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 ()
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)
void	Clear ()
void	DivideEdge (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)
void	RemoveDeletedNodesAndElements (VertexElementMap &rElementMap)
void	RemoveDeletedNodes ()
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	CheckForT1Swaps (VertexElementMap &rElementMap)
bool	CheckForT2Swaps (VertexElementMap &rElementMap)
bool	CheckForIntersections ()
void	IdentifySwapType (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB, VertexElementMap &rElementMap)
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)
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
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 vertex-based mesh class, for use in vertex-based cell-based simulations.

Definition at line 50 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 rearrangment (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 rearrangment node separation after remeshing (defaults to 1.5)

Definition at line 36 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 102 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 113 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 238 of file MutableVertexMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and VertexElement< 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 219 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 to check if elements have intersected and to correct them if required

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

Returns:: whether to recheck the mesh again

Definition at line 889 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 >::CheckForT1Swaps ( VertexElementMap & rElementMap ) [inline, protected]

Helper method for ReMesh to check if any neighbouring nodes in an element are within the mCellRearrangementThreshold and perform any T1Swaps if required

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

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 to recheck the mesh again

Todo:: use iterators to tidy this up

Definition at line 797 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, protected]

Helper method for ReMesh to check if any elements are smaller than the mT2Threshold and perform any T2Swaps, removing elements, if required

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

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 to recheck the mesh again

Definition at line 860 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 MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements().

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

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 167 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 T1Swaps

Definition at line 207 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT1Swaps.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Helper method to clear the stored T3Swaps

Definition at line 213 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT3Swaps.

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

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 578 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 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 602 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 609 of file MutableVertexMesh.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), Node< SPACE_DIM >::GetIndex(), 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

Definition at line 450 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddElement(), VertexElement< 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.

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

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)

Definition at line 261 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.

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

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 435 of file MutableVertexMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: mCellRearrangementRatio

Definition at line 131 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 119 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 137 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mCheckForInternalIntersections.

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 T1Swaps

Definition at line 195 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT1Swaps.

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

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 T3Swaps

Definition at line 201 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mLocationsOfT3Swaps.

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

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 182 of file MutableVertexMesh.cpp.

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

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

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 176 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 >::GetNumNodes(), 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 125 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,
		VertexElementMap &	rElementMap
	)			`[inline, protected]`

Helper method for ReMesh to Identify the type of swap when nodes are too close, T2Swap or NodeMerge.

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

Parameters:

	pNodeA	one of the nodes to perform the swap with
	pNodeB	the other node to perform the swap
	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 955 of file MutableVertexMesh.cpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT1Swaps().

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 to perform an element swap to fix overlaping elements

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

Parameters:

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

Definition at line 1510 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 to merge nodes when needed. Replaces the node contained in the least number of elements with the other node.

Parameters:

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

Definition at line 1281 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 to perform the T1 Swap

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

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? (#1884)

Definition at line 1332 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 to perform the T2 Swap

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

Parameters:

rElement

the element to remove

Definition at line 1682 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]`

Called by ReMesh(). Moves a node, which has been found to overlap an element, back onto the edge of that element and associates it with the element and adds new nodes to maitain three elemets a node.

Parameters:

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

Definition at line 1784 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() to remove a triangular void in which one of the edges is less than the cell rearrangement threshold.

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 2445 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 does not require a VertexElementMap. Note: inherited classes should overload ReMesh(VertexElementMap&).

Definition at line 790 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]

Re-mesh the mesh.

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:: put code for remeshing in 3D here - see #866 and the paper doi:10.1016/j.jtbi.2003.10.001

Definition at line 740 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT1Swaps(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT2Swaps(), EXCEPTION, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodesAndElements().

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 714 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 675 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 >::CheckForT2Swaps(), and 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

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Cylindrical2dVertexMesh.

Definition at line 229 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 155 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 143 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 161 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 255 of file MutableVertexMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

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

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 149 of file MutableVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::mT2Threshold.

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.

Definition at line 216 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 64 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(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCellRearrangementRatio().

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 58 of file MutableVertexMesh.hpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT1Swaps(), 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(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetCellRearrangementThreshold().

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 70 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 76 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 73 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 T1Swaps (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 82 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 T3Swaps (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 88 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 67 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: