#include <AbstractTetrahedralMeshWriter.hpp>

Inheritance diagram for AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	AbstractTetrahedralMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

virtual	~AbstractTetrahedralMeshWriter ()

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

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 ()

virtual void	WriteFiles ()=0

void	WriteFilesUsingMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

Protected Attributes
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	PostElement (unsigned globalIndex, unsigned indices[], unsigned numIndices, unsigned tag, double attribute)

void	UnpackElement (ElementData &rElementData, unsigned globalIndex, unsigned numIndices, unsigned tag)

virtual void	WriteFilesUsingParallelMesh (bool keepOriginalElementIndexing=true)

void	WriteNclFile (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool invertMeshPermutation=false)

virtual void	CreateFilesWithHeaders ()

virtual void	AppendLocalDataToFiles ()

virtual void	WriteFilesFooter ()

Private Attributes
NodeMap *	mpNodeMap

Detailed Description

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

An abstract tetrahedral mesh writer class.

Definition at line 88 of file AbstractTetrahedralMeshWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::AbstractTetrahedralMeshWriter	(	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 72 of file AbstractTetrahedralMeshWriter.cpp.

References AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::~AbstractTetrahedralMeshWriter ( )

virtual

Destructor just deletes the node map if memory has been allocated for it

Definition at line 95 of file AbstractTetrahedralMeshWriter.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles ( )

privatevirtual

Append local mesh data to output files.

Reimplemented in CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >, CmguiMeshWriter< DIM, DIM >, and MeshalyzerMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 654 of file AbstractTetrahedralMeshWriter.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders ( )

privatevirtual

Create output files and add headers.

Reimplemented in CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >, CmguiMeshWriter< DIM, DIM >, and MeshalyzerMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 646 of file AbstractTetrahedralMeshWriter.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ElementData AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextBoundaryElement ( )

virtual

Returns: the data (indices) of the next boundary element to be written to file

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 230 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), ElementData::AttributeValue, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextBoundaryElement(), and ElementData::NodeIndices.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ElementData AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextCableElement ( )

virtual

Returns: the data (indices/attributes) of the next cable element to be written to file

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 289 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), ElementData::AttributeValue, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetAttribute(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextCableElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::IsDeleted(), and ElementData::NodeIndices.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ElementData AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement ( )

virtual

Returns: the data (indices/attributes) of the next element to be written to file

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 170 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), ElementData::AttributeValue, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetAttribute(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::IsDeleted(), and ElementData::NodeIndices.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< double > AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode ( )

virtual

Returns: the coordinates of the next node to be written to file

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 120 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), and AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::PostElement	(	unsigned	globalIndex,
		unsigned	indices[],
		unsigned	numIndices,
		unsigned	tag,
		double	attribute
	)

inlineprivate

Post an element from a slave process to the master for concentration

Parameters

globalIndex	index of this element
indices	the node index data for this element
numIndices	number of indices
tag	temporary
attribute

Definition at line 99 of file AbstractTetrahedralMeshWriter.hpp.

References GenericEventHandler< 11, MeshEventHandler >::BeginEvent(), and GenericEventHandler< 11, MeshEventHandler >::EndEvent().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::UnpackElement	(	ElementData &	rElementData,
		unsigned	globalIndex,
		unsigned	numIndices,
		unsigned	tag
	)

inlineprivate

Unpack an element from a slave process on the master for concentration

Parameters

rElementData	the output structure to fill (should have the NodeIndices structure of the correct size
globalIndex	index of this element
numIndices	number of indices
tag	temporary

Definition at line 120 of file AbstractTetrahedralMeshWriter.hpp.

References ElementData::AttributeValue, GenericEventHandler< 11, MeshEventHandler >::BeginEvent(), GenericEventHandler< 11, MeshEventHandler >::EndEvent(), and ElementData::NodeIndices.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesFooter ( )

privatevirtual

Append footers to output files.

Reimplemented in CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >, CmguiMeshWriter< DIM, DIM >, and MeshalyzerMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 662 of file AbstractTetrahedralMeshWriter.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Write a const mesh to file. Used by the serialization methods and avoids iterators...

Parameters

rMesh	the mesh
keepOriginalElementIndexing	Whether to write the mesh with the same element ordering as in memory. Optimisations can be applied if this is not needed.

Todo:: #1322 Mesh should really be const!

Todo:: #1322 Mesh should be const

Todo:: #1322 This should be const too

Todo:: #1322, This should be const too

Reimplemented in VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >, and XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 442 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and NodeMap::SetNewIndex().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise(), CellBasedPdeHandler< DIM >::OpenResultsFiles(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMeshReaderAndMesh	(	AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &	rMeshReader,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh
	)

Write a const mesh to file. Used by the serialization methods and avoids iterators. The master process will use the mesh reader to copy over most of the mesh files, converting them to binary format. However, the mesh is used to write a .ncl file which contains node connectivity information.

Parameters

rMeshReader	a reader of the original mesh files on disk
rMesh	the mesh object in memory

Definition at line 524 of file AbstractTetrahedralMeshWriter.cpp.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh ( bool keepOriginalElementIndexing = true )

privatevirtual

Write a parallel mesh to file. Used by the serialization methods.

Parameters

keepOriginalElementIndexing Whether to write the mesh with the same element ordering as in memory. Optimisations can be applied if this is not needed.

Todo:: #2351 Also exclude VTK writer

Definition at line 533 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::Barrier(), GenericEventHandler< 11, MeshEventHandler >::BeginEvent(), PetscTools::BeginRoundRobin(), GenericEventHandler< 11, MeshEventHandler >::EndEvent(), PetscTools::EndRoundRobin(), PetscTools::GetMyRank(), and PetscTools::GetNumProcs().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		bool	invertMeshPermutation = `false`
	)

private

Write out a node connectivity information file (collectively called, involves some communication).

Parameters

rMesh	the mesh object in memory
invertMeshPermutation	whether to permute the file using the inverse of the mesh's permutation

Definition at line 332 of file AbstractTetrahedralMeshWriter.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::Barrier(), GenericEventHandler< 11, MeshEventHandler >::BeginEvent(), PetscTools::BeginRoundRobin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumContainingElementsPerProcess(), GenericEventHandler< 11, MeshEventHandler >::EndEvent(), PetscTools::EndRoundRobin(), FileFinder::GetAbsolutePath(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ChasteBuildInfo::GetProvenanceString(), PetscTools::IsSequential(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementCounterForParallelMesh

protected

Used by master process for polling processes for the next boundary element

Definition at line 198 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mCableElementCounterForParallelMesh

protected

Used by master process for polling processes for the next cable element

Definition at line 199 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mElementCounterForParallelMesh

protected

Used by master process for polling processes for the next element

Definition at line 197 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mFilesAreBinary

protected

Whether all data is to be written as binary - used in derived class TrianglesMeshWriter

Definition at line 200 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mIndexFromZero

protected

True if input data is numbered from zero, false otherwise

Definition at line 194 of file AbstractTetrahedralMeshWriter.hpp.

Referenced by CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CmguiMeshWriter(), MeshalyzerMeshWriter< ELEMENT_DIM, SPACE_DIM >::MeshalyzerMeshWriter(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::VtkMeshWriter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodeCounterForParallelMesh

protected

Used by master process for polling processes for the next node

Definition at line 196 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesPerBoundaryElement

protected

Same as (ELEMENT_DIM), except when writing a quadratic mesh!

Definition at line 187 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesPerElement

protected

Same as (ELEMENT_DIM+1), except when writing a quadratic mesh!

Definition at line 186 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpDistributedMesh

protected

Another pointer to the mesh, produced by dynamic cast

Definition at line 190 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshWriterIterators<ELEMENT_DIM,SPACE_DIM>* AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters

protected

Handy iterators so that we know the next node/element to be written

Definition at line 192 of file AbstractTetrahedralMeshWriter.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh

protected

Pointer to the mesh (if we are writing from a mesh)

Definition at line 189 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMixedMesh

protected

Another pointer to the mesh, produced by dynamic cast

Definition at line 191 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

NodeMap* AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodeMap

private

Node map to be used when writing a mesh that has deleted nodes

Definition at line 182 of file AbstractTetrahedralMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mWriteMetaFile

protected

Whether to write a metafile (only used by MeshylazerMeshWriter)

Definition at line 195 of file AbstractTetrahedralMeshWriter.hpp.

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

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

mesh/src/writer/AbstractTetrahedralMeshWriter.hpp
mesh/src/writer/AbstractTetrahedralMeshWriter.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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