Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <Hdf5ToXdmfConverter.hpp>

Inheritance diagram for Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	Hdf5ToXdmfConverter (const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
void	AddDataOnNodes (XERCES_CPP_NAMESPACE_QUALIFIER DOMElement *pGridElement, XERCES_CPP_NAMESPACE_QUALIFIER DOMDocument *pDomDocument, unsigned timeStep)
Public Member Functions inherited from AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >
	AbstractHdf5Converter (const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, const std::string &rSubdirectoryName, unsigned precision)
void	WriteInfoFile ()
	~AbstractHdf5Converter ()
std::string	GetSubdirectory ()
Public Member Functions inherited from XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >
	XdmfMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)
void	WriteFiles ()
void	WriteFilesUsingMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool keepOriginalElementIndexing=true)
Public Member Functions inherited from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractTetrahedralMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)
virtual	~AbstractTetrahedralMeshWriter ()
void	WriteFilesUsingMeshReaderAndMesh (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
std::vector< double >	GetNextNode ()
ElementData	GetNextElement ()
ElementData	GetNextBoundaryElement ()
ElementData	GetNextCableElement ()
Public Member Functions inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)
virtual	~AbstractMeshWriter ()
std::string	GetOutputDirectory ()
virtual unsigned	GetNumNodes ()
unsigned	GetNumElements ()
unsigned	GetNumBoundaryFaces ()
unsigned	GetNumCableElements ()
void	WriteFilesUsingMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

Additional Inherited Members
Protected Member Functions inherited from AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >
bool	MoveOntoNextDataset ()
Protected Attributes inherited from AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >
const FileFinder &	mrH5Folder
boost::shared_ptr< Hdf5DataReader >	mpReader
unsigned	mNumVariables
std::string	mFileBaseName
std::vector< std::string >	mDatasetNames
unsigned	mOpenDatasetIndex
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh
OutputFileHandler *	mpOutputFileHandler
std::string	mRelativeSubdirectory
unsigned	mPrecision
Protected Attributes inherited from XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >
unsigned	mNumberOfTimePoints
double	mTimeStep
Protected Attributes inherited from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
unsigned	mNodesPerElement
unsigned	mNodesPerBoundaryElement
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh
DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpDistributedMesh
MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *	mpMixedMesh
MeshWriterIterators< ELEMENT_DIM, SPACE_DIM > *	mpIters
bool	mIndexFromZero
bool	mWriteMetaFile
unsigned	mNodeCounterForParallelMesh
unsigned	mElementCounterForParallelMesh
unsigned	mBoundaryElementCounterForParallelMesh
unsigned	mCableElementCounterForParallelMesh
bool	mFilesAreBinary
Protected Attributes inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
OutputFileHandler *	mpOutputFileHandler
std::string	mBaseName
AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > *	mpMeshReader
unsigned	mNumNodes
unsigned	mNumElements
unsigned	mNumBoundaryElements
unsigned	mNumCableElements

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >

This class "converts" from Hdf5 format to XDMF format. The output will be one .xdmf master file with separate geometry/topology files. The HDF5 data is not converted, but is rather linked to by the .xdmf master file

Definition at line 47 of file Hdf5ToXdmfConverter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToXdmfConverter	(	const FileFinder &	rInputDirectory,
		const std::string &	rFileBaseName,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh
	)

Constructor, which does the conversion and writes the .vtu file.

Note

This method is collective, and hence must be called by all processes.

Parameters

rInputDirectory	The input directory, relative to CHASTE_TEST_OUTPUT, where the .h5 file has been written
rFileBaseName	The base name of the data file.
pMesh	Pointer to the mesh.

Definition at line 39 of file Hdf5ToXdmfConverter.cpp.

References XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumberOfTimePoints, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader, XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::mTimeStep, and XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >::AddDataOnNodes ( XERCES_CPP_NAMESPACE_QUALIFIER DOMElement *  pGridElement, XERCES_CPP_NAMESPACE_QUALIFIER DOMDocument *  pDomDocument, unsigned  timeStep  )

virtual

Generate Attribute tags and append to the element. Here this is a dummy class, but can be overloaded with real variables elsewhere (see pde/src/postprocesssing/Hdf5toXdmfConverter).

Parameters

pGridElement	Pointer to DOMElement to append Attribute tags to.
pDomDocument	Pointer to DOMDocument to generate new elements.
timeStep	Index of time point to write.

Todo:

#1157 Make this work in parallel

Reimplemented from XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 62 of file Hdf5ToXdmfConverter.cpp.

References AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mNumVariables, and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader.

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The documentation for this class was generated from the following files:

• pde/src/postprocessing/Hdf5ToXdmfConverter.hpp
• pde/src/postprocessing/Hdf5ToXdmfConverter.cpp