some doxygen formatting fixes

- consistent indentation of comments
- put @ref on separate line
- some minor fixes

(this is done with wrapcomments.py and checking things manually)

include/deal.II/algorithms/timestep_control.h

@@ -174,7 +174,7 @@ namespace Algorithms
     double start_val;
 
     /**
-     *The end of the time interval.
+     * The end of the time interval.
      */
     double final_val;
 

include/deal.II/arborx/access_traits.h

@@ -245,10 +245,10 @@ namespace ArborXWrappers
 
 
   /**
-   *  This class defines a predicate used by ArborXWrappers::BVH to determine
-   *  for given spheres which of the bounding boxes used to build the
-   *  ArborXWrappers::BVH intersect with them.
-   *  @note The class is not supposed to be used in a polymorphic context.
+   * This class defines a predicate used by ArborXWrappers::BVH to determine
+   * for given spheres which of the bounding boxes used to build the
+   * ArborXWrappers::BVH intersect with them.
+   * @note The class is not supposed to be used in a polymorphic context.
    */
   class SphereIntersectPredicate : private SpherePredicate
   {

include/deal.II/base/data_out_base.h

@@ -702,7 +702,7 @@ namespace DataOutBase
   {
     /**
      * Default constructor. Sets up the dimension labels with the default values
-     of <tt>"x"</tt>, <tt>"y"</tt>, and <tt>"z"</tt>.
+     * of <tt>"x"</tt>, <tt>"y"</tt>, and <tt>"z"</tt>.
      */
     GnuplotFlags();
 
@@ -1536,7 +1536,8 @@ namespace DataOutBase
     unsigned int node_dim;
 
     /**
-     * The number of cells stored in @ref filtered_cells.
+     * The number of cells stored in
+     * @ref filtered_cells.
      */
     unsigned int num_cells;
 

include/deal.II/base/discrete_time.h

@@ -401,7 +401,7 @@ class DiscreteTime
   double start_time;
 
   /**
-   *The end of the time interval.
+   * The end of the time interval.
    */
   double end_time;
 

include/deal.II/base/function.h

@@ -774,7 +774,8 @@ class ComponentSelectFunction
  * component, and consequently is not shown in boldface. Then assume
  * that we want this $u_h(x)$ to be used as a boundary condition for a 2d
  * problem at the line $y=0$. Let's say that this line corresponds to
- * @ref GlossBoundaryIndicator "boundary indicator" 123.
+ * @ref GlossBoundaryIndicator "boundary indicator"
+ * 123.
  * If we say that the 2d problem is associated with
  * @code
  *   DoFHandler<2> dof_handler_2d;

include/deal.II/base/hdf5.h

@@ -1122,7 +1122,8 @@ namespace HDF5
 
   namespace internal
   {
-    /** This function returns the HDF5 datatype corresponding to the C++ type.
+    /**
+     * This function returns the HDF5 datatype corresponding to the C++ type.
      * In the case of std::complex types the HDF5 handlers are automatically
      * freed using the destructor of `std::shared_ptr`. `std::shared_ptr` is
      * used instead of `std::unique_ptr` because the destructor of
@@ -1136,7 +1137,8 @@ namespace HDF5
     std::shared_ptr<hid_t>
     get_hdf5_datatype();
 
-    /** Return the dimensions of `data`. For a std::vector this function returns
+    /**
+     * Return the dimensions of `data`. For a std::vector this function returns
      * `std::vector<hsize_t>{vector_size}`.
      *
      * Several HDF5 functions such as H5Screate_simple() require a
@@ -1148,42 +1150,48 @@ namespace HDF5
     std::vector<hsize_t>
     get_container_dimensions(const std::vector<number> &data);
 
-    /** Return the dimensions of `data`. For a Vector this function returns
+    /**
+     * Return the dimensions of `data`. For a Vector this function returns
      * `std::vector<hsize_t>{vector_size}`.
      */
     template <typename number>
     std::vector<hsize_t>
     get_container_dimensions(const Vector<number> &data);
 
-    /** Return the dimensions of `data`. For a FullMatrix the function returns
+    /**
+     * Return the dimensions of `data`. For a FullMatrix the function returns
      * `std::vector<hsize_t>{rows, columns}`.
      */
     template <typename number>
     std::vector<hsize_t>
     get_container_dimensions(const FullMatrix<number> &data);
 
-    /** This function returns the total size of the container. For a std::vector
+    /**
+     * This function returns the total size of the container. For a std::vector
      * the function returns `int(vector_size)`.
      */
     template <typename number>
     unsigned int
     get_container_size(const std::vector<number> &data);
 
-    /** This function returns the total size of the container. For a Vector the
+    /**
+     * This function returns the total size of the container. For a Vector the
      * function returns `int(vector_size)`.
      */
     template <typename number>
     unsigned int
     get_container_size(const Vector<number> &data);
 
-    /** This function returns the total size of the container. For a FullMatrix
+    /**
+     * This function returns the total size of the container. For a FullMatrix
      * the function returns `int(rows*columns)`.
      */
     template <typename number>
     unsigned int
     get_container_size(const FullMatrix<number> &data);
 
-    /** This function initializes and returns a container of type std::vector,
+    /**
+     * This function initializes and returns a container of type std::vector,
      * Vector or FullMatrix. The function does not set the values of the
      * elements of the container. The container can store data of a HDF5 dataset
      * or a HDF5 selection. The dimensions parameter holds the dimensions of the
@@ -1207,15 +1215,17 @@ namespace HDF5
       Container>::type
     initialize_container(const std::vector<hsize_t> &dimensions);
 
-    /** Same as above.
+    /**
+     * Same as above.
      */
     template <typename Container>
     typename std::enable_if<
       std::is_same<Container, Vector<typename Container::value_type>>::value,
       Container>::type
     initialize_container(const std::vector<hsize_t> &dimensions);
 
-    /** Same as above.
+    /**
+     * Same as above.
      */
     template <typename Container>
     typename std::enable_if<
@@ -1224,15 +1234,17 @@ namespace HDF5
       Container>::type
     initialize_container(const std::vector<hsize_t> &dimensions);
 
-    /** This helper function sets the property list of the read and write
+    /**
+     * This helper function sets the property list of the read and write
      * operations of DataSet. A property list has to be created for the MPI
      * driver. For the serial driver the default H5P_DEFAULT can be used. In
      * addition H5Pset_dxpl_mpio is used to set the MPI mode to collective.
      */
     inline void
     set_plist(hid_t &plist, const bool mpi);
 
-    /** This helper function releases the property list handler of the read and
+    /**
+     * This helper function releases the property list handler of the read and
      * write operations of DataSet. For the serial version there is no need to
      * release the property list handler because H5P_DEFAULT has been used. If
      * query_io_mode is True then H5Pget_mpio_actual_io_mode and
@@ -1247,7 +1259,8 @@ namespace HDF5
                   const bool                 mpi,
                   const bool                 query_io_mode);
 
-    /** Convert a HDF5 no_collective_cause code to a human readable string.
+    /**
+     * Convert a HDF5 no_collective_cause code to a human readable string.
      */
     inline std::string
     no_collective_cause_to_string(const uint32_t no_collective_cause);

include/deal.II/base/vectorization.h

@@ -756,7 +756,7 @@ inline DEAL_II_ALWAYS_INLINE VectorizedArray<Number, width>
  * Create a vectorized array of given type and broadcast the scalar value
  * to all array elements.
  *
- *  @relatesalso VectorizedArray
+ * @relatesalso VectorizedArray
  */
 template <typename VectorizedArrayType>
 inline DEAL_II_ALWAYS_INLINE VectorizedArrayType
@@ -1111,7 +1111,8 @@ class VectorizedArray<double, 8>
     _mm512_storeu_pd(ptr, data);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    * @note Memory must be aligned by 64 bytes.
    */
   DEAL_II_ALWAYS_INLINE
@@ -1668,7 +1669,8 @@ class VectorizedArray<float, 16>
     _mm512_storeu_ps(ptr, data);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    * @note Memory must be aligned by 64 bytes.
    */
   DEAL_II_ALWAYS_INLINE
@@ -2321,7 +2323,8 @@ class VectorizedArray<double, 4>
     _mm256_storeu_pd(ptr, data);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    * @note Memory must be aligned by 32 bytes.
    */
   DEAL_II_ALWAYS_INLINE
@@ -2837,7 +2840,8 @@ class VectorizedArray<float, 8>
     _mm256_storeu_ps(ptr, data);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    * @note Memory must be aligned by 32 bytes.
    */
   DEAL_II_ALWAYS_INLINE
@@ -3383,7 +3387,8 @@ class VectorizedArray<double, 2>
     _mm_storeu_pd(ptr, data);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    * @note Memory must be aligned by 16 bytes.
    */
   DEAL_II_ALWAYS_INLINE
@@ -3830,7 +3835,8 @@ class VectorizedArray<float, 4>
     _mm_storeu_ps(ptr, data);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    * @note Memory must be aligned by 16 bytes.
    */
   DEAL_II_ALWAYS_INLINE
@@ -4299,7 +4305,8 @@ class VectorizedArray<double, 2>
     vec_vsx_st(data, 0, ptr);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    */
   DEAL_II_ALWAYS_INLINE
   void
@@ -4308,7 +4315,8 @@ class VectorizedArray<double, 2>
     store(ptr);
   }
 
-  /** @copydoc VectorizedArray<Number>::gather()
+  /**
+   * @copydoc VectorizedArray<Number>::gather()
    */
   DEAL_II_ALWAYS_INLINE
   void
@@ -4318,7 +4326,8 @@ class VectorizedArray<double, 2>
       *(reinterpret_cast<double *>(&data) + i) = base_ptr[offsets[i]];
   }
 
-  /** @copydoc VectorizedArray<Number>::scatter
+  /**
+   * @copydoc VectorizedArray<Number>::scatter
    */
   DEAL_II_ALWAYS_INLINE
   void
@@ -4543,7 +4552,8 @@ class VectorizedArray<float, 4>
     vec_vsx_st(data, 0, ptr);
   }
 
-  /** @copydoc VectorizedArray<Number>::streaming_store()
+  /**
+   * @copydoc VectorizedArray<Number>::streaming_store()
    */
   DEAL_II_ALWAYS_INLINE
   void
@@ -4552,7 +4562,8 @@ class VectorizedArray<float, 4>
     store(ptr);
   }
 
-  /** @copydoc VectorizedArray<Number>::gather()
+  /**
+   * @copydoc VectorizedArray<Number>::gather()
    */
   DEAL_II_ALWAYS_INLINE
   void
@@ -4562,7 +4573,8 @@ class VectorizedArray<float, 4>
       *(reinterpret_cast<float *>(&data) + i) = base_ptr[offsets[i]];
   }
 
-  /** @copydoc VectorizedArray<Number>::scatter
+  /**
+   * @copydoc VectorizedArray<Number>::scatter
    */
   DEAL_II_ALWAYS_INLINE
   void

include/deal.II/distributed/tria_base.h

@@ -66,7 +66,8 @@ namespace parallel
    * @ref GlossMPICommunicator "MPI communicators"
    * or that they have
    * @ref GlossLocallyOwnedCell "locally owned",
-   * @ref GlossGhostCell "ghost", and possibly
+   * @ref GlossGhostCell "ghost",
+   * and possibly
    * @ref GlossArtificialCell "artificial cells".
    * This class provides
    * a number of member functions that allows querying some information
@@ -685,7 +686,8 @@ namespace parallel
      * Save additional cell-attached data into the given file. The first
      * arguments are used to determine the offsets where to write buffers to.
      *
-     * Called by @ref save.
+     * Called by
+     * @ref save.
      */
     void
     save_attached_data(const unsigned int global_first_cell,
@@ -697,7 +699,8 @@ namespace parallel
      * The first arguments are used to determine the offsets where to read
      * buffers from.
      *
-     * Called by @ref load.
+     * Called by
+     * @ref load.
      */
     void
     load_attached_data(const unsigned int global_first_cell,

include/deal.II/dofs/dof_accessor.h

@@ -140,7 +140,8 @@ namespace internal
  * A class that gives access to the degrees of freedom stored in a DoFHandler
  * object. Accessors are used to access the data that pertains to edges,
  * faces, and cells of a triangulation. The concept is explained in more
- * detail in connection to @ref Iterators.
+ * detail in connection to
+ * @ref Iterators.
  *
  * This class follows mainly the route laid out by the accessor library
  * declared in the triangulation library (TriaAccessor). It enables the user

include/deal.II/fe/fe_interface_values.h

@@ -47,7 +47,7 @@ namespace FEInterfaceViews
   public:
     /**
      * The constructor.
-     **/
+     */
     Base(const FEInterfaceValues<dim, spacedim> &fe_interface);
 
   protected:

include/deal.II/fe/fe_nedelec.h

@@ -66,13 +66,15 @@ DEAL_II_NAMESPACE_OPEN
  * field must be continuous across the line (or surface) even though
  * the normal component may not be. As a consequence, the
  * Nédélec element is constructed in such a way that (i) it is
- * @ref vector_valued "vector-valued", (ii) the shape functions are
+ * @ref vector_valued "vector-valued",
+ * (ii) the shape functions are
  * discontinuous, but (iii) the tangential component(s) of the vector field
  * represented by each shape function are continuous across the faces
  * of cells.
  *
  * Other properties of the Nédélec element are that (i) it is
- * @ref GlossPrimitive "not a primitive element"; (ii) the shape functions
+ * @ref GlossPrimitive "not a primitive element"
+ * ; (ii) the shape functions
  * are defined so that certain integrals over the faces are either zero
  * or one, rather than the common case of certain point values being
  * either zero or one.
@@ -406,7 +408,9 @@ class FE_Nedelec : public FE_PolyTensor<dim>
    * the 3D version of FE_Nedelec has 12 degrees of freedom for `order = 0`
    * and 54 for `degree = 1`. It is important to have enough quadrature points
    * in order to perform the quadrature with sufficient accuracy.
-   * For example [QGauss<dim>(order + 2)](@ref QGauss) can be used for the
+   * For example
+   * [QGauss<dim>(order + 2)](@ref QGauss)
+   * can be used for the
    * quadrature formula, where `order` is the order of FE_Nedelec.
    */
   FE_Nedelec(const unsigned int order);