#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)
	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 57 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`
	)

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 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 109 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 120 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 245 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 226 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections ( ) [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 896 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForT1Swaps ( VertexElementMap & rElementMap ) [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 804 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 ) [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 867 of file MutableVertexMesh.cpp.

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 174 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 T1Swaps

Definition at line 214 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Helper method to clear the stored T3Swaps

Definition at line 220 of file MutableVertexMesh.cpp.

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 585 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 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 609 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 616 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), 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

Definition at line 457 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.

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 268 of file MutableVertexMesh.cpp.

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

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 442 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 138 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: mCellRearrangementThreshold

Definition at line 126 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 144 of file MutableVertexMesh.cpp.

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 T1Swaps

Definition at line 202 of file MutableVertexMesh.cpp.

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 T3Swaps

Definition at line 208 of file MutableVertexMesh.cpp.

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 189 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 183 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns:: mT2Threshold

Definition at line 132 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB,
		VertexElementMap &	rElementMap
	)		`[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 962 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(), 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 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 1517 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 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 1288 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 >::PerformT1Swap	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB,
		std::set< unsigned > &	rElementsContainingNodes
	)		`[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 1339 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 to perform the T2 Swap

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

Parameters:

rElement the element to remove

Definition at line 1689 of file MutableVertexMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap	(	Node< SPACE_DIM > *	pNode,
		unsigned	elementIndex
	)		`[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 1791 of file MutableVertexMesh.cpp.

References MutableElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), EXCEPTION, Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), Node< SPACE_DIM >::GetNumContainingElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::IsBoundaryNode(), NEVER_REACHED, 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 >::PerformVoidRemoval	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB,
		Node< SPACE_DIM > *	pNodeC
	)		`[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 2452 of file MutableVertexMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), 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 ( )

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

Definition at line 797 of file MutableVertexMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 747 of file MutableVertexMesh.cpp.

References EXCEPTION.

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 721 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 682 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
	)		`[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 236 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 162 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 150 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 168 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 262 of file MutableVertexMesh.cpp.

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 156 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.

Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Cylindrical2dVertexMesh.

Definition at line 223 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 71 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 65 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 77 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 83 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 80 of file MutableVertexMesh.hpp.

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

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 89 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 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 95 of file MutableVertexMesh.hpp.

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 74 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

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 >