#include <VtkMeshWriter.hpp>

Inheritance diagram for VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >:

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

void	WriteFiles ()

void	AddCellData (std::string name, std::vector< double > data)

void	AddCellData (std::string name, std::vector< c_vector< double, SPACE_DIM > > data)

void	AddTensorCellData (std::string name, std::vector< c_vector< double, SPACE_DIM *(SPACE_DIM+1)/2 > > data)

void	AddTensorCellData (std::string name, std::vector< c_matrix< double, SPACE_DIM, SPACE_DIM > > data)

void	AddPointData (std::string name, std::vector< double > data)

void	AddPointData (std::string name, std::vector< c_vector< double, SPACE_DIM > > data)

void	AddTensorPointData (std::string name, std::vector< c_matrix< double, SPACE_DIM, SPACE_DIM > > data)

void	SetParallelFiles (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

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

void	AddProvenance (std::string fileName)

virtual	~VtkMeshWriter ()

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)

Private Member Functions
void	MakeVtkMesh ()

void	AugmentCellData ()

Private Attributes
bool	mWriteParallelFiles

std::map< unsigned, unsigned >	mGlobalToNodeIndexMap

std::vector< std::vector< unsigned > >	mNodesToSendPerProcess

std::vector< std::vector< unsigned > >	mNodesToReceivePerProcess

NodesOnlyMesh< SPACE_DIM > *	mpNodesOnlyMesh

vtkUnstructuredGrid *	mpVtkUnstructedMesh

Additional Inherited Members
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 VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >

VtkMeshWriter

Writes a mesh in VTK .vtu format (that's an XML-based, data compressed unstructured mesh)

Definition at line 71 of file VtkMeshWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::VtkMeshWriter	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		const bool &	rCleanDirectory = `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
rCleanDirectory	whether to clean the directory (defaults to true)

Definition at line 51 of file VtkMeshWriter.cpp.

References AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mIndexFromZero, and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor.

Definition at line 64 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData	(	std::string	name,
		std::vector< double >	data
	)

Add a scalar data field to each element (known as "cell" in VTK).

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the element numbering The length of the data vector is assumed to match the number of elements in the mesh. Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 207 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), VtkNonlinearElasticitySolutionWriter< DIM >::Write(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData	(	std::string	name,
		std::vector< c_vector< double, SPACE_DIM > >	data
	)

Add a vector data field to each element (known as "cell" in VTK).

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the element numbering The length of the data vector is assumed to match the number of elements in the mesh. Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 255 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData	(	std::string	name,
		std::vector< double >	data
	)

Add a scalar data field to each node (known as "point" in VTK).

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the node numbering The length of the data vector is assumed to match the number of nodes in the mesh Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 352 of file VtkMeshWriter.cpp.

References PetscTools::GetMyRank(), PetscTools::GetNumProcs(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGlobalToNodeIndexMap, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesToReceivePerProcess, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesToSendPerProcess, AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpDistributedMesh, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mWriteParallelFiles, and UNUSED_OPT.

Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), AbstractPdeModifier< DIM >::UpdateAtEndOfOutputTimeStep(), VtkNonlinearElasticitySolutionWriter< DIM >::Write(), and LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData	(	std::string	name,
		std::vector< c_vector< double, SPACE_DIM > >	data
	)

Add a vector data field to each node (known as "point" in VTK).

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the node numbering The length of the data vector is assumed to match the number of nodes in the mesh Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 426 of file VtkMeshWriter.cpp.

References PetscTools::GetMyRank(), PetscTools::GetNumProcs(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGlobalToNodeIndexMap, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesToReceivePerProcess, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesToSendPerProcess, AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpDistributedMesh, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mWriteParallelFiles, and UNUSED_OPT.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddProvenance ( std::string fileName )

Add Chaste provenance data to a VTK file as an XML comment string

Parameters

fileName is the file name relative to mpOutputFileHandler The file is assumed have been written to and to be closed - so that it can safely be appended to.

Definition at line 173 of file VtkMeshWriter.cpp.

References ChasteBuildInfo::GetProvenanceString(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, and OutputFileHandler::OpenOutputFile().

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddTensorCellData	(	std::string	name,
		std::vector< c_vector< double, SPACE_DIM *(SPACE_DIM+1)/2 > >	data
	)

Add a symmetric tensor data field to each element (known as "cell" in VTK).

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the element numbering The length of the data vector is assumed to match the number of elements in the mesh. The data vector represents the lower half of the tensor Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 279 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

Referenced by VtkNonlinearElasticitySolutionWriter< DIM >::Write().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddTensorCellData	(	std::string	name,
		std::vector< c_matrix< double, SPACE_DIM, SPACE_DIM > >	data
	)

Add a tensor data field to each element (known as "cell" in VTK).

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the element numbering The length of the data vector is assumed to match the number of elements in the mesh. Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 315 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddTensorPointData	(	std::string	name,
		std::vector< c_matrix< double, SPACE_DIM, SPACE_DIM > >	data
	)

Add a tensor data field to each point.

Parameters

name	is a meaningful name with which to annotate the data
data	is the data which should appear in the same order as the node numbering The length of the data vector is assumed to match the number of nodes in the mesh Checking cannot be done at this stage since the data is associated with an empty VTK mesh structure.

Definition at line 510 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AugmentCellData ( )

private

At the time of adding VTK cell data, it is assumed that there is one piece of data for each element in the original mesh. If the mesh is mixed-dimension (elements and cable elements) the VTK mesh makes no distinction between the two types of cells. All data associated with cells must be the same length as the overall number of cells. This method inspects each cell data component and adds dummy data to cover the cable elements.

Definition at line 222 of file VtkMeshWriter.cpp.

References AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumCableElements(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpDistributedMesh, AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMixedMesh, VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh, and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mWriteParallelFiles.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh ( )

private

Private helper method which copies the mesh details into the waiting VTK mesh structure. Called by WriteFiles().

Todo:: #2351 Temporary workaround for parallel writer

Definition at line 70 of file VtkMeshWriter.cpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Should be called to enable files to be written in parallel (i.e. a .pvtu file and .vtu files for each process's sub-mesh).

Parameters

rMesh the mesh (must be a DistributedTetrahedralMesh)

Definition at line 546 of file VtkMeshWriter.cpp.

Referenced by Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Write mesh data to files.

Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 184 of file VtkMeshWriter.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddProvenance(), OutputFileHandler::GetOutputDirectoryFullPath(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Write files. Overrides the method implemented in AbstractTetrahedralMeshWriter, which concentrates mesh data onto a single file in order to output a monolithic file. For VTK, a DistributedTetrahedralMesh in parallel is instead written out as a set of .vtu files (one for each sub-mesh) and a .pvtu file that provides the visualizer with information about them.

Parameters

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

Todo:: #1322 Mesh should really be const!

Todo:: #1322 Mesh should be const

Todo:: This ought to look exactly like the other MakeVtkMesh

Add to the main file

Todo:: #1494 Do we need a barrier?

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 596 of file VtkMeshWriter.cpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), AbstractPdeModifier< DIM >::UpdateAtEndOfOutputTimeStep(), VtkNonlinearElasticitySolutionWriter< DIM >::Write(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGlobalToNodeIndexMap

private

Map a global node index into a local index (into mNodes and mHaloNodes as if they were concatenated)

Definition at line 79 of file VtkMeshWriter.hpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::vector<unsigned> > VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesToReceivePerProcess

private

Used to communicate node-wise halo data

Definition at line 82 of file VtkMeshWriter.hpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::vector<unsigned> > VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesToSendPerProcess

private

Used to communicate node-wise halo data

Definition at line 81 of file VtkMeshWriter.hpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

NodesOnlyMesh<SPACE_DIM>* VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpNodesOnlyMesh

private

A pointer to a NodesOnlyMesh to write to file, created by dynamic cast

Definition at line 85 of file VtkMeshWriter.hpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

vtkUnstructuredGrid* VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh

private

A VTK mesh data structure. Created at construction, has data associated with it by AddCellData and AddCellPoint, then is filled with mesh geometry by MakeVtkMesh() in WriteFiles().

Definition at line 93 of file VtkMeshWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::mWriteParallelFiles

private

Whether to write parallel (.pvtu + .vtu for each process) files, defaults to false

Definition at line 77 of file VtkMeshWriter.hpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AugmentCellData(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

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

mesh/src/writer/VtkMeshWriter.hpp
mesh/src/writer/VtkMeshWriter.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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