#include <NodeBasedCellPopulationWithBuskeUpdate.hpp>

Inheritance diagram for NodeBasedCellPopulationWithBuskeUpdate< DIM >:

Collaboration diagram for NodeBasedCellPopulationWithBuskeUpdate< DIM >:

Public Member Functions
	NodeBasedCellPopulationWithBuskeUpdate (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)

	NodeBasedCellPopulationWithBuskeUpdate (NodesOnlyMesh< DIM > &rMesh)

virtual void	UpdateNodeLocations (double dt)

void	OutputCellPopulationParameters (out_stream &rParamsFile)

Public Member Functions inherited from NodeBasedCellPopulation< DIM >
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)

	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)

	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh)

virtual	~NodeBasedCellPopulation ()

NodesOnlyMesh< DIM > &	rGetMesh ()

const NodesOnlyMesh< DIM > &	rGetMesh () const

virtual TetrahedralMesh< DIM, DIM > *	GetTetrahedralMeshForPdeModifier ()

unsigned	GetNumNodes ()

virtual CellPtr	GetCellUsingLocationIndex (unsigned index)

Node< DIM > *	GetNode (unsigned index)

unsigned	RemoveDeadCells ()

void	Clear ()

void	Update (bool hasHadBirthsOrDeaths=true)

std::vector< std::pair< Node < DIM > , Node< DIM > > > &	rGetNodePairs ()

virtual void	AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > > pPopulationWriter)

virtual void	AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > > pPopulationCountWriter)

virtual void	AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< DIM, DIM > > pCellWriter, CellPtr pCell)

double	GetMechanicsCutOffLength ()

bool	GetUseVariableRadii ()

void	SetUseVariableRadii (bool useVariableRadii=true)

void	SetLoadBalanceMesh (bool loadBalanceMesh)

void	SetLoadBalanceFrequency (unsigned loadBalanceFrequency)

double	GetWidth (const unsigned &rDimension)

c_vector< double, DIM >	GetSizeOfCellPopulation ()

std::set< unsigned >	GetNodesWithinNeighbourhoodRadius (unsigned index, double neighbourhoodRadius)

std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)

virtual CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell)

double	GetVolumeOfCell (CellPtr pCell)

void	SendCellsToNeighbourProcesses ()

void	NonBlockingSendCellsToNeighbourProcesses ()

void	GetReceivedCells ()

std::pair< CellPtr, Node< DIM > * >	GetCellNodePair (unsigned nodeIndex)

void	AddReceivedCells ()

virtual void	UpdateCellProcessLocation ()

Public Member Functions inherited from AbstractCentreBasedCellPopulation< DIM >
	AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

c_vector< double, ELEMENT_DIM >	GetLocationOfCellCentre (CellPtr pCell)

Node< ELEMENT_DIM > *	GetNodeCorrespondingToCell (CellPtr pCell)

virtual double	GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)

CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell=CellPtr())

std::pair< CellPtr, CellPtr >	CreateCellPair (CellPtr pCell1, CellPtr pCell2)

bool	IsMarkedSpring (const std::pair< CellPtr, CellPtr > &rCellPair)

void	MarkSpring (std::pair< CellPtr, CellPtr > &rCellPair)

void	UnmarkSpring (std::pair< CellPtr, CellPtr > &rCellPair)

bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)

virtual std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)

virtual void	CheckForStepSizeException (unsigned nodeIndex, c_vector< double, ELEMENT_DIM > &rDisplacement, double dt)

virtual double	GetDampingConstant (unsigned nodeIndex)

virtual bool	IsGhostNode (unsigned index)

virtual bool	IsParticle (unsigned index)

double	GetMeinekeDivisionSeparation ()

void	SetMeinekeDivisionSeparation (double divisionSeparation)

boost::shared_ptr < AbstractCentreBasedDivisionRule < ELEMENT_DIM, ELEMENT_DIM > >	GetCentreBasedDivisionRule ()

void	SetCentreBasedDivisionRule (boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, ELEMENT_DIM > > pCentreBasedDivisionRule)

virtual double	GetDefaultTimeStep ()

Public Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >
	AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

virtual unsigned	AddNode (Node< SPACE_DIM > *pNewNode)=0

virtual void	SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation)=0

virtual void	CheckForStepSizeException (unsigned nodeIndex, c_vector< double, SPACE_DIM > &rDisplacement, double dt)=0

void	SetDampingConstantNormal (double dampingConstantNormal)

void	SetDampingConstantMutant (double dampingConstantMutant)

void	SetAbsoluteMovementThreshold (double absoluteMovementThreshold)

double	GetAbsoluteMovementThreshold ()

double	GetDampingConstantNormal ()

double	GetDampingConstantMutant ()

Public Member Functions inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

void	SetDataOnAllCells (const std::string &rDataName, double dataValue)

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

std::list< CellPtr > &	rGetCells ()

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

std::vector< unsigned >	GetCellMutationStateCount ()

std::vector< unsigned >	GetCellProliferativeTypeCount ()

std::vector< unsigned >	GetCellCyclePhaseCount ()

unsigned	GetNumRealCells ()

unsigned	GetNumAllCells ()

void	SetCellAncestorsToLocationIndices ()

std::set< unsigned >	GetCellAncestors ()

std::set< CellPtr >	GetCellsUsingLocationIndex (unsigned index)

virtual bool	IsCellAttachedToLocationIndex (unsigned index)

void	SetCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	AddCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)

void	MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index)

unsigned	GetLocationIndexUsingCell (CellPtr pCell)

boost::shared_ptr < CellPropertyRegistry >	GetCellPropertyRegistry ()

void	SetDefaultCellMutationStateAndProliferativeTypeOrdering ()

c_vector< double, SPACE_DIM >	GetCentroidOfCellPopulation ()

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

void	CloseWritersFiles ()

virtual void	WriteResultsToFiles (const std::string &rDirectory)

virtual void	AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)=0

virtual void	AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter)=0

virtual void	AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter, CellPtr pCell)=0

void	OutputCellPopulationInfo (out_stream &rParamsFile)

virtual void	SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > *pSimulation)

bool	GetOutputResultsForChasteVisualizer ()

template<template< unsigned, unsigned > class T>
void	AddPopulationWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellPopulationCountWriter ()

void	AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)

void	AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter)

void	AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationCountWriter)

template<template< unsigned, unsigned > class T>
bool	HasWriter () const

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, SPACE_DIM >	GetSizeOfCellPopulation ()

virtual bool	IsRoomToDivide (CellPtr pCell)

std::pair< unsigned, unsigned >	CreateOrderedPair (unsigned index1, unsigned index2)

Iterator	Begin ()

Iterator	End ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	TestNodeBasedCellPopulationWithBuskeUpdate

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from NodeBasedCellPopulation< DIM >
virtual void	UpdateParticlesAfterReMesh (NodeMap &rMap)

virtual void	Validate ()

Protected Member Functions inherited from AbstractCentreBasedCellPopulation< DIM >
	AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh)

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >
	AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

Protected Member Functions inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

Protected Attributes inherited from NodeBasedCellPopulation< DIM >
NodesOnlyMesh< DIM > *	mpNodesOnlyMesh

Protected Attributes inherited from AbstractCentreBasedCellPopulation< DIM >
double	mMeinekeDivisionSeparation

std::set< std::pair< CellPtr, CellPtr > >	mMarkedSprings

boost::shared_ptr < AbstractCentreBasedDivisionRule < ELEMENT_DIM, ELEMENT_DIM > >	mpCentreBasedDivisionRule

Protected Attributes inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >
double	mDampingConstantNormal

double	mDampingConstantMutant

double	mAbsoluteMovementThreshold

Protected Attributes inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
std::map< unsigned, std::set < CellPtr > >	mLocationCellMap

std::map< Cell *, unsigned >	mCellLocationMap

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	mrMesh

std::list< CellPtr >	mCells

c_vector< double, SPACE_DIM >	mCentroid

out_stream	mpVtkMetaFile

boost::shared_ptr < CellPropertyRegistry >	mpCellPropertyRegistry

bool	mOutputResultsForChasteVisualizer

std::vector< boost::shared_ptr < AbstractCellWriter < ELEMENT_DIM, SPACE_DIM > > >	mCellWriters

std::vector< boost::shared_ptr < AbstractCellPopulationWriter < ELEMENT_DIM, SPACE_DIM > > >	mCellPopulationWriters

std::vector< boost::shared_ptr < AbstractCellPopulationCountWriter < ELEMENT_DIM, SPACE_DIM > > >	mCellPopulationCountWriters

Detailed Description

template<unsigned DIM>
class NodeBasedCellPopulationWithBuskeUpdate< DIM >

A NodeBasedCellPopulationWithBuskeUpdate is a CellPopulation consisting of only nodes in space with associated cells. There are no elements and no mesh. The cell positions are updated according to Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).

Definition at line 50 of file NodeBasedCellPopulationWithBuskeUpdate.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

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 41 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

template<unsigned DIM>

NodeBasedCellPopulationWithBuskeUpdate< DIM >::NodeBasedCellPopulationWithBuskeUpdate ( NodesOnlyMesh< DIM > & rMesh )

Constructor for use by the de-serializer.

Parameters

rMesh a mutable nodes-only mesh

Definition at line 50 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

Member Function Documentation

template<unsigned DIM>

void NodeBasedCellPopulationWithBuskeUpdate< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile )

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 NodeBasedCellPopulation< DIM >.

Definition at line 202 of file NodeBasedCellPopulationWithBuskeUpdate.cpp.

References NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

template<class Archive >

void NodeBasedCellPopulationWithBuskeUpdate< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

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