Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
VtkMeshWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#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< doubleGetNextNode ()
 
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, unsignedmGlobalToNodeIndexMap
 
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 >
OutputFileHandlermpOutputFileHandler
 
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

◆ VtkMeshWriter()

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
rDirectorythe directory in which to write the mesh to file
rBaseNamethe base name of the files in which to write the mesh data
rCleanDirectorywhether 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.

◆ ~VtkMeshWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::~VtkMeshWriter ( )
virtual

Destructor.

Definition at line 64 of file VtkMeshWriter.cpp.

Member Function Documentation

◆ AddCellData() [1/2]

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
nameis a meaningful name with which to annotate the data
datais 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.

◆ AddCellData() [2/2]

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
nameis a meaningful name with which to annotate the data
datais 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.

Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), and VtkNonlinearElasticitySolutionWriter< DIM >::Write().

◆ AddPointData() [1/2]

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
nameis a meaningful name with which to annotate the data
datais 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(), and UNUSED_OPT.

◆ AddPointData() [2/2]

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

◆ AddProvenance()

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
fileNameis 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().

◆ AddTensorCellData() [1/2]

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
nameis a meaningful name with which to annotate the data
datais 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.

◆ AddTensorCellData() [2/2]

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
nameis a meaningful name with which to annotate the data
datais 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.

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

◆ AddTensorPointData()

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
nameis a meaningful name with which to annotate the data
datais 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.

◆ AugmentCellData()

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.

◆ MakeVtkMesh()

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.

References ElementData::AttributeValue, and ElementData::NodeIndices.

◆ SetParallelFiles()

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

◆ WriteFiles()

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.

◆ WriteFilesUsingMesh()

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
rMeshthe mesh
keepOriginalElementIndexingWhether 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.

References PetscTools::AmMaster(), 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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements(), PetscTools::GetNumProcs(), PetscTools::IsSequential(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

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

Member Data Documentation

◆ mGlobalToNodeIndexMap

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.

◆ mNodesToReceivePerProcess

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.

◆ mNodesToSendPerProcess

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.

◆ mpNodesOnlyMesh

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.

◆ mpVtkUnstructedMesh

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.

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

◆ mWriteParallelFiles

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.


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