MutableVertexMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <MutableVertexMesh.hpp>

Inherits VertexMesh< 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)
	MutableVertexMesh ()
virtual	~MutableVertexMesh ()
void	SetCellRearrangementThreshold (double cellRearrangementThreshold)
void	SetT2Threshold (double t2Threshold)
void	SetCellRearrangementRatio (double cellRearrangementRatio)
virtual void	SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > point)
void	SetCheckForInternalIntersections (bool checkForInternalIntersections)
double	GetCellRearrangementThreshold () const
double	GetT2Threshold () const
double	GetCellRearrangementRatio () 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 ()
Protected Member Functions
unsigned	DivideElement (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned nodeAIndex, unsigned nodeBIndex, bool placeOriginalElementBelow=false)
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)
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 Attributes
double	mCellRearrangementThreshold
double	mCellRearrangementRatio
double	mT2Threshold
bool	mCheckForInternalIntersections
std::vector< unsigned >	mDeletedNodeIndices
std::vector< unsigned >	mDeletedElementIndices
std::vector< c_vector< double, SPACE_DIM > >	mLocationsOfT1Swaps
c_vector< double, SPACE_DIM >	mLastT2SwapLocation
std::vector< c_vector< double, SPACE_DIM > >	mLocationsOfT3Swaps
Friends
class	TestMutableVertexMesh
class	TestMutableVertexMeshReMesh
class	boost::serialization::access

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 64 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`
	)			`[inline]`

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)

Definition at line 42 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 ( ) [inline]

Default constructor for use by serializer.

Definition at line 110 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 ( ) [inline, virtual]

Destructor.

Definition at line 122 of file MutableVertexMesh.cpp.

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

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Add an element to the mesh.

Parameters:

pNewElement

the new element

Returns:: the index of the new element in the mesh

Definition at line 246 of file MutableVertexMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 227 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and Node< SPACE_DIM >::SetIndex().

Referenced by VertexBasedCellPopulation< DIM >::AddNode(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections ( ) [inline, 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 908 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges ( ) [inline, protected]

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 822 of file MutableVertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), Node< SPACE_DIM >::GetIndex(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementThreshold, and Node< SPACE_DIM >::rGetContainingElementIndices().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 883 of file MutableVertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetT2Threshold(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), and VertexElementMap::SetDeleted().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear ( ) [inline, virtual]

Delete mNodes and mElements.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 176 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT1Swaps ( ) [inline]

Helper method to clear the stored T1 swaps

Definition at line 215 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT1Swaps.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT3Swaps ( ) [inline]

Helper method to clear the stored T3 swaps

Definition at line 221 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT3Swaps.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 594 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), Node< SPACE_DIM >::GetIndex(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, Node< SPACE_DIM >::rGetContainingElementIndices(), and Node< SPACE_DIM >::SetAsBoundaryNode().

Referenced by VertexBasedCellPopulation< DIM >::RemoveDeadCells().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 618 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)			`[inline]`

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 625 of file MutableVertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), Node< SPACE_DIM >::GetIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), Node< SPACE_DIM >::IsBoundaryNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, 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`
	)			`[inline, 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 468 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddElement(), MutableElement< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, and VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

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

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`
	)			`[inline]`

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 269 of file MutableVertexMesh.cpp.

Referenced by VertexBasedCellPopulation< DIM >::AddCell(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongShortAxis().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 455 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetShortAxisOfElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: mCellRearrangementRatio

Definition at line 140 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementRatio.

Referenced by VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: mCellRearrangementThreshold

Definition at line 128 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementThreshold.

Referenced by VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and VertexBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Definition at line 146 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCheckForInternalIntersections.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: the location of the last T2 swap

Definition at line 203 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLastT2SwapLocation.

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 ( ) [inline]

Returns:: the locations of the T1 swaps

Definition at line 197 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT1Swaps.

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 ( ) [inline]

Returns:: the locations of the T3 swaps

Definition at line 209 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT3Swaps.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const [inline, virtual]

Returns:: the number of VertexElements in the mesh.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 191 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, and VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by VertexBasedCellPopulation< DIM >::GetNumElements(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const [inline, virtual]

Returns:: the number of Nodes in the mesh.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 185 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: mT2Threshold

Definition at line 134 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mT2Threshold.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps(), and VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)			`[inline, protected, virtual]`

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 982 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap	(	Node< SPACE_DIM > *	pNode,
		unsigned	elementIndex
	)			`[inline, 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 1486 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)			`[inline, 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 1294 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

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

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
	)			`[inline, 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 1345 of file MutableVertexMesh.cpp.

References EXCEPTION, Node< SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::GetNumContainingElements(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), Node< SPACE_DIM >::IsBoundaryNode(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementRatio, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementThreshold, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT1Swaps, Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), Node< SPACE_DIM >::rGetModifiableLocation(), and Node< SPACE_DIM >::SetAsBoundaryNode().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap ( VertexElement< ELEMENT_DIM, SPACE_DIM > & rElement ) [inline, 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 1652 of file MutableVertexMesh.cpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap	(	Node< SPACE_DIM > *	pNode,
		unsigned	elementIndex
	)			`[inline, 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 1724 of file MutableVertexMesh.cpp.

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

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
	)			`[inline, 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 2431 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes(), Node< SPACE_DIM >::rGetLocation(), Node< SPACE_DIM >::rGetModifiableLocation(), and Node< SPACE_DIM >::SetAsBoundaryNode().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( ) [inline]

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 815 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( VertexElementMap & rElementMap ) [inline, 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 771 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements(), and VertexElementMap::Resize().

Referenced by VertexBasedCellPopulation< DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes ( ) [inline]

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

Definition at line 740 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 701 of file MutableVertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes(), VertexElementMap::Resize(), VertexElementMap::SetDeleted(), and VertexElementMap::SetNewIndex().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, protected]`

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?

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Cylindrical2dVertexMesh, and Toroidal2dVertexMesh.

Definition at line 262 of file MutableVertexMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Set method for mCellRearrangementRatio.

Parameters:

cellRearrangementRatio

Definition at line 164 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementRatio.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Set method for mCellRearrangementThreshold.

Parameters:

cellRearrangementThreshold

Definition at line 152 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Set method for mCheckForInternalIntersections.

Parameters:

checkForInternalIntersections

Definition at line 170 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCheckForInternalIntersections.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< SPACE_DIM >	point
	)			`[inline, 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 263 of file MutableVertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by VertexBasedCellPopulation< DIM >::SetNode(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::WidenEdgeOrCorrectIntersectionLocationIfNecessary().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Set method for mT2Threshold.

Parameters:

t2Threshold

Definition at line 158 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mT2Threshold.

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
	)			`[inline, 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 2457 of file MutableVertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementRatio, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCellRearrangementThreshold, and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

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

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Cylindrical2dVertexMesh, and Toroidal2dVertexMesh.

Definition at line 249 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 78 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementRatio(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), MutableVertexMesh< DIM, DIM >::serialize(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCellRearrangementRatio(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::WidenEdgeOrCorrectIntersectionLocationIfNecessary().

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 72 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCellRearrangementThreshold(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), MutableVertexMesh< DIM, DIM >::serialize(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCellRearrangementThreshold(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::WidenEdgeOrCorrectIntersectionLocationIfNecessary().

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 84 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCheckForInternalIntersections(), MutableVertexMesh< DIM, DIM >::serialize(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCheckForInternalIntersections().

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 90 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElement(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements(), and 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 87 of file MutableVertexMesh.hpp.

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 101 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLastT2SwapLocation(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap().

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 96 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT1Swaps(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocationsOfT1Swaps(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap().

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 107 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ClearLocationsOfT3Swaps(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocationsOfT3Swaps(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap().

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 81 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetT2Threshold(), MutableVertexMesh< DIM, DIM >::serialize(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetT2Threshold().

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