Doxygen update

-> eliminated some doxygen warnings.

Cantera/src/base/Array.h

@@ -27,6 +27,13 @@ namespace Cantera {
     /**
      *  A class for 2D arrays stored in column-major
      *  (Fortran-compatible) form.
+     *  In this form, the data entry for an n row, m col 
+     *  matrix is 
+     *       index = i + (n-1) * j
+     *  where
+     *     J(i,j) = data_start + index 
+     *         i = row
+     *         j = column
      */
     class Array2D {
 
@@ -69,7 +76,12 @@ namespace Cantera {
 	    return *this;
         }
 
-        /// resize the array, and fill the new entries with 'v'
+        //! resize the array, and fill the new entries with 'v'
+        /*!
+         * @param n  This is the number of rows
+         * @param m  This is the number of columns in the new matrix
+         * @param v  Default fill value -> defaults to zero.
+         */
         void resize(int n, int m, doublereal v = 0.0) {
             m_nrows = n;
             m_ncols = m;
@@ -147,6 +159,13 @@ namespace Cantera {
          */ 
         doublereal operator() ( int i, int j) const {return value(i,j);}
 
+        //! Returns a changeable reference to position in the matrix
+        /*!
+         * This is a key entry. Returns a reference to the matrixes (i,j)
+         * element. This may be used as an L value.
+         * @param i   The row index
+         * @param j   The column index
+         */
         doublereal& value( int i, int j) {return m_data[m_nrows*j + i];}
         doublereal value( int i, int j) const {return m_data[m_nrows*j + i];}
 

Cantera/src/base/misc.cpp

@@ -244,7 +244,7 @@ namespace Cantera {
        *
        * @ingroup errorhandling
        */
-      void getErrors( std::ostream& f) ;
+      void getErrors(std::ostream& f) ;
 
       //!  Prints all of the error messages using writelog
       /*!
@@ -427,37 +427,47 @@ namespace Cantera {
     } ;
     
 #ifdef THREAD_SAFE_CANTERA
+      //! Typedef for thread specific messages
       typedef boost::shared_ptr< Messages >   pMessages_t ;
+
+      //! Typedef for map between a thread and the message
       typedef std::map< cthreadId_t, pMessages_t > threadMsgMap_t ;
+
       class ThreadMessages
       {
       public:
-         ThreadMessages()
-         {
-         }
-
-         Messages* operator->()
-         {
-            MSG_LOCK() ;
-            cthreadId_t curId = getThisThreadId() ;
-            threadMsgMap_t::iterator iter = m_threadMsgMap.find( curId ) ;
-            if ( iter != m_threadMsgMap.end() )
+	//! Constructor
+	ThreadMessages()
+	{
+	}
+	
+	//! Provide a pointer deferencing overloaded operator
+	/*!
+	 * @return  returns a pointer to Messages
+	 */
+	Messages* operator->()
+	{
+	  MSG_LOCK() ;
+	  cthreadId_t curId = getThisThreadId() ;
+	  threadMsgMap_t::iterator iter = m_threadMsgMap.find( curId ) ;
+	  if ( iter != m_threadMsgMap.end() )
             {
-               return (iter->second.get()) ;
+	      return (iter->second.get()) ;
             }
-            pMessages_t pMsgs( new Messages() ) ;
-            m_threadMsgMap.insert( std::pair< cthreadId_t, pMessages_t >( curId, pMsgs ) ) ;
-            return pMsgs.get() ;
-         }
+	  pMessages_t pMsgs( new Messages() ) ;
+	  m_threadMsgMap.insert( std::pair< cthreadId_t, pMessages_t >( curId, pMsgs ) ) ;
+	  return pMsgs.get() ;
+	}
 
-         void removeThreadMessages() {
-            MSG_LOCK() ;
-            cthreadId_t curId = getThisThreadId() ;
-            threadMsgMap_t::iterator iter = m_threadMsgMap.find( curId ) ;
-            if ( iter != m_threadMsgMap.end() ) {
-               m_threadMsgMap.erase( iter ) ;
-            }
-         }
+	//! Remove a local thread message
+	void removeThreadMessages() {
+	  MSG_LOCK() ;
+	  cthreadId_t curId = getThisThreadId() ;
+	  threadMsgMap_t::iterator iter = m_threadMsgMap.find( curId ) ;
+	  if ( iter != m_threadMsgMap.end() ) {
+	    m_threadMsgMap.erase( iter ) ;
+	  }
+	}
 
       private:
 	//! Thread Msg Map

Cantera/src/base/units.h

@@ -169,7 +169,8 @@ namespace Cantera {
     std::map<std::string, doublereal> m_act_u;
 
 #if defined(THREAD_SAFE_CANTERA)
-      static boost::mutex units_mutex;
+    //! Decl for static locker for Units singelton 
+    static boost::mutex units_mutex;
 #endif
 
     /*!