fix issue with cppcheck and macro

Author: rrsettgast

src/common/macros.hpp

@@ -61,4 +61,6 @@
         __pragma(warning(pop))
 #else
 #define HPCREACT_NO_MISSING_BRACES( ... ) __VA_ARGS__ // No-op for unknown compilers
+#define HPCREACT_NO_MISSING_BRACES_OPEN
+#define HPCREACT_NO_MISSING_BRACES_CLOSE
 #endif

src/common/symmetricMatrix.hpp

@@ -1,25 +1,69 @@
 #pragma once
 
+/**
+ * @file
+ * @brief This file contains the definition of a symmetric matrix.
+ *       It is used to store the symmetric part of a matrix in a
+ *      compact way.
+ */
+
+/**
+ * @brief A symmetric matrix is a matrix that is equal to its transpose.
+ *        This class stores the symmetric part of a matrix in a compact way.
+ * @tparam T The type of the elements of the matrix.
+ * @tparam INDEX_TYPE The type of the indices of the matrix.
+ * @tparam N The size of the matrix.
+ * @details 
+ *   The matrix is stored in a 1D array, where the elements are
+ *   stored in a compact way. 
+ * 
+ *   The linear index is calculated using
+ *   the formula (i*(i+1))/2 + j, where i and j are the indices of
+ *   the matrix. This corrosponds to filling the lower triangular
+ *   part of the matrix row by row. So each row i has i+1 elements.
+ * 
+ *   The size of the matrix is calculated using the
+ *   formula (N*(N+1))/2, where N is the size of the matrix.
+ */
 template< typename T, typename INDEX_TYPE, int N >
 struct symmetricMatrix
 {
+  /**
+   * @brief the storage size of the matrix
+   */
   static constexpr INDEX_TYPE size() { return ( N*(N+1) ) / 2; }
 
-  static inline INDEX_TYPE linearIndex( INDEX_TYPE const i, INDEX_TYPE const j )
+  /**
+   * @brief calculates the linear index of the element at (i,j)
+   */
+  static inline INDEX_TYPE linearIndex( INDEX_TYPE const i, INDEX_TYPE const j ) const
   {
     return (( i*(i+1) ) >> 1) + j;
   }
 
+  /**
+   * @brief non-const access operator
+   * @param i the row index
+   * @param j the column index
+   * @return reference to the element at (i,j)
+   */
   inline T & operator()( INDEX_TYPE const i, INDEX_TYPE const j )
   {
     return m_data[linearIndex( i, j )];
   }
 
+  /**
+   * @brief const access operator
+   * @param i the row index
+   * @param j the column index
+   * @return reference to the element at (i,j)
+   */
   inline T const & operator()( INDEX_TYPE const i, INDEX_TYPE const j ) const
   {
     return m_data[linearIndex( i, j )];
   }
 
+  /// Matrix is stored in a 1D c-array.
   T m_data[ size() ];
 
 };

src/docs/doxygen/Doxyfile.in

@@ -1040,7 +1040,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = */cmake/* **/unitTests/*.cpp
+EXCLUDE_PATTERNS       = */cmake/* **/unitTests/*.cpp */Parameters.hpp
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

src/reactions/bulkGeneric/EquilibriumReactions.hpp

@@ -13,16 +13,29 @@ namespace hpcReact
 namespace bulkGeneric
 {
 
+/**
+ * @brief This class implements components required to calculate equilibrium 
+ *        reactions for a given set of species. The class also proovides
+ *        device callable methods to enforce equilibrium pointwise and also
+ *        provides methods to launch batch processing of material points.
+ * @tparam REAL_TYPE The type of the real numbers used in the class.
+ * @tparam INT_TYPE The type of the integers used in the class.
+ * @tparam INDEX_TYPE The type of the indices used in the class.
+ */
 template< typename REAL_TYPE,
           typename INT_TYPE,
           typename INDEX_TYPE >
 class EquilibriumReactions
 {
 public:
+  /// alias for type of the real numbers used in the class.
   using RealType = REAL_TYPE;
+
+  /// alias for type of the integers used in the class.
   using IntType = INT_TYPE;
+  
+  /// alias for type of the indices used in the class.
   using IndexType = INDEX_TYPE;
-//  constexpr static int formulation = FORMULATION;
 
   template< typename PARAMS_DATA,
             typename ARRAY_1D,
@@ -37,7 +50,9 @@ class EquilibriumReactions
                               ARRAY_1D & residual,
                               ARRAY_2D & jacobian );
 
-
+  /**
+   * @brief This method enforces equilibrium for a given set of species using 
+   *        reaction extents.
   template< typename PARAMS_DATA,
             typename ARRAY_1D,
             typename ARRAY_1D_TO_CONST >