XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <XdmfMeshWriter.hpp>

Inheritance diagram for XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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)

Protected Attributes
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

Private Member Functions
void	WriteXdmfMasterFile (unsigned numberOfChunks=1u)
virtual void	AddDataOnNodes (XERCES_CPP_NAMESPACE_QUALIFIER DOMElement *pGridElement, XERCES_CPP_NAMESPACE_QUALIFIER DOMDocument *pDomDocument, unsigned timeStep)

Detailed Description

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

A class for writing from a Chaste mesh to the geometry/topology components of an XDMF file.

Definition at line 62 of file XdmfMeshWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::XdmfMeshWriter	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		const bool	clearOutputDir = true
	)

Constructor.

Parameters

rDirectory	the directory in which to write the mesh to file
rBaseName	the base name of the files in which to write the mesh data
clearOutputDir	whether to clean the directory (defaults to true)

Definition at line 44 of file XdmfMeshWriter.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

inlineprivatevirtual

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.

Reimplemented in Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 83 of file XdmfMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles ( )

virtual

Write the files using a mesh reader. Called from WriteFilesUsingMeshReader in the base class.

Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 183 of file XdmfMeshWriter.cpp.

References PetscTools::AmMaster(), EXCEPTION, and ChasteBuildInfo::GetProvenanceString().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &  rMesh, bool  keepOriginalElementIndexing = true  )

virtual

Write the files using mesh – this allows the parallel distributed case to write only local data.

Parameters

rMesh	the mesh
keepOriginalElementIndexing	Whether to write the mesh with the same element ordering. Ignored in this derived class

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 54 of file XdmfMeshWriter.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), PetscTools::GetMyRank(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::GetNumProcs(), ChasteBuildInfo::GetProvenanceString(), and PetscTools::IsParallel().

Referenced by Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToXdmfConverter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteXdmfMasterFile ( unsigned  numberOfChunks = 1u )

private

Write the master file. This just contains references to the geometry/topology files.

Parameters

numberOfChunks

is the number of geometric pieces which is 1 for sequential code and for non-distributed meshes.

Definition at line 247 of file XdmfMeshWriter.cpp.

References PetscTools::AmMaster(), and ChasteBuildInfo::GetProvenanceString().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumberOfTimePoints

protected

Defaults to 1, when we are writing geometry only. Used in HDF5 converter which has "protected" access as a derived class.

Definition at line 65 of file XdmfMeshWriter.hpp.

Referenced by Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToXdmfConverter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::mTimeStep

protected

Defaults to 1.0.

Definition at line 66 of file XdmfMeshWriter.hpp.

Referenced by Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToXdmfConverter().

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

• mesh/src/writer/XdmfMeshWriter.hpp
• mesh/src/writer/XdmfMeshWriter.cpp