#include <MutableVertexMesh.hpp>

Inheritance diagram for MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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)
	Alternative 2D 'Voronoi' constructor. More...

	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)

virtual VertexMesh < ELEMENT_DIM, SPACE_DIM > *	GetMeshForVtk ()

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	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)

template<class Archive >
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
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

Friends
class	TestMutableVertexMesh

class	TestMutableVertexMeshReMesh

class	TestMutableVertexMeshRosetteMethods

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 MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >

A mutable vertex-based mesh class, which inherits from VertexMesh and allows for local remeshing. This is implemented through simple operations including node merging, neighbour exchange ("T1 swap"), node/edge merging in the case of intersections ("T3 swap") and removal of small triangular elements ("T2 swap").

MutableVertexMesh 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 65 of file MutableVertexMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::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`
	)

Default constructor.

Parameters

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)
cellRearrangementRatio	ratio between the minimum threshold distance for element rearrangement node separation after remeshing (defaults to 1.5)
protorosetteFormationProbability	the probability of a protorosette formation event happening instead of a T1 swap
protorosetteResolutionProbabilityPerTimestep	the probability that, in a given timestep, a protorosette will resolve (similar to the completion of a T1 swap)
rosetteResolutionProbabilityPerTimestep	the probability that, in a given timestep, a rosette will resolve (reduce the number of cells sharing a common vertex by 1)

Definition at line 43 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::AddElement(), MutableVertexMesh< 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>

MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh ( )

Default constructor for use by serializer.

Definition at line 124 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor.

Definition at line 140 of file MutableVertexMesh.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Add an element to the mesh.

Parameters

pNewElement the new element

Returns: the index of the new element in the mesh

Definition at line 347 of file MutableVertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and MutableElement< ELEMENT_DIM, SPACE_DIM >::RegisterWithNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode ( Node< SPACE_DIM > * pNewNode )

Add a node to the mesh.

Note: After calling this one or more times, you must then call ReMesh.

Parameters

pNewNode pointer to the new node

Returns: the global index of the new node in the mesh.

Definition at line 328 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), and Node< SPACE_DIM >::SetIndex().

Referenced by Cylindrical2dVertexMesh::AddNode(), and Toroidal2dVertexMesh::AddNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections ( )

protected

Helper method for ReMesh().

Check if any elements have become intersected and correct this by implementing the appropriate local remeshing operation (a T3 swap or node merge).

Returns: whether to recheck the mesh again

Todo:: Change to only loop over neighbouring elements (see #2401)

Definition at line 1016 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForRosettes ( )

protected

Helper method for ReMesh().

Check whether the mesh contains rosettes or protorosettes, and implement resolution events if necessary.

First, we loop over each node and populate vectors of protorosette and rosette nodes which need to undergo resolution.

We do not perform the resolution events in this initial loop because the resolution events involve changing nodes in the mesh.

Finally, we loop over the contents of each node vector and perform the necessary resolution events.

Because each resolution event changes nodes, we include several assertions to catch possible unconsidered behaviour.

Definition at line 3065 of file MutableVertexMesh.cpp.

References RandomNumberGenerator::Instance(), Node< SPACE_DIM >::IsDeleted(), and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges ( )

protectedvirtual

Helper method for ReMesh().

Check if any neighbouring nodes in an element are closer than the mCellRearrangementThreshold and are not contained in any triangular elements. If any such pair of nodes are found, then call IdentifySwapType(), which in turn implements the appropriate local remeshing operation (a T1 swap, void removal, or node merge).

Returns: whether we need to check for, and implement, any further local remeshing operations (true if any swaps are performed).

Todo:: Could we search more efficiently by just iterating over edges? (see #2401)

Todo:: Use iterators to tidy this up (see #2401)

Definition at line 930 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps ( VertexElementMap & rElementMap )

Helper method for ReMesh().

Check for any triangular element whose area is smaller than mT2Threshold and call PerformT2Swap() on any such element.

Parameters

rElementMap a VertexElementMap which associates the indices of VertexElements in the old mesh with indices of VertexElements in the new mesh. This should be created with the correct size, GetNumElements()

Returns: whether we need to check for, and implement, any further local remeshing operations

Todo:: : cover this line in a test

Definition at line 991 of file MutableVertexMesh.cpp.

References VertexElementMap::SetDeleted().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Delete mNodes and mElements.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 277 of file MutableVertexMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT1Swaps ( )

Helper method to clear the stored T1 swaps

Definition at line 316 of file MutableVertexMesh.cpp.

Referenced by VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT3Swaps ( )

Helper method to clear the stored T3 swaps

Definition at line 322 of file MutableVertexMesh.cpp.

Referenced by VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh ( unsigned index )

Mark an element as deleted. Note that it DOES NOT deal with the associated nodes and therefore should only be called immediately prior to a ReMesh() being called.

Parameters

index the global index of a specified vertex element

Definition at line 695 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::rGetContainingElementIndices(), and Node< SPACE_DIM >::SetAsBoundaryNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh ( unsigned index )

Mark a given node as deleted. Note that this method DOES NOT deal with the associated elements and therefore should only be called immediately prior to a ReMesh() being called.

Parameters

index The index of the node to delete

Definition at line 719 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)

Add a node on the edge between two nodes.

Parameters

pNodeA	a pointer to one node
pNodeB	a pointer to the other nodes

Definition at line 726 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::IsBoundaryNode(), Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::SetPoint().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElement	(	VertexElement< ELEMENT_DIM, SPACE_DIM > *	pElement,
		unsigned	nodeAIndex,
		unsigned	nodeBIndex,
		bool	placeOriginalElementBelow = `false`
	)

protected

Divide an element along the axis passing through two of its nodes.

Todo:: This method currently assumes SPACE_DIM = 2 (see #866)

Parameters

pElement	the element to divide
nodeAIndex	the local index of one node within this element
nodeBIndex	the local index of another node within this element
placeOriginalElementBelow	whether to place the original element below (in the y direction) the new element (defaults to false)

Returns: the index of the new element

Remove the correct nodes from each element. If placeOriginalElementBelow is true, place the original element below (in the y direction) the new element; otherwise, place it above.

Todo:: this could be more efficient (see #2401)

Definition at line 569 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Divide an element along a specified axis.

If the new nodes (intersections of axis with element) are within mCellRearrangementThreshold of existing nodes then they are moved 2*mCellRearrangementThreshold away.

Parameters

pElement	the element to divide
axisOfDivision	axis to divide the element by
placeOriginalElementBelow	whether to place the original element below (in the y direction) the new element (defaults to false)

Returns: the index of the new element

Todo:: or should we move a and b apart, it may interfere with neighbouring edges? (see #1399 and #2401)

Definition at line 370 of file MutableVertexMesh.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::IsBoundaryNode(), Node< SPACE_DIM >::rGetContainingElementIndices(), and Node< SPACE_DIM >::rGetLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Divide an element along its short axis.

Parameters

pElement	the element to divide
placeOriginalElementBelow	whether to place the original element below (in the y direction) the new element (defaults to false)

Returns: the index of the new element

Definition at line 556 of file MutableVertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementRatio ( ) const

Returns: mCellRearrangementRatio

Definition at line 158 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementThreshold ( ) const

Returns: mCellRearrangementThreshold

Definition at line 146 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCheckForInternalIntersections ( ) const

Returns: mCheckForInternalIntersections, either to check for edges intersections or not.

Definition at line 196 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceForT3SwapChecking ( ) const

Get Distance for T3 swap checking.

Returns: mDistanceForT3SwapChecking

Definition at line 188 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLastT2SwapLocation ( )

Returns: the location of the last T2 swap

Definition at line 304 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns: the locations of the T1 swaps

Definition at line 298 of file MutableVertexMesh.cpp.

Referenced by VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns: the locations of the T3 swaps

Definition at line 310 of file MutableVertexMesh.cpp.

Referenced by VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns: the number of VertexElements in the mesh.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 292 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns: the number of Nodes in the mesh.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 286 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetProtorosetteFormationProbability ( ) const

Get method for mProtoRosetteFormationProbability.

Returns: mProtoRosetteFormationProbability

Definition at line 164 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetProtorosetteResolutionProbabilityPerTimestep ( ) const

Get method for mProtoRosetteResolutionProbabilityPerTimestep.

Returns: mProtoRosetteResolutionProbabilityPerTimestep

Definition at line 170 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetRosetteResolutionProbabilityPerTimestep ( ) const

Get method for mRosetteResolutionProbabilityPerTimestep.

Returns: mRosetteResolutionProbabilityPerTimestep

Definition at line 176 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetT2Threshold ( ) const

Returns: mT2Threshold

Definition at line 152 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::HandleHighOrderJunctions	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)

protectedvirtual

Helper method for ReMesh(), called by IdentifySwapType().

Handles the case where a swap involves a junction with more than three adjacent elements. This is implemented in a separate method to allow child classes to override this behaviour and implement junction remodelling with high-order nodes (see #2664).

Parameters

pNodeA	one of the nodes to perform the swap with
pNodeB	the other node to perform the swap

Definition at line 2598 of file MutableVertexMesh.cpp.

References EXCEPTION, and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)

protectedvirtual

Helper method for ReMesh(), called by CheckForSwapsFromShortEdges() when neighbouring nodes in an element have been found to be closer than the mCellRearrangementThreshold and do not share any triangular elements.

Identify the type of local remeshing operation required (T1 swap, void removal, or node merge).

Parameters

pNodeA	one of the nodes to perform the swap with
pNodeB	the other node to perform the swap

Here, the triangular element would be along the short edge. Since we are already checking in CheckForSwapsFromShortEdges() whether the element is triangular, this exception is redundant for simulations. We leave it in for clarity. ///

Todo:: : consider removing the checking for this exception (see #2401)

If this is true then one of the elements adjacent to the triangular void is triangular. This element will then not share the short edge that is considered for a swap. Nevertheless, it would loose an edge during the swap. We are currently not able to deal with this situation. Related to #2533 and #2401.

Definition at line 1108 of file MutableVertexMesh.cpp.

References EXCEPTION, Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), RandomNumberGenerator::Instance(), Node< SPACE_DIM >::IsBoundaryNode(), NEVER_REACHED, and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Helper method for ReMesh(), called by CheckForIntersections().

Perform an element swap to resolve the situation where a given node has been found to overlap a given element not containing it.

Parameters

pNode	pointer to the node
elementIndex	global index of the element in the mesh

Definition at line 1617 of file MutableVertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::rGetContainingElementIndices(), and Node< SPACE_DIM >::rGetLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)

protected

Helper method for ReMesh(), called by IdentifySwapType().

Merge two given nodes in the mesh and update node/element ownership, by replacing the node contained in the least number of elements with the other node. The merged node is moved to the centre between the two old node positions.

Parameters

pNodeA	one of the nodes to perform the merge with
pNodeB	the other node to perform the merge with

Definition at line 1438 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformProtorosetteResolution ( Node< SPACE_DIM > * pProtorosetteNode )

protected

Helper method for ReMesh(), called by CheckForRosettes().

Split protorosette in random direction. Create new node and redistribute nodes along line joining centres of randomly selected cell and cell opposite it.

Parameters

pProtorosetteNode node at centre of protorosette

Ordering elements as follows:

\ A / \ / \ / B X D / \ / \ / C \

Element A is the randomly chosen element. Element C, which is directly opposite A, will end up separated from A, while the two elements B and D which start adjacent to A will end up sharing a common edge:

\ A / \ / \ / | B | D | / \ / \ / C \

Next, we compute where to place the two nodes which will replace the single protorosette node.

We place each node along the line joining the protorosette node to the centroid of element which will contain it, and the distance along this line is half of the swap distance.

To do this, we will move the existing protorosette node in to element A, and create a new node in element C. We then need to tidy up the nodes by adding the new node to elements B, C and D, and removing the protorosette node from element C.

NOTE: as the protorosette node was not necessarily on the line joining the centroids of elements A and C, unlike in a T1 swap, the new node locations will not necessarily be the full swap distance apart.

Here, we add the new node to elements B, C and D.

The method AddNode() takes the local index of a node i, where the new node is to be inserted between nodes i and i+1, so we need to find the local idx of the node directly before (clockwise from) where we wish to insert it.

For elements C and D, we just need the local index of the protorosette node, but for element B we need the one before, modulo number of elements.

Definition at line 2704 of file MutableVertexMesh.cpp.

References MutableElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), RandomNumberGenerator::Instance(), RandomNumberGenerator::randMod(), Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankDecrease ( Node< SPACE_DIM > * pRosetteNode )

protected

Helper method for ReMesh(), called by CheckForRosettes().

Split rosette by removing one cell at random. Create new node positioned along line joining rosette node and centre of randomly selected cell. Rosette node will remain unmoved.

Parameters

pRosetteNode node at centre of rosette

We have now picked a vertex element at random from the rosette. This element will now be disconnected from the rosette in a manner analogous to performing a T1 swap.

