VertexMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#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 104 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 461 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, and VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor.

Definition at line 469 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear().

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

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 152 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 241 of file VertexMesh.cpp.

References VertexElement< ELEMENT_DIM, SPACE_DIM >::AddFace(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), Node< SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::IsBoundaryNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mVoronoiElementIndexMap, Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), and VectorProduct().

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 1524 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateUnitNormalToFaceWithArea(), EXPORT_TEMPLATE_CLASS_ALL_DIMS, and NEVER_REACHED.

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), and VertexMesh< DIM, DIM >::load().

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 1311 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB().

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElongationShapeFactorOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetShortAxisOfElement(), and VertexMesh< DIM, DIM >::load().

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 1495 of file VertexMesh.cpp.

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

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateAreaOfFace(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), and VertexMesh< DIM, DIM >::load().

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 573 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), VertexMesh< DIM, DIM >::load(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh(), 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< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), and 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 1128 of file VertexMesh.cpp.

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

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

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 384 of file VertexMesh.cpp.

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

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 1418 of file VertexMesh.cpp.

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

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

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 636 of file VertexMesh.cpp.

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

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), VertexBasedCellPopulation< DIM >::GetLocationOfCellCentre(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexMesh< DIM, DIM >::load(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformProtorosetteResolution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankDecrease(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap().

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 497 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mVoronoiElementIndexMap, and UNSIGNED_UNSET.

Referenced by VertexMesh< DIM, DIM >::load(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile().

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 409 of file VertexMesh.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by VertexMesh< DIM, DIM >::load(), and 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 622 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::ElementIncludesPoint(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement(), VertexBasedCellPopulation< DIM >::GetElement(), VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocalIndexForElementEdgeClosestToPoint(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeNotAlsoInElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetRosetteRankOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), VertexMesh< DIM, DIM >::load(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformProtorosetteResolution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankDecrease(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), and 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.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator::VertexElementIterator().

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps(), Toroidal2dVertexMesh::GetMeshForVtk(), Cylindrical2dVertexMesh::GetMeshForVtk(), VertexMesh< DIM, DIM >::load(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexBasedCellPopulation< 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.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator::VertexElementIterator().

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps(), Toroidal2dVertexMesh::GetMeshForVtk(), Cylindrical2dVertexMesh::GetMeshForVtk(), VertexMesh< DIM, DIM >::load(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile().

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 444 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement().

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

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 629 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces.

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

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 1247 of file VertexMesh.cpp.

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

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap().

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 777 of file VertexMesh.cpp.

References VertexElementData::AttributeValue, ElementData::AttributeValue, VertexMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), EXCEPTION, VertexElementData::Faces, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElementAttributes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::HasNodePermutation(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, VertexElementData::NodeIndices, ElementData::NodeIndices, AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset(), Node< SPACE_DIM >::rGetContainingElementIndices(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetAttribute(), and UNUSED_OPT.

Referenced by IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), VertexBasedCellPopulation< DIM >::GetNeighbouringLocationIndices(), VertexMesh< DIM, DIM >::load(), 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 707 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode().

Referenced by VertexBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeNotAlsoInElement(), and VertexMesh< DIM, DIM >::load().

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 737 of file VertexMesh.cpp.

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

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

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 1462 of file VertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB().

Referenced by FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPerimeterGradientOfElementAtNode(), and VertexMesh< DIM, DIM >::load().

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 610 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by T2SwapCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), VertexMesh< DIM, DIM >::load(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements(), and VertexBasedCellPopulation< DIM >::Update().

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 604 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

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

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 616 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mFaces.

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

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 598 of file VertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by VertexMesh< DIM, DIM >::load(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh().

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 1480 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode().

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

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 1441 of file VertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB().

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPerimeterGradientOfElementAtNode(), VertexMesh< DIM, DIM >::load(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap().

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 549 of file VertexMesh.cpp.

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

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

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

Definition at line 1365 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement(), RandomNumberGenerator::Instance(), and RandomNumberGenerator::ranf().

Referenced by ShortAxisVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongShortAxis(), and VertexMesh< DIM, DIM >::load().

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 1092 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateAreaOfFace(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), 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(), VertexMesh< DIM, DIM >::load(), 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 1018 of file VertexMesh.cpp.

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

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateUnitNormalToFaceWithArea(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::ElementIncludesPoint(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocalIndexForElementEdgeClosestToPoint(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), VertexMesh< DIM, DIM >::load(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::WidenEdgeOrCorrectIntersectionLocationIfNecessary().

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 1034 of file VertexMesh.cpp.

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

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps(), Toroidal2dVertexMesh::ConstructFromMeshReader(), VertexBasedCellPopulation< DIM >::GetVolumeOfCell(), VertexMesh< DIM, DIM >::load(), 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 523 of file VertexMesh.cpp.

References EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mVoronoiElementIndexMap, and UNSIGNED_UNSET.

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

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 489 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 482 of file VertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

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 475 of file VertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

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 MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), Toroidal2dVertexMesh::ConstructFromMeshReader(), Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator::IsAtEnd(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankIncrease(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), 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 VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetFace(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumFaces(), 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(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), 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 >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(), and 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