#include <VertexMesh.hpp>

Inheritance diagram for VertexMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for VertexMesh< ELEMENT_DIM, SPACE_DIM >:

Classes
class	VertexElementIterator

Public Member Functions
VertexElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)

VertexElementIterator	GetElementIteratorEnd ()

	VertexMesh (std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements)

	VertexMesh (std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM-1, SPACE_DIM > * > faces, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements)

	VertexMesh (TetrahedralMesh< 2, 2 > &rMesh, bool isPeriodic=false)

	VertexMesh (TetrahedralMesh< 3, 3 > &rMesh)

	VertexMesh ()

virtual	~VertexMesh ()

virtual unsigned	GetNumNodes () const

virtual unsigned	GetNumElements () const

unsigned	GetNumAllElements () const

virtual unsigned	GetNumFaces () const

VertexElement< ELEMENT_DIM, SPACE_DIM > *	GetElement (unsigned index) const

VertexElement< ELEMENT_DIM-1, SPACE_DIM > *	GetFace (unsigned index) const

virtual c_vector< double, SPACE_DIM >	GetCentroidOfElement (unsigned index)

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

virtual void	Clear ()

unsigned	GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex (unsigned elementIndex)

unsigned	GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex (unsigned nodeIndex)

unsigned	GetRosetteRankOfElement (unsigned index)

virtual c_vector< double, SPACE_DIM >	GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)

virtual double	GetVolumeOfElement (unsigned index)

virtual double	GetSurfaceAreaOfElement (unsigned index)

c_vector< double, SPACE_DIM >	GetAreaGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)

c_vector< double, SPACE_DIM >	GetPreviousEdgeGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)

c_vector< double, SPACE_DIM >	GetNextEdgeGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)

c_vector< double, SPACE_DIM >	GetPerimeterGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)

virtual c_vector< double, 3 >	CalculateMomentsOfElement (unsigned index)

double	GetEdgeLength (unsigned elementIndex1, unsigned elementIndex2)

double	GetElongationShapeFactorOfElement (unsigned elementIndex)

double	CalculateUnitNormalToFaceWithArea (VertexElement< ELEMENT_DIM-1, SPACE_DIM > *pFace, c_vector< double, SPACE_DIM > &rNormal)

virtual double	CalculateAreaOfFace (VertexElement< ELEMENT_DIM-1, SPACE_DIM > *pFace)

c_vector< double, SPACE_DIM >	GetShortAxisOfElement (unsigned index)

std::set< unsigned >	GetNeighbouringNodeIndices (unsigned nodeIndex)

std::set< unsigned >	GetNeighbouringNodeNotAlsoInElement (unsigned nodeIndex, unsigned elemIndex)

std::set< unsigned >	GetNeighbouringElementIndices (unsigned elementIndex)

template<>
	VertexMesh (TetrahedralMesh< 2, 2 > &rMesh, bool isPeriodic)

template<>
	VertexMesh (TetrahedralMesh< 3, 3 > &rMesh)

Public Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
NodeIterator	GetNodeIteratorBegin (bool skipDeletedNodes=true)

NodeIterator	GetNodeIteratorEnd ()

	AbstractMesh ()

virtual	~AbstractMesh ()

unsigned	GetNumBoundaryNodes () const

virtual unsigned	GetNumAllNodes () const

unsigned	GetNumNodeAttributes () const

Node< SPACE_DIM > *	GetNode (unsigned index) const

virtual Node< SPACE_DIM > *	GetNodeOrHaloNode (unsigned index) const

Node< SPACE_DIM > *	GetNodeFromPrePermutationIndex (unsigned index) const

virtual void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

virtual DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

virtual void	PermuteNodes ()

BoundaryNodeIterator	GetBoundaryNodeIteratorBegin () const

BoundaryNodeIterator	GetBoundaryNodeIteratorEnd () const

std::string	GetMeshFileBaseName () const

bool	IsMeshOnDisk () const

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

double	GetDistanceBetweenNodes (unsigned indexA, unsigned indexB)

virtual double	GetWidth (const unsigned &rDimension) const

virtual ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const

virtual unsigned	GetNearestNodeIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

virtual void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)

virtual void	Translate (const c_vector< double, SPACE_DIM > &rDisplacement)

void	Translate (const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0)

virtual void	Rotate (c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)

void	Rotate (c_vector< double, 3 > axis, double angle)

void	RotateX (const double theta)

void	RotateY (const double theta)

void	RotateZ (const double theta)

void	Rotate (double theta)

virtual void	RefreshMesh ()

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

Protected Member Functions
unsigned	SolveNodeMapping (unsigned index) const

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

void	GenerateVerticesFromElementCircumcentres (TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

bool	ElementIncludesPoint (const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex)

unsigned	GetLocalIndexForElementEdgeClosestToPoint (const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex)

template<class Archive >
void	save (Archive &archive, const unsigned int version) const

template<class Archive >
void	load (Archive &archive, const unsigned int version)

Protected Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
virtual void	SetElementOwnerships ()

ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

Protected Attributes
std::vector< VertexElement < ELEMENT_DIM, SPACE_DIM > * >	mElements

std::vector< VertexElement < ELEMENT_DIM-1, SPACE_DIM > * >	mFaces

std::map< unsigned, unsigned >	mVoronoiElementIndexMap

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpDelaunayMesh

Protected Attributes inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< Node< SPACE_DIM > * >	mNodes

std::vector< Node< SPACE_DIM > * >	mBoundaryNodes

DistributedVectorFactory *	mpDistributedVectorFactory

std::vector< unsigned >	mNodePermutation

std::string	mMeshFileBaseName

bool	mMeshChangesDuringSimulation

Friends
class	TestVertexMesh

class	boost::serialization::access

Additional Inherited Members
Public Types inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node < SPACE_DIM > * >::const_iterator	BoundaryNodeIterator

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class VertexMesh< ELEMENT_DIM, SPACE_DIM >

A vertex-based mesh class, in which elements may contain different numbers of nodes. This is facilitated by the VertexElement class.

This class has two applications in the cell_based code.

First, VertexMesh is used as a member of the MeshBasedCellPopulation class to represent a Voronoi tessellation, the dual to a Delaunay mesh, which allows the shapes of cells to be visualised in simulations of a class of off-lattice cell centre-based models.

Second, VertexMesh serves as a parent class for MutableVertexMesh, which is used as a member of the VertexBasedCellPopulation class to represent the junctional network of cells that forms the basis of simulations of off-lattice vertex-based models.

Definition at line 74 of file VertexMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh	(	std::vector< Node< SPACE_DIM > * >	nodes,
		std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * >	vertexElements
	)

Default constructor.

Parameters

nodes	vector of pointers to nodes
vertexElements	vector of pointers to VertexElements

Definition at line 41 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh	(	std::vector< Node< SPACE_DIM > * >	nodes,
		std::vector< VertexElement< ELEMENT_DIM-1, SPACE_DIM > * >	faces,
		std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * >	vertexElements
	)

Constructor.

Parameters

nodes	vector of pointers to nodes
faces	vector of pointer to VertexElements
vertexElements	vector of pointers to VertexElement<3,3>s

Definition at line 105 of file VertexMesh.cpp.

References Node< SPACE_DIM >::AddElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh	(	TetrahedralMesh< 2, 2 > &	rMesh,
		bool	isPeriodic = `false`
	)

Alternative 2D 'Voronoi' constructor. Creates a Voronoi tessellation of a given tetrahedral mesh, which must be Delaunay (see TetrahedralMesh::CheckIsVoronoi).

Todo:: Merge with 3D Voronoi constructor? (see #1075)

Parameters

rMesh	a tetrahedral mesh
isPeriodic	a boolean that indicates whether the mesh is periodic or not

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh ( TetrahedralMesh< 3, 3 > & rMesh )

Alternative 3D 'Voronoi' constructor. Creates a Voronoi tessellation of a given tetrahedral mesh, which must be Delaunay (see TetrahedralMesh::CheckIsVoronoi).

Todo:: Merge with 2D Voronoi constructor? (see #1075)

Parameters

rMesh a tetrahedral mesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh ( )

Default constructor for use by serializer.

Definition at line 465 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor.

Definition at line 474 of file VertexMesh.cpp.

template<>

VertexMesh< 2, 2 >::VertexMesh	(	TetrahedralMesh< 2, 2 > &	rMesh,
		bool	isPeriodic
	)

This VertexMesh constructor is currently only defined for 2D meshes.

Parameters

rMesh	a tetrahedral mesh
isPeriodic	a boolean that indicates whether the mesh is periodic or not

Create a std::vector of pairs, where each pair comprises the angle between the centre of the Voronoi element and each node with that node's global index in the Voronoi mesh.

Definition at line 154 of file VertexMesh.cpp.

References MutableElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh.

template<>

VertexMesh< 3, 3 >::VertexMesh ( TetrahedralMesh< 3, 3 > & rMesh )

This VertexMesh constructor is currently only defined for 3D meshes.

Parameters

rMesh a tetrahedral mesh

Create a std::vector of pairs, where each pair comprises the angle between the centre of the Voronoi element and each node with that node's global index in the Voronoi mesh.

Definition at line 244 of file VertexMesh.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateAreaOfFace ( VertexElement< ELEMENT_DIM-1, SPACE_DIM > * pFace )

virtual

Get the area of a given face in 3D. Uses CalculateUnitNormalToFaceWithArea

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

pFace a face in the mesh

Returns: the area

Definition at line 1554 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 3 > VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement ( unsigned index )

virtual

Compute the second moments and product moment of area for a given 2D element about its centroid. These are:

I_xx, the second moment of area about an axis through the centroid of the element parallel to the x-axis;

I_yy, the second moment of area about an axis through the centroid of the element parallel to the y-axis;

and I_xy, product moment of area through the centroid of the element.

Formulae for these quantities may be found e.g. in the following reference:

Mechanics of Materials James M. Gere (Author), Barry J. Goodno. Cengage Learning; 8th edition (January 1, 2012)

This method is used within GetShortAxisOfElement() to compute the direction of the shortest principal axis passing through the centroid, or 'short axis', of the element.

Note that by definition, the second moments of area must be non-negative, while the product moment of area may not be.

Parameters

index the global index of a specified vertex element

Returns: (Ixx,Iyy,Ixy).

Definition at line 1336 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateUnitNormalToFaceWithArea	(	VertexElement< ELEMENT_DIM-1, SPACE_DIM > *	pFace,
		c_vector< double, SPACE_DIM > &	rNormal
	)

Compute the unit normal vector to a given face in 3D. This is achieved by calculating scaled normal, which is the effective sum of signed areas of triangle forming the face. Note: this may return the outward or inward normal, depending on the face chirality.

Parameters

pFace	a face in the mesh
rNormal	vector in which to return the unit normal

Returns: the area

Definition at line 1524 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VectorProduct().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear ( )

virtual

Delete mNodes, mFaces and mElements.

Reimplemented in MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >, MutableVertexMesh< 2, 2 >, and MutableVertexMesh< DIM, DIM >.

Definition at line 585 of file VertexMesh.cpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader ( AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > & rMeshReader )

Construct the mesh using a MeshReader.

Parameters

rMeshReader the mesh reader

Referenced by VertexMesh< DIM, DIM >::load().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool VertexMesh< ELEMENT_DIM, SPACE_DIM >::ElementIncludesPoint	(	const c_vector< double, SPACE_DIM > &	rTestPoint,
		unsigned	elementIndex
	)

protected

Test whether a given point lies inside a given element.

We use a winding number test, which counts the number of times the polygon associated with the element winds around the given point. The point is outside only when this "winding number" vanishes; otherwise, the point is inside.

One must decide whether a point on the polygon's boundary is inside or outside: we adopt the standard convention that a point on a left or bottom edge is inside, and a point on a right or top edge is outside. This way, if two distinct polygons share a common boundary segment, then a point on that segment will be in one polygon or the other, but not both at the same time.

Parameters

rTestPoint	the point to test
elementIndex	global index of the element in the mesh

Returns: if the point is included in the element.

Todo:: (see #2387 and #2401) Investigate why the commented implementation causes Test2DVertexBasedCryptRepresentativeSimulation to fail

Definition at line 1151 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres ( TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

protected

Populate mNodes with locations corresponding to the element circumcentres of a given TetrahedralMesh. Used by 'Voronoi' constructors.

Parameters

rMesh a tetrahedral mesh

Definition at line 386 of file VertexMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements().

Referenced by Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode	(	VertexElement< ELEMENT_DIM, SPACE_DIM > *	pElement,
		unsigned	localIndex
	)

Compute the area gradient of a 2D element at one of its nodes.

N.B. This calls GetVectorFromAtoB(), which can be overridden in daughter classes for non-Euclidean metrics.

Parameters

pElement	pointer to a specified vertex element
localIndex	local index of a node in this element

Returns: the gradient of the area of the element, evaluated at this node.

Definition at line 1442 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

Referenced by FarhadifarForce< DIM >::AddForceContribution(), and NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement ( unsigned index )

virtual

Compute the centroid of an element.

A formula for the centroid of a plane polygon may be found e.g. in the following reference:

Mechanics of Materials James M. Gere (Author), Barry J. Goodno. Cengage Learning; 8th edition (January 1, 2012)

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

index the global index of a specified vertex element

Returns: (centroid_x, centroid_y).

Todo:: compute centroid rather than centre of mass (see #1422)

Definition at line 655 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex ( unsigned elementIndex )

Returns: the global index of the corresponding element in the Delaunay mesh, given the global index of an element in the Voronoi mesh.

Parameters

elementIndex global index of an element in the Voronoi mesh

Definition at line 506 of file VertexMesh.cpp.

References UNSIGNED_UNSET.

Referenced by VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength	(	unsigned	elementIndex1,
		unsigned	elementIndex2
	)

Returns: the length of the edge separating two given elements in 2D.

Parameters

elementIndex1	index of an element in the mesh
elementIndex2	index of an element in the mesh

Definition at line 412 of file VertexMesh.cpp.

References EXCEPTION.

Referenced by HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexElement< ELEMENT_DIM, SPACE_DIM > * VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement ( unsigned index ) const

Parameters

index the global index of a specified vertex element.

Returns: a pointer to the vertex element

Definition at line 639 of file VertexMesh.cpp.

Referenced by CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin ( bool skipDeletedElements = true )

inline

Returns: an iterator to the first element in the mesh.

Parameters

skipDeletedElements whether to include deleted element

Definition at line 668 of file VertexMesh.hpp.

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), Toroidal2dVertexMesh::GetMeshForVtk(), Cylindrical2dVertexMesh::GetMeshForVtk(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexBasedCellPopulation< SPACE_DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd ( )

inline

Returns: an iterator to one past the last element in the mesh.

Definition at line 675 of file VertexMesh.hpp.

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), Toroidal2dVertexMesh::GetMeshForVtk(), Cylindrical2dVertexMesh::GetMeshForVtk(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElongationShapeFactorOfElement ( unsigned elementIndex )

Get the elongation shape factor of a given element. This is defined as the square root of the ratio of the two second moments of the element around its principal axes.

Parameters

elementIndex index of an element in the mesh

Returns: the elongation shape factor of the element.

Definition at line 447 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexElement< ELEMENT_DIM-1, SPACE_DIM > * VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetFace ( unsigned index ) const

Parameters

index the global index of a specified face.

Returns: a pointer to the face

Definition at line 647 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocalIndexForElementEdgeClosestToPoint	(	const c_vector< double, SPACE_DIM > &	rTestPoint,
		unsigned	elementIndex
	)

protected

Get the local index of a given element which is the start vertex of the edge of the element that the overlapping point rTestPoint is closest to.

Parameters

rTestPoint	the point to test
elementIndex	global index of the element in the mesh

Returns: the local index

Definition at line 1271 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and SmallPow().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices ( unsigned elementIndex )

Given an element, find a set containing the indices of its neighbouring elements.

Parameters

elementIndex global index of the element

Returns: its neighbouring element indices

Definition at line 799 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and Node< SPACE_DIM >::rGetContainingElementIndices().

Referenced by IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices ( unsigned nodeIndex )

Given a node, find a set containing the indices of its neighbouring nodes.

Parameters

nodeIndex global index of the node

Returns: its neighbouring node indices

Definition at line 727 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeNotAlsoInElement	(	unsigned	nodeIndex,
		unsigned	elemIndex
	)

Given a node and one of its containing elements, find a set containing the indices of those neighbouring node(s) that are NOT also in the element.

