ENH: Add XdmfExodusReader for reading ExodusII files into Xdmf. Add ability...

ENH: Add XdmfExodusReader for reading ExodusII files into Xdmf.  Add ability for XdmfArray::initialize() to take a size value to initialize the array to.

CMake/FindExodus.cmake

+#
+# Find the Exodus finite element data model library from Sandia
+#
+#  EXODUS_FOUND - System has Exodus
+#  EXODUS_INCLUDE_DIR - The LibXml2 include directory
+#  EXODUS_LIBRARIES - The libraries needed to use LibXml2
+
+FIND_PACKAGE(NetCDF REQUIRED)
+
+FIND_PATH(EXODUS_INCLUDE_DIR NAMES exodusII.h)
+
+FIND_LIBRARY(EXODUS_LIBRARIES NAMES exodusii exodusIIv2c)
+
+INCLUDE(FindPackageHandleStandardArgs)
+
+# handle the QUIETLY and REQUIRED arguments and set EXODUS_FOUND to TRUE if 
+# all listed variables are TRUE
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Exodus DEFAULT_MSG EXODUS_LIBRARIES EXODUS_INCLUDE_DIR)
+
+MARK_AS_ADVANCED(EXODUS_INCLUDE_DIR EXODUS_LIBRARIES)
+

CMake/FindNetCDF.cmake

+#
+# Find NetCDF include directories and libraries
+#
+# NetCDF_FOUND - System has NetCDF
+# NetCDF_INCLUDE_DIR - The NetCDF include directory
+# NetCDF_LIBRARIES - The libraries needed to use NetCDF
+
+FIND_PATH(NetCDF_INCLUDE_DIR netcdf.h)
+
+FIND_LIBRARY(NetCDF_LIBRARIES
+  NAMES netcdf
+  ${NetCDF_PREFIX}
+  ${NetCDF_PREFIX}/lib64
+  ${NetCDF_PREFIX}/lib
+  /usr/local/lib64
+  /usr/lib64
+  /usr/lib64/netcdf-3
+  /usr/local/lib
+  /usr/lib
+  /usr/lib/netcdf-3
+)
+
+INCLUDE(FindPackageHandleStandardArgs)
+
+# handle the QUIETLY and REQUIRED arguments and set EXODUS_FOUND to TRUE if 
+# all listed variables are TRUE
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NetCDF_INCLUDE_DIR NetCDF_LIBRARIES)
+
+MARK_AS_ADVANCED(NetCDF_INCLUDE_DIR NetCDF_LIBRARIES)

XdmfTopologyType.cpp

@@ -95,6 +95,12 @@ boost::shared_ptr<const XdmfTopologyType> XdmfTopologyType::Quadrilateral_8()
 	return p;
 }
 
+boost::shared_ptr<const XdmfTopologyType> XdmfTopologyType::Quadrilateral_9()
+{
+	static boost::shared_ptr<const XdmfTopologyType> p(new XdmfTopologyType(9, "Quadrilateral_9", Quadratic));
+	return p;
+}
+
 boost::shared_ptr<const XdmfTopologyType> XdmfTopologyType::Tetrahedron_10()
 {
 	static boost::shared_ptr<const XdmfTopologyType> p(new XdmfTopologyType(10, "Tetrahedron_10", Quadratic));
@@ -113,6 +119,12 @@ boost::shared_ptr<const XdmfTopologyType> XdmfTopologyType::Wedge_15()
 	return p;
 }
 
+boost::shared_ptr<const XdmfTopologyType> XdmfTopologyType::Wedge_18()
+{
+	static boost::shared_ptr<const XdmfTopologyType> p(new XdmfTopologyType(18, "Wedge_18", Quadratic));
+	return p;
+}
+
 boost::shared_ptr<const XdmfTopologyType> XdmfTopologyType::Hexahedron_20()
 {
 	static boost::shared_ptr<const XdmfTopologyType> p(new XdmfTopologyType(20, "Hexahedron_20", Quadratic));

XdmfTopologyType.hpp

@@ -23,6 +23,7 @@
  * 	Edge_3
  * 	Triangle_6
  * 	Quadrilateral_8
+ * 	Quadrilateral_9
  * 	Tetrahedron_10
  * 	Pyramid_13
  * 	Wedge_15
@@ -37,7 +38,7 @@
  * 	TwoDCoRectMesh
  * 	ThreeDSMesh
  * 	ThreeDRectMesh
- *	ThreeDCoRectMesh
+ * 	ThreeDCoRectMesh
  */
 class XdmfTopologyType : public XdmfItemProperty {
 
@@ -65,9 +66,11 @@ public:
 	static boost::shared_ptr<const XdmfTopologyType> Edge_3();
 	static boost::shared_ptr<const XdmfTopologyType> Triangle_6();
 	static boost::shared_ptr<const XdmfTopologyType> Quadrilateral_8();
+	static boost::shared_ptr<const XdmfTopologyType> Quadrilateral_9();
 	static boost::shared_ptr<const XdmfTopologyType> Tetrahedron_10();
 	static boost::shared_ptr<const XdmfTopologyType> Pyramid_13();
 	static boost::shared_ptr<const XdmfTopologyType> Wedge_15();
+	static boost::shared_ptr<const XdmfTopologyType> Wedge_18();
 	static boost::shared_ptr<const XdmfTopologyType> Hexahedron_20();
 	static boost::shared_ptr<const XdmfTopologyType> Hexahedron_24();
 	static boost::shared_ptr<const XdmfTopologyType> Hexahedron_27();

core/XdmfArray.cpp

@@ -471,43 +471,43 @@ std::string XdmfArray::getValuesString() const
 	return "";
 }
 
-void XdmfArray::initialize(const boost::shared_ptr<const XdmfArrayType> arrayType)
+void XdmfArray::initialize(const boost::shared_ptr<const XdmfArrayType> arrayType, const unsigned int size)
 {
 	if(arrayType == XdmfArrayType::Int8())
 	{
-		this->initialize<char>();
+		this->initialize<char>(size);
 	}
 	else if(arrayType == XdmfArrayType::Int16())
 	{
-		this->initialize<short>();
+		this->initialize<short>(size);
 	}
 	else if(arrayType == XdmfArrayType::Int32())
 	{
-		this->initialize<int>();
+		this->initialize<int>(size);
 	}
 	else if(arrayType == XdmfArrayType::Int64())
 	{
-		this->initialize<long>();
+		this->initialize<long>(size);
 	}
 	else if(arrayType == XdmfArrayType::Float32())
 	{
-		this->initialize<float>();
+		this->initialize<float>(size);
 	}
 	else if(arrayType == XdmfArrayType::Float64())
 	{
-		this->initialize<double>();
+		this->initialize<double>(size);
 	}
 	else if(arrayType == XdmfArrayType::UInt8())
 	{
-		this->initialize<unsigned char>();
+		this->initialize<unsigned char>(size);
 	}
 	else if(arrayType == XdmfArrayType::UInt16())
 	{
-		this->initialize<unsigned short>();
+		this->initialize<unsigned short>(size);
 	}
 	else if(arrayType == XdmfArrayType::UInt32())
 	{
-		this->initialize<unsigned int>();
+		this->initialize<unsigned int>(size);
 	}
 	else if(arrayType == XdmfArrayType::Uninitialized())
 	{

core/XdmfArray.hpp

@@ -187,15 +187,19 @@ public:
 	/**
 	 * Initializes the array to contain an empty container of a particular type.
 	 *
+	 * @param size the number of values in the initialized array.
 	 * @return a smart pointer to the internal vector of values initialized in this array.
 	 */
 	template <typename T>
-	boost::shared_ptr<std::vector<T> > initialize();
+	boost::shared_ptr<std::vector<T> > initialize(const unsigned int size = 0);
 
 	/**
 	 * Initializes the array to contain an empty container of a particular XdmfArrayType.
+	 *
+	 * @param arrayType the type of array to initialize.
+	 * @param size the number of values in the initialized array.
 	 */
-	void initialize(const boost::shared_ptr<const XdmfArrayType> arrayType);
+	void initialize(const boost::shared_ptr<const XdmfArrayType> arrayType, const unsigned int size = 0);
 
 	/**
 	 * Returns whether the array is initialized (contains values in memory).

core/XdmfArray.tpp

@@ -198,14 +198,14 @@ void XdmfArray::getValuesCopy(const unsigned int startIndex, T * const valuesPoi
 }
 
 template <typename T>
-boost::shared_ptr<std::vector<T> > XdmfArray::initialize()
+boost::shared_ptr<std::vector<T> > XdmfArray::initialize(const unsigned int size)
 {
 	if(mHaveArrayPointer)
 	{
 		releaseArrayPointer();
 	}
 	// Set type of variant to type of pointer
-	boost::shared_ptr<std::vector<T> > newArray(new std::vector<T>());
+	boost::shared_ptr<std::vector<T> > newArray(new std::vector<T>(size));
 	if(mTmpReserveSize > 0)
 	{
 		newArray->reserve(mTmpReserveSize);

core/XdmfHDF5Controller.cpp

@@ -49,8 +49,7 @@ void XdmfHDF5Controller::read(XdmfArray * const array)
 	hssize_t numVals = H5Sget_simple_extent_npoints(dataspace);
 	hid_t datatype = H5Dget_type(dataset);
 
-	array->initialize(mType);
-	array->resize(numVals, 0);
+	array->initialize(mType, numVals);
 	H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, array->getValuesPointer());
 
 	herr_t status;

utils/CMakeLists.txt

 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 
+option(XDMF_BUILD_EXODUS_IO OFF)
 option(XDMF_BUILD_PARTITIONER OFF)
 
 set(XdmfUtilsExecutables)
@@ -8,6 +9,15 @@ set(XdmfUtilsSources
 )
 set(XdmfUtilsLinkLibraries Xdmf)
 
+if(XDMF_BUILD_EXODUS_IO)
+	find_package(Exodus REQUIRED)
+	if(EXODUS_FOUND)
+		include_directories(${EXODUS_INCLUDE_DIR} ${NetCDF_INCLUDE_DIR})
+	endif(EXODUS_FOUND)
+	set(XdmfUtilsSources ${XdmfUtilsSources} XdmfExodusReader)
+	set(XdmfUtilsLinkLibraries ${XdmfUtilsLinkLibraries} ${EXODUS_LIBRARIES} ${NetCDF_LIBRARIES})
+endif(XDMF_BUILD_EXODUS_IO)
+
 if(XDMF_BUILD_PARTITIONER)
 	find_package(Metis REQUIRED)
 	if(METIS_FOUND)

utils/XdmfExodusReader.hpp

+#ifndef XDMFEXODUSREADER_HPP_
+#define XDMFEXODUSREADER_HPP_
+
+// Forward Declarations
+class XdmfGrid;
+class XdmfTopologyType;
+
+// Includes
+#include <boost/shared_ptr.hpp>
+#include <string>
+
+/*!
+ * @brief XdmfExodusReader reads an ExodusII file from disk into an Xdmf structure in memory.
+ */
+class XdmfExodusReader {
+
+public:
+
+	/**
+	 * Create a new XdmfExodusReader.
+	 *
+	 * @return constructed XdmfExodusReader.
+	 */
+	static boost::shared_ptr<XdmfExodusReader> New();
+
+	virtual ~XdmfExodusReader();
+
+    /*!
+     * Read the contents of an ExodusII file from disk into an Xdmf structure in memory..
+     *
+     * @param fileName containing the path of the exodus file to read.
+     *
+     * @return XdmfGrid containing the mesh stored in the ExodusII file.
+     */
+	boost::shared_ptr<XdmfGrid> read(const std::string & fileName) const;
+
+protected:
+
+	XdmfExodusReader();
+
+private:
+
+	XdmfExodusReader(const XdmfExodusReader & exodusReader);  // Not implemented.
+	void operator=(const XdmfExodusReader & exodusReader);  // Not implemented.
+
+	/**
+	 * Convert an Exodus topology type to an XdmfTopologyType.
+	 *
+	 * @param exodusTopologyType a string containing the name of the exodus topology type to convert.
+	 * @param pointsPerCell the number of points per cell for the exodus topology type to convert.
+	 *
+	 * @return the equivalent XdmfTopologyType.
+	 */
+	boost::shared_ptr<const XdmfTopologyType> exodusToXdmfTopologyType(std::string exodusTopologyType, const int pointsPerCell) const;
+};
+
+#endif /* XDMFEXODUSREADER_HPP_ */

utils/XdmfPartitioner.cpp

@@ -49,6 +49,12 @@ extern "C"
 #include "XdmfTopology.hpp"
 #include "XdmfTopologyType.hpp"
 
+boost::shared_ptr<XdmfPartitioner> XdmfPartitioner::New()
+{
+	boost::shared_ptr<XdmfPartitioner> p(new XdmfPartitioner());
+	return p;
+}
+
 XdmfPartitioner::XdmfPartitioner()
 {
 }
@@ -203,8 +209,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(const boost::sh
 			partitioned->getGeometry()->setType(gridToPartition->getGeometry()->getType());
 			boost::shared_ptr<XdmfArray> geometryVals = partitioned->getGeometry();
 			unsigned int numDimensions = partitioned->getGeometry()->getType()->getDimensions();
-			geometryVals->initialize(gridToPartition->getGeometry()->getArrayType());
-			geometryVals->resize<unsigned int>(currNodeMap.size() * numDimensions);
+			geometryVals->initialize(gridToPartition->getGeometry()->getArrayType(), currNodeMap.size() * numDimensions);
 
 			for(std::map<unsigned int, unsigned int>::const_iterator iter = currNodeMap.begin(); iter != currNodeMap.end(); ++iter)
 			{
@@ -220,8 +225,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(const boost::sh
 			// Fill in topology for this partition
 			partitioned->getTopology()->setType(gridToPartition->getTopology()->getType());
 			boost::shared_ptr<XdmfArray> topologyVals = partitioned->getTopology();
-			topologyVals->initialize(gridToPartition->getTopology()->getArrayType());
-			topologyVals->resize<unsigned int>(currElemIds.size() * topologyType->getNodesPerElement());
+			topologyVals->initialize(gridToPartition->getTopology()->getArrayType(), currElemIds.size() * topologyType->getNodesPerElement());
 
 			unsigned int index = 0;
 			for(std::vector<unsigned int>::const_iterator iter = currElemIds.begin(); iter != currElemIds.end(); ++iter)
@@ -303,8 +307,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(const boost::sh
 					createdAttribute->setType(currAttribute->getType());
 					unsigned int index = 0;
 					unsigned int numValsPerComponent = currAttribute->size() / gridToPartition->getTopology()->getNumberElements();
-					createdAttribute->initialize(currAttribute->getArrayType());
-					createdAttribute->resize<unsigned int>(currElemIds.size() * numValsPerComponent);
+					createdAttribute->initialize(currAttribute->getArrayType(), currElemIds.size() * numValsPerComponent);
 					for(std::vector<unsigned int>::const_iterator iter = currElemIds.begin(); iter != currElemIds.end(); ++iter)
 					{
 						createdAttribute->copyValues(index, currAttribute, *iter * numValsPerComponent, numValsPerComponent);
@@ -317,8 +320,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(const boost::sh
 					createdAttribute->setName(currAttribute->getName());
 					createdAttribute->setCenter(currAttribute->getCenter());
 					createdAttribute->setType(currAttribute->getType());
-					createdAttribute->initialize(currAttribute->getArrayType());
-					createdAttribute->resize<unsigned int>(currNodeMap.size());
+					createdAttribute->initialize(currAttribute->getArrayType(), currNodeMap.size());
 					for(std::map<unsigned int, unsigned int>::const_iterator iter = currNodeMap.begin(); iter != currNodeMap.end(); ++iter)
 					{
 						createdAttribute->copyValues(iter->second, currAttribute, iter->first, 1);

utils/XdmfPartitioner.hpp

@@ -6,6 +6,9 @@ class XdmfGrid;
 class XdmfGridCollection;
 class XdmfHDF5Writer;
 
+// Includes
+#include <boost/shared_ptr.hpp>
+
 /*!
  * @brief XdmfPartitioner partitions an XdmfGrid using the metis library.
  *
@@ -20,11 +23,7 @@ public:
 	 *
 	 * @return constructed XdmfPartitioner.
 	 */
-	static boost::shared_ptr<XdmfPartitioner> New()
-	{
-		boost::shared_ptr<XdmfPartitioner> p(new XdmfPartitioner());
-		return p;
-	};
+	static boost::shared_ptr<XdmfPartitioner> New();
 
 	virtual ~XdmfPartitioner();
 

