#include <AbstractOffLatticeCellPopulation.hpp>

Inheritance diagram for AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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)

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

virtual double	GetDampingConstant (unsigned nodeIndex)=0

void	SetDampingConstantNormal (double dampingConstantNormal)

void	SetDampingConstantMutant (double dampingConstantMutant)

void	SetAbsoluteMovementThreshold (double absoluteMovementThreshold)

double	GetAbsoluteMovementThreshold ()

double	GetDampingConstantNormal ()

double	GetDampingConstantMutant ()

virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)

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)

virtual double	GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)=0

std::list< CellPtr > &	rGetCells ()

virtual unsigned	GetNumNodes ()=0

virtual c_vector< double, SPACE_DIM >	GetLocationOfCellCentre (CellPtr pCell)=0

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

virtual bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

virtual CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell=CellPtr())=0

virtual double	GetDefaultTimeStep ()=0

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

virtual std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)=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
	AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

Protected Member Functions inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
virtual void	Validate ()=0

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

	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Attributes
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	boost::serialization::access

Detailed Description

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

An abstract facade class encapsulating an off-lattice (centre- or vertex-based) cell population.

Definition at line 46 of file AbstractOffLatticeCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractOffLatticeCellPopulation ( 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 50 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Default constructor.

Parameters

rMesh	a refernce 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 39 of file AbstractOffLatticeCellPopulation.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual unsigned AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddNode ( Node< SPACE_DIM > * pNewNode )

pure virtual

Add a new node to the cell population.

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

Parameters

pNewNode pointer to the new node

Returns: global index of new node in cell population.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

pure 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.

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

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

Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAbsoluteMovementThreshold ( )

Returns: mAbsoluteMovementThreshold

Definition at line 97 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

pure virtual

Get the damping constant for this node - ie d in drdt = F/d.

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

Parameters

nodeIndex the global index of this node

Returns: the damping constant at the node.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantMutant ( )

Returns: mDampingConstantMutant

Definition at line 91 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantNormal ( )

Returns: mDampingConstantNormal

Definition at line 85 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Overridden OutputCellPopulationParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

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

Definition at line 103 of file AbstractOffLatticeCellPopulation.cpp.

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

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and VertexBasedCellPopulation< SPACE_DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void AbstractOffLatticeCellPopulation< 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 59 of file AbstractOffLatticeCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAbsoluteMovementThreshold ( double absoluteMovementThreshold )

Set mAbsoluteMovementThreshold.

Parameters

absoluteMovementThreshold the new value of mAbsoluteMovementThreshold

Definition at line 79 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantMutant ( double dampingConstantMutant )

Set mDampingConstantMutant.

Parameters

dampingConstantMutant the new value of mDampingConstantMutant

Definition at line 72 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantNormal ( double dampingConstantNormal )

Set mDampingConstantNormal.

Parameters

dampingConstantNormal the new value of mDampingConstantNormal

Definition at line 65 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< SPACE_DIM > &	rNewLocation
	)

pure virtual

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

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

Parameters

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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations ( double dt )

virtual

This is a deprecated method and only used in NodesOnlyCellPopulationWithBuskeUpdate.

Update the location of each node in the cell population given a vector of forces on nodes and a time step over which to integrate the equations of motion.

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

Parameters

dt time step

Reimplemented in NodeBasedCellPopulationWithBuskeUpdate< DIM >.

Definition at line 57 of file AbstractOffLatticeCellPopulation.cpp.

References NEVER_REACHED.

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 51 of file AbstractOffLatticeCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAbsoluteMovementThreshold

protected

The absolute distance which a cell is permitted to move in one time-step. Movement beyond this threshold will trigger UpdateNodeLocations to throw an exception

Definition at line 86 of file AbstractOffLatticeCellPopulation.hpp.

Referenced by AbstractOffLatticeCellPopulation< DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantMutant

protected

Damping constant for mutant cells has units of kg s^-1.

Definition at line 79 of file AbstractOffLatticeCellPopulation.hpp.

Referenced by AbstractOffLatticeCellPopulation< DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantNormal

protected

Damping constant for normal cells has units of kg s^-1 Represented by the parameter eta in the model by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 74 of file AbstractOffLatticeCellPopulation.hpp.

Referenced by AbstractOffLatticeCellPopulation< DIM >::serialize().

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

cell_based/src/population/AbstractOffLatticeCellPopulation.hpp
cell_based/src/population/AbstractOffLatticeCellPopulation.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 AbstractOffLatticeCellPopulation< 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 AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >