#include <DiscreteContinuumMesh.hpp>

Inheritance diagram for DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	DiscreteContinuumMesh ()

	~DiscreteContinuumMesh ()

std::vector< std::vector< unsigned > >	GetConnectivity ()

std::vector< c_vector< double, SPACE_DIM > >	GetNodeLocations ()

std::vector< c_vector< double, SPACE_DIM > >	GetElementCentroids ()

std::vector< DimensionalChastePoint< SPACE_DIM > >	GetNodeLocationsAsPoints ()

std::vector< unsigned >	GetElementRegionMarkers ()

units::quantity< unit::length >	GetReferenceLengthScale ()

std::vector< std::vector< unsigned > >	GetPointElementMap (std::vector< DimensionalChastePoint< SPACE_DIM > > points)

const std::vector< std::vector< CellPtr > > &	GetElementCellMap (bool update=true)

std::vector< std::vector< boost::shared_ptr< VesselSegment< SPACE_DIM > > > >	GetElementSegmentMap (bool update=true, bool useVesselSurface=false)

vtkSmartPointer< vtkUnstructuredGrid >	GetAsVtkUnstructuredGrid ()

void	SetAttributes (std::vector< unsigned > attributes)

void	SetCellPopulation (AbstractCellPopulation< SPACE_DIM > &rCellPopulation, units::quantity< unit::length > cellLengthScale)

void	SetVesselNetwork (boost::shared_ptr< VesselNetwork< SPACE_DIM > > pNetwork)

void	ImportDiscreteContinuumMeshFromTetgen (tetgen::tetgenio &mesherOutput, unsigned numberOfElements, int elementList, unsigned numberOfFaces, int faceList, int *edgeMarkerList)

Static Public Member Functions
static boost::shared_ptr< DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM > >	Create ()

Private Attributes
std::vector< unsigned >	mAttributes

units::quantity< unit::length >	mReferenceLength

vtkSmartPointer< vtkUnstructuredGrid >	mpVtkMesh

vtkSmartPointer< vtkCellLocator >	mpVtkCellLocator

bool	mVtkRepresentationUpToDate

std::vector< std::vector< unsigned > >	mPointElementMap

std::vector< std::vector< boost::shared_ptr< VesselSegment< SPACE_DIM > > > >	mSegmentElementMap

std::vector< std::vector< CellPtr > >	mCellElementMap

boost::shared_ptr< VesselNetwork< SPACE_DIM > >	mpNetwork

AbstractCellPopulation< SPACE_DIM > *	mpCellPopulation

units::quantity< unit::length >	mCellPopulationReferenceLength

Friends
class	DiscreteContinuumMeshGenerator< ELEMENT_DIM, SPACE_DIM >

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >

This is a TetrahedralMesh with some extra functions for point locating, output of node locations and connectivity and attribute storage. It uses its own version of ImportFromTetgen with fewer template arguements. There is scope for merging this versions with the one in TetrahedralMesh.

Definition at line 67 of file DiscreteContinuumMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::DiscreteContinuumMesh ( )

Constructor

Definition at line 58 of file DiscreteContinuumMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Destructor

Definition at line 82 of file DiscreteContinuumMesh.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

boost::shared_ptr< DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::Create ( )

static

Factory constructor method

Returns: a shared pointer to a new mesh

Definition at line 75 of file DiscreteContinuumMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

vtkSmartPointer< vtkUnstructuredGrid > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid ( )

Return the mesh as a vtk unstructured grid

Returns: the mesh as a vtk unstructured grid

Definition at line 94 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetConnectivity(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeLocations(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkCellLocator, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkMesh, and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mVtkRepresentationUpToDate.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetPointElementMap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< std::vector< unsigned > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetConnectivity ( )

Return the element connectivity

Returns: the element connectivity

Definition at line 315 of file DiscreteContinuumMesh.cpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< std::vector< CellPtr > > & DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap ( bool update = true )

Return the point cell map

Parameters

update update the map

Returns: the point cell map

Definition at line 207 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mCellElementMap, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mCellPopulationReferenceLength, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpCellPopulation, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkCellLocator, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mReferenceLength, and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mVtkRepresentationUpToDate.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_vector< double, SPACE_DIM > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCentroids ( )

Return the element centroids

Returns: the element centroids

Definition at line 159 of file DiscreteContinuumMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< unsigned > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementRegionMarkers ( )

Return the element-wise region markers

Returns: the element-wise region markers

Definition at line 153 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mAttributes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< std::vector< boost::shared_ptr< VesselSegment< SPACE_DIM > > > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementSegmentMap	(	bool	update = `true`,
		bool	useVesselSurface = `false`
	)

Return the point segments map

Parameters

update	update the map
useVesselSurface	use a surface based representation for vessels

Returns: the point segment map

Definition at line 256 of file DiscreteContinuumMesh.cpp.