utils/XdmfTopologyConverter.cpp

@@ -108,8 +108,7 @@ public:
 		toReturn->getTopology()->setType(XdmfTopologyType::Hexahedron_64());
 
 		boost::shared_ptr<XdmfArray> newPoints = toReturn->getGeometry();
-		newPoints->initialize(gridToConvert->getGeometry()->getArrayType());
-		newPoints->resize(gridToConvert->getGeometry()->size(), 0);
+		newPoints->initialize(gridToConvert->getGeometry()->getArrayType(), gridToConvert->getGeometry()->size());
 
 		if(!gridToConvert->getGeometry()->isInitialized())
 		{
@@ -389,8 +388,7 @@ public:
 		toReturn->getTopology()->setType(XdmfTopologyType::Hexahedron_125());
 
 		boost::shared_ptr<XdmfArray> newPoints = toReturn->getGeometry();
-		newPoints->initialize(gridToConvert->getGeometry()->getArrayType());
-		newPoints->resize(gridToConvert->getGeometry()->size(), 0);
+		newPoints->initialize(gridToConvert->getGeometry()->getArrayType(), gridToConvert->getGeometry()->size());
 
 		if(!gridToConvert->getGeometry()->isInitialized())
 		{
@@ -810,8 +808,7 @@ public:
 
 		boost::shared_ptr<XdmfArray> oldConnectivity = gridToConvert->getTopology();
 		boost::shared_ptr<XdmfArray> newConnectivity = toReturn->getTopology();
-		newConnectivity->initialize(oldConnectivity->getArrayType());
-		newConnectivity->resize(216 * gridToConvert->getTopology()->getNumberElements(), 0);
+		newConnectivity->initialize(oldConnectivity->getArrayType(), 216 * gridToConvert->getTopology()->getNumberElements());
 
 		if(!oldConnectivity->isInitialized())
 		{
@@ -1060,8 +1057,7 @@ public:
 				newAttribute->setCenter(currAttribute->getCenter());
 
 				boost::shared_ptr<XdmfArray> vals = newAttribute;
-				vals->initialize(currAttribute->getArrayType());
-				vals->resize(currAttribute->size() * 27, 0);
+				vals->initialize(currAttribute->getArrayType(), currAttribute->size() * 27);
 				for(unsigned int j=0; j<currAttribute->size(); ++j)
 				{
 					vals->copyValues(j * 27, currAttribute, j, 27, 1, 0);
@@ -1073,6 +1069,12 @@ public:
 	}
 };
 
+boost::shared_ptr<XdmfTopologyConverter> XdmfTopologyConverter::New()
+{
+	boost::shared_ptr<XdmfTopologyConverter> p(new XdmfTopologyConverter());
+	return p;
+}
+
 XdmfTopologyConverter::XdmfTopologyConverter()
 {
 }

utils/XdmfTopologyConverter.hpp

@@ -5,6 +5,9 @@
 class XdmfGrid;
 class XdmfTopologyType;
 
+// Includes
+#include <boost/shared_ptr.hpp>
+
 /*!
  * @brief XdmfTopologyConverter converts an XdmfGrid to different topology types.  XdmfAttributes and XdmfSets attached to the XdmfGrid
  * are adjusted to remain valid for the new topology type.
@@ -25,11 +28,7 @@ public:
 	 *
 	 * @return constructed XdmfTopologyConverter.
 	 */
-	static boost::shared_ptr<XdmfTopologyConverter> New()
-	{
-		boost::shared_ptr<XdmfTopologyConverter> p(new XdmfTopologyConverter());
-		return p;
-	};
+	static boost::shared_ptr<XdmfTopologyConverter> New();
 
 	virtual ~XdmfTopologyConverter();
 

utils/tests/Cxx/TestXdmfTopologyConverter.cpp

 #include <math.h>
 #include "XdmfArray.hpp"
+#include "XdmfArrayType.hpp"
 #include "XdmfGeometry.hpp"
 #include "XdmfGeometryType.hpp"
 #include "XdmfGrid.hpp"
 #include "XdmfTopology.hpp"
 #include "XdmfTopologyConverter.hpp"
 #include "XdmfTopologyType.hpp"
-
-#include "XdmfArrayType.hpp"
 #include "XdmfWriter.hpp"
 
 int main(int argc, char* argv[])