Note that we allow for more than one such index, since there is no reason a priori to assume that each node is contained by exactly three elements.

Parameters

nodeIndex	global index of the node
elemIndex	global index of the element

Returns: its neighbouring nodes that are not in the element

Definition at line 758 of file VertexMesh.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode	(	VertexElement< ELEMENT_DIM, SPACE_DIM > *	pElement,
		unsigned	localIndex
	)

Compute the gradient of the edge of a 2D element starting at its nodes.

N.B. This calls GetVectorFromAtoB(), which can be overridden in daughter classes for non-Euclidean metrics.

Parameters

pElement	pointer to a specified vertex element
localIndex	local index of a node in this element

Returns: the gradient of the edge of the element that starts at this node.

Definition at line 1488 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

Referenced by FarhadifarForce< DIM >::AddForceContribution(), and NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements ( ) const

Returns: the number of VertexElements in the mesh, including those marked as deleted.

Definition at line 625 of file VertexMesh.cpp.

Referenced by T2SwapCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const

virtual

Returns: the number of VertexElements in the mesh.

Reimplemented in MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >, MutableVertexMesh< 2, 2 >, and MutableVertexMesh< DIM, DIM >.

Definition at line 618 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumFaces ( ) const

virtual

Returns: the number of Faces in the mesh.

Definition at line 632 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const

virtual

Returns: the number of Nodes in the mesh.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >, MutableVertexMesh< 2, 2 >, and MutableVertexMesh< DIM, DIM >.

Definition at line 611 of file VertexMesh.cpp.

Referenced by VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPerimeterGradientOfElementAtNode	(	VertexElement< ELEMENT_DIM, SPACE_DIM > *	pElement,
		unsigned	localIndex
	)

Compute the gradient of the perimeter of a 2D element at its nodes. This returns the sum of GetPreviousEdgeGradientAtNode() and GetNextEdgeGradientAtNode().

Parameters

pElement	pointer to a specified vertex element
localIndex	local index of a node in this element

Returns: the gradient of the perimeter of the element, evaluated at this node.

Definition at line 1507 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode	(	VertexElement< ELEMENT_DIM, SPACE_DIM > *	pElement,
		unsigned	localIndex
	)

Compute the gradient of the edge of a 2D element ending at its nodes.

N.B. This calls GetVectorFromAtoB(), which can be overridden in daughter classes for non-Euclidean metrics.

Parameters

pElement	pointer to a specified vertex element
localIndex	local index of a node in this element

Returns: the gradient of the edge of the element that ends at this node.

Definition at line 1466 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetRosetteRankOfElement ( unsigned index )

Get the "rosette rank" of an element.

This is defined as the maximum number of elements shared by any node in the specified element.

Parameters

index the global index of a specified vertex element

Returns: the rosette rank of the element

Definition at line 560 of file VertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetShortAxisOfElement ( unsigned index )

Compute the direction of the shortest principal axis passing through the centroid, or 'short axis', of a given element. This is the eigenvector associated with the eigenvalue of largest magnitude of the inertia matrix

J = ( I_xx -I_xy ) ( -I_xy I_yy )

whose entries are computed by calling the method CalculateMomentsOfElement().

Note that if the nodes owned by the element are supplied in clockwise rather than anticlockwise manner, or if this arises when any periodicity is enforced, then the sign of each moment may be incorrect change. This means that we need to consider the eigenvalue of largest magnitude rather than largest value when computing the short axis of the element.

If the element is a regular polygon then the eigenvalues of the inertia tensor are equal: in this case we return a random unit vector.

This method is only implemented in 2D at present.

Parameters

index the global index of a specified vertex element

Returns: a unit vector giving the direction of the short axis

Todo:: remove magic number? (see #1884 and #2401)

Definition at line 1391 of file VertexMesh.cpp.

References RandomNumberGenerator::Instance(), and RandomNumberGenerator::ranf().

Referenced by ShortAxisVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement ( unsigned index )

virtual

Compute the surface area (or perimeter in 2D) of an element.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

index the global index of a specified vertex element

Returns: the surfacearea of the element

Definition at line 1114 of file VertexMesh.cpp.

