CaBasedCellPopulation< DIM > Class Template Reference

#include <CaBasedCellPopulation.hpp>

Inherits AbstractOnLatticeCellPopulation< DIM >.

Collaboration diagram for CaBasedCellPopulation< DIM >:

Public Member Functions
	CaBasedCellPopulation (PottsMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices, unsigned latticeCarryingCapacity=1u, bool deleteMesh=false, bool validate=false)
	CaBasedCellPopulation (PottsMesh< DIM > &rMesh)
virtual	~CaBasedCellPopulation ()
std::vector< unsigned > &	rGetAvailableSpaces ()
virtual bool	IsSiteAvailable (unsigned index, CellPtr pCell)
PottsMesh< DIM > &	rGetMesh ()
const PottsMesh< DIM > &	rGetMesh () const
Node< DIM > *	GetNode (unsigned index)
unsigned	GetNumNodes ()
std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)
c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)
void	AddCellUsingLocationIndex (unsigned index, CellPtr pCell)
void	RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)
Node< DIM > *	GetNodeCorrespondingToCell (CellPtr pCell)
CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())
virtual double	EvaluateDivisionPropensity (unsigned currentNodeIndex, unsigned targetNodeIndex, CellPtr pCell)
unsigned	RemoveDeadCells ()
virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)
void	UpdateCellLocations (double dt)
bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)
void	Update (bool hasHadBirthsOrDeaths=true)
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	GetVolumeOfCell (CellPtr pCell)
double	GetWidth (const unsigned &rDimension)
void	AddUpdateRule (boost::shared_ptr< AbstractCaUpdateRule< DIM > > pUpdateRule)
void	RemoveAllUpdateRules ()
const std::vector < boost::shared_ptr < AbstractCaUpdateRule< DIM > > > &	rGetUpdateRuleCollection () const
void	OutputCellPopulationParameters (out_stream &rParamsFile)
bool	IsRoomToDivide (CellPtr pCell)
Private Member Functions
void	SetEmptySites (const std::set< unsigned > &rEmptySiteIndices)
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
void	Validate ()
virtual void	WriteVtkResultsToFile (const std::string &rDirectory)
Private Attributes
unsigned	mLatticeCarryingCapacity
std::vector< boost::shared_ptr < AbstractCaUpdateRule< DIM > > >	mUpdateRuleCollection
std::vector< unsigned >	mAvailableSpaces
Friends
class	TestCaBasedCellPopulation
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class CaBasedCellPopulation< DIM >

A facade class encapsulating a cell population under the Cellular Automaton (CA) framework.

Contains a group of cells and maintains the associations between CellPtrs and nodes in a specialised PottsMesh class.

When used here the PottsMesh has no elements as Cells are associated with nodes. The PottsMesh is used to define node connectivity.

Multiple cells can be associated at a single node.

Definition at line 65 of file CaBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CaBasedCellPopulation< DIM >::CaBasedCellPopulation	(	PottsMesh< DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices,
		unsigned	latticeCarryingCapacity = `1u`,
		bool	deleteMesh = `false`,
		bool	validate = `false`
	)			`[inline]`

Create a new cell population facade from a mesh, a vector of location indices and a collection of cells.

There must be precisely one CellPtr for each entry of the locationIndices vector.

Parameters:

	rMesh	reference to a PottsMesh
	rCells	reference to a vector of CellPtrs
	locationIndices	a vector of location indices that correspond to real cells
	latticeCarryingCapacity	an optional parameter to allow more than one cell per site
	deleteMesh	set to true if you want the cell population to free the mesh memory on destruction (defaults to false)
	validate	whether to validate the cell population when it is created (defaults to false as not used in CA simulations)

Definition at line 66 of file CaBasedCellPopulation.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), CaBasedCellPopulation< DIM >::GetNumNodes(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), CaBasedCellPopulation< DIM >::mAvailableSpaces, AbstractCellPopulation< DIM >::mCells, and AbstractCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

CaBasedCellPopulation< DIM >::CaBasedCellPopulation ( PottsMesh< DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a vertex mesh.

Definition at line 106 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

CaBasedCellPopulation< DIM >::~CaBasedCellPopulation ( ) [inline, virtual]

Destructor, which frees any memory allocated by the constructor.

Definition at line 112 of file CaBasedCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::mDeleteMesh, and AbstractCellPopulation< DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AcceptCellWriter	(	boost::shared_ptr< AbstractCellWriter< DIM, DIM > >	pCellWriter,
		CellPtr	pCell
	)			`[inline, virtual]`

A virtual method to accept a cell writer so it can write data from this object to file.

Parameters:

	pCellWriter	the population writer.
	pCell	the cell whose data is being written.

Definition at line 459 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > > pPopulationCountWriter ) [inline, virtual]

A virtual method to accept a cell population count writer so it can write data from this object to file.

Parameters:

pPopulationCountWriter

the population count writer.

Definition at line 453 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > > pPopulationWriter ) [inline, virtual]

A virtual method to accept a cell population writer so it can write data from this object to file.

Parameters:

pPopulationWriter

the population writer.

Definition at line 447 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

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

Overridden AddCell() method.

Add a new cell to the cell population.

Parameters:

	pNewCell	the cell to add
	rCellDivisionVector	this parameter is not yet used in this class (see #1737)
	pParentCell	pointer to a parent cell (if required)

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

Definition at line 238 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::AddCellUsingLocationIndex(), CaBasedCellPopulation< DIM >::EvaluateDivisionPropensity(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), RandomNumberGenerator::Instance(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mrMesh, RandomNumberGenerator::ranf(), and UNSIGNED_UNSET.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AddCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)			`[inline, virtual]`

Overridden AddCellUsingLocationIndex method to add a cell to a given location index. Also updates mAvailableSpaces

Parameters:

	index	the location index
	pCell	the cell.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 190 of file CaBasedCellPopulation.cpp.

References EXCEPTION, CaBasedCellPopulation< DIM >::IsSiteAvailable(), and CaBasedCellPopulation< DIM >::mAvailableSpaces.

Referenced by CaBasedCellPopulation< DIM >::AddCell().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::AddUpdateRule ( boost::shared_ptr< AbstractCaUpdateRule< DIM > > pUpdateRule ) [inline]

Add an update rule to be used in this simulation (use this to set up how cells move).

Parameters:

pUpdateRule

pointer to an update rule

Definition at line 493 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::mUpdateRuleCollection.

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::EvaluateDivisionPropensity	(	unsigned	currentNodeIndex,
		unsigned	targetNodeIndex,
		CellPtr	pCell
	)			`[inline, virtual]`

Calculate the propensity of a dividing into a given site. Overridden in child classes to define other division methods. eg directed division.

Parameters:

	currentNodeIndex	The index of the current node/lattice site
	targetNodeIndex	The index of the target node/lattice site
	pCell	a pointer to the cell (needed if more than one cell per lattice site

Returns:: The probability of the cell dividing from the current node to the target node

Definition at line 312 of file CaBasedCellPopulation.cpp.

Referenced by CaBasedCellPopulation< DIM >::AddCell().

template<unsigned DIM>

c_vector< double, DIM > CaBasedCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr pCell ) [inline, 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< DIM >.

Definition at line 178 of file CaBasedCellPopulation.cpp.

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

template<unsigned DIM>

std::set< unsigned > CaBasedCellPopulation< DIM >::GetNeighbouringLocationIndices ( CellPtr pCell ) [inline, virtual]

Overridden GetNeighbouringLocationIndices() method.

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

Note: In keeping with other parts of the code in this class, we assume a Moore neighbourhood. Also, at present this method assumes a unit carrying capacity at each lattice site.

Parameters:

pCell

a cell

Returns:: the set of neighbouring location indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 158 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), and AbstractCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

Node< DIM > * CaBasedCellPopulation< DIM >::GetNode ( unsigned index ) [inline, virtual]

Overridden GetNode() method.

Parameters:

index

global index of the specified node

Returns:: a pointer to the node.

Implements AbstractCellPopulation< DIM >.

Definition at line 146 of file CaBasedCellPopulation.cpp.

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

Referenced by DiffusionCaUpdateRule< DIM >::EvaluateProbability().

template<unsigned DIM>

Node< DIM > * CaBasedCellPopulation< DIM >::GetNodeCorrespondingToCell ( CellPtr pCell ) [inline]

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

Parameters:

pCell

the cell

Returns:: pointer to the node.

Definition at line 184 of file CaBasedCellPopulation.cpp.

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

template<unsigned DIM>

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

Overridden GetNumNodes() method.

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

Implements AbstractCellPopulation< DIM >.

Definition at line 152 of file CaBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and AbstractCellPopulation< DIM >::mrMesh.

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

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::GetVolumeOfCell ( CellPtr pCell ) [inline, virtual]

Overridden GetVolumeOfCell() method.

Parameters:

pCell

boost shared pointer to a cell

Returns:: volume via associated mesh element

Implements AbstractCellPopulation< DIM >.

Definition at line 479 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

double CaBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension ) [inline, virtual]

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the cell population by calling GetWidth() on the mesh.

Note this returns the size of the underlying mesh not the population of cells so here it will be the same for all time.

Parameters:

rDimension

a dimension (0,1 or 2)

Returns:: The maximum distance between any nodes in this dimension.

Implements AbstractCellPopulation< DIM >.

Definition at line 486 of file CaBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and AbstractCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell ) [inline, virtual]

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters:

pCell

the cell

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

Implements AbstractCellPopulation< DIM >.

Definition at line 436 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsRoomToDivide ( CellPtr pCell ) [inline, virtual]

Overridden IsRoomToDivide() method. Returns whether there are any available neighbouring sites to the one occupied by a given cell.

Parameters:

pCell

pointer to a cell

Returns:: whether the cell has any free neighbouring sites

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 212 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), and AbstractCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

bool CaBasedCellPopulation< DIM >::IsSiteAvailable	(	unsigned	index,
		CellPtr	pCell
	)			`[inline, virtual]`

Find if a given node has space available. Overridden in subclasses to implement different division regimes.

Todo:: Which subclasses? Why is the second input argument needed?

Parameters:

	index	The global index of a specified node.
	pCell	The cell wanting to divide into the lattice site (defaults to NULL).

Returns:: whether the node is an empty site

Todo:: this is where to deal with carrying capacity

Definition at line 127 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::mAvailableSpaces.

Referenced by CaBasedCellPopulation< DIM >::AddCell(), CaBasedCellPopulation< DIM >::AddCellUsingLocationIndex(), CaBasedCellPopulation< DIM >::CaBasedCellPopulation(), CaBasedCellPopulation< DIM >::GetNeighbouringLocationIndices(), CaBasedCellPopulation< DIM >::IsRoomToDivide(), and CaBasedCellPopulation< DIM >::UpdateCellLocations().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::OpenWritersFiles ( OutputFileHandler & rOutputFileHandler ) [inline, virtual]

Overridden OpenWritersFiles() method.

Open all files in mCellPopulationWriters and mCellWriters for writing (not appending).

Parameters:

rOutputFileHandler

handler for the directory in which to open this file.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 465 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputResultsForChasteVisualizer.

template<unsigned DIM>

void CaBasedCellPopulation< 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 AbstractOnLatticeCellPopulation< DIM >.

Definition at line 511 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::RemoveAllUpdateRules ( ) [inline]

Method to remove all the update rules

Definition at line 499 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::mUpdateRuleCollection.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::RemoveCellUsingLocationIndex	(	unsigned	index,
		CellPtr	pCell
	)			`[inline, virtual]`

Overridden AddCellUsingLocationIndex method to remove a cell from a given location index. Also updates mAvailableSpaces

Parameters:

	index	the location index
	pCell	the cell.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 202 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::mAvailableSpaces, and CaBasedCellPopulation< DIM >::mLatticeCarryingCapacity.

Referenced by CaBasedCellPopulation< DIM >::RemoveDeadCells().

template<unsigned DIM>

unsigned CaBasedCellPopulation< 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 320 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< DIM >::mCells, and CaBasedCellPopulation< DIM >::RemoveCellUsingLocationIndex().

template<unsigned DIM>

std::vector< unsigned > & CaBasedCellPopulation< DIM >::rGetAvailableSpaces ( ) [inline]

Returns:: mAvailableSpaces.

Definition at line 121 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::mAvailableSpaces.

template<unsigned DIM>

const PottsMesh< DIM > & CaBasedCellPopulation< DIM >::rGetMesh ( ) const [inline]

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

Definition at line 140 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

PottsMesh< DIM > & CaBasedCellPopulation< DIM >::rGetMesh ( ) [inline]

Returns:: reference to mrMesh.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 134 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mrMesh.

Referenced by DiffusionCaUpdateRule< DIM >::EvaluateProbability().

template<unsigned DIM>

const std::vector< boost::shared_ptr< AbstractCaUpdateRule< DIM > > > & CaBasedCellPopulation< DIM >::rGetUpdateRuleCollection ( ) const [inline]

Get the collection of update rules to be used in this simulation.

Returns:: the update rule collection

Definition at line 505 of file CaBasedCellPopulation.cpp.

References CaBasedCellPopulation< DIM >::mUpdateRuleCollection.

template<unsigned DIM>

template<class Archive >

void CaBasedCellPopulation< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Note that serialization of the mesh and cells is handled by load/save_construct_data.

