NodeBasedTissue< DIM > Class Template Reference

#include <NodeBasedTissue.hpp>

Inherits AbstractCellCentreBasedTissue< DIM >.

Collaboration diagram for NodeBasedTissue< DIM >:

Public Member Functions
	NodeBasedTissue (const std::vector< Node< DIM > * > nodes, std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteNodes=true)
	NodeBasedTissue (const std::vector< Node< DIM > * > nodes, bool deleteNodes=true)
	NodeBasedTissue (const AbstractMesh< DIM, DIM > &rMesh, std::vector< TissueCell > &rCells)
	~NodeBasedTissue ()
unsigned	GetNumNodes ()
Node< DIM > *	GetNode (unsigned index)
unsigned	RemoveDeadCells ()
void	Clear ()
void	Update (bool hasHadBirthsOrDeaths=true)
std::vector< Node< DIM > * > &	rGetNodes ()
const std::vector< Node< DIM > * > &	rGetNodes () const
BoxCollection< DIM > *	GetBoxCollection ()
std::set< std::pair< Node< DIM > , Node< DIM > > > &	rGetNodePairs ()
Protected Attributes
std::vector< Node< DIM > * >	mNodes
std::vector< unsigned >	mDeletedNodeIndices
bool	mAddedNodes
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
unsigned	AddNode (Node< DIM > *pNewNode)
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
void	Validate ()
void	SplitUpIntoBoxes (double cutOffLength, c_vector< double, 2 *DIM > domainSize)
void	FindMaxAndMin ()
Private Attributes
BoxCollection< DIM > *	mpBoxCollection
c_vector< double, DIM >	mMinSpatialPositions
c_vector< double, DIM >	mMaxSpatialPositions
std::set< std::pair< Node< DIM > , Node< DIM > > >	mNodePairs
bool	mDeleteNodes
Friends
class	TestNodeBasedTissue
class	TestBoxCollection
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class NodeBasedTissue< DIM >

A NodeBasedTissue is a Tissue consisting of only nodes in space with associated cells. There are no elements and no mesh.

Definition at line 45 of file NodeBasedTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NodeBasedTissue< DIM >::NodeBasedTissue	(	const std::vector< Node< DIM > * >	nodes,
		std::vector< TissueCell > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteNodes = `true`
	)			`[inline]`

Default constructor.

Note that the tissue will take responsibility for freeing the memory used by the nodes.

Parameters:

	nodes	a vector of Nodes
	rCells	a vector of TissueCells
	locationIndices	an optional vector of location indices that correspond to real cells
	deleteNodes	whether to delete nodes in destructor

Definition at line 32 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

NodeBasedTissue< DIM >::NodeBasedTissue	(	const std::vector< Node< DIM > * >	nodes,
		bool	deleteNodes = `true`
	)			`[inline]`

Constructor for use by the archiving - doesn't take in cells, since these are dealt with by the serialize method of our base class.

Note that the tissue will take responsibility for freeing the memory used by the nodes.

Parameters:

	nodes	a vector of Nodes
	deleteNodes	whether to delete nodes in destructor

Definition at line 47 of file NodeBasedTissue.cpp.

template<unsigned DIM>

NodeBasedTissue< DIM >::NodeBasedTissue	(	const AbstractMesh< DIM, DIM > &	rMesh,
		std::vector< TissueCell > &	rCells
	)			`[inline]`

Constructor which takes in a mesh and takes a copy of its nodes. The mesh is not changed and no references to any of its data are created.

This constructor is a helper constructor: it is generally easier for the user to create a mesh than a set of nodes.

Parameters:

	rMesh	any mesh.
	rCells	a vector of TissueCells.

Definition at line 59 of file NodeBasedTissue.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), NodeBasedTissue< DIM >::mAddedNodes, NodeBasedTissue< DIM >::mNodes, and NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

NodeBasedTissue< DIM >::~NodeBasedTissue ( ) [inline]

Destructor.

Frees all our node memory.

Definition at line 78 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::Clear(), NodeBasedTissue< DIM >::mDeleteNodes, and NodeBasedTissue< DIM >::mNodes.

Member Function Documentation

template<unsigned DIM>

unsigned NodeBasedTissue< DIM >::AddNode ( Node< DIM > * pNewNode ) [inline, private, virtual]

Overridden AddNode() method.

Add a new node to the tissue.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in tissue

Implements AbstractTissue< DIM >.

Definition at line 319 of file NodeBasedTissue.cpp.

References Node< SPACE_DIM >::GetIndex(), NodeBasedTissue< DIM >::mAddedNodes, NodeBasedTissue< DIM >::mDeletedNodeIndices, NodeBasedTissue< DIM >::mNodes, and Node< SPACE_DIM >::SetIndex().

template<unsigned DIM>

void NodeBasedTissue< DIM >::Clear ( ) [inline]

Reset the member variables mDeletedNodeIndices, mAddedNodes, mNodePairs, and mpBoxCollection.

Definition at line 94 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mAddedNodes, NodeBasedTissue< DIM >::mDeletedNodeIndices, NodeBasedTissue< DIM >::mNodePairs, and NodeBasedTissue< DIM >::mpBoxCollection.

Referenced by NodeBasedTissue< DIM >::Update(), and NodeBasedTissue< DIM >::~NodeBasedTissue().

template<unsigned DIM>

void NodeBasedTissue< DIM >::FindMaxAndMin ( ) [inline, private]

Loops over nodes and sets mMinSpatialPositions and mMaxSpatialPositions

Definition at line 160 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::GetNode(), NodeBasedTissue< DIM >::mMaxSpatialPositions, NodeBasedTissue< DIM >::mMinSpatialPositions, and NodeBasedTissue< DIM >::mNodes.

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

template<unsigned DIM>

BoxCollection< DIM > * NodeBasedTissue< DIM >::GetBoxCollection ( ) [inline]

Returns:: pointer to a node box collection.

Definition at line 347 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mpBoxCollection.

template<unsigned DIM>

Node< DIM > * NodeBasedTissue< DIM >::GetNode ( unsigned index ) [inline, virtual]

Overridden GetNode() method.

Parameters:

index

global index of the specified node

Returns:: a pointer to the node with a given index.

Implements AbstractTissue< DIM >.

Definition at line 197 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

Referenced by NodeBasedTissue< DIM >::FindMaxAndMin().

template<unsigned DIM>

unsigned NodeBasedTissue< DIM >::GetNumNodes ( ) [inline, virtual]

Returns:: the number of nodes in the tissue.

Implements AbstractTissue< DIM >.

Definition at line 340 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mDeletedNodeIndices, and NodeBasedTissue< DIM >::mNodes.

Referenced by NodeBasedTissue< DIM >::Validate().

template<unsigned DIM>

unsigned NodeBasedTissue< DIM >::RemoveDeadCells ( ) [inline, virtual]

Remove all cells labelled as dead.

Note that after calling this method the tissue will be in an inconsistent state until the equivalent of a 'remesh' is performed! So don't try iterating over cells or anything like that.

Returns:: number of cells removed

Implements AbstractTissue< DIM >.

Definition at line 296 of file NodeBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCells, and NodeBasedTissue< DIM >::mDeletedNodeIndices.

template<unsigned DIM>

std::set< std::pair< Node< DIM > *, Node< DIM > * > > & NodeBasedTissue< DIM >::rGetNodePairs ( ) [inline]

Returns:: Node pairs for force calculation.

Definition at line 354 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodePairs.

template<unsigned DIM>

const std::vector< Node< DIM > * > & NodeBasedTissue< DIM >::rGetNodes ( ) const [inline]

Method for getting all nodes in the tissue (for archiving).

Returns:: vector of Nodes

Definition at line 139 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

template<unsigned DIM>

std::vector< Node< DIM > * > & NodeBasedTissue< DIM >::rGetNodes ( ) [inline]

Method for getting all nodes in the tissue.

Returns:: vector of Nodes

Definition at line 132 of file NodeBasedTissue.cpp.

References NodeBasedTissue< DIM >::mNodes.

template<unsigned DIM>

template<class Archive >

void NodeBasedTissue< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Note that serialization of the nodes is handled by load/save_construct_data, so we don't actually have to do anything here except delegate to the base class.

Parameters: