Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
|
#include <VtkMeshWriter.hpp>
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 |
Writes a mesh in VTK .vtu format (that's an XML-based, data compressed unstructured mesh)
Definition at line 71 of file VtkMeshWriter.hpp.
VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::VtkMeshWriter | ( | const std::string & | rDirectory, |
const std::string & | rBaseName, | ||
const bool & | rCleanDirectory = true |
||
) |
Constructor.
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.
|
virtual |
Destructor.
Definition at line 64 of file VtkMeshWriter.cpp.
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).
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.
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).
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.
Referenced by AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), and VtkNonlinearElasticitySolutionWriter< DIM >::Write().
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).
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(), and UNUSED_OPT.
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).
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(), and UNUSED_OPT.
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().
void VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddProvenance | ( | std::string | fileName | ) |
Add Chaste provenance data to a VTK file as an XML comment string
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().
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).
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.
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).
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.
Referenced by VtkNonlinearElasticitySolutionWriter< DIM >::Write().
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.
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.
|
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.
|
private |
Private helper method which copies the mesh details into the waiting VTK mesh structure. Called by WriteFiles().
Definition at line 70 of file VtkMeshWriter.cpp.
References ElementData::AttributeValue, and ElementData::NodeIndices.
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).
rMesh | the mesh (must be a DistributedTetrahedralMesh) |
Definition at line 546 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(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile().
|
virtual |
Write mesh data to files.
Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 184 of file VtkMeshWriter.cpp.
|
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.
rMesh | the mesh |
keepOriginalElementIndexing | Whether to write the mesh with the same element ordering. Optimisations can be applied if this is not needed. |
Add to the main file
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().
|
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.
|
private |
Used to communicate node-wise halo data
Definition at line 82 of file VtkMeshWriter.hpp.
|
private |
Used to communicate node-wise halo data
Definition at line 81 of file VtkMeshWriter.hpp.
|
private |
A pointer to a NodesOnlyMesh to write to file, created by dynamic cast
Definition at line 85 of file VtkMeshWriter.hpp.
|
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().
|
private |
Whether to write parallel (.pvtu + .vtu for each process) files, defaults to false
Definition at line 77 of file VtkMeshWriter.hpp.