#include <AbstractCentreBasedCellPopulation.hpp>

Inheritance diagram for AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

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

c_vector< double, SPACE_DIM >	GetLocationOfCellCentre (CellPtr pCell)

Node< SPACE_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, SPACE_DIM > &rDisplacement, double dt)

virtual double	GetDampingConstant (unsigned nodeIndex)

virtual bool	IsGhostNode (unsigned index)

virtual bool	IsParticle (unsigned index)

virtual std::vector< std::pair< Node< SPACE_DIM > , Node< SPACE_DIM > > > &	rGetNodePairs ()=0

double	GetMeinekeDivisionSeparation ()

void	SetMeinekeDivisionSeparation (double divisionSeparation)

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

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

virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)

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	UpdateNodeLocations (double dt)

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 TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	GetTetrahedralMeshForPdeModifier ()=0

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

std::list< CellPtr > &	rGetCells ()

virtual unsigned	GetNumNodes ()=0

virtual Node< SPACE_DIM > *	GetNode (unsigned index)=0

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

virtual unsigned	RemoveDeadCells ()=0

virtual void	Update (bool hasHadBirthsOrDeaths=true)=0

std::vector< unsigned >	GetCellMutationStateCount ()

std::vector< unsigned >	GetCellProliferativeTypeCount ()

std::vector< unsigned >	GetCellCyclePhaseCount ()

unsigned	GetNumRealCells ()

unsigned	GetNumAllCells ()

void	SetCellAncestorsToLocationIndices ()

std::set< unsigned >	GetCellAncestors ()

virtual CellPtr	GetCellUsingLocationIndex (unsigned index)

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 ()

virtual double	GetWidth (const unsigned &rDimension)=0

virtual double	GetVolumeOfCell (CellPtr pCell)=0

virtual std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)=0

c_vector< double, SPACE_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

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

Protected Member Functions
	AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

virtual void	WriteVtkResultsToFile (const std::string &rDirectory)=0

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 >
virtual void	Validate ()=0

	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

Protected Attributes
double	mMeinekeDivisionSeparation

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

boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_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

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

Friends
class	TestCentreBasedDivisionRules

class	boost::serialization::access

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >

An abstract facade class encapsulating a centre-based cell population, in which each cell corresponds to a Node.

Definition at line 49 of file AbstractCentreBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation ( AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

protected

Constructor that just takes in a mesh.

Parameters

rMesh the mesh for the cell population.

Definition at line 63 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation	(	AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`
	)

Default constructor.

Parameters

rMesh	a reference to the mesh underlying the cell population
rCells	a vector of cells
locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 43 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCentreBasedDivisionRule.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWritersAcrossPopulation ( )

protectedvirtual

Call AcceptCellWriter across the whole population, iterating in an appropriate way for this type of cell population.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 260 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CellPtr AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell	(	CellPtr	pNewCell,
		CellPtr	pParentCell = `CellPtr()`
	)

virtual

Add a new cell to the cell population.

Parameters

pNewCell	the cell to add
pParentCell	pointer to a parent cell (if required)

Returns: address of cell as it appears in the cell list

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 96 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by NodeBasedCellPopulationWithParticles< DIM >::AddCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), and NodeBasedCellPopulation< DIM >::AddCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckForStepSizeException	(	unsigned	nodeIndex,
		c_vector< double, SPACE_DIM > &	rDisplacement,
		double	dt
	)

virtual

Checks whether a given node displacement violates the movement threshold for this population. If so, a stepSizeException is generated that contains a warning/error message and a suggested smaller dt that should avoid the problem.

Parameters

nodeIndex	Index of the node in question (allows us to check whether this is a ghost or particle)
rDisplacement	Movement vector of the node at this time step
dt	Current time step size

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 195 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsGhostNode(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsParticle(), and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAbsoluteMovementThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns: a an ordered pair of pointers to two given Cells. Used by the spring marking routines. Elements in the returned pair are ordered by cell ID number - the cell in the pair will have a smaller ID.

Parameters

pCell1	a Cell
pCell2	a Cell

Definition at line 134 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), CryptProjectionForce::CalculateForceBetweenNodes(), and GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellDataItemAtPdeNode	(	unsigned	pdeNodeIndex,
		std::string &	rVariableName,
		bool	dirichletBoundaryConditionApplies = `false`,
		double	dirichletBoundaryValue = `0.0`
	)

virtual

Overridden GetCellDataItemAtPdeNode() method.

Parameters

pdeNodeIndex	index of a node in a tetrahedral mesh for use with a PDE modifier
rVariableName	the name of the cell data item to get
dirichletBoundaryConditionApplies	where a Dirichlet boundary condition is used (optional; defaults to false)
dirichletBoundaryValue	the value of the Dirichlet boundary condition, if used (optional; defaults to 0.0)

Returns: the value of a CellData item (interpolated if necessary) at a node, specified by its index in a tetrahedral mesh for use with a PDE modifier. This method can be called by PDE modifier classes.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 83 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Returns: The division rule that is currently being used.

Definition at line 277 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCentreBasedDivisionRule.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant ( unsigned nodeIndex )

virtual

Overridden GetDampingConstant() method.

Get the damping constant for the cell associated with this node, i.e. d in drdt = F/d.

If the cell is wild-type, then the normal damping constant is returned. If the cell has a mutation, then the mutant damping constant is returned.

Note that by default, the normal and mutant damping constants are the same. To alter the damping constant for mutant cells, call the method SetDampingConstantMutant() on the CellPopulation.

Parameters

nodeIndex the global index of this node

Returns: the damping constant at the Cell associated with this node

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 213 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantMutant(), AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantNormal(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsGhostNode(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsParticle().

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDefaultTimeStep ( )

virtual

Overridden GetDefaultTimeStep() method.

Returns: a default value for the time step to use when simulating the cell population.

A hard-coded value of 1/120 is returned. However, note that the time step can be reset by calling SetDt() on the simulation object used to simulate the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 303 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre ( CellPtr pCell )

virtual

Overridden GetLocationOfCellCentre() method. Find where a given cell is in space.

Parameters

pCell the cell

Returns: the location of the node corresponding to this cell.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 70 of file AbstractCentreBasedCellPopulation.cpp.

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

Referenced by CryptCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector(), RandomDirectionCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector(), FixedCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector(), CryptProjectionStatistics::GetCryptSection(), CryptStatistics::GetCryptSection(), and RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetMeinekeDivisionSeparation ( )

Returns: mMeinekeDivisionSeparation

Definition at line 246 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMeinekeDivisionSeparation.

Referenced by CryptCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector(), and RandomDirectionCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices ( CellPtr pCell )

virtual

Overridden GetNeighbouringLocationIndices() method.

Given a cell, returns the set of location indices corresponding to neighbouring cells.

Parameters

pCell a cell

Returns: the set of neighbouring location indices.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 188 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices().

Referenced by CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNodeCorrespondingToCell ( CellPtr pCell )

Get a pointer to the node corresponding to a given cell.

Parameters

pCell the cell

Returns: address of the node

Definition at line 76 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode().

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAssociatedWithADeletedLocation(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell )

virtual

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters

pCell the cell

Returns: whether a given cell is associated with a deleted node.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 182 of file AbstractCentreBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsGhostNode ( unsigned index )

virtual

Find if a given node is a ghost node. The method always returns false but is overridden in MeshBasedCellPopulationWithGhostNodes.

Parameters

index the global index of a specified node

Returns: whether the node is a ghost node

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 234 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckForStepSizeException(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant(), CellwiseDataGradient< DIM >::SetupGradients(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Parameters

rCellPair a set of pointers to Cells

Returns: whether the spring between two given cells is marked.

Definition at line 155 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings.

Referenced by CryptProjectionForce::CalculateForceBetweenNodes(), and GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsParticle ( unsigned index )

virtual

Find if a given node is a particle. The method always returns false but is overridden in NodeBasedCellPopulationWithParticles.

Parameters

index the global index of a specified node

Returns: whether the node is a particle

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 240 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckForStepSizeException(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Mark the spring between the given cells.

Parameters

rCellPair a set of pointers to Cells

Definition at line 164 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellPopulationParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, NodeBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulationWithParticles< DIM >, and NodeBasedCellPopulationWithBuskeUpdate< DIM >.

Definition at line 289 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMeinekeDivisionSeparation, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCentreBasedDivisionRule, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

Referenced by NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual std::vector< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > >& AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs ( )

pure virtual

Method to return the connected nodes in a centre based simulation.

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

Returns: Node pairs for force calculation.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and NodeBasedCellPopulation< DIM >.

Referenced by AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 66 of file AbstractCentreBasedCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Set the division rule for this population.

Parameters

pCentreBasedDivisionRule pointer to the new division rule

Definition at line 283 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCentreBasedDivisionRule.

Referenced by CryptSimulation1d::CryptSimulation1d().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetMeinekeDivisionSeparation ( double divisionSeparation )

Set mMeinekeDivisionSeparation.

Parameters

divisionSeparation the new value of mMeinekeDivisionSeparation

Definition at line 252 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMeinekeDivisionSeparation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Stop marking the spring between the given cells.

Parameters

rCellPair a set of pointers to Cells

Definition at line 173 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings.

Referenced by CryptProjectionForce::CalculateForceBetweenNodes(), and GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile ( const std::string & rDirectory )

protectedpure virtual

Write the current results to mpVtkMetaFile.

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

Parameters

rDirectory pathname of the output directory, relative to where Chaste output is stored

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 58 of file AbstractCentreBasedCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class TestCentreBasedDivisionRules

friend

This test uses the private constructor to simplify testing.

Definition at line 55 of file AbstractCentreBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::set<std::pair<CellPtr,CellPtr> > AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings

protected

Special springs that we want to keep track of for some reason. Currently used to track cells in the process of dividing (which are represented as two cells joined by a shorter spring).

Definition at line 86 of file AbstractCentreBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsMarkedSpring(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MarkSpring(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells(), AbstractCentreBasedCellPopulation< DIM >::serialize(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UnmarkSpring(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMeinekeDivisionSeparation

protected

Initial separation placement of mother/daughter cells at birth. Has units of cell size at equilibrium rest length

Definition at line 79 of file AbstractCentreBasedCellPopulation.hpp.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetMeinekeDivisionSeparation(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), AbstractCentreBasedCellPopulation< DIM >::serialize(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetMeinekeDivisionSeparation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

protected

A pointer to a division rule that is used to generate the locations of daughter cells when a cell divides. This is a specialisation for centre-based models.

Definition at line 91 of file AbstractCentreBasedCellPopulation.hpp.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentreBasedDivisionRule(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), AbstractCentreBasedCellPopulation< DIM >::serialize(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCentreBasedDivisionRule().

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

cell_based/src/population/AbstractCentreBasedCellPopulation.hpp
cell_based/src/population/AbstractCentreBasedCellPopulation.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM> class AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >