#include <ImmersedBoundaryMeshWriter.hpp>

Inheritance diagram for ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >:

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

	~ImmersedBoundaryMeshWriter ()

void	WriteFilesUsingMesh (ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

void	WriteVtkUsingMesh (ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::string stamp="")

void	MakeVtkMesh (ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

void	AddCellData (std::string dataName, std::vector< double > dataPayload)

void	AddPointData (std::string dataName, std::vector< double > dataPayload)

std::vector< double >	GetNextNode ()

ImmersedBoundaryElementData	GetNextImmersedBoundaryElement ()

ImmersedBoundaryElementData	GetNextImmersedBoundaryLamina ()

void	WriteFiles ()

void	FindElementOverlaps (ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

const std::vector< std::vector< unsigned > > &	rGetElementParts () const

void	MakeVtkMesh (ImmersedBoundaryMesh< 1, 1 > &rMesh)

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 ElementData	GetNextElement ()

virtual ElementData	GetNextBoundaryElement ()

virtual ElementData	GetNextCableElement ()

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

Private Types
using	geom_point = boost::geometry::model::point< double, 2, boost::geometry::cs::cartesian >

using	geom_segment = boost::geometry::model::segment< geom_point >

Private Member Functions
c_vector< double, SPACE_DIM >	GetIntersectionOfEdgeWithBoundary (const c_vector< double, SPACE_DIM > &rStart, const c_vector< double, SPACE_DIM > &rEnd)

c_vector< double, SPACE_DIM >	GetNearestCorner (const c_vector< double, SPACE_DIM > &rA, const c_vector< double, SPACE_DIM > &rB) const

Private Attributes
ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

MeshWriterIterators< ELEMENT_DIM, SPACE_DIM > *	mpIters

unsigned	mNumLaminas

std::vector< std::vector< unsigned > >	mElementParts

std::array< geom_segment, 4 >	mBoundaryEdges

vtkUnstructuredGrid *	mpVtkUnstructedMesh

Additional Inherited Members
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 ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >

A mesh writer class for immersed boundary meshes.

Definition at line 76 of file ImmersedBoundaryMeshWriter.hpp.

Member Typedef Documentation

◆ geom_point

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

using ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::geom_point = boost::geometry::model::point<double, 2, boost::geometry::cs::cartesian>

private

Shorthand for a 2d cartesian point

Definition at line 96 of file ImmersedBoundaryMeshWriter.hpp.

◆ geom_segment

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

using ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::geom_segment = boost::geometry::model::segment<geom_point>

private

Shorthand for a segment of geom_points

Definition at line 99 of file ImmersedBoundaryMeshWriter.hpp.

Constructor & Destructor Documentation

◆ ImmersedBoundaryMeshWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::ImmersedBoundaryMeshWriter	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		bool	clearOutputDir = `true`
	)

Constructor.

Parameters

rDirectory	reference to the output directory, relative to where Chaste output is stored
rBaseName	reference to the base name for results files
clearOutputDir	whether to clear the output directory prior to writing files (defaults to true)

Definition at line 63 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBoundaryEdges, ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpIters, ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh, and NEVER_REACHED.

◆ ~ImmersedBoundaryMeshWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Destructor.

Definition at line 102 of file ImmersedBoundaryMeshWriter.cpp.

Member Function Documentation

◆ AddCellData()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData	(	std::string	dataName,
		std::vector< double >	dataPayload
	)

Add data to a future VTK file.

Parameters

dataName	a tag to go into the VTK file
dataPayload	a pay-load of length (number of elements)

Definition at line 483 of file ImmersedBoundaryMeshWriter.cpp.

Referenced by ImmersedBoundaryCellPopulation< DIM >::WriteVtkResultsToFile().

◆ AddPointData()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData	(	std::string	dataName,
		std::vector< double >	dataPayload
	)

Add data to a future VTK file.

Parameters

dataName	a tag to go into the VTK file
dataPayload	a pay-load of length (number of nodes)

Definition at line 500 of file ImmersedBoundaryMeshWriter.cpp.

Referenced by ImmersedBoundaryCellPopulation< DIM >::WriteVtkResultsToFile().

◆ FindElementOverlaps()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::FindElementOverlaps ( ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Analyses the mesh to determine where (if at all) each element overlaps due to the periodic boundaries.

Parameters

rMesh the immersed boundary mesh

Definition at line 734 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), and NEVER_REACHED.

Referenced by ImmersedBoundaryCellPopulation< DIM >::WriteVtkResultsToFile().

◆ GetIntersectionOfEdgeWithBoundary()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetIntersectionOfEdgeWithBoundary	(	const c_vector< double, SPACE_DIM > &	rStart,
		const c_vector< double, SPACE_DIM > &	rEnd
	)

private

When elements cross the periodic boundary they are broken up into pieces for visualisation. Some additional points are needed where the element edge crosses the boundary to produce good output polygons.

This function returns the location on the boundary where an edge (given by rStart and rEnd) crosses d[0,1]x[0,1].

Parameters

rStart	the start point of the edge that crosses the boundary
rEnd	the end point of the edge that crosses the boundary

Returns: the point at which the edge rStart->rEnd crosses d[0,1]x[0,1]

Definition at line 769 of file ImmersedBoundaryMeshWriter.cpp.

References NEVER_REACHED.

◆ GetNearestCorner()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNearestCorner	(	const c_vector< double, SPACE_DIM > &	rA,
		const c_vector< double, SPACE_DIM > &	rB
	)		const

private

Helper function to get the nearest corner to the average of two points on the boundary.

Parameters

rA	one of the boundary points
rB	the other boundary point

Returns: the coordinates of the nearest corner of [0,1]x[0,1]

Definition at line 801 of file ImmersedBoundaryMeshWriter.cpp.

◆ GetNextImmersedBoundaryElement()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ImmersedBoundaryElementData ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextImmersedBoundaryElement ( )

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

Definition at line 147 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryElementData::AttributeValue, ImmersedBoundaryElementData::averageNodeSpacing, ImmersedBoundaryElementData::cornerNodeIndices, EXCEPTION, ImmersedBoundaryElementData::fluidSourceIndex, ImmersedBoundaryElementData::hasFluidSource, ImmersedBoundaryElementData::isBoundaryElement, and ImmersedBoundaryElementData::NodeIndices.

◆ GetNextImmersedBoundaryLamina()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ImmersedBoundaryElementData ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextImmersedBoundaryLamina ( )

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

Definition at line 192 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryElementData::AttributeValue, ImmersedBoundaryElementData::averageNodeSpacing, ImmersedBoundaryElementData::cornerNodeIndices, EXCEPTION, ImmersedBoundaryElementData::fluidSourceIndex, ImmersedBoundaryElementData::hasFluidSource, ImmersedBoundaryElementData::isBoundaryElement, and ImmersedBoundaryElementData::NodeIndices.

◆ GetNextNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< double > ImmersedBoundaryMeshWriter< 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 ImmersedBoundaryMeshWriter.cpp.

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

◆ MakeVtkMesh() [1/2]

void ImmersedBoundaryMeshWriter< 1, 1 >::MakeVtkMesh ( ImmersedBoundaryMesh< 1, 1 > & rMesh )

Template instnantiation for unused code path

Parameters

rMesh the mesh

Definition at line 477 of file ImmersedBoundaryMeshWriter.cpp.

◆ MakeVtkMesh() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh ( ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Populate mpVtkUnstructedMesh using a vertex-based mesh. Called by WriteVtkUsingMesh().

Parameters

rMesh reference to the vertex-based mesh

To allow viewing in Paraview, we have to treat differently cells which overlap the boundaries, as there is no support for periodicity in Paraview.

We overcome this by first identifying which cells overlap, and breaking them in to pieces as necessary, so that each cell when displayed stays contiguous.

Cell overlaps should have already been calculated - this is done by a call to FindElementOverlaps() from ImmersedBoundaryCellPopulation::WriteVtkResultsToFile().

Because no node can be present in more than one cell, it is safe to add points to mpVtkUnstructuredMesh as we go through each cell, rather than having to add nodes before cells.

Definition at line 283 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), Node< SPACE_DIM >::GetIndex(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetLaminaIteratorBegin(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetLaminaIteratorEnd(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), NEVER_REACHED, and Node< SPACE_DIM >::rGetLocation().

◆ rGetElementParts()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< std::vector< unsigned > > & ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::rGetElementParts ( ) const

Returns: reference to mElementParts

Definition at line 812 of file ImmersedBoundaryMeshWriter.cpp.

Referenced by ImmersedBoundaryCellPopulation< DIM >::WriteVtkResultsToFile().

◆ WriteFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Write mesh data to files. This method must be overridden in concrete classes.

Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 539 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryElementData::AttributeValue, ImmersedBoundaryElementData::averageNodeSpacing, ImmersedBoundaryElementData::cornerNodeIndices, ImmersedBoundaryElementData::fluidSourceIndex, ChasteBuildInfo::GetProvenanceString(), ImmersedBoundaryElementData::hasFluidSource, ImmersedBoundaryElementData::isBoundaryElement, and ImmersedBoundaryElementData::NodeIndices.

◆ WriteFilesUsingMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh ( ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Write files using a mesh.

Parameters

rMesh reference to the vertex-based mesh

Definition at line 517 of file ImmersedBoundaryMeshWriter.cpp.

References ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

Referenced by ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::save().

◆ WriteVtkUsingMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh	(	ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::string	stamp = `""`
	)

Write VTK file using a mesh.

Parameters

rMesh	reference to the immersed boundary mesh
stamp	is an optional stamp (like a time-stamp) to put into the name of the file

Definition at line 244 of file ImmersedBoundaryMeshWriter.cpp.

References NEVER_REACHED.

Referenced by ImmersedBoundaryCellPopulation< DIM >::WriteVtkResultsToFile().

Member Data Documentation

◆ mBoundaryEdges

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::array<geom_segment, 4> ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBoundaryEdges

private

Array of geom_segments; a helper array, filled by the constructor, for GetIntersectionOfEdgeWithBoundary

Definition at line 102 of file ImmersedBoundaryMeshWriter.hpp.

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

◆ mElementParts

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::vector<unsigned> > ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mElementParts

private

Vector containing, for each element, the node indices at which it must be split for visualisation

Definition at line 92 of file ImmersedBoundaryMeshWriter.hpp.

◆ mNumLaminas

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumLaminas

private

The number of laminas in the mesh

Definition at line 89 of file ImmersedBoundaryMeshWriter.hpp.

◆ mpIters

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

private

Iterators over the mesh

Definition at line 86 of file ImmersedBoundaryMeshWriter.hpp.

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

◆ mpMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ImmersedBoundaryMesh<ELEMENT_DIM,SPACE_DIM>* ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpMesh

private

If writing from a mesh object, the mesh to write to disk. Otherwise NULL.

Definition at line 83 of file ImmersedBoundaryMeshWriter.hpp.

◆ mpVtkUnstructedMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

vtkUnstructuredGrid* ImmersedBoundaryMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpVtkUnstructedMesh

private

Todo:: Merge into VtkMeshWriter (#1076)

Definition at line 129 of file ImmersedBoundaryMeshWriter.hpp.

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

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

mesh/src/immersed_boundary/ImmersedBoundaryMesh.hpp
mesh/src/immersed_boundary/ImmersedBoundaryMeshWriter.hpp
mesh/src/immersed_boundary/ImmersedBoundaryMeshWriter.cpp

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ geom_point

◆ geom_segment

Constructor & Destructor Documentation

◆ ImmersedBoundaryMeshWriter()

◆ ~ImmersedBoundaryMeshWriter()

Member Function Documentation

◆ AddCellData()

◆ AddPointData()

◆ FindElementOverlaps()

◆ GetIntersectionOfEdgeWithBoundary()

◆ GetNearestCorner()

◆ GetNextImmersedBoundaryElement()

◆ GetNextImmersedBoundaryLamina()

◆ GetNextNode()

◆ MakeVtkMesh() [1/2]

◆ MakeVtkMesh() [2/2]

◆ rGetElementParts()

◆ WriteFiles()

◆ WriteFilesUsingMesh()

◆ WriteVtkUsingMesh()

Member Data Documentation

◆ mBoundaryEdges

◆ mElementParts

◆ mNumLaminas

◆ mpIters

◆ mpMesh

◆ mpVtkUnstructedMesh