ENH: Add XdmfGridCollection and begin adding XdmfPartitioner.

CMake/FindMetis.cmake

+# - Try to find the Metis graph partitioning library
+# Once done this will define
+#
+#  METIS_FOUND - System has metis
+#  METIS_INCLUDE_DIR - The metis include directory
+#  METIS_LIBRARIES - The libraries needed to use metis
+
+FIND_PATH(METIS_INCLUDE_DIR NAMES metis.h)
+
+FIND_LIBRARY(METIS_LIBRARIES NAMES metis)
+
+INCLUDE(FindPackageHandleStandardArgs)
+
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Metis DEFAULT_MSG METIS_LIBRARIES METIS_INCLUDE_DIR)
+
+MARK_AS_ADVANCED(METIS_INCLUDE_DIR METIS_LIBRARIES)

CMakeLists.txt

@@ -42,6 +42,8 @@ set(XdmfSources
 	XdmfGeometry
 	XdmfGeometryType
 	XdmfGrid
+	XdmfGridCollection
+	XdmfGridCollectionType
 	XdmfHDF5Controller
 	XdmfHDF5Writer
 	XdmfItem
@@ -70,3 +72,8 @@ if(BUILD_TESTING)
 	include(CTest)
 	add_subdirectory(tests)
 endif(BUILD_TESTING)
+
+option(BUILD_UTILS OFF)
+if(BUILD_UTILS)
+  add_subdirectory(utils)
+endif(BUILD_UTILS)

Xdmf.i

@@ -14,6 +14,8 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 	#include <XdmfGeometry.hpp>
 	#include <XdmfGeometryType.hpp>
 	#include <XdmfGrid.hpp>
+	#include <XdmfGridCollection.hpp>
+	#include <XdmfGridCollectionType.hpp>
 	#include <XdmfHDF5Controller.hpp>
 	#include <XdmfHDF5Writer.hpp>
 	#include <XdmfItem.hpp>
@@ -57,6 +59,7 @@ namespace boost {
 %template(XdmfDomainPtr) boost::shared_ptr<XdmfDomain>;
 %template(XdmfGeometryPtr) boost::shared_ptr<XdmfGeometry>;
 %template(XdmfGridPtr) boost::shared_ptr<XdmfGrid>;
+%template(XdmfGridCollectionPtr) boost::shared_ptr<XdmfGridCollection>;
 %template(XdmfHDF5ControllerPtr) boost::shared_ptr<XdmfHDF5Controller>;
 %template(XdmfHDF5WriterPtr) boost::shared_ptr<XdmfHDF5Writer>;
 %template(XdmfItemPtr) boost::shared_ptr<XdmfItem>;
@@ -91,6 +94,9 @@ SWIG_SHARED_PTR_DERIVED(XdmfGeometry, XdmfItem);
 SWIG_SHARED_PTR_DERIVED(XdmfGeometry, XdmfObject);
 SWIG_SHARED_PTR_DERIVED(XdmfGrid, XdmfItem);
 SWIG_SHARED_PTR_DERIVED(XdmfGrid, XdmfObject);
+SWIG_SHARED_PTR_DERIVED(XdmfGridCollection, XdmfGrid);
+SWIG_SHARED_PTR_DERIVED(XdmfGridCollection, XdmfItem);
+SWIG_SHARED_PTR_DERIVED(XdmfGridCollection, XdmfObject);
 SWIG_SHARED_PTR_DERIVED(XdmfHDF5Controller, XdmfObject);
 SWIG_SHARED_PTR_DERIVED(XdmfHDF5Writer, XdmfVisitor);
 SWIG_SHARED_PTR_DERIVED(XdmfHDF5Writer, Loki::BaseVisitor);
@@ -134,6 +140,9 @@ SWIG_SHARED_PTR_DERIVED(XdmfWriter, XdmfObject);
 %include XdmfTopology.hpp
 %include XdmfTopologyType.hpp
 
+%include XdmfGridCollection.hpp
+%include XdmfGridCollectionType.hpp
+
 // Provide accessors from python lists to XdmfArrays
 %extend XdmfArray {
 	void copyValueAsChar(int index, char value) {

XdmfArray.hpp

@@ -8,7 +8,6 @@ class XdmfHDF5Controller;
 #include "XdmfItem.hpp"
 #include <boost/shared_array.hpp>
 #include <boost/variant.hpp>
-#include <vector>
 
 /**
  * @brief Provides a single interface for storing a wide variety of data types.
@@ -46,6 +45,7 @@ class XdmfHDF5Controller;
  * 	Unsigned Int
  */
 class XdmfArray : public XdmfItem {
+
 public:
 
 	XdmfNewMacro(XdmfArray);

XdmfAttributeCenter.hpp

@@ -2,7 +2,6 @@
 #define XDMFATTRIBUTECENTER_HPP_
 
 // Includes
-#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfAttributeType.hpp

@@ -2,7 +2,6 @@
 #define XDMFATTRIBUTETYPE_HPP_
 
 // Includes
-#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfDomain.cpp

@@ -69,6 +69,15 @@ void XdmfDomain::populateItem(const std::map<std::string, std::string> & itemPro
 	}
 }
 
+void XdmfDomain::removeGrid(const unsigned int index)
+{
+	if(index >= mGrids.size())
+	{
+		assert(false);
+	}
+	mGrids.erase(mGrids.begin() + index);
+}
+
 void XdmfDomain::traverse(boost::shared_ptr<Loki::BaseVisitor> visitor)
 {
 	for(std::vector<boost::shared_ptr<XdmfGrid> >::const_iterator iter = mGrids.begin(); iter != mGrids.end(); ++iter)

XdmfDomain.hpp

@@ -5,7 +5,6 @@
 class XdmfGrid;
 
 // Includes
-#include <vector>
 #include "XdmfItem.hpp"
 
 /**
@@ -56,6 +55,13 @@ public:
 	 */
 	void insert(boost::shared_ptr<XdmfGrid> grid);
 
+	/**
+	 * Remove an XdmfGrid from the domain.
+	 *
+	 * @param index of the XdmfGrid to remove.
+	 */
+	void removeGrid(const unsigned int index);
+
 	virtual void traverse(boost::shared_ptr<Loki::BaseVisitor> visitor);
 
 protected:

XdmfGeometryType.cpp

@@ -5,7 +5,6 @@
  *      Author: kleiter
  */
 
-#include <map>
 #include "XdmfGeometryType.hpp"
 
 // Supported XdmfGeometryTypes

XdmfGeometryType.hpp

@@ -2,7 +2,6 @@
 #define XDMFGEOMETRYTYPE_HPP_
 
 // Includes
-#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfGrid.cpp

@@ -140,7 +140,7 @@ void XdmfGrid::populateItem(const std::map<std::string, std::string> & itemPrope
 		{
 			mGeometry = geometry;
 		}
-		if(boost::shared_ptr<XdmfSet> set = boost::shared_dynamic_cast<XdmfSet>(*iter))
+		else if(boost::shared_ptr<XdmfSet> set = boost::shared_dynamic_cast<XdmfSet>(*iter))
 		{
 			this->insert(set);
 		}
@@ -148,6 +148,10 @@ void XdmfGrid::populateItem(const std::map<std::string, std::string> & itemPrope
 		{
 			mTopology = topology;
 		}
+		else
+		{
+			assert(false);
+		}
 	}
 }
 

XdmfGrid.hpp

@@ -9,7 +9,6 @@ class XdmfTopology;
 
 // Includes
 #include "XdmfItem.hpp"
-#include <vector>
 
 /**
  * @brief A mesh that consists of elements, points, and values attached to the mesh.
@@ -169,6 +168,8 @@ protected:
 	virtual ~XdmfGrid();
 	virtual void populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems);
 
+	std::string mName;
+
 private:
 
 	XdmfGrid(const XdmfGrid & grid);  // Not implemented.
@@ -178,7 +179,6 @@ private:
 	boost::shared_ptr<XdmfGeometry> mGeometry;
 	std::vector<boost::shared_ptr<XdmfSet> > mSets;
 	boost::shared_ptr<XdmfTopology> mTopology;
-	std::string mName;
 };
 
 #endif /* XDMFGRID_HPP_ */

XdmfGridCollection.cpp

+/*
+ * XdmfGridCollection.cpp
+ *
+ *  Created on: Jan 25, 2010
+ *      Author: kleiter
+ */
+
+#include "XdmfGridCollection.hpp"
+
+XdmfGridCollection::XdmfGridCollection() :
+	mCollectionType(XdmfGridCollectionType::NoCollectionType())
+{
+	mName = "Collection";
+	std::cout << "Created Collection " << this << std::endl;
+}
+
+XdmfGridCollection::~XdmfGridCollection()
+{
+  std::cout << "Deleted Collection " << this << std::endl;
+}
+
+std::string XdmfGridCollection::ItemTag = "Grid";
+
+boost::shared_ptr<XdmfGrid> XdmfGridCollection::getGrid(unsigned int index)
+{
+	if(index >= mGrids.size())
+	{
+		assert(false);
+	}
+	return mGrids[index];
+}
+
+boost::shared_ptr<const XdmfGrid> XdmfGridCollection::getGrid(unsigned int index) const
+{
+	if(index >= mGrids.size())
+	{
+		assert(false);
+	}
+	return mGrids[index];
+}
+
+XdmfGridCollectionType XdmfGridCollection::getGridCollectionType() const
+{
+	return mCollectionType;
+}
+
+std::map<std::string, std::string> XdmfGridCollection::getItemProperties() const
+{
+	std::map<std::string, std::string> collectionProperties;
+	collectionProperties["Name"] = mName;
+	collectionProperties["GridType"] = "Collection";
+	mCollectionType.getProperties(collectionProperties);
+	return collectionProperties;
+}
+
+unsigned int XdmfGridCollection::getNumberOfGrids() const
+{
+	return mGrids.size();
+}
+
+void XdmfGridCollection::insert(boost::shared_ptr<XdmfGrid> grid)
+{
+	mGrids.push_back(grid);
+}
+
+void XdmfGridCollection::populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems)
+{
+	for(std::vector<boost::shared_ptr<XdmfItem> >::const_iterator iter = childItems.begin(); iter != childItems.end(); ++iter)
+	{
+		if(boost::shared_ptr<XdmfGrid> grid = boost::shared_dynamic_cast<XdmfGrid>(*iter))
+		{
+			this->insert(grid);
+		}
+		else
+		{
+			assert(false);
+		}
+	}
+	XdmfGrid::populateItem(itemProperties, childItems);
+}
+
+void XdmfGridCollection::removeGrid(const unsigned int index)
+{
+	if(index >= mGrids.size())
+	{
+		assert(false);
+	}
+	mGrids.erase(mGrids.begin() + index);
+}
+
+void XdmfGridCollection::setGridCollectionType(const XdmfGridCollectionType & collectionType)
+{
+	mCollectionType = collectionType;
+}
+
+void XdmfGridCollection::traverse(boost::shared_ptr<Loki::BaseVisitor> visitor)
+{
+	for(std::vector<boost::shared_ptr<XdmfGrid> >::const_iterator iter = mGrids.begin(); iter != mGrids.end(); ++iter)
+	{
+		(*iter)->accept(visitor);
+	}
+}

XdmfGridCollection.hpp

+#ifndef XDMFGRIDCOLLECTION_HPP_
+#define XDMFGRIDCOLLECTION_HPP_
+
+// Includes
+#include "XdmfGrid.hpp"
+#include "XdmfGridCollectionType.hpp"
+
+/**
+ * @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.
+ *
+ * It is valid to nest collections.  A spatial collection within a temporal collection is commonly used.
+ */
+class XdmfGridCollection : public XdmfGrid {
+
+public:
+
+	XdmfNewMacro(XdmfGridCollection);
+	LOKI_DEFINE_VISITABLE(XdmfGridCollection, XdmfGrid)
+	static std::string ItemTag;
+
+	/**
+	 * Get a grid from this collection.
+	 *
+	 * @param index of grid to retrieve.
+	 * @return the requested XdmfGrid.
+	 */
+	boost::shared_ptr<XdmfGrid> getGrid(unsigned int index);
+
+	/**
+	 * Get a grid from this collection (const version).
+	 *
+	 * @param index of the grid to retrieve.
+	 * @return the requested XdmfGrid.
+	 */
+	boost::shared_ptr<const XdmfGrid> getGrid(unsigned int index) const;
+
+	/**
+	 * Get the XdmfGridCollectionType associated with this grid collection.
+	 *
+	 * @return XdmfGridCollectionType of this collection.
+	 */
+	XdmfGridCollectionType getGridCollectionType() const;
+
+	std::map<std::string, std::string> getItemProperties() const;
+
+	/**
+	 * Get the number of grids in this collection.
+	 *
+	 * @return unsigned int containing the number of XdmfGrids in this collection.
+	 */
+	unsigned int getNumberOfGrids() const;
+
+	/**
+	 * Insert a grid into this collection.
+	 *
+	 * @param grid an XdmfGrid to insert into this collection.
+	 */
+	void insert(boost::shared_ptr<XdmfGrid> grid);
+
+	/**
+	 * Remove a grid from this collection.
+	 *
+	 * @param index of the XdmfGrid to remove.
+	 */
+	void removeGrid(const unsigned int index);
+
+	/**
+	 * Set the XdmfGridCollectionType associated with this grid collection.
+	 *
+	 * @param collectionType the XdmfGridCollectionType to set.
+	 */
+	void setGridCollectionType(const XdmfGridCollectionType & collectionType);
+
+	virtual void traverse(boost::shared_ptr<Loki::BaseVisitor> visitor);
+
+protected:
+
+	XdmfGridCollection();
+	virtual ~XdmfGridCollection();
+	virtual void populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems);
+
+private:
+
+	XdmfGridCollection(const XdmfGridCollection & collection);  // Not implemented.
+	void operator=(const XdmfGridCollection & collection);  // Not implemented.
+
+	XdmfGridCollectionType mCollectionType;
+	std::vector<boost::shared_ptr<XdmfGrid> > mGrids;
+};
+
+#endif /* XDMFGRID_HPP_ */

XdmfGridCollectionType.cpp

+/*
+ * XdmfGridCollectionType.cpp
+ *
+ *  Created on: Jan 29, 2010
+ *      Author: kleiter
+ */
+
+#include "XdmfGridCollectionType.hpp"
+
+// Supported XdmfGridCollectionTypes
+XdmfGridCollectionType XdmfGridCollectionType::NoCollectionType()
+{
+	return XdmfGridCollectionType("None");
+}
+
+XdmfGridCollectionType XdmfGridCollectionType::Spatial()
+{
+	return XdmfGridCollectionType("Spatial");
+}
+
+XdmfGridCollectionType XdmfGridCollectionType::Temporal()
+{
+	return XdmfGridCollectionType("Temporal");
+}
+
+XdmfGridCollectionType::XdmfGridCollectionType(const std::string & name) :
+	mName(name)
+{
+}
+
+XdmfGridCollectionType::XdmfGridCollectionType(const XdmfGridCollectionType & collectionType):
+	mName(collectionType.mName)
+{
+}
+
+XdmfGridCollectionType XdmfGridCollectionType::New(const std::map<std::string, std::string> & itemProperties)
+{
+	std::map<std::string, std::string>::const_iterator type = itemProperties.find("CollectionType");
+	if(type != itemProperties.end())
+	{
+		const std::string typeVal = type->second;
+		if(typeVal.compare("None") == 0)
+		{
+			return NoCollectionType();
+		}
+		else if(typeVal.compare("Spatial") == 0)
+		{
+			return Spatial();
+		}
+		else if(typeVal.compare("Temporal") == 0)
+		{
+			return Temporal();
+		}
+		else
+		{
+			assert(false);
+		}
+	}
+	assert(false);
+}
+
+XdmfGridCollectionType & XdmfGridCollectionType::operator=(const XdmfGridCollectionType & collectionType)
+{
+	if(this != &collectionType)
+	{
+		mName = collectionType.mName;
+	}
+	return *this;
+}
+
+bool XdmfGridCollectionType::operator==(const XdmfGridCollectionType & collectionType) const
+{
+	return mName.compare(collectionType.mName) == 0;
+}
+
+bool XdmfGridCollectionType::operator!=(const XdmfGridCollectionType & collectionType) const
+{
+	return !this->operator==(collectionType);
+}
+
+void XdmfGridCollectionType::getProperties(std::map<std::string, std::string> & collectedProperties) const
+{
+	collectedProperties["CollectionType"] = mName;
+}

XdmfGridCollectionType.hpp

+#ifndef XDMFGRIDCOLLECTIONTYPE_HPP_
+#define XDMFGRIDCOLLECTIONTYPE_HPP_
+
+// Includes
+#include "XdmfItemProperty.hpp"
+
+/**
+ * @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().
+ *
+ * Xdmf supports the following collection types:
+ * 	NoCollectionType
+ * 	Spatial
+ * 	Temporal
+ */
+class XdmfGridCollectionType : public XdmfItemProperty {
+
+public:
+
+	friend class XdmfGridCollection;
+
+	// Supported XdmfGridCollectionTypes
+	static XdmfGridCollectionType NoCollectionType();
+	static XdmfGridCollectionType Spatial();
+	static XdmfGridCollectionType Temporal();
+
+	void getProperties(std::map<std::string, std::string> & collectedProperties) const;
+
+	/*
+	 * Compare two XdmfGridCollectionTypes for equality.
+	 *
+	 * @param collectionType an XdmfGridCollectionType to compare equality to.
+	 * @return true if the XdmfGridCollectionTypes are equal.
+	 */
+	bool operator==(const XdmfGridCollectionType & collectionype) const;
+
+	/**
+	 * Compare two XdmfGridCollectionTypes for inequality.
+	 *
+	 * @param collectionType an XdmfGridCollectionType to compare inequality to.
+	 * @return true if the XdmfGridCollectionTypes are not equal.
+	 */
+	bool operator!=(const XdmfGridCollectionType & collectionType) const;
+
+	XdmfGridCollectionType(const XdmfGridCollectionType & collectionType);
+	XdmfGridCollectionType & operator=(const XdmfGridCollectionType & collectionType);
+
+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().
+	 *
+	 * @param name the name of the XdmfGridCollectionType to construct.
+	 */
+	XdmfGridCollectionType(const std::string & name);
+
+private:
+
+	static XdmfGridCollectionType New(const std::map<std::string, std::string> & itemProperties);
+
+	std::string mName;
+};
+
+#endif /* XDMFGRIDCOLLECTIONTYPE_HPP_ */

XdmfHDF5Controller.cpp

@@ -3,7 +3,6 @@
 
 #include <hdf5.h>
 #include <sstream>
-#include <vector>
 #include "XdmfArray.hpp"
 #include "XdmfHDF5Controller.hpp"
 

XdmfHDF5Controller.hpp

@@ -5,7 +5,6 @@
 class XdmfArray;
 
 // Includes
-#include <string>
 #include "XdmfObject.hpp"
 
 /**

XdmfItem.hpp

@@ -57,7 +57,7 @@ protected:
 	virtual ~XdmfItem();
 
 	/**
-	 * Populates an item using a map of key/value property pairs and a vector of its child items.  This is intended to be used to
+	 * Populates an item using a map of key/value property pairs and a vector of its child items.  This is used to
 	 * support generic reading of XdmfItems from disk.
 	 *
 	 * @param itemProperties a map of key/value properties associated with this XdmfItem.

XdmfReader.cpp

@@ -11,7 +11,6 @@
 
 
 #include <libxml/xmlreader.h>
-#include <map>
 #include "XdmfReader.hpp"
 
 /**

XdmfSet.hpp

@@ -9,9 +9,9 @@
  * @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 record a set of nodes along a boundary.  The individual elements making up the
- * set are determined by their id.  An XdmfSet can have XdmfAttributes attached that give extra values
- * attached to the components of the set.
+ * a simulation may want to hold a set of nodes along 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 XdmfSet : public XdmfDataItem {
 

XdmfSetType.hpp

@@ -2,7 +2,6 @@
 #define XDMFSETTYPE_HPP_
 
 // Includes
-#include <string>
 #include "XdmfItemProperty.hpp"
 
 /**

XdmfTopologyType.hpp

@@ -2,7 +2,6 @@
 #define XDMFTOPOLOGYTYPE_HPP_
 
 // Includes
-#include <string>
 #include "XdmfItemProperty.hpp"
 /**
  * @brief Property describing the types of elements stored in an XdmfTopology.

utils/CMakeLists.txt

+option(BUILD_PARTITIONER OFF)