The node at the centre of the rosette will not move, and a new node will be created a suitable distance away, along a line joining the rosette node and the centroid of the element we have randomly selected to move.

Ordering of elements is as follows:

\ S / \ / N \ / P —–X—– / \ / \ / \

where element S is the selected element, N is the next (counterclockwise) element from S, and P is the previous (clockwise) element from S.

Elements N and P will end up sharing an edge:

\ S / \ / \ / N | P | —–*—– / \ / \ / \

Next, we compute where to place the new node which will separate the rosette node from element S.

We place this node along the line joining the rosette node to the centroid of element S, at a distance of the swap distance ( (rearrangement ratio) x (rearrangement threshold) )

To do this, we create a new node in element S. We then need to tidy up the nodes by adding the new node to elements S, N and P, and by removing the rosette node from element S.

Here, we add the new node to elements S, N and P, and remove the rosette node from element S.

The method AddNode() takes the local index of a node i, where the new node is to be inserted between nodes i and i+1, so we need to find the local idx of the node directly before (clockwise from) where we wish to insert it.

For elements S and P, we just need the local index of the rosette node, but for element N we need the one before, modulo number of elements.

Definition at line 2890 of file MutableVertexMesh.cpp.

References MutableElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), RandomNumberGenerator::Instance(), RandomNumberGenerator::randMod(), Node< SPACE_DIM >::rGetContainingElementIndices(), and Node< SPACE_DIM >::rGetLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankIncrease	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)

protected

Helper method for ReMesh(), called by HandleHighOrderJunctions().

Merge a node of a non-rosette cell with the central node of a rosette, by replacing the node in the non-rosette cell with that of the rosette centre, keeping the rosette centre in the same position.

Parameters

pNodeA	one of the nodes to perform the merge with
pNodeB	the other node to perform the merge with

The picture below shows the situation we are in. The central node (marked with an 'X') is contained in (at least) four elements already (A, B, C and D), and this is the rosette node which we have designated as hi_rank_node.

The node shared by elements C, D and E has come within the cell rearrangement threshold of the rosette node in order for this method to have been called. We have designated this node lo_rank_node.

We now 'merge' hi_rank_node and lo_rank_node, but keep hi_rank_node where it is (which is why we don't call PerformNodeMerge(), as that would move both nodes to their average location).

To accomplish this merge, we need do nothing to elements A and B. We remove lo_rank_node from elements C and D, and we replace lo_rank_node by hi_rank_node in element E.

\ A / \ / \ / B X C / \ ______ / \ / D \ E

Definition at line 2617 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Helper method for ReMesh(), called by IdentifySwapType().

Perform a T1 swap on two given nodes contained in a given set of elements. This involves replacing the two nodes with two new nodes placed on either side of the previous shared edge, such that the edge formed by the two new nodes is the perpendicular bisector of the previous shared edge, and 'just larger' (by a factor mCellRearrangementRatio) than mThresholdDistance.

Parameters

pNodeA	one of the nodes to perform the swap with
pNodeB	the other node to perform the swap
rElementsContainingNodes	set of common elements

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

Definition at line 1476 of file MutableVertexMesh.cpp.

References EXCEPTION, Node< SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::GetNumContainingElements(), Node< SPACE_DIM >::IsBoundaryNode(), Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), Node< SPACE_DIM >::rGetModifiableLocation(), and Node< SPACE_DIM >::SetAsBoundaryNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Helper method for ReMesh(), called by CheckForT2Swaps().

Perform a T2 swap on a given triangular element whose area is smaller than mT2Threshold by replacing it with a new node located at the centroid of the former element and updating node/element ownership.

Parameters

rElement the element to remove

Definition at line 1784 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Helper method for ReMesh(), called by CheckForIntersections().

Perform a T3 swap on a given node that has been found to overlap a given element by moving the node back onto the edge of that element, associating it with the element and adding new nodes to maintain three elements per node.

Parameters

pNode	pointer to the node
elementIndex	global index of the element in the mesh

Todo:: the intersection location is sometimes overwritten when WidenEdgeOrCorrectIntersectionLocationIfNecessary

Definition at line 1852 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Helper method for ReMesh(), called by IdentifySwapType().

Remove a triangular void bounded by three given nodes, in which one of the edges is less than mCellRearrangementThreshold, through calls to PerformNodeMerge().

Parameters

pNodeA	one of the nodes on the short edge
pNodeB	the other node on the short edge
pNodeC	the other node in the triangular void

Definition at line 2560 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::IsDeleted(), Node< SPACE_DIM >::rGetLocation(), Node< SPACE_DIM >::rGetModifiableLocation(), and Node< SPACE_DIM >::SetAsBoundaryNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( VertexElementMap & rElementMap )

virtual

Update the state of the mesh by implementing any local remeshing operations (node merging, or T1, T2 or T3 swaps) that are required, and store any changes in element indices using the given VertexElementMap.

This method calls several other methods, in particular CheckForT2Swaps(), CheckForSwapsFromShortEdges() and CheckForIntersections().

Parameters

rElementMap a VertexElementMap which associates the indices of VertexElements in the old mesh with indices of VertexElements in the new mesh. This should be created with the correct size, GetNumElements()

Todo:: Implement ReMesh() in 3D (see #1422)

Definition at line 872 of file MutableVertexMesh.cpp.

References EXCEPTION, and VertexElementMap::Resize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( )

Alternative version of ReMesh which takes no parameters and does not require a VertexElementMap. Note: inherited classes should overload ReMesh(VertexElementMap&).

Todo:: This method seems to be redundant; remove it? (#2401)

Definition at line 923 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes ( )

Helper method for ReMesh(). Removes the deleted nodes from the mesh and relabels the node indices.

Definition at line 841 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements ( VertexElementMap & rElementMap )

Helper method for ReMesh(). Removes the deleted nodes and elements from the mesh and updates the rElementMap accordingly.

Parameters

rElementMap a VertexElementMap which associates the indices of VertexElements in the old mesh with indices of VertexElements in the new mesh. This should be created with the correct size, GetNumElements()

Definition at line 802 of file MutableVertexMesh.cpp.

References VertexElementMap::Resize(), VertexElementMap::SetDeleted(), and VertexElementMap::SetNewIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inlineprotected

Serialize the mesh.

Note that if you are calling this method (from subclasses) you should archive your member variables FIRST. So that this method can call a ReMesh (to convert from TrianglesMeshReader input format into your native format).

Parameters

archive	the archive
version	the current version of this class

Todo:: : maybe we should archive the mLocationsOfT1Swaps and mDeletedNodeIndices etc. as well?

Definition at line 337 of file MutableVertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCellRearrangementRatio ( double cellRearrangementRatio )

Set method for mCellRearrangementRatio.

Parameters

cellRearrangementRatio

Definition at line 214 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCellRearrangementThreshold ( double cellRearrangementThreshold )

Set method for mCellRearrangementThreshold.

Parameters

cellRearrangementThreshold

Definition at line 202 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCheckForInternalIntersections ( bool checkForInternalIntersections )

Set method for mCheckForInternalIntersections.

Parameters

checkForInternalIntersections

Definition at line 271 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetDistanceForT3SwapChecking ( double distanceForT3SwapChecking )

Set distance for T3 swap checking. At each time step we check for each boundary node whether it intersects with any boundary elements (cells) whose centroids lie within this distance to the node. Note that T3 swaps may not be resolved correctly if this distance is chosen too small, while large values for mDistanceForT3SwapChecking may slow down the simulation.

Parameters

distanceForT3SwapChecking

Definition at line 182 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< SPACE_DIM >	point
	)

virtual

Move the node with a particular index to a new point in space.

Parameters

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

Definition at line 364 of file MutableVertexMesh.cpp.

Referenced by Cylindrical2dVertexMesh::SetNode(), and Toroidal2dVertexMesh::SetNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetProtorosetteFormationProbability ( double protorosetteFormationProbability )

Set method for mProtoRosetteFormationProbability.

Parameters

protorosetteFormationProbability the new value of mProtoRosetteFormationProbability

Definition at line 220 of file MutableVertexMesh.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetProtorosetteResolutionProbabilityPerTimestep ( double protorosetteResolutionProbabilityPerTimestep )

Set method for mProtoRosetteResolutionProbabilityPerTimestep.

Parameters

protorosetteResolutionProbabilityPerTimestep the new value of mProtoRosetteResolutionProbabilityPerTimestep

Definition at line 237 of file MutableVertexMesh.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetRosetteResolutionProbabilityPerTimestep ( double rosetteResolutionProbabilityPerTimestep )

Set method for mRosetteResolutionProbabilityPerTimestep.

Parameters

rosetteResolutionProbabilityPerTimestep the new value of mRosetteResolutionProbabilityPerTimestep

Definition at line 254 of file MutableVertexMesh.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetT2Threshold ( double t2Threshold )

Set method for mT2Threshold.

Parameters

t2Threshold

Definition at line 208 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 2 > MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::WidenEdgeOrCorrectIntersectionLocationIfNecessary	(	unsigned	indexA,
		unsigned	indexB,
		c_vector< double, 2 >	intersection
	)

protected

Helper method for ReMesh(), called by PerformT3Swap(). During T3 swaps nodes are merged onto edges. This method checks if the edge is too short and moves its vertices apart if necessary in order to prevent T1 swaps from happening right away. The method also checks that the location where the merged node is going to end up at is not too close to one of the neighbouring vertices and moves it if necessary to prevent T1 swaps.

Parameters

indexA	index of one of the nodes on the short edge
indexB	index of the other node on the short edge
intersection	the intersection location, i.e. the location where we are planning to put the merged node

Returns: intersection, the corrected location of where we are planning to put the merged node

If the edge is shorter than 4.0*mCellRearrangementRatio*mCellRearrangementThreshold move vertexA and vertexB 4.0*mCellRearrangementRatio*mCellRearrangementThreshold apart.

Todo:: investigate if moving A and B causes other issues with nearby nodes (see #2401)

Note: this distance is so that there is always enough room for new nodes (if necessary)

Todo:: currently this assumes a worst case scenario of 3 nodes between A and B could be less movement for other cases (see #1399 and #2401)

If the intersection is within mCellRearrangementRatio^2*mCellRearrangementThreshold of vertexA or vertexB move it mCellRearrangementRatio^2*mCellRearrangementThreshold away.

Note: this distance so that there is always enough room for new nodes (if necessary).

Todo:: currently this assumes a worst case scenario of 3 nodes between A and B; could be less movement for other cases (see #2401)

Definition at line 3144 of file MutableVertexMesh.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 324 of file MutableVertexMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementRatio

protected

The ratio between the minimum distance apart that two nodes in the mesh can be without causing element rearrangement and their separation after remeshing.

Definition at line 80 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementThreshold

protected

The minimum distance apart that two nodes in the mesh can be without causing element rearrangement.

Definition at line 74 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCheckForInternalIntersections

protected

Whether to check for edges intersections (true) or not (false).

Definition at line 95 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices

protected

Indices of elements that have been deleted. These indices can be reused when adding new elements.

Definition at line 101 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices

protected

Indices of nodes that have been deleted. These indices can be reused when adding new elements/nodes.

Definition at line 98 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDistanceForT3SwapChecking

protected

Distance for T3 swap checking. At each time step we check for each boundary node whether it intersects with any boundary elements (cells) whose centroids lie within this distance to the node. Note that T3 swaps may not be resolved correctly if this distance is chosen too small, while large values for mDistanceForT3SwapChecking may slow down the simulation.

Definition at line 109 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector<double, SPACE_DIM> MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLastT2SwapLocation

protected

The location of the last T2 swap (the centre of the removed triangle), stored so it can be accessed by the T2SwapCellKiller.

Definition at line 120 of file MutableVertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Locations of T1 swaps (the mid point of the moving nodes), stored so they can be accessed and output by the cell population. The locations are stored until they are cleared by ClearLocationsOfT1Swaps().

Definition at line 115 of file MutableVertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protected

Locations of T3 swaps (the location of the intersection with the edge), stored so they can be accessed and output by the cell population. The locations are stored until they are cleared by ClearLocationsOfT3Swaps().

Definition at line 126 of file MutableVertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mProtorosetteFormationProbability

protected

The probability that, instead of a T1 swap, the relevant nodes merge to form a protorosette

Definition at line 86 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mProtorosetteResolutionProbabilityPerTimestep

protected

The probability that, in a given timestep, a protorosette node resolves into two rank-3 nodes

Definition at line 89 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mRosetteResolutionProbabilityPerTimestep

protected

The probability that, in a given timestep, a rosette node resolves into two lower-rank nodes

Definition at line 92 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mT2Threshold

protected

The area threshold at which T2 swaps occur in an apoptotic, triangular cell/element.

Definition at line 83 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< DIM, DIM >::serialize().

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

mesh/src/vertex/MutableVertexMesh.hpp
mesh/src/vertex/MutableVertexMesh.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

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