Chaste Release::3.1
Public Member Functions | Private Member Functions | Private Attributes
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 >:

List of all members.

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

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
vtkUnstructuredGrid * mpVtkUnstructedMesh

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 66 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:
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 49 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 62 of file VtkMeshWriter.cpp.

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:
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 196 of file VtkMeshWriter.cpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput().

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 244 of file VtkMeshWriter.cpp.

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:
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 269 of file VtkMeshWriter.cpp.

References PetscTools::GetMyRank(), and PetscTools::GetNumProcs().

Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), 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:
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 359 of file VtkMeshWriter.cpp.

References PetscTools::GetMyRank(), and PetscTools::GetNumProcs().

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 161 of file VtkMeshWriter.cpp.

References ChasteBuildInfo::GetProvenanceString().

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 211 of file VtkMeshWriter.cpp.

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().

Definition at line 68 of file VtkMeshWriter.cpp.

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

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:
rMeshthe mesh (must be a DistributedTetrahedralMesh)

Definition at line 461 of file VtkMeshWriter.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), and PetscTools::IsSequential().

Referenced by Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter().

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 172 of file VtkMeshWriter.cpp.

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

Add to the main file

Todo:
#1494 Do we need a barrier?

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 508 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 AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), and Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter().

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 74 of file VtkMeshWriter.hpp.

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 77 of file VtkMeshWriter.hpp.

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 76 of file VtkMeshWriter.hpp.

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 86 of file VtkMeshWriter.hpp.

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

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 72 of file VtkMeshWriter.hpp.

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