ENH: Modify documentation for completeness.

Added documentation to several methods. Modified Doxygen configuration file to
correctly process macros (tested using Doxygen 1.7.1). Correctly format
documentation to 80 characters per line.

CMake/VersionSuite/SetUpVersion.cmake

@@ -3,9 +3,9 @@
 # Descrition: 	This small suite allows you to add support
 #		for versioning in your projects
 
-# This allows you to turn on and off the auto 
+# This allows you to turn on and off the auto
 # update of the (project name)Version.hpp file
-SET(VERSION_CONTROL_AUTOUPDATE ON CACHE BOOL "Automaticaly Update The Version")
+SET(VERSION_CONTROL_AUTOUPDATE OFF CACHE BOOL "Automaticaly Update The Version")
 MARK_AS_ADVANCED(VERSION_CONTROL_AUTOUPDATE)
 
 # We need to make sure we have the header file
@@ -37,7 +37,7 @@ MACRO(VersionCalculate)
         FOREACH(r ${return})
             MATH(EXPR count "${count} + 1")
         ENDFOREACH(r ${return})
-        SET(vMinor ${count})       
+        SET(vMinor ${count})
     ELSE(GIT_FOUND)
         SET(vMinor "X")
     ENDIF(GIT_FOUND)
@@ -49,8 +49,8 @@ MACRO(VersionWrite vProjectName export_name)
     FOREACH(il ${include_list})
         SET(includes "${includes}\n\#include \"${il}\"")
     ENDFOREACH(il ${include_list})
-    FILE(WRITE ${CMAKE_BINARY_DIR}/${vProjectName}Version.hpp 
-"/* Current Version of ${vProjectName} 
+    FILE(WRITE ${CMAKE_BINARY_DIR}/${vProjectName}Version.hpp
+"/* Current Version of ${vProjectName}
  * Major is: ${vMajor}
  * Minor is: ${vMinor}
  */
@@ -59,9 +59,9 @@ ${includes}
 extern ${export_name} ProjectVersion ${vProjectName}Version;\n"
     )
 
-	FILE(WRITE ${CMAKE_BINARY_DIR}/${vProjectName}Version.cpp 
+	FILE(WRITE ${CMAKE_BINARY_DIR}/${vProjectName}Version.cpp
 "/* Current Version of ${vProjectName}
- * Make sure to include this file in your built sources 
+ * Make sure to include this file in your built sources
  */
 \#include \"${vProjectName}Version.hpp\"
 ProjectVersion ${vProjectName}Version = ProjectVersion(\"${vProjectName}\", \"${vMajor}\", \"${vMinor}\");\n"

Xdmf.hpp

 #ifndef _XDMF_HPP
 #define _XDMF_HPP
+
+/*! \mainpage XDMF API
+*
+* \section intro Introduction
+*
+* The eXtensible Data Model and Format (XDMF) is a distributed data
+* hub for accessing scientific data in High Performance Computing
+* (HPC) applications. XDMF defines a data model and format as well as
+* facilities for accessing the data in a distributed environment.
+*
+* XDMF differs from other data model and format efforts in that the
+* "light data" is logically (and possibly physically) separated from
+* the "heavy data". Light data is considered to be both "data about
+* the data" such as dimensions and name, as well as small quantities
+* of computed data. Heavy data is considered to be large amounts of
+* data. For example, in a three dimensional structural mechanics
+* calculation, the size and dimensions of the computational grid are
+* light data while the actual X, Y, and Z values for the grid are
+* heavy data. Calculated values like "Pressure at a node" are heavy,
+* while "Total Residual Mass" for the entire calculation is light.
+* Light data is stored on disk in a machine parsable language like
+* XML. Heavy data is stored in a format suitable for large amounts of
+* data like HDF5.
+*
+* While use of the XDMF API is not necessary to produce or consume
+* valid datasets, it is extremely useful for handling the wide variety
+* of files that are possible and its use is highly recommended. The
+* XDMF API is written in C++ and is wrapped for access from other
+* languages including Python and Java.
+*
+* XDMF utilizes reference counting shared pointers to handle ownership
+* of XDMF objects. This allows multiple objects to reference a single
+* XDMF object. An object is deleted and memory is reclaimed when no
+* other XDMF objects hold a reference to the object. This allows
+* flexibility in constructing XDMF structures, as simple structures
+* can be shared instead of copied.
+*
+* All XDMF objects are constructed by calling New(), which returns a
+* shared pointer to a newly constructed object. All default
+* constructors in the XDMF API are protected, ensuring that only
+* shared pointers can be created. These pointers are freed
+* automatically by the shared pointer reference counting mechanism.
+*/
+
 /* Keep all our Win32 Conversions here */
 #ifdef _WIN32
 /* Used to export/import from the dlls */

XdmfAttribute.hpp

@@ -12,11 +12,11 @@ class XdmfAttributeType;
 /**
  * @brief Holds values located at specific parts of an XdmfGrid.
  *
- * XdmfAttribute holds values centered at specific locations of an XdmfGrid.
- * An attribute contains two properties that should be set,
- * XdmfAttributeCenter, which describes where the values are centered, and
- * XdmfAttributeType, which describes what types of values the attribute
- * contains.
+ * XdmfAttribute holds values centered at specific locations of an
+ * XdmfGrid. An attribute contains two properties that should be set,
+ * XdmfAttributeCenter, which describes where the values are centered,
+ * and XdmfAttributeType, which describes what types of values the
+ * attribute contains.
  */
 class XDMF_EXPORT XdmfAttribute : public XdmfArray {
 

XdmfAttributeCenter.hpp

@@ -8,10 +8,10 @@
 /**
  * @brief Property describing where XdmfAttribute values are centered.
  *
- * XdmfAttributeCenter is a property used by XdmfAttribute to specify where
- * its values are centered on an XdmfGrid. A specific XdmfAttributeCenter can
- * be created by calling on of the static methods in the class, i.e.
- * XdmfAttributeCenter::Cell().
+ * XdmfAttributeCenter is a property used by XdmfAttribute to specify
+ * where its values are centered on an XdmfGrid. A specific
+ * XdmfAttributeCenter can be created by calling on of the static
+ * methods in the class, i.e.  XdmfAttributeCenter::Cell().
  *
  * Xdmf supports the following attribute centers:
  *   Grid
@@ -42,10 +42,11 @@ class XDMF_EXPORT XdmfAttributeCenter : public XdmfItemProperty {
  protected:
 
   /**
-   * Protected constructor for XdmfAttributeCenter.  The constructor is
-   * protected because all attribute centers supported by Xdmf should be
-   * accessed through more specific static methods that construct
-   * XdmfAttributeCenters - i.e. XdmfAttributeCenter::Node().
+   * Protected constructor for XdmfAttributeCenter.  The constructor
+   * is protected because all attribute centers supported by Xdmf
+   * should be accessed through more specific static methods that
+   * construct XdmfAttributeCenters -
+   * i.e. XdmfAttributeCenter::Node().
    *
    * @param name the name of the XdmfAttributeCenter to construct.
    */

XdmfAttributeType.hpp

@@ -6,12 +6,13 @@
 #include "XdmfItemProperty.hpp"
 
 /**
- * @brief Property describing the type of values an XdmfAttribute contains.
+ * @brief Property describing the type of values an XdmfAttribute
+ * contains.
  *
- * XdmfAttributeType is a property used by XdmfAttribute to specify what type
- * of values the XdmfAttribute contains. A specific XdmfAttributeType can be
- * created by calling one of the static methods in the class,
- * i.e. XdmfAttributeType::Scalar().
+ * XdmfAttributeType is a property used by XdmfAttribute to specify
+ * what type of values the XdmfAttribute contains. A specific
+ * XdmfAttributeType can be created by calling one of the static
+ * methods in the class, i.e. XdmfAttributeType::Scalar().
  *
  * Xdmf supports the following attribute types:
  *   NoAttributeType

XdmfCurvilinearGrid.hpp

@@ -9,14 +9,14 @@ class XdmfArray;
 #include "XdmfGrid.hpp"
 
 /**
- * @brief A curvilinear (or structured) grid consisting of cells and points
- * arranged on a regular lattice in space.
+ * @brief A curvilinear (or structured) grid consisting of cells and
+ * points arranged on a regular lattice in space.
  *
- * XdmfCurvilinearGrid represents a mesh of cells and points arranged with
- * regular topology and irregular geometry.
+ * XdmfCurvilinearGrid represents a mesh of cells and points arranged
+ * with regular topology and irregular geometry.
  *
- * In order to define a curvilinear grid, the dimensions of the grid must be
- * supplied along with the coordinates of each point.
+ * In order to define a curvilinear grid, the dimensions of the grid
+ * must be supplied along with the coordinates of each point.
  *
  */
 class XDMF_EXPORT XdmfCurvilinearGrid : public XdmfGrid {
@@ -40,7 +40,7 @@ class XDMF_EXPORT XdmfCurvilinearGrid : public XdmfGrid {
    *
    * @param xNumPoints the number of points in the x direction.
    * @param yNumPoints the number of points in the y direction.
-   * @param yNumPoints the number of points in the z direction.
+   * @param zNumPoints the number of points in the z direction.
    *
    * @return constructed curvilinear grid.
    */
@@ -65,15 +65,16 @@ class XDMF_EXPORT XdmfCurvilinearGrid : public XdmfGrid {
   static const std::string ItemTag;
 
   /**
-   * Get the dimensions of the grid, the number of points in each direction.
+   * Get the dimensions of the grid, the number of points in each
+   * direction.
    *
    * @return XdmfArray containing dimensions of this grid.
    */
   boost::shared_ptr<XdmfArray> getDimensions();
 
   /**
-   * Get the dimensions of the grid, the number of points in each direction
-   * (const version).
+   * Get the dimensions of the grid, the number of points in each
+   * direction (const version).
    *
    * @return XdmfArray containing the dimensions of this grid.
    */
@@ -87,7 +88,8 @@ class XDMF_EXPORT XdmfCurvilinearGrid : public XdmfGrid {
   boost::shared_ptr<XdmfGeometry> getGeometry();
 
   /**
-   * Set the dimensions of the grid, the number of points in each direction.
+   * Set the dimensions of the grid, the number of points in each
+   * direction.
    *
    * @param dimensions the dimension of the grid.
    */

XdmfDomain.hpp

@@ -15,9 +15,9 @@ class XdmfUnstructuredGrid;
 /**
  * @brief The root XdmfItem that holds XdmfGrids.
  *
- * XdmfDomain is the top XdmfItem in an Xdmf structure.
- * It can store a number of grids and provides methods to insert, retrieve,
- * and remove these grids.
+ * XdmfDomain is the top XdmfItem in an Xdmf structure.  It can store
+ * a number of grids and provides methods to insert, retrieve, and
+ * remove these grids.
  */
 class XDMF_EXPORT XdmfDomain : public virtual XdmfItem {
 

XdmfGeometry.hpp

@@ -11,10 +11,10 @@ class XdmfGeometryType;
 /**
  * @brief Handles the coordinate positions of points in an XdmfGrid.
  *
- * XdmfGeometry is a required part of an XdmfGrid. It stores the coordinate
- * locations of all points contained in an XdmfGrid. XdmfGeometry contains an
- * XdmfGeometryType property which should be set that specifies the types of
- * coordinate values stored.
+ * XdmfGeometry is a required part of an XdmfGrid. It stores the
+ * coordinate locations of all points contained in an
+ * XdmfGrid. XdmfGeometry contains an XdmfGeometryType property which
+ * should be set that specifies the types of coordinate values stored.
  */
 class XDMF_EXPORT XdmfGeometry : public XdmfArray {
 

XdmfGeometryType.hpp

@@ -6,13 +6,13 @@
 #include "XdmfItemProperty.hpp"
 
 /**
- * @brief Property describing the types of coordinate values stored in an
- * XdmfGeometry.
+ * @brief Property describing the types of coordinate values stored in
+ * an XdmfGeometry.
  *
- * XdmfGeometryType is a property used by XdmfGeometry to specify the type of
- * coordinate values stored in the XdmfGeometry. A specific XdmfGeometryType
- * can be created by calling one of the static methods in the class, i.e.
- * XdmfAttributeType::XYZ().
+ * XdmfGeometryType is a property used by XdmfGeometry to specify the
+ * type of coordinate values stored in the XdmfGeometry. A specific
+ * XdmfGeometryType can be created by calling one of the static
+ * methods in the class, i.e.  XdmfAttributeType::XYZ().
  *
  * Xdmf supports the following geometry types:
  *   NoGeometryType
@@ -52,10 +52,10 @@ class XDMF_EXPORT XdmfGeometryType : public XdmfItemProperty {
  protected:
 
   /**
-   * Protected constructor for XdmfGeometryType.  The constructor is protected
-   * because all geometry types supported by Xdmf should be accessed through
-   * more specific static methods that construct XdmfGeometryTypes - i.e.
-   * XdmfGeometryType::XYZ().
+   * Protected constructor for XdmfGeometryType.  The constructor is
+   * protected because all geometry types supported by Xdmf should be
+   * accessed through more specific static methods that construct
+   * XdmfGeometryTypes - i.e.  XdmfGeometryType::XYZ().
    *
    * @param name a std::string containing the name of the geometry type..
    * @param dimensions an int containing the dimensions of the geometry type.

XdmfGrid.hpp

@@ -14,17 +14,19 @@ class XdmfTopology;
 #include "XdmfItem.hpp"
 
 /**
- * @brief A mesh containing elements, points, and fields attached to the mesh.
+ * @brief A mesh containing elements, points, and fields attached to
+ * the mesh.
  *
- * XdmfGrid represents a mesh. It is required to contain two other Xdmf data
- * structures, an XdmfGeometry that stores point locations and an XdmfTopology
- * that store connectivity information. XdmfAttributes can be inserted into
- * the XdmfGrid to specify fields centered on various parts of the mesh.
- * XdmfSets can be inserted into XdmfGrids to specify collections of mesh
- * elements.
+ * XdmfGrid represents a mesh. It is required to contain two other
+ * Xdmf data structures, an XdmfGeometry that stores point locations
+ * and an XdmfTopology that store connectivity
+ * information. XdmfAttributes can be inserted into the XdmfGrid to
+ * specify fields centered on various parts of the mesh.  XdmfSets can
+ * be inserted into XdmfGrids to specify collections of mesh elements.
  *
- * XdmfGrid is an abstract base class.  There are several implementations for
- * representing both structured and unstructured grids.
+ * XdmfGrid is an abstract base class. There are several
+ * implementations for representing both structured and unstructured
+ * grids.
  */
 class XDMF_EXPORT XdmfGrid : public virtual XdmfItem {
 
@@ -73,16 +75,16 @@ class XDMF_EXPORT XdmfGrid : public virtual XdmfItem {
   /**
    * Get the time associated with this grid.
    *
-   * @return pointer to the XdmfTime attached to this grid. If no XdmfTime is
-   * attached, return a NULL pointer.
+   * @return pointer to the XdmfTime attached to this grid. If no
+   * XdmfTime is attached, return a NULL pointer.
    */
   boost::shared_ptr<XdmfTime> getTime();
 
   /**
    * Get the time associated with this grid (const version).
    *
-   * @return pointer to the XdmfTime attached to this grid. If no XdmfTime is
-   * attached, return a NULL pointer.
+   * @return pointer to the XdmfTime attached to this grid. If no
+   * XdmfTime is attached, return a NULL pointer.
    */
   boost::shared_ptr<const XdmfTime> getTime() const;
 

XdmfGridCollection.hpp

@@ -12,13 +12,13 @@ class XdmfGridCollectionType;
 /**
  * @brief A spatial or temporal collection of XdmfGrids.
  *
- * A temporal collection is timestep data.  Each child grid represents the
- * state at a single timestep.
- * A spatial collection consists of XdmfGrids that are arranged together in
- * space. E.g. a partitioned mesh.
+ * A temporal collection is timestep data.  Each child grid represents
+ * the state at a single timestep.  A spatial collection consists of
+ * XdmfGrids that are arranged together in space. E.g. a partitioned
+ * mesh.
  *
- * It is valid to nest collections. A spatial collection inside a temporal
- * collection is commonly used.
+ * It is valid to nest collections. A spatial collection inside a
+ * temporal collection is commonly used.
  */
 class XDMF_EXPORT XdmfGridCollection : public XdmfDomain,
                                        public XdmfGrid {
@@ -52,14 +52,15 @@ class XDMF_EXPORT XdmfGridCollection : public XdmfDomain,
   using XdmfGrid::insert;
 
   /**
-   * Insert an information into the grid collection..
+   * Insert an information into the grid collection.
    *
    * @param information an XdmfInformation to attach to this item.
    */
   void insert(const boost::shared_ptr<XdmfInformation> information);
 
   /**
-   * Set the XdmfGridCollectionType associated with this grid collection.
+   * Set the XdmfGridCollectionType associated with this grid
+   * collection.
    *
    * @param type the XdmfGridCollectionType to set.
    */

XdmfGridCollectionType.hpp

@@ -8,10 +8,11 @@
 /**
  * @brief Property describing the type of an XdmfGridCollection.
  *
- * XdmfGridCollectionType is a property used by XdmfGridCollection to specify
- * what type of collection the XdmfGridCollection contains. A specific
- * XdmfGridCollectionType can be created by calling one of the static methods
- * in the class, i.e. XdmfGridCollectionType::Temporal().
+ * XdmfGridCollectionType is a property used by XdmfGridCollection to
+ * specify what type of collection the XdmfGridCollection contains. A
+ * specific XdmfGridCollectionType can be created by calling one of
+ * the static methods in the class,
+ * i.e. XdmfGridCollectionType::Temporal().
  *
  * Xdmf supports the following collection types:
  *   NoCollectionType
@@ -37,10 +38,11 @@ class XDMF_EXPORT XdmfGridCollectionType : public XdmfItemProperty {
  protected:
 
   /**
-   * Protected constructor for XdmfGridCollectionType. The constructor is
-   * protected because all collection types supported by Xdmf should be
-   * accessed through more specific static methods that construct
-   * XdmfGridCollectionType - i.e. XdmfGridCollectionType::Temporal().
+   * Protected constructor for XdmfGridCollectionType. The constructor
+   * is protected because all collection types supported by Xdmf
+   * should be accessed through more specific static methods that
+   * construct XdmfGridCollectionType -
+   * i.e. XdmfGridCollectionType::Temporal().
    *
    * @param name the name of the XdmfGridCollectionType to construct.
    */

XdmfMap.hpp

@@ -11,20 +11,23 @@ class XdmfHeavyDataController;
 #include "XdmfItem.hpp"
 
 /**
- * @brief Boundary communicator map for partitioned spatial collections.
+ * @brief Boundary communicator map for partitioned spatial
+ * collections.
  *
- * Provides mechanism for mapping nodes across partition boundaries. Each
- * partitioned grid contains its own map, mapping its own nodes to all other
- * nodes in the global system.
+ * Provides mechanism for mapping nodes across partition
+ * boundaries. Each partitioned grid contains its own map, mapping its
+ * own nodes to all other nodes in the global system.
  *
  * There are two methods for constructing XdmfMaps:
- * Calling New() with no parameters will construct an empty map. The map can be
- * filled manually with subsequent insert commands.
+ *
+ * Calling New() with no parameters will construct an empty map. The
+ * map can be filled manually with subsequent insert commands.
+ *
  * Calling New(const std::vector<boost::shared_ptr<XdmfAttribute> > &
- * globalNodeIds) will construct XdmfMaps for each grid in an entire global
- * system. Each entry in the vector contains the globalNodeIds for that
- * partition. The constructor accepts global node ids for each partition to
- * construct the proper XdmfMaps.
+ * globalNodeIds) will construct XdmfMaps for each grid in an entire
+ * global system. Each entry in the vector contains the globalNodeIds
+ * for that partition. The constructor accepts global node ids for
+ * each partition to construct the proper XdmfMaps.
  */
 class XDMF_EXPORT XdmfMap : public XdmfItem {
 
@@ -38,8 +41,9 @@ class XDMF_EXPORT XdmfMap : public XdmfItem {
   static boost::shared_ptr<XdmfMap> New();
 
   /**
-   * Create XdmfMaps for each grid in a domain decomposed mesh. Each entry in
-   * the globalNodeIds vector contains the global node ids for that partition.
+   * Create XdmfMaps for each grid in a domain decomposed mesh. Each
+   * entry in the globalNodeIds vector contains the global node ids
+   * for that partition.
    *
    * @param globalNodeIds a vector of attributes containing globalNodeId
    * values for each partition to be mapped.
@@ -57,7 +61,8 @@ class XDMF_EXPORT XdmfMap : public XdmfItem {
   std::map<std::string, std::string> getItemProperties() const;
 
   /**
-   * Given a local node id return a map containing equivalent remote node ids
+   * Given a local node id return a map containing equivalent remote
+   * node ids
    */
   std::map<unsigned int, unsigned int>
   getRemoteNodeIds(const unsigned int localNodeId);
@@ -71,7 +76,8 @@ class XDMF_EXPORT XdmfMap : public XdmfItem {
               const unsigned int remoteLocalNodeId);
 
   /**
-   * Returns whether the map is initialized (contains values in memory).
+   * Returns whether the map is initialized (contains values in
+   * memory).
    */
   bool isInitialized() const;
 
@@ -81,7 +87,7 @@ class XDMF_EXPORT XdmfMap : public XdmfItem {
   void read();
 
   /**
-   * Release all data held in memory.  The heavy data remain attached.
+   * Release all data held in memory. The heavy data remain attached.
    */
   void release();
 

XdmfReader.hpp

@@ -8,10 +8,10 @@
 /**
  * @brief Reads an Xdmf file stored on disk into memory.
  *
- * Reads an Xdmf file stored on disk into an Xdmf structure in memory. All
- * light data is parsed in order to create appropriate Xdmf objects. Heavy
- * data controllers are created and attached to XdmfArrays but no heavy data
- * is read into memory.
+ * Reads an Xdmf file stored on disk into an Xdmf structure in
+ * memory. All light data is parsed in order to create appropriate
+ * Xdmf objects. Heavy data controllers are created and attached to
+ * XdmfArrays but no heavy data is read into memory.
  */
 class XDMF_EXPORT XdmfReader : public XdmfCoreReader {
 

XdmfRectilinearGrid.hpp

@@ -9,15 +9,15 @@ class XdmfArray;
 #include "XdmfGrid.hpp"
 
 /**
- * @brief A rectilinear grid consists of cells and points arranged on a
- * regular lattice in space.
+ * @brief A rectilinear grid consists of cells and points arranged on
+ * a regular lattice in space.
  *
- * XdmfRectilinearGrid represents a mesh of cells and points arranged on a
- * regular lattice in space. Points are arranged along coordinate axes, but
- * the spacing between points may vary.
+ * XdmfRectilinearGrid represents a mesh of cells and points arranged
+ * on a regular lattice in space. Points are arranged along coordinate
+ * axes, but the spacing between points may vary.
  *
- * In order to define a rectilinear grid, the coordinates along each axis
- * direction must be specified.
+ * In order to define a rectilinear grid, the coordinates along each
+ * axis direction must be specified.
  *
  */
 class XDMF_EXPORT XdmfRectilinearGrid : public XdmfGrid {
@@ -68,18 +68,19 @@ class XDMF_EXPORT XdmfRectilinearGrid : public XdmfGrid {
   /**
    * Get the coordinates of the grid along a single axis.
    *
-   * @param axisIndex the index of the axis to retrieve, (i.e. 0 for x-axis).
-   * If no array exists at the index, return NULL.
+   * @param axisIndex the index of the axis to retrieve, (i.e. 0 for
+   * x-axis). If no array exists at the index, return NULL.
    *
    * @return array of coordinates along
    */
   boost::shared_ptr<XdmfArray> getCoordinates(const unsigned int axisIndex);
 
   /**
-   * Get the coordinates of the grid along a single axis (const version).
+   * Get the coordinates of the grid along a single axis (const
+   * version).
    *
-   * @param axisIndex the index of the axis to retrieve (i.e. 0 for x-axis).
-   * If no array exists at the index, return NULL.
+   * @param axisIndex the index of the axis to retrieve (i.e. 0 for
+   * x-axis). If no array exists at the index, return NULL.
    *
    * @return array of coordinates along
    */
@@ -89,27 +90,30 @@ class XDMF_EXPORT XdmfRectilinearGrid : public XdmfGrid {
   /**
    * Get the coordinates of the grid along all axes.
    *
-   * @return vector containing an array of coordinates along each direction.
+   * @return vector containing an array of coordinates along each
+   * direction.
    */
   std::vector<boost::shared_ptr<XdmfArray> > getCoordinates();
 
   /**
    * Get the coordinates of the grid along all axes (const version).
    *
-   * @return vector containing an array of coordinates along each direction.
+   * @return vector containing an array of coordinates along each
+   * direction.
    */
   const std::vector<boost::shared_ptr<XdmfArray> > getCoordinates() const;
 
   /**
-   * Get the dimensions of the grid, the number of points in each direction.
+   * Get the dimensions of the grid, the number of points in each
+   * direction.
    *
    * @return XdmfArray containing dimensions of this grid.
    */
   boost::shared_ptr<XdmfArray> getDimensions();
 
   /**
-   * Get the dimensions of the grid, the number of points in each direction
-   * (const version).
+   * Get the dimensions of the grid, the number of points in each
+   * direction (const version).
    *
    * @return XdmfArray containing the dimensions of this grid.
    */
@@ -119,7 +123,8 @@ class XDMF_EXPORT XdmfRectilinearGrid : public XdmfGrid {
    * Set the coordinates of the grid along a single axis.
    *
    * @param axisIndex the index of the axis to set (i.e. 0 for x-axis).
-   * @param axisCoordinates the coordinates of points along a single axis to set.
+   * @param axisCoordinates the coordinates of points along a single axis to
+   * set.
    */
   void setCoordinates(const unsigned int axisIndex,
                       const boost::shared_ptr<XdmfArray> axisCoordinates);

XdmfRegularGrid.hpp

@@ -9,12 +9,12 @@ class XdmfArray;
 #include "XdmfGrid.hpp"
 
 /**
- * @brief A regular grid consists of congruent points arranged regularly in
- * space.
+ * @brief A regular grid consists of congruent points arranged
+ * regularly in space.
  *
- * XdmfRegularGrid represents a regular mesh of congruent points arranged in
- * space. In order to define a regular grid, three sets of terms need to be
- * supplied:
+ * XdmfRegularGrid represents a regular mesh of congruent points
+ * arranged in space. In order to define a regular grid, three sets of
+ * terms need to be supplied:
  *
  * Brick Size (Dx, Dy, (Dz)) - Size of an individual brick.
  * Dimensions (X, Y, (Z)) - Number of points in X, Y, and Z directions
@@ -102,15 +102,16 @@ class XDMF_EXPORT XdmfRegularGrid : public XdmfGrid {
   boost::shared_ptr<const XdmfArray> getBrickSize() const;
 
   /**
-   * Get the dimensions of the grid, the number of points in each direction.
+   * Get the dimensions of the grid, the number of points in each
+   * direction.
    *
    * @return XdmfArray containing dimensions of this grid.
    */
   boost::shared_ptr<XdmfArray> getDimensions();
 
   /**
-   * Get the dimensions of the grid, the number of points in each direction
-   * (const version).
+   * Get the dimensions of the grid, the number of points in each
+   * direction (const version).
    *
    * @return XdmfArray containing the dimensions of this grid.
    */
@@ -119,28 +120,31 @@ class XDMF_EXPORT XdmfRegularGrid : public XdmfGrid {
   /**
    * Get the location of the origin of the grid.
    *
-   * @return XdmfArray containing the location of the origin of the grid.
+   * @return XdmfArray containing the location of the origin of the
+   * grid.
    */
   boost::shared_ptr<XdmfArray> getOrigin();
 
   /**
    * Get the location of the origin of the grid.
    *
-   * @return XdmfArray containing the location of the origin of the grid
-   * (const version).
+   * @return XdmfArray containing the location of the origin of the
+   * grid (const version).
    */
   boost::shared_ptr<const XdmfArray> getOrigin() const;
 
   /**
    * Set the size of the points composing the grid.
    *
-   * @param brickSize the sizes of the points composing the mesh. This should
-   * have the same number of terms as the dimensionality of the mesh.
+   * @param brickSize the sizes of the points composing the mesh. This
+   * should have the same number of terms as the dimensionality of the
+   * mesh.
    */
   void setBrickSize(const boost::shared_ptr<XdmfArray> brickSize);
 
   /**
-   * Set the dimensions of the grid, the number of points in each direction.
+   * Set the dimensions of the grid, the number of points in each
+   * direction.
    *
    * @param dimensions the dimension of the grid.
    */
@@ -149,8 +153,8 @@ class XDMF_EXPORT XdmfRegularGrid : public XdmfGrid {
   /**
    * Set the origin of the grid.
    *
-   * @param origin location of the origin of the grid.  This should have
-   * the same number of terms as the dimensionality of the mesh.
+   * @param origin location of the origin of the grid.  This should
+   * have the same number of terms as the dimensionality of the mesh.
    */
   void setOrigin(const boost::shared_ptr<XdmfArray> origin);
 

XdmfSet.hpp

@@ -11,14 +11,15 @@ class XdmfSetType;
 #include "XdmfArray.hpp"
 
 /**
- * @brief Holds a collection of individual nodes, cells, faces, or edges that
- * are part of an XdmfGrid.
+ * @brief Holds a collection of individual nodes, cells, faces, or
+ * edges that are part of an XdmfGrid.
  *
- * An XdmfSet holds a collection of nodes, cells, faces, or edges that are
- * part of an XdmfGrid. For instance, a simulation may want to hold a set of
- * nodes on a boundary. The individual elements making up the set are
- * determined by their id. An XdmfSet can have XdmfAttributes attached that
- * contain extra values attached to the elements in the set.
+ * An XdmfSet holds a collection of nodes, cells, faces, or edges that
+ * are part of an XdmfGrid. For instance, a simulation may want to
+ * hold a set of nodes on a boundary. The individual elements making
+ * up the set are determined by their id. An XdmfSet can have
+ * XdmfAttributes attached that contain extra values attached to the
+ * elements in the set.
  */
 class XDMF_EXPORT XdmfSet : public XdmfArray {
 

XdmfSetType.hpp

@@ -8,9 +8,9 @@
 /**
  * @brief Property describing the type of ids an XdmfSet contains.
  *
- * An XdmfSet holds ids for a collection of nodes, cells, faces, or edges
- * that are part of an XdmfGrid. This property indicates which type the set
- * contains.
+ * An XdmfSet holds ids for a collection of nodes, cells, faces, or
+ * edges that are part of an XdmfGrid. This property indicates which
+ * type the set contains.
  *
  * Xdmf supports the following set types:
  *   NoSetType
@@ -40,10 +40,10 @@ class XDMF_EXPORT XdmfSetType : public XdmfItemProperty {
  protected:
 
   /**
-   * Protected constructor for XdmfSetType. The constructor is protected
-   * because all set types supported by Xdmf should be accessed through more
-   * specific static methods that construct XdmfSetTypes -
-   * i.e. XdmfSetType::Node().
+   * Protected constructor for XdmfSetType. The constructor is
+   * protected because all set types supported by Xdmf should be
+   * accessed through more specific static methods that construct
+   * XdmfSetTypes - i.e. XdmfSetType::Node().
    *
    * @param name a std::string containing the name of the XdmfSetType.
    */

XdmfTopology.hpp

@@ -11,10 +11,10 @@ class XdmfTopologyType;
 /**
  * @brief Holds the connectivity information in an XdmfGrid.
  *
- * XdmfTopology is a required part of an XdmfGrid. It stores the connectivity
- * information for all points contained in an XdmfGrid. XdmfTopology contains
- * an XdmfTopologyType property which should be set that specifies the
- * element type stored.
+ * XdmfTopology is a required part of an XdmfGrid. It stores the
+ * connectivity information for all points contained in an
+ * XdmfGrid. XdmfTopology contains an XdmfTopologyType property which
+ * should be set that specifies the element type stored.
  */
 class XDMF_EXPORT XdmfTopology : public XdmfArray {
 

XdmfTopologyType.hpp

@@ -6,11 +6,13 @@
 #include "XdmfItemProperty.hpp"
 
 /**