NodeBasedCellPopulation< DIM > Class Template Reference

#include <NodeBasedCellPopulation.hpp>

Inherits AbstractCentreBasedCellPopulation< DIM >.

Inherited by NodeBasedCellPopulationWithBuskeUpdate< DIM >.

Collaboration diagram for NodeBasedCellPopulation< DIM >:

Public Member Functions
	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)
	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh)
	~NodeBasedCellPopulation ()
NodesOnlyMesh< DIM > &	rGetMesh ()
const NodesOnlyMesh< DIM > &	rGetMesh () const
unsigned	GetNumNodes ()
Node< DIM > *	GetNode (unsigned index)
unsigned	RemoveDeadCells ()
void	Clear ()
void	Update (bool hasHadBirthsOrDeaths=true)
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)
std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)
virtual CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())
Protected Member Functions
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
Protected Attributes
NodesOnlyMesh< DIM > &	mrMesh
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
unsigned	AddNode (Node< DIM > *pNewNode)
void	Validate ()
void	SplitUpIntoBoxes (double cutOffLength, c_vector< double, 2 *DIM > domainSize)
void	FindMaxAndMin ()
void	WriteCellVolumeResultsToFile ()
void	WriteVtkResultsToFile ()
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	mDeleteMesh
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 44 of file NodeBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation	(	NodesOnlyMesh< DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`
	)			`[inline]`

Default constructor.

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

Parameters:

	rMesh	a mutable nodes-only mesh
	rCells	a vector of cells
	locationIndices	an optional vector of location indices that correspond to real cells
	deleteMesh	whether to delete nodes-only mesh in destructor

Definition at line 34 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation ( NodesOnlyMesh< DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a mutable nodes-only mesh

Definition at line 48 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

Destructor.

Frees all our node memory.

Definition at line 59 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::Clear(), NodeBasedCellPopulation< DIM >::mDeleteMesh, and NodeBasedCellPopulation< DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>

CellPtr NodeBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell = `CellPtr()`
	)			`[inline, virtual]`

Overridden AddCell() method.

Add a new cell to the cell population and update the vector of cell radii in the NodesOnlyMesh.

Parameters:

	pNewCell	the cell to add
	rCellDivisionVector	the position in space at which to put it
	pParentCell	pointer to a parent cell - this is required for mesh-based cell populations

Returns:: address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)

Todo:: set the correct cell radius and properly test this (#1808)

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 553 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), NodeBasedCellPopulation< DIM >::mrMesh, and NodesOnlyMesh< SPACE_DIM >::SetCellRadius().

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 AbstractOffLatticeCellPopulation< DIM >.

Definition at line 276 of file NodeBasedCellPopulation.cpp.

References NodesOnlyMesh< SPACE_DIM >::AddNode(), and NodeBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

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

Reset the member variables mNodePairs and mpBoxCollection.

Definition at line 81 of file NodeBasedCellPopulation.cpp.

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

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

template<unsigned DIM>

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

Loops over nodes and sets mMinSpatialPositions and mMaxSpatialPositions

Definition at line 126 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::GetNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), NodeBasedCellPopulation< DIM >::mMaxSpatialPositions, NodeBasedCellPopulation< DIM >::mMinSpatialPositions, and NodeBasedCellPopulation< DIM >::mrMesh.

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

template<unsigned DIM>

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

Returns:: pointer to a node box collection.

Definition at line 288 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpBoxCollection.

template<unsigned DIM>

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

Returns:: mMechanicsCutOffLength

Definition at line 320 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength.

template<unsigned DIM>

std::set< unsigned > NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned index ) [inline, virtual]

Overridden GetNeighbouringNodeIndices() method.

Parameters:

index

the node index

Returns:: the set of neighbouring node indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 338 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), NodesOnlyMesh< SPACE_DIM >::GetCellRadius(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), NodeBasedCellPopulation< DIM >::GetNode(), and NodeBasedCellPopulation< DIM >::mrMesh.

Referenced by BuskeCompressionForce< DIM >::AddForceContribution(), and NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations().

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 164 of file NodeBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), and NodeBasedCellPopulation< DIM >::mrMesh.

Referenced by NodeBasedCellPopulation< DIM >::FindMaxAndMin(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::SplitUpIntoBoxes(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), and NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile().

template<unsigned DIM>

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

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

Implements AbstractCellPopulation< DIM >.

Definition at line 282 of file NodeBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), and NodeBasedCellPopulation< DIM >::mrMesh.

Referenced by NodeBasedCellPopulation< DIM >::Validate(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

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 326 of file NodeBasedCellPopulation.cpp.

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

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 >.

Reimplemented in NodeBasedCellPopulationWithBuskeUpdate< DIM >.

Definition at line 304 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mMechanicsCutOffLength.

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 248 of file NodeBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, and NodeBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

const NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh ( ) const [inline]

Returns:: const reference to mrMesh (used in archiving).

Definition at line 75 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh ( ) [inline]

Returns:: reference to mrMesh.

Definition at line 69 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mrMesh.

Referenced by NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations().

template<unsigned DIM>

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

Returns:: Node pairs for force calculation.

Definition at line 294 of file NodeBasedCellPopulation.cpp.

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

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: