#include <Cylindrical2dVertexMesh.hpp>

Inheritance diagram for Cylindrical2dVertexMesh:

Collaboration diagram for Cylindrical2dVertexMesh:

Public Member Functions
	Cylindrical2dVertexMesh (double width, std::vector< Node< 2 > * > nodes, std::vector< VertexElement< 2, 2 > * > vertexElements, double cellRearrangementThreshold=0.01, double t2Threshold=0.001)

	Cylindrical2dVertexMesh (Cylindrical2dMesh &rMesh)

	~Cylindrical2dVertexMesh ()

c_vector< double, 2 >	GetVectorFromAtoB (const c_vector< double, 2 > &rLocation1, const c_vector< double, 2 > &rLocation2)

void	SetNode (unsigned nodeIndex, ChastePoint< 2 > point)

double	GetWidth (const unsigned &rDimension) const

unsigned	AddNode (Node< 2 > *pNewNode)

void	Scale (const double xScale=1.0, const double yScale=1.0, const double zScale=1.0)

MutableVertexMesh< 2, 2 > *	GetMeshForVtk ()

Public Member Functions inherited from MutableVertexMesh< 2, 2 >
	MutableVertexMesh (std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements, double cellRearrangementThreshold=0.01, double t2Threshold=0.001, double cellRearrangementRatio=1.5, double protorosetteFormationProbability=0.0, double protorosetteResolutionProbabilityPerTimestep=0.0, double rosetteResolutionProbabilityPerTimestep=0.0)

	MutableVertexMesh ()

virtual	~MutableVertexMesh ()

void	SetCellRearrangementThreshold (double cellRearrangementThreshold)

void	SetT2Threshold (double t2Threshold)

void	SetCellRearrangementRatio (double cellRearrangementRatio)

void	SetProtorosetteFormationProbability (double protorosetteFormationProbability)

void	SetProtorosetteResolutionProbabilityPerTimestep (double protorosetteResolutionProbabilityPerTimestep)

void	SetRosetteResolutionProbabilityPerTimestep (double rosetteResolutionProbabilityPerTimestep)

virtual void	SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > point)

void	SetCheckForInternalIntersections (bool checkForInternalIntersections)

double	GetCellRearrangementThreshold () const

double	GetT2Threshold () const

double	GetCellRearrangementRatio () const

double	GetProtorosetteFormationProbability () const

double	GetProtorosetteResolutionProbabilityPerTimestep () const

double	GetRosetteResolutionProbabilityPerTimestep () const

void	SetDistanceForT3SwapChecking (double distanceForT3SwapChecking)

double	GetDistanceForT3SwapChecking () const

unsigned	GetNumNodes () const

unsigned	GetNumElements () const

bool	GetCheckForInternalIntersections () const

std::vector< c_vector< double, SPACE_DIM > >	GetLocationsOfT1Swaps ()

c_vector< double, SPACE_DIM >	GetLastT2SwapLocation ()

std::vector< c_vector< double, SPACE_DIM > >	GetLocationsOfT3Swaps ()

void	ClearLocationsOfT1Swaps ()

void	ClearLocationsOfT3Swaps ()

unsigned	AddNode (Node< SPACE_DIM > *pNewNode)

void	DeleteElementPriorToReMesh (unsigned index)

void	DeleteNodePriorToReMesh (unsigned index)

unsigned	DivideElementAlongShortAxis (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, bool placeOriginalElementBelow=false)

unsigned	DivideElementAlongGivenAxis (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, c_vector< double, SPACE_DIM > axisOfDivision, bool placeOriginalElementBelow=false)

unsigned	AddElement (VertexElement< ELEMENT_DIM, SPACE_DIM > *pNewElement)

bool	CheckForT2Swaps (VertexElementMap &rElementMap)

void	Clear ()

void	DivideEdge (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

void	RemoveDeletedNodesAndElements (VertexElementMap &rElementMap)

void	RemoveDeletedNodes ()

virtual void	ReMesh (VertexElementMap &rElementMap)

void	ReMesh ()

Public Member Functions inherited from VertexMesh< ELEMENT_DIM, SPACE_DIM >
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 ()

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)

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 ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const

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

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 ()

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

	Cylindrical2dVertexMesh ()

Private Attributes
double	mWidth

Friends
class	TestCylindrical2dVertexMesh

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

Protected Member Functions inherited from MutableVertexMesh< 2, 2 >
unsigned	DivideElement (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned nodeAIndex, unsigned nodeBIndex, bool placeOriginalElementBelow=false)

virtual bool	CheckForSwapsFromShortEdges ()

bool	CheckForIntersections ()

virtual void	IdentifySwapType (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

void	PerformNodeMerge (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

void	PerformT1Swap (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB, std::set< unsigned > &rElementsContainingNodes)

void	PerformIntersectionSwap (Node< SPACE_DIM > *pNode, unsigned elementIndex)

void	PerformT2Swap (VertexElement< ELEMENT_DIM, SPACE_DIM > &rElement)

void	PerformT3Swap (Node< SPACE_DIM > *pNode, unsigned elementIndex)

void	PerformVoidRemoval (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB, Node< SPACE_DIM > *pNodeC)

virtual void	HandleHighOrderJunctions (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

void	PerformRosetteRankIncrease (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

void	PerformProtorosetteResolution (Node< SPACE_DIM > *pProtorosetteNode)

void	PerformRosetteRankDecrease (Node< SPACE_DIM > *pRosetteNode)

void	CheckForRosettes ()

c_vector< double, 2 >	WidenEdgeOrCorrectIntersectionLocationIfNecessary (unsigned indexA, unsigned indexB, c_vector< double, 2 > intersection)

void	serialize (Archive &archive, const unsigned int version)

Protected Member Functions inherited from VertexMesh< ELEMENT_DIM, SPACE_DIM >
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 inherited from MutableVertexMesh< 2, 2 >
double	mCellRearrangementThreshold

double	mCellRearrangementRatio

double	mT2Threshold

double	mProtorosetteFormationProbability

double	mProtorosetteResolutionProbabilityPerTimestep

double	mRosetteResolutionProbabilityPerTimestep

bool	mCheckForInternalIntersections

std::vector< unsigned >	mDeletedNodeIndices

std::vector< unsigned >	mDeletedElementIndices

double	mDistanceForT3SwapChecking

std::vector< c_vector< double, SPACE_DIM > >	mLocationsOfT1Swaps

c_vector< double, SPACE_DIM >	mLastT2SwapLocation

std::vector< c_vector< double, SPACE_DIM > >	mLocationsOfT3Swaps

Protected Attributes inherited from VertexMesh< ELEMENT_DIM, SPACE_DIM >
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

Detailed Description

A subclass of MutableVertexMesh<2,2> for a rectangular mesh with periodic left and right boundaries, representing a cylindrical geometry.

The class works by overriding calls such as ReMesh() and GetVectorFromAtoB() so that simulation classes can treat this class in exactly the same way as a MutableMesh<2,2>.

Definition at line 53 of file Cylindrical2dVertexMesh.hpp.

Constructor & Destructor Documentation

Cylindrical2dVertexMesh::Cylindrical2dVertexMesh ( )

private

Constructor - used for serialization only.

Definition at line 147 of file Cylindrical2dVertexMesh.cpp.

Referenced by serialize().

Cylindrical2dVertexMesh::Cylindrical2dVertexMesh	(	double	width,
		std::vector< Node< 2 > * >	nodes,
		std::vector< VertexElement< 2, 2 > * >	vertexElements,
		double	cellRearrangementThreshold = `0.01`,
		double	t2Threshold = `0.001`
	)

Default constructor.

Parameters

width	the width (circumference) of the mesh
nodes	vector of pointers to nodes
vertexElements	vector of pointers to VertexElements
cellRearrangementThreshold	the minimum threshold distance for element rearrangement (defaults to 0.01)
t2Threshold	the maximum threshold distance for Type 2 swaps (defaults to 0.001)

Definition at line 39 of file Cylindrical2dVertexMesh.cpp.

References MutableVertexMesh< 2, 2 >::ReMesh().

Cylindrical2dVertexMesh::Cylindrical2dVertexMesh ( Cylindrical2dMesh & rMesh )

Alternative constructor. Creates a Voronoi tessellation of a given Cylindrical2dMesh, which must be Delaunay (see TetrahedralMesh::CheckIsVoronoi).

Parameters

rMesh a Cylindrical2dMesh

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 51 of file Cylindrical2dVertexMesh.cpp.

References MutableElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableVertexMesh< 2, 2 >::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, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh, and mWidth.

Cylindrical2dVertexMesh::~Cylindrical2dVertexMesh ( )

Destructor.

Definition at line 151 of file Cylindrical2dVertexMesh.cpp.

Referenced by serialize().

Member Function Documentation

unsigned Cylindrical2dVertexMesh::AddNode ( Node< 2 > * pNewNode )

Overridden AddNode() method.

Parameters

pNewNode the node to be added to the mesh

Returns: the global index of the new node

Definition at line 209 of file Cylindrical2dVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), Node< SPACE_DIM >::GetPoint(), and SetNode().

Referenced by serialize().

MutableVertexMesh< 2, 2 > * Cylindrical2dVertexMesh::GetMeshForVtk ( )

Return a pointer to an extended mesh that is a 'non-periodic' version of our mesh. This can then be used when writing to VTK.

Returns: a non-periodic vertex mesh

Definition at line 230 of file Cylindrical2dVertexMesh.cpp.

References CHASTE_CLASS_EXPORT, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), Node< SPACE_DIM >::GetIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), MutableVertexMesh< 2, 2 >::GetNumNodes(), MutableVertexMesh< 2, 2 >::mCellRearrangementThreshold, MutableVertexMesh< 2, 2 >::mT2Threshold, mWidth, and AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetIndex().

Referenced by serialize().

c_vector< double, 2 > Cylindrical2dVertexMesh::GetVectorFromAtoB	(	const c_vector< double, 2 > &	rLocation1,
		const c_vector< double, 2 > &	rLocation2
	)

Overridden GetVectorFromAtoB() method. This method evaluates the (surface) distance between two points in a 2D cylindrical geometry.

Parameters

rLocation1	the x and y co-ordinates of point 1
rLocation2	the x and y co-ordinates of point 2

Returns: the vector from location1 to location2

Definition at line 155 of file Cylindrical2dVertexMesh.cpp.

References mWidth.

Referenced by serialize().

double Cylindrical2dVertexMesh::GetWidth ( const unsigned & rDimension ) const

virtual

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the mesh, taking periodicity into account.

Parameters

rDimension a dimension (0 or 1)

Returns: The maximum distance between any nodes in this dimension.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 194 of file Cylindrical2dVertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and mWidth.

Referenced by serialize().

void Cylindrical2dVertexMesh::Scale	(	const double	xScale = `1.0`,
		const double	yScale = `1.0`,
		const double	zScale = `1.0`
	)

virtual

Overridden Scale method to also scale the width (mWidth) of the mesh

Parameters

xScale	is the scale in the x-direction (defaults to 1.0)
yScale	is the scale in the y-direction (defaults to 1.0)
zScale	is the scale in the z-direction (defaults to 1.0) note this has to be 1.0 as only a 2d Mesh

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 220 of file Cylindrical2dVertexMesh.cpp.

References mWidth, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale().

Referenced by serialize().

template<class Archive >

void Cylindrical2dVertexMesh::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archives the member variables of the object which have to be preserved during its lifetime.

The remaining member variables are re-initialised before being used by each ReMesh() call so they do not need to be archived.

Parameters

archive	the archive
version	the current version of this class

Definition at line 75 of file Cylindrical2dVertexMesh.hpp.

References AddNode(), CHASTE_CLASS_EXPORT, Cylindrical2dVertexMesh(), GetMeshForVtk(), GetVectorFromAtoB(), GetWidth(), mWidth, Scale(), SetNode(), and ~Cylindrical2dVertexMesh().

void Cylindrical2dVertexMesh::SetNode	(	unsigned	nodeIndex,
		ChastePoint< 2 >	point
	)

Overridden SetNode() method.

If the location should be set outside a cylindrical boundary move it back onto the cylinder.

Parameters

nodeIndex	is the index of the node to be moved
point	is the new target location of the node

Definition at line 174 of file Cylindrical2dVertexMesh.cpp.

References mWidth, ChastePoint< DIM >::rGetLocation(), ChastePoint< DIM >::SetCoordinate(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

Referenced by AddNode(), and serialize().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 63 of file Cylindrical2dVertexMesh.hpp.

Member Data Documentation

double Cylindrical2dVertexMesh::mWidth

private

The circumference of the cylinder.

Definition at line 60 of file Cylindrical2dVertexMesh.hpp.

Referenced by Cylindrical2dVertexMesh(), GetMeshForVtk(), GetVectorFromAtoB(), GetWidth(), Scale(), serialize(), and SetNode().

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

mesh/src/vertex/Cylindrical2dVertexMesh.hpp
mesh/src/vertex/Cylindrical2dVertexMesh.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation