#include <NodeBasedCellPopulationWithParticles.hpp>

Inheritance diagram for NodeBasedCellPopulationWithParticles< DIM >:

Collaboration diagram for NodeBasedCellPopulationWithParticles< DIM >:

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

	NodeBasedCellPopulationWithParticles (NodesOnlyMesh< DIM > &rMesh)

void	UpdateParticlePositions (double dt)

void	UpdateParticlesAfterReMesh (NodeMap &rMap)

void	UpdateNodeLocations (double dt)

bool	IsParticle (unsigned index)

std::set< unsigned >	GetParticleIndices ()

CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)

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

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

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)

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)

CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, ELEMENT_DIM > &rCellDivisionVector, 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 double	GetDampingConstant (unsigned nodeIndex)

virtual bool	IsGhostNode (unsigned index)

double	GetMeinekeDivisionSeparation ()

void	SetMeinekeDivisionSeparation (double divisionSeparation)

Public Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_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

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 ()

std::list< CellPtr > &	rGetCells ()

virtual CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, SPACE_DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())=0

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)

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)

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

Protected Member Functions
void	Validate ()

virtual void	AcceptCellWritersAcrossPopulation ()

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

Protected Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_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)

Private Member Functions
void	SetParticles (const std::set< unsigned > &rParticleIndices)

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

Friends
class	TestNodeBasedCellPopulationWithParticles

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from NodeBasedCellPopulation< DIM >
NodesOnlyMesh< DIM > *	mpNodesOnlyMesh

Protected Attributes inherited from AbstractCentreBasedCellPopulation< DIM >
double	mMeinekeDivisionSeparation

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

Protected Attributes inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_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 NodeBasedCellPopulationWithParticles< DIM >

A NodeBasedCellPopulationWithParticles is a NodeBasedCellPopulation with cells interacting with particles, such as ECM or fluid particles.

Definition at line 50 of file NodeBasedCellPopulationWithParticles.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NodeBasedCellPopulationWithParticles< DIM >::NodeBasedCellPopulationWithParticles	(	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 46 of file NodeBasedCellPopulationWithParticles.cpp.

References EXCEPT_IF_NOT, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), PetscTools::IsSequential(), NodeBasedCellPopulationWithParticles< DIM >::SetParticles(), and NodeBasedCellPopulationWithParticles< DIM >::Validate().

template<unsigned DIM>

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

Constructor for use by the de-serializer.

Parameters

rMesh a mutable nodes-only mesh

Definition at line 91 of file NodeBasedCellPopulationWithParticles.cpp.

Member Function Documentation

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::AcceptCellWritersAcrossPopulation ( )

protectedvirtual

Overridden AcceptCellWritersAcrossPopulation() method.

Calls AcceptCellWriter() across the whole population, iterating in an appropriate way to skip particle nodes.

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 233 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd().

template<unsigned DIM>

CellPtr NodeBasedCellPopulationWithParticles< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell
	)

virtual

Overridden AddCell() method.

Add a new cell to the cell population and update mIsParticle.

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)

Reimplemented from NodeBasedCellPopulation< DIM >.

Definition at line 170 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell().

template<unsigned DIM>

std::set< unsigned > NodeBasedCellPopulationWithParticles< DIM >::GetParticleIndices ( )

Returns: the indices of those nodes that are particles.

Definition at line 103 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin().

template<unsigned DIM>

bool NodeBasedCellPopulationWithParticles< DIM >::IsParticle ( unsigned index )

virtual

IsParticle() method.

Find if a given node is a particle

Parameters

index the global index of a specified node

Returns: whether the node is a particle

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 97 of file NodeBasedCellPopulationWithParticles.cpp.

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< 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 379 of file NodeBasedCellPopulationWithParticles.cpp.

References NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

template<class Archive >

void NodeBasedCellPopulationWithParticles< 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

archive	the archive
version	the current version of this class

Definition at line 89 of file NodeBasedCellPopulationWithParticles.hpp.

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::SetParticles ( const std::set< unsigned > & rParticleIndices )

private

Set the particles by taking in a set of which nodes indices are particles.

Parameters

rParticleIndices set of node indices corresponding to particles

Definition at line 121 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), and NodeBasedCellPopulationWithParticles< DIM >::Validate().

Referenced by NodeBasedCellPopulationWithParticles< DIM >::NodeBasedCellPopulationWithParticles().

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::UpdateNodeLocations ( double dt )

virtual

Overridden UpdateNodeLocation() method.

Update the location of each node in the cell population given a two vectors of forces on cells and particles and a time step over which to integrate the equations of motion.

Parameters

dt time step

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Definition at line 223 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations().

template<unsigned DIM>

void NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions ( double dt )

Update particle positions.

Parameters

dt

Definition at line 136 of file NodeBasedCellPopulationWithParticles.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin().