ENH: Add graphs to Xdmf.

Graphs are stored in compressed sparse row format (XdmfSparseMatrix).
Added ability to partition graphs in XdmfPartitioner.
Added tests for new sparse matrix and graph classes.

CMakeLists.txt

@@ -211,6 +211,7 @@ if(NOT XDMF_BUILD_CORE_ONLY)
     XdmfDomain
     XdmfGeometry
     XdmfGeometryType
+    XdmfGraph
     XdmfGrid
     XdmfGridCollection
     XdmfGridCollectionType

Xdmf.i

@@ -25,6 +25,7 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     #include <XdmfItem.hpp>
     #include <XdmfItemProperty.hpp>
     #include <XdmfSharedPtr.hpp>
+    #include <XdmfSparseMatrix.hpp>
     #include <XdmfSystemUtils.hpp>
     #include <XdmfVisitor.hpp>
     #include <XdmfWriter.hpp>
@@ -37,6 +38,7 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     #include <XdmfDomain.hpp>
     #include <XdmfGeometry.hpp>
     #include <XdmfGeometryType.hpp>
+    #include <XdmfGraph.hpp>
     #include <XdmfGrid.hpp>
     #include <XdmfGridCollection.hpp>
     #include <XdmfGridCollectionType.hpp>
@@ -139,6 +141,7 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 %ignore XdmfCurvilinearGrid::ItemTag;
 %ignore XdmfDomain::ItemTag;
 %ignore XdmfGeometry::ItemTag;
+%ignore XdmfGraph::ItemTag;
 %ignore XdmfGrid::ItemTag;
 %ignore XdmfGridCollection::ItemTag;
 %ignore XdmfMap::ItemTag;
@@ -190,6 +193,9 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     else if(shared_ptr<XdmfGeometry> geometry = shared_dynamic_cast<XdmfGeometry>($1)) {
         $result = SWIG_NewPointerObj(SWIG_as_voidptr(new shared_ptr<XdmfGeometry>(geometry)), SWIGTYPE_p_boost__shared_ptrT_XdmfGeometry_t, SWIG_POINTER_OWN);
     }
+    else if(shared_ptr<XdmfGraph> graph = shared_dynamic_cast<XdmfGraph>($1)) {
+        $result = SWIG_NewPointerObj(SWIG_as_voidptr(new shared_ptr<XdmfGraph>(graph)), SWIGTYPE_p_boost__shared_ptrT_XdmfGraph_t, SWIG_POINTER_OWN);
+    }
     else if(shared_ptr<XdmfGridCollection> gridCollection = shared_dynamic_cast<XdmfGridCollection>($1)) {
         $result = SWIG_NewPointerObj(SWIG_as_voidptr(new shared_ptr<XdmfGridCollection>(gridCollection)), SWIGTYPE_p_boost__shared_ptrT_XdmfGridCollection_t, SWIG_POINTER_OWN);
     }
@@ -268,6 +274,7 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 %shared_ptr(XdmfDomain)
 %shared_ptr(XdmfGeometry)
 %shared_ptr(XdmfGeometryType)
+%shared_ptr(XdmfGraph)
 %shared_ptr(XdmfGrid)
 %shared_ptr(XdmfGridCollection)
 %shared_ptr(XdmfGridCollectionType)
@@ -293,6 +300,7 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 %include XdmfDomain.hpp
 %include XdmfGeometry.hpp
 %include XdmfGeometryType.hpp
+%include XdmfGraph.hpp
 %include XdmfGridCollection.hpp
 %include XdmfGridCollectionType.hpp
 %include XdmfItemFactory.hpp

XdmfDomain.cpp

@@ -23,6 +23,7 @@
 
 #include "XdmfDomain.hpp"
 #include "XdmfCurvilinearGrid.hpp"
+#include "XdmfGraph.hpp"
 #include "XdmfGridCollection.hpp"
 #include "XdmfRectilinearGrid.hpp"
 #include "XdmfRegularGrid.hpp"
@@ -36,6 +37,10 @@ XDMF_CHILDREN_IMPLEMENTATION(XdmfDomain,
                              XdmfCurvilinearGrid,
                              CurvilinearGrid,
                              Name)
+XDMF_CHILDREN_IMPLEMENTATION(XdmfDomain,
+                             XdmfGraph,
+                             Graph,
+                             Name)
 XDMF_CHILDREN_IMPLEMENTATION(XdmfDomain,
                              XdmfRectilinearGrid,
                              RectilinearGrid,
@@ -85,7 +90,7 @@ XdmfDomain::populateItem(const std::map<std::string, std::string> & itemProperti
                          const XdmfCoreReader * const reader)
 {
   XdmfItem::populateItem(itemProperties, childItems, reader);
-  for(std::vector<shared_ptr<XdmfItem> >::const_iterator iter = 
+  for(std::vector<shared_ptr<XdmfItem> >::const_iterator iter =
         childItems.begin();
       iter != childItems.end();
       ++iter) {
@@ -97,6 +102,10 @@ XdmfDomain::populateItem(const std::map<std::string, std::string> & itemProperti
             shared_dynamic_cast<XdmfCurvilinearGrid>(*iter)) {
       this->insert(grid);
     }
+    else if(shared_ptr<XdmfGraph> graph =
+            shared_dynamic_cast<XdmfGraph>(*iter)) {
+      this->insert(graph);
+    }
     else if(shared_ptr<XdmfRectilinearGrid> grid =
             shared_dynamic_cast<XdmfRectilinearGrid>(*iter)) {
       this->insert(grid);
@@ -116,31 +125,37 @@ void
 XdmfDomain::traverse(const shared_ptr<XdmfBaseVisitor> visitor)
 {
   XdmfItem::traverse(visitor);
-  for(std::vector<shared_ptr<XdmfGridCollection> >::const_iterator iter = 
+  for(std::vector<shared_ptr<XdmfGridCollection> >::const_iterator iter =
         mGridCollections.begin();
       iter != mGridCollections.end();
       ++iter) {
     (*iter)->accept(visitor);
   }
-  for(std::vector<shared_ptr<XdmfCurvilinearGrid> >::const_iterator iter = 
+  for(std::vector<shared_ptr<XdmfCurvilinearGrid> >::const_iterator iter =
         mCurvilinearGrids.begin();
       iter != mCurvilinearGrids.end();
       ++iter) {
     (*iter)->accept(visitor);
   }
-  for(std::vector<shared_ptr<XdmfRectilinearGrid> >::const_iterator iter = 
+  for(std::vector<shared_ptr<XdmfGraph> >::const_iterator iter =
+        mGraphs.begin();
+      iter != mGraphs.end();
+      ++iter) {
+    (*iter)->accept(visitor);
+  }
+  for(std::vector<shared_ptr<XdmfRectilinearGrid> >::const_iterator iter =
         mRectilinearGrids.begin();
       iter != mRectilinearGrids.end();
       ++iter) {
     (*iter)->accept(visitor);
   }
-  for(std::vector<shared_ptr<XdmfRegularGrid> >::const_iterator iter = 
+  for(std::vector<shared_ptr<XdmfRegularGrid> >::const_iterator iter =
         mRegularGrids.begin();
       iter != mRegularGrids.end();
       ++iter) {
     (*iter)->accept(visitor);
   }
-  for(std::vector<shared_ptr<XdmfUnstructuredGrid> >::const_iterator iter = 
+  for(std::vector<shared_ptr<XdmfUnstructuredGrid> >::const_iterator iter =
         mUnstructuredGrids.begin();
       iter != mUnstructuredGrids.end();
       ++iter) {

XdmfDomain.hpp

@@ -26,6 +26,7 @@
 
 // Forward Declarations
 class XdmfCurvilinearGrid;
+class XdmfGraph;
 class XdmfGridCollection;
 class XdmfRectilinearGrid;
 class XdmfRegularGrid;
@@ -56,8 +57,9 @@ public:
   virtual ~XdmfDomain();
 
   LOKI_DEFINE_VISITABLE(XdmfDomain, XdmfItem);
-  XDMF_CHILDREN(XdmfGridCollection, GridCollection, Name);
   XDMF_CHILDREN(XdmfCurvilinearGrid, CurvilinearGrid, Name);
+  XDMF_CHILDREN(XdmfGraph, Graph, Name);
+  XDMF_CHILDREN(XdmfGridCollection, GridCollection, Name);
   XDMF_CHILDREN(XdmfRectilinearGrid, RectilinearGrid, Name);
   XDMF_CHILDREN(XdmfRegularGrid, RegularGrid, Name);
   XDMF_CHILDREN(XdmfUnstructuredGrid, UnstructuredGrid, Name);

XdmfGraph.cpp

+/*****************************************************************************/
+/*                                    XDMF                                   */
+/*                       eXtensible Data Model and Format                    */
+/*                                                                           */
+/*  Id : XdmfGraph.cpp                                                       */
+/*                                                                           */
+/*  Author:                                                                  */
+/*     Kenneth Leiter                                                        */
+/*     kenneth.leiter@arl.army.mil                                           */
+/*     US Army Research Laboratory                                           */
+/*     Aberdeen Proving Ground, MD                                           */
+/*                                                                           */
+/*     Copyright @ 2011 US Army Research Laboratory                          */
+/*     All Rights Reserved                                                   */
+/*     See Copyright.txt for details                                         */
+/*                                                                           */
+/*     This software is distributed WITHOUT ANY WARRANTY; without            */
+/*     even the implied warranty of MERCHANTABILITY or FITNESS               */
+/*     FOR A PARTICULAR PURPOSE.  See the above copyright notice             */
+/*     for more information.                                                 */
+/*                                                                           */
+/*****************************************************************************/
+
+#include "XdmfAttribute.hpp"
+#include "XdmfGraph.hpp"
+
+XDMF_CHILDREN_IMPLEMENTATION(XdmfGraph, XdmfAttribute, Attribute, Name)
+
+shared_ptr<XdmfGraph>
+XdmfGraph::New(const unsigned int numberNodes)
+{
+  shared_ptr<XdmfGraph> p(new XdmfGraph(numberNodes));
+  return p;
+}
+
+XdmfGraph::XdmfGraph(const unsigned int numberNodes) :
+  XdmfSparseMatrix(numberNodes,
+                   numberNodes)
+{
+}
+
+XdmfGraph::~XdmfGraph()
+{
+}
+
+const std::string XdmfGraph::ItemTag = "Graph";
+
+std::string
+XdmfGraph::getItemTag() const
+{
+  return ItemTag;
+}
+
+unsigned int
+XdmfGraph::getNumberNodes() const
+{
+  return this->getNumberRows();
+}
+
+void
+XdmfGraph::populateItem(const std::map<std::string, std::string> & itemProperties,
+                        const std::vector<shared_ptr<XdmfItem> > & childItems,
+                        const XdmfCoreReader * const reader)
+{
+  XdmfSparseMatrix::populateItem(itemProperties,
+                                 childItems,
+                                 reader);
+  for(std::vector<shared_ptr<XdmfItem> >::const_iterator iter =
+        childItems.begin();
+      iter != childItems.end();
+      ++iter) {
+    if(shared_ptr<XdmfAttribute> attribute =
+       shared_dynamic_cast<XdmfAttribute>(*iter)) {
+      this->insert(attribute);
+    }
+  }
+}
+
+void
+XdmfGraph::traverse(const shared_ptr<XdmfBaseVisitor> visitor)
+{
+  XdmfSparseMatrix::traverse(visitor);
+  for(std::vector<shared_ptr<XdmfAttribute> >::const_iterator iter =
+        mAttributes.begin();
+      iter != mAttributes.end();
+      ++iter) {
+    (*iter)->accept(visitor);
+  }
+}

XdmfGraph.hpp

+/*****************************************************************************/
+/*                                    XDMF                                   */
+/*                       eXtensible Data Model and Format                    */
+/*                                                                           */
+/*  Id : XdmfGraph.hpp                                                       */
+/*                                                                           */
+/*  Author:                                                                  */
+/*     Kenneth Leiter                                                        */
+/*     kenneth.leiter@arl.army.mil                                           */
+/*     US Army Research Laboratory                                           */
+/*     Aberdeen Proving Ground, MD                                           */
+/*                                                                           */
+/*     Copyright @ 2011 US Army Research Laboratory                          */
+/*     All Rights Reserved                                                   */
+/*     See Copyright.txt for details                                         */
+/*                                                                           */
+/*     This software is distributed WITHOUT ANY WARRANTY; without            */
+/*     even the implied warranty of MERCHANTABILITY or FITNESS               */
+/*     FOR A PARTICULAR PURPOSE.  See the above copyright notice             */
+/*     for more information.                                                 */
+/*                                                                           */
+/*****************************************************************************/
+
+#ifndef XDMFGRAPH_HPP_
+#define XDMFGRAPH_HPP_
+
+// Forward Declarations
+class XdmfAttribute;
+
+// Includes
+#include "Xdmf.hpp"
+#include "XdmfSparseMatrix.hpp"
+
+/**
+ * @brief Graph stored in sparse matrix form.
+ *
+ * Stores graph information in sparse matrix form. Attributes defining
+ * node and edge information can be inserted.
+ */
+class XDMF_EXPORT XdmfGraph : public XdmfSparseMatrix {
+
+public:
+
+  /**
+   * Create a new XdmfGraph.
+   *
+   * @param numberNodes number of nodes in graph.
+   *
+   * @return constructed XdmfGraph.
+   */
+  static shared_ptr<XdmfGraph> New(const unsigned int numberNodes);
+
+  virtual ~XdmfGraph();
+
+  LOKI_DEFINE_VISITABLE(XdmfGraph, XdmfSparseMatrix);
+  XDMF_CHILDREN(XdmfAttribute, Attribute, Name);
+  static const std::string ItemTag;
+
+  std::string getItemTag() const;
+
+  unsigned int getNumberNodes() const;
+
+  void traverse(const shared_ptr<XdmfBaseVisitor> visitor);
+
+protected:
+
+  XdmfGraph(const unsigned int numberNodes);
+
+  virtual void
+  populateItem(const std::map<std::string, std::string> & itemProperties,
+               const std::vector<shared_ptr<XdmfItem> > & childItems,
+               const XdmfCoreReader * const reader);
+
+private:
+
+  XdmfGraph(const XdmfGraph &);  // Not implemented.
+  void operator=(const XdmfGraph &);  // Not implemented.
+};
+
+#ifdef _WIN32
+#endif
+
+#endif /* XDMFGRAPH_HPP_ */

XdmfItemFactory.cpp

@@ -28,6 +28,7 @@
 #include "XdmfDomain.hpp"
 #include "XdmfGeometry.hpp"
 #include "XdmfGeometryType.hpp"
+#include "XdmfGraph.hpp"
 #include "XdmfGridCollection.hpp"
 #include "XdmfInformation.hpp"
 #include "XdmfItemFactory.hpp"
@@ -35,6 +36,7 @@
 #include "XdmfRectilinearGrid.hpp"
 #include "XdmfRegularGrid.hpp"
 #include "XdmfSet.hpp"
+#include "XdmfSparseMatrix.hpp"
 #include "XdmfTime.hpp"
 #include "XdmfTopology.hpp"
 #include "XdmfUnstructuredGrid.hpp"
@@ -124,6 +126,9 @@ XdmfItemFactory::createItem(const std::string & itemTag,
     }
     return XdmfGeometry::New();
   }
+  else if(itemTag.compare(XdmfGraph::ItemTag) == 0) {
+    return XdmfGraph::New(0);
+  }
   else if(itemTag.compare(XdmfGrid::ItemTag) == 0) {
     // For backwards compatibility with the old format, this tag can
     // correspond to multiple XdmfItems.
@@ -165,6 +170,9 @@ XdmfItemFactory::createItem(const std::string & itemTag,
   else if(itemTag.compare(XdmfSet::ItemTag) == 0) {
     return XdmfSet::New();
   }
+  else if(itemTag.compare(XdmfSparseMatrix::ItemTag) == 0) {
+    return XdmfSparseMatrix::New(0, 0);
+  }
   else if(itemTag.compare(XdmfTime::ItemTag) == 0) {
     return XdmfTime::New();
   }

core/CMakeLists.txt

@@ -79,6 +79,7 @@ set(XdmfCoreSources
   XdmfInformation
   XdmfItem
   XdmfItemProperty
+  XdmfSparseMatrix
   XdmfSystemUtils
   ${CMAKE_BINARY_DIR}/XdmfVersion
   XdmfVisitor

core/XdmfArray.hpp

@@ -183,6 +183,8 @@ public:
   /**
    * Get a copy of a single value stored in this array.
    *
+   * @param index the index in the array to copy.
+   *
    * @return the requested value.
    */
   template <typename T>
@@ -323,7 +325,7 @@ public:
   template<typename T>
   void insert(const unsigned int startIndex,
               const T * const valuesPointer,
-              const unsigned int numValues = 1,
+              const unsigned int numValues,
               const unsigned int arrayStride = 1,
               const unsigned int valuesStride = 1);
 
@@ -538,7 +540,7 @@ private:
     boost::shared_array<const double>,
     boost::shared_array<const unsigned char>,
     boost::shared_array<const unsigned short>,
-    boost::shared_array<const unsigned int>  > ArrayVariant;
+    boost::shared_array<const unsigned int> > ArrayVariant;
   
   ArrayVariant mArray;
   unsigned int mArrayPointerNumValues;

core/XdmfCore.i

@@ -23,6 +23,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
     #include <XdmfItem.hpp>
     #include <XdmfItemProperty.hpp>
     #include <XdmfSharedPtr.hpp>
+    #include <XdmfSparseMatrix.hpp>
     #include <XdmfSystemUtils.hpp>
     #include <XdmfVersion.hpp>
     #include <XdmfVisitor.hpp>
@@ -45,6 +46,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 // Ignore ItemTags
 %ignore XdmfArray::ItemTag;
 %ignore XdmfInformation::ItemTag;
+%ignore XdmfSparseMatrix::ItemTag;
 
 // Define equality operators
 %extend XdmfItem {
@@ -296,6 +298,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %shared_ptr(XdmfInformation)
 %shared_ptr(XdmfItem)
 %shared_ptr(XdmfItemProperty)
+%shared_ptr(XdmfSparseMatrix)
 %shared_ptr(XdmfVisitor)
 %shared_ptr(XdmfWriter)
 
@@ -317,6 +320,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %include XdmfInformation.hpp
 %include XdmfHDF5Controller.hpp
 %include XdmfHDF5Writer.hpp
+%include XdmfSparseMatrix.hpp
 %include XdmfWriter.hpp
 
 %include CMake/VersionSuite/ProjectVersion.hpp
@@ -395,4 +399,3 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 
 %template(UIntVector) std::vector<unsigned int>;
 %template(ItemVector) std::vector<boost::shared_ptr<XdmfItem> >;
-

core/XdmfSparseMatrix.cpp

+/*****************************************************************************/
+/*                                    XDMF                                   */
+/*                       eXtensible Data Model and Format                    */
+/*                                                                           */
+/*  Id : XdmfSparseMatrix.cpp                                                */
+/*                                                                           */
+/*  Author:                                                                  */
+/*     Kenneth Leiter                                                        */
+/*     kenneth.leiter@arl.army.mil                                           */
+/*     US Army Research Laboratory                                           */
+/*     Aberdeen Proving Ground, MD                                           */
+/*                                                                           */
+/*     Copyright @ 2011 US Army Research Laboratory                          */
+/*     All Rights Reserved                                                   */
+/*     See Copyright.txt for details                                         */
+/*                                                                           */
+/*     This software is distributed WITHOUT ANY WARRANTY; without            */
+/*     even the implied warranty of MERCHANTABILITY or FITNESS               */
+/*     FOR A PARTICULAR PURPOSE.  See the above copyright notice             */
+/*     for more information.                                                 */
+/*                                                                           */
+/*****************************************************************************/
+
+#include <iostream>
+
+#include <sstream>
+#include "XdmfSparseMatrix.hpp"
+#include "XdmfError.hpp"
+
+shared_ptr<XdmfSparseMatrix>
+XdmfSparseMatrix::New(const unsigned int numberRows,
+                      const unsigned int numberColumns)
+{
+  shared_ptr<XdmfSparseMatrix> p(new XdmfSparseMatrix(numberRows,
+                                                      numberColumns));
+  return p;
+}
+
+XdmfSparseMatrix::XdmfSparseMatrix(const unsigned int numberRows,
+                                   const unsigned int numberColumns) :
+  mColumnIndex(XdmfArray::New()),
+  mName(""),
+  mNumberColumns(numberColumns),
+  mNumberRows(numberRows),
+  mRowPointer(XdmfArray::New()),
+  mValues(XdmfArray::New())
+{
+  mRowPointer->resize<unsigned int>(mNumberRows + 1, 0);
+}
+
+XdmfSparseMatrix::~XdmfSparseMatrix()
+{
+}
+
+const std::string XdmfSparseMatrix::ItemTag = "SparseMatrix";
+
+shared_ptr<XdmfArray>
+XdmfSparseMatrix::getColumnIndex()
+{
+  return mColumnIndex;
+}
+
+std::map<std::string, std::string>
+XdmfSparseMatrix::getItemProperties() const
+{
+  std::map<std::string, std::string> sparseMatrixProperties;
+  sparseMatrixProperties.insert(std::make_pair("Name", mName));
+  std::stringstream numberRowsString;
+  numberRowsString << mNumberRows;
+  sparseMatrixProperties.insert(std::make_pair("NumberRows",
+                                               numberRowsString.str()));
+  std::stringstream numberColumnsString;
+  numberColumnsString << mNumberColumns;
+  sparseMatrixProperties.insert(std::make_pair("NumberColumns",
+                                               numberColumnsString.str()));
+  return sparseMatrixProperties;
+}
+
+std::string
+XdmfSparseMatrix::getItemTag() const
+{
+  return ItemTag;
+}
+
+std::string
+XdmfSparseMatrix::getName() const
+{
+  return mName;
+}
+
+unsigned int
+XdmfSparseMatrix::getNumberColumns() const
+{
+  return mNumberColumns;
+}
+
+unsigned int
+XdmfSparseMatrix::getNumberRows() const
+{
+  return mNumberRows;
+}
+
+shared_ptr<XdmfArray>
+XdmfSparseMatrix::getRowPointer()
+{
+  return mRowPointer;
+}
+
+shared_ptr<XdmfArray>
+XdmfSparseMatrix::getValues()
+{
+  return mValues;
+}
+
+std::string
+XdmfSparseMatrix::getValuesString() const
+{
+
+  std::stringstream toReturn;
+  for(unsigned int i=0; i<mNumberRows; ++i) {
+    unsigned int index = 0;
+    for(unsigned int j=mRowPointer->getValue<unsigned int>(i);
+        j<mRowPointer->getValue<unsigned int>(i+1);
+        ++j) {
+      const unsigned int k = mColumnIndex->getValue<unsigned int>(j);
+      while(index++ < k) {
+        toReturn << "0.0, ";
+      }
+      toReturn << mValues->getValue<double>(j) << ", ";
+    }
+    while(index++ < mNumberColumns) {
+      toReturn << "0.0, ";
+    }
+    toReturn << std::endl;
+  }
+
+  return toReturn.str();
+
+}
+
+void
+XdmfSparseMatrix::populateItem(const std::map<std::string, std::string> & itemProperties,
+                               const std::vector<shared_ptr<XdmfItem> > & childItems,
+                               const XdmfCoreReader * const reader)
+{
+  XdmfItem::populateItem(itemProperties, childItems, reader);
+  std::map<std::string, std::string>::const_iterator name =
+    itemProperties.find("Name");
+  if(name != itemProperties.end()) {
+    mName = name->second;
+  }
+  else  {
+    XdmfError::message(XdmfError::FATAL,
+                       "'Name' not found in itemProperties in "
+                       "XdmfSparseMatrix::populateItem");
+  }
+  std::map<std::string, std::string>::const_iterator numberRows =
+    itemProperties.find("NumberRows");
+  if(numberRows != itemProperties.end()) {
+    mNumberRows = std::atoi(numberRows->second.c_str());
+  }
+  else  {
+    XdmfError::message(XdmfError::FATAL,
+                       "'NumberRows' not found in itemProperties in "
+                       "XdmfSparseMatrix::populateItem");
+  }
+  std::map<std::string, std::string>::const_iterator numberColumns =
+    itemProperties.find("NumberColumns");
+  if(numberColumns != itemProperties.end()) {
+    mNumberColumns = std::atoi(numberColumns->second.c_str());
+  }
+  else  {
+    XdmfError::message(XdmfError::FATAL,
+                       "'NumberColumns' not found in itemProperties in "
+                       "XdmfSparseMatrix::populateItem");
+  }
+
+  std::vector<shared_ptr<XdmfArray> > arrayVector;
+  arrayVector.reserve(3);
+  for(std::vector<shared_ptr<XdmfItem> >::const_iterator iter =
+        childItems.begin();
+      iter != childItems.end();
+      ++iter) {
+    if(shared_ptr<XdmfArray> array = shared_dynamic_cast<XdmfArray>(*iter)) {
+      arrayVector.push_back(array);
+    }
+  }
+
+  if(arrayVector.size() < 3) {
+    XdmfError::message(XdmfError::FATAL,
+                       "Expected 3 arrays attached to "
+                       "XdmfSparseMatrix::populateItem");
+  }
+  mRowPointer = arrayVector[0];
+  mColumnIndex = arrayVector[1];
+  mValues = arrayVector[2];
+}
+
+void
+XdmfSparseMatrix::setColumnIndex(const shared_ptr<XdmfArray> columnIndex)
+{
+  mColumnIndex = columnIndex;
+}
+
+void
+XdmfSparseMatrix::setName(const std::string & name)
+{
+  mName = name;
+}
+
+void
+XdmfSparseMatrix::setRowPointer(const shared_ptr<XdmfArray> rowPointer)
+{
+  mRowPointer = rowPointer;
+}
+
+void
+XdmfSparseMatrix::setValues(const shared_ptr<XdmfArray> values)
+{
+  mValues = values;
+}
+
+void
+XdmfSparseMatrix::traverse(const shared_ptr<XdmfBaseVisitor> visitor)
+{
+  XdmfItem::traverse(visitor);
+  mRowPointer->accept(visitor);
+  mColumnIndex->accept(visitor);
+  mValues->accept(visitor);
+}

core/XdmfSparseMatrix.hpp

+/*****************************************************************************/
+/*                                    XDMF                                   */
+/*                       eXtensible Data Model and Format                    */
+/*                                                                           */
+/*  Id : XdmfSparseMatrix.hpp                                                */
+/*                                                                           */
+/*  Author:                                                                  */
+/*     Kenneth Leiter                                                        */
+/*     kenneth.leiter@arl.army.mil                                           */
+/*     US Army Research Laboratory                                           */
+/*     Aberdeen Proving Ground, MD                                           */
+/*                                                                           */
+/*     Copyright @ 2011 US Army Research Laboratory                          */
+/*     All Rights Reserved                                                   */
+/*     See Copyright.txt for details                                         */
+/*                                                                           */
+/*     This software is distributed WITHOUT ANY WARRANTY; without            */
+/*     even the implied warranty of MERCHANTABILITY or FITNESS               */
+/*     FOR A PARTICULAR PURPOSE.  See the above copyright notice             */
+/*     for more information.                                                 */
+/*                                                                           */
+/*****************************************************************************/
+
+#ifndef XDMFSPARSEMATRIX_HPP_
+#define XDMFSPARSEMATRIX_HPP_
+
+// Includes
+#include "XdmfCore.hpp"
+#include "XdmfArray.hpp"
+
+/**
+ * @brief Sparse matrix implemented as compressed row storage.
+ *
+ * An XdmfSparseMatrix provides routines for interacting with a sparse
+ * matrix.  It is stored internally in compressed row storage.
+ */
+class XDMFCORE_EXPORT XdmfSparseMatrix : public XdmfItem {
+
+public:
+
+  /**
+   * Create a new XdmfSparseMatrix.
+   *
+   * @param numberRows number of rows in matrix.
+   * @param numberColumns number of columns in matrix.
+   *
+   * @return constructed XdmfSparseMatrix.
+   */
+  static shared_ptr<XdmfSparseMatrix> New(const unsigned int numberRows,
+                                          const unsigned int numberColumns);
+
+  virtual ~XdmfSparseMatrix();
+
+  LOKI_DEFINE_VISITABLE(XdmfSparseMatrix, XdmfItem);
+  static const std::string ItemTag;
+
+  /**
+   * Get the column index array.
+   *
+   * @return array containing column indices for nonzero entries of
+   * matrix. This is the same size as values.
+   */