References VertexElement< ELEMENT_DIM, SPACE_DIM >::GetFace(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), VertexElement< ELEMENT_DIM, SPACE_DIM >::GetNumFaces(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), and VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB	(	const c_vector< double, SPACE_DIM > &	rLocationA,
		const c_vector< double, SPACE_DIM > &	rLocationB
	)

virtual

Overridden GetVectorFromAtoB() method. Returns a vector between two points in space.

If the mesh is being used to represent a Voronoi tessellation, and mpDelaunayMesh is not NULL, then use that to compute GetVectorFromAtoB.

Parameters

rLocationA	a c_vector of coordinates
rLocationB	a c_vector of coordinates

Returns: c_vector from location A to location B.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1037 of file VertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB().

Referenced by WelikyOsterForce< DIM >::AddForceContribution().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement ( unsigned index )

virtual

Get the volume (or area in 2D, or length in 1D) of an element.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

index the global index of a specified vertex element

Returns: the volume of the element

Definition at line 1054 of file VertexMesh.cpp.

References VertexElement< ELEMENT_DIM, SPACE_DIM >::GetFace(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), VertexElement< ELEMENT_DIM, SPACE_DIM >::GetNumFaces(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), Toroidal2dVertexMesh::ConstructFromMeshReader(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex ( unsigned nodeIndex )

Returns: the global index of the corresponding element in the Voronoi mesh given the global index of a node in the Delaunay mesh, or throws an exception if this does not exist.

Parameters

nodeIndex global index of a node in the Delaunay mesh

Definition at line 533 of file VertexMesh.cpp.

References EXCEPTION, and UNSIGNED_UNSET.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void VertexMesh< ELEMENT_DIM, SPACE_DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprotected

Load a mesh by using VertexMeshReader and the location in ArchiveLocationInfo.

Parameters

archive	the archive
version	the current version of this class

Definition at line 202 of file VertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void VertexMesh< ELEMENT_DIM, SPACE_DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprotected

Archive the VertexMesh and its member variables. Note that this will write out a VertexMeshWriter file to wherever ArchiveLocationInfo has specified.

Parameters

archive	the archive
version	the current version of this class

Definition at line 184 of file VertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping ( unsigned index ) const

protected

Solve boundary element mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters

index the global index of the boundary element

Returns: local index

Todo:: sort out boundary elements in a vertex mesh (#1263)

Definition at line 497 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping ( unsigned index ) const

protected

Solve element mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters

index the global index of the element

Returns: local index

Definition at line 489 of file VertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned VertexMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping ( unsigned index ) const

protectedvirtual

Solve node mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters

index the global index of the node

Returns: local index

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 481 of file VertexMesh.cpp.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 174 of file VertexMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements

protected

Vector of pointers to VertexElements.

Definition at line 81 of file VertexMesh.hpp.

Referenced by Toroidal2dVertexMesh::ConstructFromMeshReader(), Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator::VertexElementIterator(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<VertexElement<ELEMENT_DIM-1, SPACE_DIM>*> VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces

protected

Vector of pointers to VertexElements.

Definition at line 84 of file VertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh

protected

Delaunay tetrahedral mesh that is used only when the vertex mesh is used to represent a Voronoi tessellation. A pointer to the Delaunay mesh is required in this case because the Delaunay mesh may be a subclass of TetrahedralMesh, which overrides methods such as GetVectorFromAtoB().

Definition at line 102 of file VertexMesh.hpp.

Referenced by Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> VertexMesh< ELEMENT_DIM, SPACE_DIM >::mVoronoiElementIndexMap

protected

Map that is used only when the vertex mesh is used to represent a Voronoi tessellation, the dual to a Delaunay tetrahedral mesh. The map consists of pairs (index1, index2), where index1 denotes the global index of a node in the Delaunay mesh and index2 denotes the global index of the corresponding element in the Voronoi mesh.

Definition at line 93 of file VertexMesh.hpp.

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

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

mesh/src/vertex/VertexMesh.hpp
mesh/src/vertex/VertexMesh.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class VertexMesh< 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>
class VertexMesh< ELEMENT_DIM, SPACE_DIM >