Added subset; modified Array's interaction with Function; added new...

Added subset; modified Array's interaction with Function; added new functionality to XdmfInformation subarrays; adjusted documentation to make more uniform

XdmfAttribute.hpp

@@ -62,7 +62,7 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @return	constructed XdmfAttribute.
+   * @return	Constructed XdmfAttribute.
    */
   static shared_ptr<XdmfAttribute> New();
 
@@ -129,7 +129,7 @@ public:
    * @skipline #//getName
    * @until #//getName
    *
-   * @return	a string containing the name of the attribute.
+   * @return	A string containing the name of the attribute.
    */
   std::string getName() const;
 
@@ -183,7 +183,7 @@ public:
    * @skipline #//setCenter
    * @until #//setCenter
    *
-   * @param	center	the XdmfAttributeCenter to set.
+   * @param	center	The XdmfAttributeCenter to set.
    */
   void setCenter(const shared_ptr<const XdmfAttributeCenter> center);
 
@@ -208,7 +208,7 @@ public:
    * @skipline #//setName
    * @until #//setName
    *
-   * @param	name	a string containing the name to set.
+   * @param	name	A string containing the name to set.
    */
   void setName(const std::string & name);
 

XdmfAttributeCenter.hpp

@@ -93,7 +93,7 @@ protected:
    * construct XdmfAttributeCenters -
    * i.e. XdmfAttributeCenter::Node().
    *
-   * @param name the name of the XdmfAttributeCenter to construct.
+   * @param	name	The name of the XdmfAttributeCenter to construct.
    */
   XdmfAttributeCenter(const std::string & name);
 

XdmfAttributeType.hpp

@@ -96,7 +96,7 @@ protected:
    * accessed through more specific static methods that construct
    * XdmfAttributeTypes - i.e. XdmfAttributeType::Scalar().
    *
-   * @param name the name of the XdmfAttributeType to construct.
+   * @param	name	The name of the XdmfAttributeType to construct.
    */
   XdmfAttributeType(const std::string & name);
 

XdmfCurvilinearGrid.hpp

@@ -65,10 +65,10 @@ public:
    * @skipline #//constructor2
    * @until #//constructor2
    *
-   * @param	xNumPoints	the number of points in the x direction.
-   * @param	yNumPoints	the number of points in the y direction.
+   * @param	xNumPoints	The number of points in the x direction.
+   * @param	yNumPoints	The number of points in the y direction.
    *
-   * @return			constructed curvilinear grid.
+   * @return			Constructed curvilinear grid.
    */
   static shared_ptr<XdmfCurvilinearGrid>
   New(const unsigned int xNumPoints,
@@ -93,11 +93,11 @@ public:
    * @skipline #//constructor3
    * @until #//constructor3
    *
-   * @param	xNumPoints	the number of points in the x direction.
-   * @param	yNumPoints	the number of points in the y direction.
-   * @param	zNumPoints	the number of points in the z direction.
+   * @param	xNumPoints	The number of points in the x direction.
+   * @param	yNumPoints	The number of points in the y direction.
+   * @param	zNumPoints	The number of points in the z direction.
    *
-   * @return			constructed curvilinear grid.
+   * @return			Constructed curvilinear grid.
    */
   static shared_ptr<XdmfCurvilinearGrid>
   New(const unsigned int xNumPoints,
@@ -123,9 +123,9 @@ public:
    * @skipline #//constructorvector
    * @until #//constructorvector
    *
-   * @param	numPoints	the number of points in each direction.
+   * @param	numPoints	The number of points in each direction.
    *
-   * @return			constructed curvilinear grid.
+   * @return			Constructed curvilinear grid.
    */
   static shared_ptr<XdmfCurvilinearGrid>
   New(const shared_ptr<XdmfArray> numPoints);
@@ -216,7 +216,7 @@ public:
    * @skipline #//getGeometry
    * @until #//getGeometry
    *
-   * @return	the geometry associated with this grid.
+   * @return	The geometry associated with this grid.
    */
   shared_ptr<XdmfGeometry> getGeometry();
 
@@ -244,7 +244,7 @@ public:
    * @skipline #//setDimensions
    * @until #//setDimensions
    *
-   * @param	dimensions	the dimension of the grid.
+   * @param	dimensions	The dimension of the grid.
    */
   void setDimensions(const shared_ptr<XdmfArray> dimensions);
 
@@ -271,7 +271,7 @@ public:
    * @skipline #//setGeometry
    * @until #//setGeometry
    *
-   * @param	geometry	an XdmfGeometry to associate with this grid.
+   * @param	geometry	An XdmfGeometry to associate with this grid.
    */
   void setGeometry(const shared_ptr<XdmfGeometry> geometry);
 

XdmfDomain.hpp

@@ -64,7 +64,7 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @return constructed XdmfDomain.
+   * @return	Constructed XdmfDomain.
    */
   static shared_ptr<XdmfDomain> New();
 

XdmfGeometry.hpp

@@ -60,7 +60,7 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @return	constructed XdmfGeometry.
+   * @return	Constructed XdmfGeometry.
    */
   static shared_ptr<XdmfGeometry> New();
 
@@ -142,7 +142,7 @@ public:
    * @skipline #//setType
    * @until #//setType
    *
-   * @param	type	the XdmfGeometryType to set.
+   * @param	type	The XdmfGeometryType to set.
    */
   void setType(const shared_ptr<const XdmfGeometryType> type);
 

XdmfGeometryType.hpp

@@ -88,7 +88,7 @@ public:
    * @skipline #//getDimensions
    * @until #//getDimensions
    *
-   * @return	an int containing number of dimensions.
+   * @return	An int containing number of dimensions.
    */
   virtual unsigned int getDimensions() const;
 
@@ -109,7 +109,7 @@ public:
    * @skipline #//getName
    * @until #//getName
    *
-   * @return	the name of this geometry type.
+   * @return	The name of this geometry type.
    */
   std::string getName() const;
 

XdmfGraph.hpp

@@ -60,7 +60,7 @@ public:
    *
    * @param numberNodes number of nodes in graph.
    *
-   * @return	constructed XdmfGraph.
+   * @return	Constructed XdmfGraph.
    */
   static shared_ptr<XdmfGraph> New(const unsigned int numberNodes);
 

XdmfGrid.hpp

@@ -84,7 +84,7 @@ public:
    * @skipline #//getGeometry
    * @until #//getGeometry
    *
-   * @return	the geometry associated with this grid.
+   * @return	The geometry associated with this grid.
    */
   shared_ptr<const XdmfGeometry> getGeometry() const;
 
@@ -117,7 +117,7 @@ public:
    * @skipline #//getName
    * @until #//getName
    *
-   * @return	the name of the grid.
+   * @return	The name of the grid.
    */
   std::string getName() const;
 
@@ -146,7 +146,7 @@ public:
    * @skipline #//getTime
    * @until #//getTime
    *
-   * @return	pointer to the XdmfTime attached to this grid. If no
+   * @return	Pointer to the XdmfTime attached to this grid. If no
    * 		XdmfTime is attached, return a NULL pointer.
    */
   shared_ptr<XdmfTime> getTime();
@@ -168,7 +168,7 @@ public:
    *
    * Python: Python doesn't have a constant version
    * 
-   * @return	pointer to the XdmfTime attached to this grid. If no
+   * @return	Pointer to the XdmfTime attached to this grid. If no
    * 		XdmfTime is attached, return a NULL pointer.
    */
   shared_ptr<const XdmfTime> getTime() const;
@@ -194,7 +194,7 @@ public:
    * @skipline #//getTopology
    * @until #//getTopology
    *
-   * @return	the topology associated with this grid.
+   * @return	The topology associated with this grid.
    */
   shared_ptr<const XdmfTopology> getTopology() const;
 
@@ -221,7 +221,7 @@ public:
    * @skipline #//setName
    * @until #//setName
    *
-   * @param	name	name of the grid to set.
+   * @param	name	Name of the grid to set.
    */
   void setName(const std::string & name);
 
@@ -246,7 +246,7 @@ public:
    * @skipline #//setTime
    * @until #//setTime
    *
-   * @param	time	an XdmfTime to associate with this grid.
+   * @param	time	An XdmfTime to associate with this grid.
    */
   void setTime(const shared_ptr<XdmfTime> time);
 

XdmfGridCollection.hpp

@@ -65,7 +65,7 @@ public:
    * @skipline #//initalization
    * @until #//initalization
    *
-   * @return	constructed XdmfGridCollection.
+   * @return	Constructed XdmfGridCollection.
    */
   static shared_ptr<XdmfGridCollection> New();
 
@@ -127,7 +127,7 @@ public:
    * @skipline #//insert
    * @until #//insert
    *
-   * @param	information	an XdmfInformation to attach to this item.
+   * @param	information	An XdmfInformation to attach to this item.
    */
   void insert(const shared_ptr<XdmfInformation> information);
 
@@ -153,7 +153,7 @@ public:
    * @skipline #//setType
    * @until #//setType
    *
-   * @param	type	the XdmfGridCollectionType to set.
+   * @param	type	The XdmfGridCollectionType to set.
    */
   void setType(const shared_ptr<const XdmfGridCollectionType> type);
 

XdmfItemFactory.hpp

@@ -56,7 +56,7 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @return	constructed XdmfItemFactory.
+   * @return	Constructed XdmfItemFactory.
    */
   static shared_ptr<XdmfItemFactory> New();
 

XdmfMap.hpp

@@ -79,7 +79,7 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @return 	constructed XdmfMap.
+   * @return 	Constructed XdmfMap.
    */
   static shared_ptr<XdmfMap> New();
 
@@ -102,11 +102,12 @@ public:
    * @skipline #//initializationnode
    * @until #//initializationnode
    *
-   * @param 	globalNodeIds 	a vector of attributes containing globalNodeId
+   * @param 	globalNodeIds 	A vector of attributes containing globalNodeId
    *                            values for each partition to be mapped.
    *
-   * @return constructed XdmfMaps for each partition. The size of the vector
-   *         will be the same as the globalNodeIds vector.
+   * @return 			Constructed XdmfMaps for each partition. The
+   *				size of the vector will be the same as the
+   *				globalNodeIds vector.
    */
   static std::vector<shared_ptr<XdmfMap> >
   New(const std::vector<shared_ptr<XdmfAttribute> > & globalNodeIds);
@@ -139,7 +140,7 @@ public:
    * @skipline #//getMap
    * @until #//getMap
    *
-   * @return 	stored boundary communicator map.
+   * @return 	Stored boundary communicator map.
    */
   std::map<task_id, node_id_map> getMap() const;
 
@@ -168,7 +169,7 @@ public:
    * @skipline #//getName
    * @until #//getName
    *
-   * @return 	name of boundary communicator map.
+   * @return	Name of boundary communicator map.
    */
   std::string getName() const;
 
@@ -194,10 +195,10 @@ public:
    * @skipline #//getRemoteNodeIds
    * @until #//getRemoteNodeIds
    *
-   * @param	remoteTaskId 	 task id to retrieve mapping for.
+   * @param	remoteTaskId 	Task id to retrieve mapping for.
    *
-   * @return	a map of local node ids to a vector of remote node ids on
-   *	 	remoteTaskId.
+   * @return			A map of local node ids to a vector of
+   *				remote node ids on remoteTaskId.
    */
   node_id_map getRemoteNodeIds(const task_id remoteTaskId);
 
@@ -228,8 +229,8 @@ public:
    *
    * @param 	remoteTaskId 		task id where the remoteLoalNodeId is
    *					located.
-   * @param 	localNodeId		the node id of the node being mapped.
-   * @param 	remoteLocalNodeId	a node id on the remoteTaskId that the
+   * @param 	localNodeId		The node id of the node being mapped.
+   * @param 	remoteLocalNodeId	A node id on the remoteTaskId that the
    *					localNodeId is mapped to.
    */
   void insert(const task_id  remoteTaskId,
@@ -329,11 +330,11 @@ public:
    * @skipline #//setHeavyDataController
    * @until #//setHeavyDataController
    *
-   * @param	remoteTaskIdsControllers	a vector of XdmfHeavyDataControllers 
+   * @param	remoteTaskIdsControllers	A vector of XdmfHeavyDataControllers 
    *						to the remote task ids dataset.
-   * @param	localNodeIdsControllers		a vector of XdmfHeavyDataControllers
+   * @param	localNodeIdsControllers		A vector of XdmfHeavyDataControllers
    *						to the local node ids dataset.
-   * @param	remoteLocalNodeIdsControllers	a vector of XdmfHeavyDataControllers
+   * @param	remoteLocalNodeIdsControllers	A vector of XdmfHeavyDataControllers
    *						to the remote local node ids dataset.
    */
   void
@@ -362,7 +363,7 @@ public:
    * @skipline #//setMap
    * @until #//setMap
    *
-   * @param	map	the boundary communicator map to store.
+   * @param	map	The boundary communicator map to store.
    */
   void setMap(std::map<task_id, node_id_map> map);
 
@@ -387,7 +388,7 @@ public:
    * @skipline #//setName
    * @until #//setName
    *
-   * @param	name	the name of the boundary communicator map to set.
+   * @param	name	The name of the boundary communicator map to set.
    */
   void setName(const std::string & name);
 

XdmfReader.hpp

@@ -57,7 +57,7 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @return	constructed XdmfReader.
+   * @return	Constructed XdmfReader.
    */
   static shared_ptr<XdmfReader> New();
 

XdmfRectilinearGrid.hpp

@@ -68,10 +68,10 @@ public:
    * @skipline #//initialization2
    * @until #//initialization2
    *
-   * @param 	xCoordinates 	the coordinates of points along the x axis
-   * @param 	yCoordinates 	the coordinates of points along the y axis.
+   * @param 	xCoordinates 	The coordinates of points along the x axis
+   * @param 	yCoordinates 	The coordinates of points along the y axis.
    *
-   * @return 			constructed rectilinear grid.
+   * @return 			Constructed rectilinear grid.
    */
   static shared_ptr<XdmfRectilinearGrid>
   New(const shared_ptr<XdmfArray> xCoordinates,
@@ -98,11 +98,11 @@ public:
    * @skipline #//initialization3
    * @until #//initialization3
    *
-   * @param 	xCoordinates 	the coordinates of points along the x axis
-   * @param 	yCoordinates 	the coordinates of points along the y axis.
-   * @param 	zCoordinates 	the coordinates of points along the z axis.
+   * @param 	xCoordinates 	The coordinates of points along the x axis
+   * @param 	yCoordinates 	The coordinates of points along the y axis.
+   * @param 	zCoordinates 	The coordinates of points along the z axis.
    *
-   * @return 			constructed rectilinear grid.
+   * @return 			Constructed rectilinear grid.
    */
   static shared_ptr<XdmfRectilinearGrid>
   New(const shared_ptr<XdmfArray> xCoordinates,
@@ -130,9 +130,9 @@ public:
    * @skipline #//initializationvector
    * @until #//initializationvector
    *
-   * @param 	axesCoordinates 	the coordinates of points along each axis.
+   * @param 	axesCoordinates 	The coordinates of points along each axis.
    *
-   * @return 				constructed rectilinear grid.
+   * @return 				Constructed rectilinear grid.
    */
   static shared_ptr<XdmfRectilinearGrid>
   New(const std::vector<shared_ptr<XdmfArray> > & axesCoordinates);
@@ -167,11 +167,11 @@ public:
    * @skipline #//getCoodinatessingle
    * @until #//getCoodinatessingle
    *
-   * @param 	axisIndex 	the index of the axis to retrieve, (i.e. 0 for
+   * @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
+   * @return 			Array of coordinates along requested axis
    */
   shared_ptr<XdmfArray> getCoordinates(const unsigned int axisIndex);
 
@@ -193,11 +193,11 @@ public:
    *
    * Python: does not support a constant version of this function
    *
-   * @param 	axisIndex 	the index of the axis to retrieve (i.e. 0 for
+   * @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
+   * @return 			Array of coordinates along requeste axis
    */
   shared_ptr<const XdmfArray>
   getCoordinates(const unsigned int axisIndex) const;
@@ -227,7 +227,7 @@ public:
    * @skipline #//getCoodinatesvector
    * @until #//getCoodinatesvector
    *
-   * @return 	vector containing an array of coordinates along each
+   * @return 	Vector containing an array of coordinates along each
    * 		direction.
    */
   std::vector<shared_ptr<XdmfArray> > getCoordinates();
@@ -249,7 +249,7 @@ public:
    *
    * Python: does not support a constant version of this function
    *
-   * @return 	vector containing an array of coordinates along each
+   * @return 	Vector containing an array of coordinates along each
    * 		direction.
    */
   const std::vector<shared_ptr<XdmfArray> > getCoordinates() const;
@@ -331,9 +331,9 @@ public:
    * @skipline #//setCoordinatessingle
    * @until #//setCoordinatessingle
    *
-   * @param 	axisIndex 		the index of the axis to set
+   * @param 	axisIndex 		The index of the axis to set
    *					(i.e. 0 for x-axis).
-   * @param 	axisCoordinates 	the coordinates of points along
+   * @param 	axisCoordinates 	The coordinates of points along
    *					a single axis to set.
    */
   void setCoordinates(const unsigned int axisIndex,
@@ -364,7 +364,7 @@ public:
    * @skipline #//setCoordinatesvector
    * @until #//setCoordinatesvector
    *
-   * @param 	axesCoordinates 	the coordinates of points
+   * @param 	axesCoordinates 	The coordinates of points
    * 					along each axis.
    */
   void

XdmfRegularGrid.hpp

@@ -68,14 +68,14 @@ public:
    * @skipline #//initialization2
    * @until #//initialization2
    *
-   * @param 	xBrickSize 	the size of the brick in the x direction.
-   * @param 	yBrickSize 	the size of the brick in the y direction.
-   * @param 	xNumPoints 	the number of points in the x direction.
-   * @param 	yNumPoints 	the number of points in the y direction.
-   * @param 	xOrigin 	the x coordinate of the origin.
-   * @param 	yOrigin 	the y coordinate of the origin.
-   *
-   * @return 			constructed structured grid.
+   * @param 	xBrickSize 	The size of the brick in the x direction.
+   * @param 	yBrickSize 	The size of the brick in the y direction.
+   * @param 	xNumPoints 	The number of points in the x direction.
+   * @param 	yNumPoints 	The number of points in the y direction.
+   * @param 	xOrigin 	The x coordinate of the origin.
+   * @param 	yOrigin 	The y coordinate of the origin.
+   *
+   * @return 			Constructed structured grid.
    */
   static shared_ptr<XdmfRegularGrid> New(const double xBrickSize,
                                          const double yBrickSize,
@@ -105,17 +105,17 @@ public:
    * @skipline #//initialization3
    * @until #//initialization3
    *
-   * @param 	xBrickSize 	the size of the brick in the x direction.
-   * @param 	yBrickSize 	the size of the brick in the y direction.
-   * @param 	zBrickSize 	the size of the brick in the z direction.
-   * @param 	xNumPoints 	the number of points in the x direction.
-   * @param 	yNumPoints 	the number of points in the y direction.
-   * @param 	zNumPoints 	the number of points in the z direction.
-   * @param 	xOrigin 	the x coordinate of the origin.
-   * @param 	yOrigin 	the y coordinate of the origin.
-   * @param 	zOrigin 	the z coordinate of the origin.
-   *
-   * @return 			constructed structured grid.
+   * @param 	xBrickSize 	The size of the brick in the x direction.
+   * @param 	yBrickSize 	The size of the brick in the y direction.
+   * @param 	zBrickSize 	The size of the brick in the z direction.
+   * @param 	xNumPoints 	The number of points in the x direction.
+   * @param 	yNumPoints 	The number of points in the y direction.
+   * @param 	zNumPoints 	The number of points in the z direction.
+   * @param 	xOrigin 	The x coordinate of the origin.
+   * @param 	yOrigin 	The y coordinate of the origin.
+   * @param 	zOrigin 	The z coordinate of the origin.
+   *
+   * @return 			Constructed structured grid.
    */
   static shared_ptr<XdmfRegularGrid> New(const double xBrickSize,
                                          const double yBrickSize,
@@ -144,11 +144,11 @@ public:
    * @skipline #//initializationvector
    * @until #//initializationvector
    *
-   * @param 	brickSize 	the size of the brick in each direction.
-   * @param 	numPoints 	the number of points in each direction.
-   * @param 	origin 		the coordinates of the origin.
+   * @param 	brickSize 	The size of the brick in each direction.
+   * @param 	numPoints 	The number of points in each direction.
+   * @param 	origin 		The coordinates of the origin.
    *
-   * @return 			constructed structured grid.
+   * @return 			Constructed structured grid.
    */
   static shared_ptr<XdmfRegularGrid>
   New(const shared_ptr<XdmfArray> brickSize,
@@ -335,7 +335,7 @@ public:
    * @skipline #//setBrickSize
    * @until #//setBrickSize
    *
-   * @param 	brickSize 	the sizes of the points composing the mesh. This
+   * @param 	brickSize 	The sizes of the points composing the mesh. This
    * 				should have the same number of terms as the
    *				dimensionality of the mesh.
    */
@@ -388,7 +388,7 @@ public:
    * @skipline #//setOrigin
    * @until #//setOrigin
    *
-   * @param 	origin 	location of the origin of the grid.  This should
+   * @param 	origin 	Location of the origin of the grid.  This should
    * 			have the same number of terms as the dimensionality
    *			of the mesh.
    */

XdmfSet.hpp

@@ -65,7 +65,7 @@ public:
    * @skipline #//initialize
    * @until #//initialize
    *
-   * @return 	constructed XdmfSet.
+   * @return 	Constructed XdmfSet.
    */
   static shared_ptr<XdmfSet> New();
 
@@ -104,7 +104,7 @@ public:
    * @skipline #//getName
    * @until #//getName
    *
-   * @return 	a string containing the name of the set.
+   * @return	A string containing the name of the set.
    */
   std::string getName() const;
 
@@ -164,7 +164,7 @@ public:
    * @skipline #//setName
    * @until #//setName
    *
-   * @param 	name 	a string containing the name to set.
+   * @param 	name	A string containing the name to set.
    */
   void setName(const std::string & name);
 
@@ -189,7 +189,7 @@ public:
    * @skipline //#setType
    * @until //#setType
    *
-   * @param 	type 	the XdmfSetType to set.
+   * @param	type	The XdmfSetType to set.
    */
   void setType(const shared_ptr<const XdmfSetType> type);
 

XdmfSetType.hpp

@@ -67,7 +67,7 @@ protected:
    * accessed through more specific static methods that construct
    * XdmfSetTypes - i.e. XdmfSetType::Node().
    *
-   * @param name a std::string containing the name of the XdmfSetType.
+   * @param	name	A std::string containing the name of the XdmfSetType.
    */
   XdmfSetType(const std::string & name);
 

XdmfTime.hpp

@@ -54,8 +54,8 @@ public:
    * @skipline #//initialization
    * @until #//initialization
    *
-   * @param 	value 	the timeValue of the XdmfTime to create.
-   * @return 		the new XdmfTime.
+   * @param 	value 	The timeValue of the XdmfTime to create.
+   * @return 		The new XdmfTime.
    */
   static shared_ptr<XdmfTime> New(const double & value = 0);
 
@@ -89,7 +89,7 @@ public:
    * @skipline #//getValue
    * @until #//getValue
    *
-   * @return 	a double containing the time value.
+   * @return 	A double containing the time value.
    */
   double getValue() const;
 
@@ -114,7 +114,7 @@ public:
    * @skipline #//setValue
    * @until #//setValue