are indicated by a return value of -1 for lack
      *     of convergence or -3 for a singular jacobian.
@@ -172,6 +177,7 @@ protected:
      * Set mixture to an equilibrium state consistent with specified
      * element potentials and temperature.
      *
+     * @param s mixture to be updated
      * @param x vector of non-dimensional element potentials
      * \f[ \lambda_m/RT \f].
      * @param t temperature in K.

include/cantera/kinetics/KineticsFactory.h

@@ -60,6 +60,9 @@ public:
      *              called "model", with a string value. The value of this
      *              string is used to decide which kinetics manager is used to
      *              calculate the reaction mechanism.
+     * @param th    Vector of phases. The first phase is the phase in which
+     *              the reactions occur, and the subsequent phases (if any)
+     *              are e.g. bulk phases adjacent to a reacting surface.
      *
      * @return Pointer to the new kinetics manager.
      */

src/base/units.h

@@ -54,7 +54,7 @@ public:
     /**
      * Return the multiplier required to convert an activation
      * energy to SI units.
-     * @param units activation energy units
+     * @param units_ activation energy units
      */
     doublereal actEnergyToSI(const std::string& units_) {
         if (m_act_u.find(units_) != m_act_u.end()) {
@@ -71,7 +71,7 @@ public:
      *  <string, doublereal>called  m_u[] and m_act_u for activity
      * coefficients. These maps are initialized with likely values.
      *
-     * @param units String containing the units description
+     * @param units_ String containing the units description
      */
     doublereal toSI(const std::string& units_) {
 

src/kinetics/importKinetics.cpp

@@ -79,7 +79,7 @@ public:
      *  points directly to a ctml element named "reaction". i refers
      *  to the number id of the reaction in the kinetics object.
      *
-     * @param iRxn Reaction number.
+     * @param i Reaction number.
      * @param r XML_Node containing reaction data.
      * @param kin Kinetics manager to which reaction will be added.
      * @param default_phase Default phase for locating a species
@@ -92,7 +92,7 @@ public:
      * @ingroup kineticsmgr
      */
     bool installReaction(int i, const XML_Node& r, Kinetics& kin,
-                         std::string default_phase, ReactionRules& rule,
+                         std::string default_phase, ReactionRules& rules,
                          bool validate_rxn) ;
 };