Note also that member data related to writers is not saved - output must be set up again by the caller after a restart.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractOnLatticeCellPopulation< DIM >.

Definition at line 100 of file CaBasedCellPopulation.hpp.

References CaBasedCellPopulation< DIM >::mAvailableSpaces, CaBasedCellPopulation< DIM >::mLatticeCarryingCapacity, and CaBasedCellPopulation< DIM >::mUpdateRuleCollection.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::SetEmptySites ( const std::set< unsigned > & rEmptySiteIndices ) [private]

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

Parameters:

rEmptySiteIndices

set of node indices corresponding to empty sites

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [inline, virtual]

Overridden Update() method.

Checks association of nodes with CellPtrs.

Parameters:

hasHadBirthsOrDeaths

- a bool saying whether cell population has had Births Or Deaths

Implements AbstractCellPopulation< DIM >.

Definition at line 442 of file CaBasedCellPopulation.cpp.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::UpdateCellLocations ( double dt ) [inline, virtual]

Overridden UpdateCellLocations() method.

Parameters:

dt

time step

Todo:: make this sweep random

Implements AbstractOnLatticeCellPopulation< DIM >.

Definition at line 348 of file CaBasedCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), RandomNumberGenerator::Instance(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::MoveCellInLocationMap(), AbstractCellPopulation< DIM >::mrMesh, CaBasedCellPopulation< DIM >::mUpdateRuleCollection, NEVER_REACHED, and RandomNumberGenerator::ranf().

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::Validate ( ) [inline, private, virtual]

Overriden Validate Method.

Not used in CA simulations so just contains NEVER_REACHED

Implements AbstractCellPopulation< DIM >.

Definition at line 60 of file CaBasedCellPopulation.cpp.

References NEVER_REACHED.

template<unsigned DIM>

void CaBasedCellPopulation< DIM >::WriteVtkResultsToFile ( const std::string & rDirectory ) [inline, private, virtual]

Overridden WriteVtkResultsToFile() method.

This method offsets cells so can visulaise multiple cells at a single site

Parameters:

rDirectory

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

Implements AbstractCellPopulation< DIM >.

Definition at line 518 of file CaBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractCellPopulation< DIM >::GetNumRealCells(), SimulationTime::GetTimeStepsElapsed(), RandomNumberGenerator::Instance(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mCellWriters, CaBasedCellPopulation< DIM >::mLatticeCarryingCapacity, AbstractCellPopulation< DIM >::mpVtkMetaFile, AbstractCellPopulation< DIM >::mrMesh, and RandomNumberGenerator::ranf().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractOnLatticeCellPopulation< DIM >.

Definition at line 87 of file CaBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

std::vector<unsigned> CaBasedCellPopulation< DIM >::mAvailableSpaces [private]

Records for each node the node the number of spaces available.

Definition at line 78 of file CaBasedCellPopulation.hpp.

Referenced by CaBasedCellPopulation< DIM >::AddCellUsingLocationIndex(), CaBasedCellPopulation< DIM >::CaBasedCellPopulation(), CaBasedCellPopulation< DIM >::IsSiteAvailable(), CaBasedCellPopulation< DIM >::RemoveCellUsingLocationIndex(), CaBasedCellPopulation< DIM >::rGetAvailableSpaces(), and CaBasedCellPopulation< DIM >::serialize().

template<unsigned DIM>

unsigned CaBasedCellPopulation< DIM >::mLatticeCarryingCapacity [private]

The carrying capacity (number of cells allowed per site).

Definition at line 72 of file CaBasedCellPopulation.hpp.

Referenced by CaBasedCellPopulation< DIM >::RemoveCellUsingLocationIndex(), CaBasedCellPopulation< DIM >::serialize(), and CaBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

std::vector<boost::shared_ptr<AbstractCaUpdateRule<DIM> > > CaBasedCellPopulation< DIM >::mUpdateRuleCollection [private]

The update rules used to determine the new location of the cells.

Definition at line 75 of file CaBasedCellPopulation.hpp.

Referenced by CaBasedCellPopulation< DIM >::AddUpdateRule(), CaBasedCellPopulation< DIM >::RemoveAllUpdateRules(), CaBasedCellPopulation< DIM >::rGetUpdateRuleCollection(), CaBasedCellPopulation< DIM >::serialize(), and CaBasedCellPopulation< DIM >::UpdateCellLocations().

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

cell_based/src/population/CaBasedCellPopulation.hpp
cell_based/src/population/CaBasedCellPopulation.cpp

CaBasedCellPopulation< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class CaBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class CaBasedCellPopulation< DIM >