NodeBasedCellPopulation< DIM > Class Template Reference

#include <NodeBasedCellPopulation.hpp>

Inheritance diagram for NodeBasedCellPopulation< DIM >:

Collaboration diagram for NodeBasedCellPopulation< DIM >:

List of all members.

Public Member Functions

NodeBasedCellPopulation (const std::vector< Node< DIM > * > nodes, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteNodes=true)

NodeBasedCellPopulation (const std::vector< Node< DIM > * > nodes, double mechanicsCutOffLength, bool deleteNodes=true)

NodeBasedCellPopulation (const AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells)

~NodeBasedCellPopulation ()

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 ()

void OutputCellPopulationParameters (out_stream &rParamsFile)

double GetMechanicsCutOffLength ()

void SetMechanicsCutOffLength (double mechanicsCutOffLength)

double GetWidth (const unsigned &rDimension)

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

double mMechanicsCutOffLength

Friends

class TestNodeBasedCellPopulation

class TestBoxCollection

class boost::serialization::access

Detailed Description

template<unsigned DIM>
class NodeBasedCellPopulation< DIM >

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

Definition at line 45 of file NodeBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

Default constructor.

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

Parameters:

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

Definition at line 31 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation	(	const std::vector< Node< DIM > * >	nodes,
		double	mechanicsCutOffLength,
		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 cell population will take responsibility for freeing the memory used by the nodes.

Parameters:

	nodes	a vector of Nodes
	mechanicsCutOffLength	the cut of length for mechanics uised to create the BoxedCollection to improve speed
	deleteNodes	whether to delete nodes in destructor

Definition at line 47 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation	(	const AbstractMesh< DIM, DIM > &	rMesh,
		std::vector< CellPtr > &	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 cells.

Definition at line 59 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

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

Destructor.

Frees all our node memory.

Definition at line 81 of file NodeBasedCellPopulation.cpp.

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

Member Function Documentation

template<unsigned DIM>

template<class Archive>

void NodeBasedCellPopulation< 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:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 98 of file NodeBasedCellPopulation.hpp.

References NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

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

Overridden AddNode() method.

Add a new node to the cell population.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in cell population

Implements AbstractCellPopulation< DIM >.

Definition at line 310 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)			`[inline, private, virtual]`

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

Parameters:

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

Implements AbstractCellPopulation< DIM >.

Definition at line 201 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodes.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::Validate ( ) [inline, private, virtual]

Check consistency of our internal data structures.

Implements AbstractCellPopulation< DIM >.

Definition at line 106 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), EXCEPTION, NodeBasedCellPopulation< DIM >::GetNumNodes(), and AbstractCellPopulation< DIM >::mCellLocationMap.

Referenced by NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation(), NodeBasedCellPopulation< DIM >::serialize(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SplitUpIntoBoxes	(	double	cutOffLength,
		c_vector< double, 2 *DIM >	domainSize
	)			`[inline, private]`

Method for Initially Splitting up cell population into neighbouring boxes, to decrease runtime.

Parameters:

	cutOffLength	length of spring cut off between nodes
	domainSize	c_vector of size 2*dimension reads minX, maxX, minY, maxY, etc

Definition at line 144 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodes, and NodeBasedCellPopulation< DIM >::mpBoxCollection.

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

template<unsigned DIM>

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

Loops over nodes and sets mMinSpatialPositions and mMaxSpatialPositions

Definition at line 157 of file NodeBasedCellPopulation.cpp.

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

Referenced by NodeBasedCellPopulation< DIM >::GetWidth(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

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

Returns:: the number of nodes in the cell population.

Implements AbstractCellPopulation< DIM >.

Definition at line 330 of file NodeBasedCellPopulation.cpp.

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

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

template<unsigned DIM>

Node< DIM > * NodeBasedCellPopulation< 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 AbstractCellPopulation< DIM >.

Definition at line 195 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodes.

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

template<unsigned DIM>

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

Remove all cells labelled as dead.

Note that after calling this method the cell population 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 AbstractCellPopulation< DIM >.

Definition at line 288 of file NodeBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, and NodeBasedCellPopulation< DIM >::mDeletedNodeIndices.

template<unsigned DIM>

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

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

Definition at line 96 of file NodeBasedCellPopulation.cpp.

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

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

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [inline, virtual]

Remove nodes that have been marked as deleted and update the node cell map.

Parameters:

hasHadBirthsOrDeaths

whether cell population has had Births Or Deaths

Implements AbstractCellPopulation< DIM >.

Definition at line 207 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

Method for getting all nodes in the cell population.

Returns:: vector of Nodes

Definition at line 132 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodes.

template<unsigned DIM>

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

Method for getting all nodes in the cell population (for archiving).

Returns:: vector of Nodes

Definition at line 138 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mNodes.

template<unsigned DIM>

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

Returns:: pointer to a node box collection.

Definition at line 336 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpBoxCollection.

template<unsigned DIM>

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

Returns:: Node pairs for force calculation.

Definition at line 342 of file NodeBasedCellPopulation.cpp.

References EXCEPTION, and NodeBasedCellPopulation< DIM >::mNodePairs.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs CellPopulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 352 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength, and AbstractCentreBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetMechanicsCutOffLength ( ) [inline]

Returns:: mMechanicsCutOffLength

Definition at line 371 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetMechanicsCutOffLength ( double mechanicsCutOffLength ) [inline]

Set mMechanicsCutOffLength.

Parameters:

mechanicsCutOffLength

the new value of mMechanicsCutOffLength

Definition at line 364 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength.

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension ) [inline, virtual]

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the cell population by computing the maximum distance between any nodes in this dimension.

Parameters:

rDimension

a dimension (0,1 or 2)

Returns:: The maximum distance between any nodes in this dimension.

Implements AbstractCellPopulation< DIM >.

Definition at line 377 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::FindMaxAndMin(), NodeBasedCellPopulation< DIM >::mMaxSpatialPositions, and NodeBasedCellPopulation< DIM >::mMinSpatialPositions.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 87 of file NodeBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

std::vector<Node<DIM>* > NodeBasedCellPopulation< DIM >::mNodes [protected]

List of nodes.

Definition at line 53 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::vector<unsigned> NodeBasedCellPopulation< DIM >::mDeletedNodeIndices [protected]

Indices of nodes that have been deleted, to be reused when adding new nodes.

Definition at line 56 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddNode(), NodeBasedCellPopulation< DIM >::Clear(), NodeBasedCellPopulation< DIM >::GetNumNodes(), and NodeBasedCellPopulation< DIM >::RemoveDeadCells().

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mAddedNodes [protected]

Whether nodes have been added to the cell population.

Definition at line 59 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::AddNode(), NodeBasedCellPopulation< DIM >::Clear(), and NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation().

template<unsigned DIM>

BoxCollection<DIM>* NodeBasedCellPopulation< DIM >::mpBoxCollection [private]

Pointer to a Node box collection

Definition at line 64 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::Clear(), NodeBasedCellPopulation< DIM >::GetBoxCollection(), NodeBasedCellPopulation< DIM >::SplitUpIntoBoxes(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

c_vector<double, DIM> NodeBasedCellPopulation< DIM >::mMinSpatialPositions [private]

Vector of minimal spatial positions in each dimension

Definition at line 67 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::FindMaxAndMin(), NodeBasedCellPopulation< DIM >::GetWidth(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

c_vector<double, DIM> NodeBasedCellPopulation< DIM >::mMaxSpatialPositions [private]

Vector of maximal spatial positions in each dimension

Definition at line 70 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::FindMaxAndMin(), NodeBasedCellPopulation< DIM >::GetWidth(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

std::set< std::pair<Node<DIM>*, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mNodePairs [private]

Node pairs for force calculations

Definition at line 73 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::Clear(), NodeBasedCellPopulation< DIM >::rGetNodePairs(), and NodeBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mDeleteNodes [private]

Whether to delete the nodes (taken in one of the constructors, defaults to true)

Definition at line 78 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::~NodeBasedCellPopulation().

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength [private]

Mechanics cut off length. Used in order to calculate the BoxCollection.

Definition at line 84 of file NodeBasedCellPopulation.hpp.

Referenced by NodeBasedCellPopulation< DIM >::GetMechanicsCutOffLength(), NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters(), NodeBasedCellPopulation< DIM >::SetMechanicsCutOffLength(), and NodeBasedCellPopulation< DIM >::Update().

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

cell_based/src/population/NodeBasedCellPopulation.hpp
cell_based/src/population/NodeBasedCellPopulation.cpp


Public Member Functions
	NodeBasedCellPopulation (const std::vector< Node< DIM > * > nodes, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteNodes=true)
	NodeBasedCellPopulation (const std::vector< Node< DIM > * > nodes, double mechanicsCutOffLength, bool deleteNodes=true)
	NodeBasedCellPopulation (const AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells)
	~NodeBasedCellPopulation ()
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 ()
void	OutputCellPopulationParameters (out_stream &rParamsFile)
double	GetMechanicsCutOffLength ()
void	SetMechanicsCutOffLength (double mechanicsCutOffLength)
double	GetWidth (const unsigned &rDimension)
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
double	mMechanicsCutOffLength
Friends
class	TestNodeBasedCellPopulation
class	TestBoxCollection
class	boost::serialization::access

NodeBasedCellPopulation< DIM > Class Template Reference

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class NodeBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class NodeBasedCellPopulation< DIM >