References DimensionalChastePoint< DIM >::GetLocation(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpNetwork, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkCellLocator, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mReferenceLength, and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mSegmentElementMap.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_vector< double, SPACE_DIM > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeLocations ( )

Return the node locations

Returns: the node locations

Definition at line 333 of file DiscreteContinuumMesh.cpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< DimensionalChastePoint< SPACE_DIM > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeLocationsAsPoints ( )

Return the node locations

Returns: the node locations as chaste points

Definition at line 345 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mReferenceLength.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< std::vector< unsigned > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetPointElementMap ( std::vector< DimensionalChastePoint< SPACE_DIM > > points )

Return a map of element indices corresponding to the input points

Parameters

points the input points

Returns: a map of element indices corresponding to the input points

Definition at line 170 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mPointElementMap, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkCellLocator, DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mReferenceLength, and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mVtkRepresentationUpToDate.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

units::quantity< unit::length > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetReferenceLengthScale ( )

Return the reference length scale

Returns: the reference length scale

Definition at line 88 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mReferenceLength.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::ImportDiscreteContinuumMeshFromTetgen	(	tetgen::tetgenio &	mesherOutput,
		unsigned	numberOfElements,
		int *	elementList,
		unsigned	numberOfFaces,
		int *	faceList,
		int *	edgeMarkerList
	)

This is the same as the TetrahedralMesh implementation of ImportFromMesher but avoids some templating

Parameters

mesherOutput	tetgen output
numberOfElements	the number of elements
elementList	the element list
numberOfFaces	the number of faces
faceList	the face list
edgeMarkerList	an edge marker list

Definition at line 357 of file DiscreteContinuumMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetAttributes ( std::vector< unsigned > attributes )

Set element attributes

Parameters

attributes the element attributes

Definition at line 486 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mAttributes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetCellPopulation	(	AbstractCellPopulation< SPACE_DIM > &	rCellPopulation,
		units::quantity< unit::length >	cellLengthScale
	)

Set the cell population

Parameters

rCellPopulation a reference to the cell population

Definition at line 492 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mCellPopulationReferenceLength, and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpCellPopulation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetVesselNetwork ( boost::shared_ptr< VesselNetwork< SPACE_DIM > > pNetwork )

Set the vessel network

Parameters

pNetwork the vessel network

Definition at line 500 of file DiscreteContinuumMesh.cpp.

References DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpNetwork.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class DiscreteContinuumMeshGenerator< ELEMENT_DIM, SPACE_DIM >

friend

For access to ImportFromMesher

Definition at line 72 of file DiscreteContinuumMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector<unsigned> DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mAttributes

private

Store element-wise region markers

Definition at line 77 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementRegionMarkers(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetAttributes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector<std::vector<CellPtr > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mCellElementMap

private

The cell element map

Definition at line 112 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

units::quantity<unit::length> DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mCellPopulationReferenceLength

private

The reference length scale for the mesh

Definition at line 127 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

AbstractCellPopulation<SPACE_DIM>* DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpCellPopulation

private

The cell population. This memory pointed to is not managed in this class.

Definition at line 122 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

boost::shared_ptr<VesselNetwork<SPACE_DIM> > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpNetwork

private

The vessel network

Definition at line 117 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementSegmentMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::SetVesselNetwork().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector<std::vector<unsigned> > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mPointElementMap

private

The point element map

Definition at line 102 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetPointElementMap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

vtkSmartPointer<vtkCellLocator> DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkCellLocator

private

A vtk cell locator

Definition at line 92 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementSegmentMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetPointElementMap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

vtkSmartPointer<vtkUnstructuredGrid> DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mpVtkMesh

private

A vtk representation

Definition at line 87 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

units::quantity<unit::length> DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mReferenceLength

private

The reference length scale for the mesh

Definition at line 82 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementSegmentMap(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeLocationsAsPoints(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetPointElementMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetReferenceLengthScale().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > > DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mSegmentElementMap

private

The segment element map

Definition at line 107 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementSegmentMap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::mVtkRepresentationUpToDate

private

Is the vtk representation up to date

Definition at line 97 of file DiscreteContinuumMesh.hpp.

Referenced by DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetAsVtkUnstructuredGrid(), DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetElementCellMap(), and DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >::GetPointElementMap().

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

projects/MicrovesselChaste/src/mesh/DiscreteContinuumMesh.hpp
projects/MicrovesselChaste/src/mesh/DiscreteContinuumMesh.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM> class DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM >