#include <PottsBasedCellPopulation.hpp>

Inheritance diagram for PottsBasedCellPopulation< DIM >:

Collaboration diagram for PottsBasedCellPopulation< DIM >:

Public Member Functions
	PottsBasedCellPopulation (PottsMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, bool deleteMesh=false, bool validate=true, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

	PottsBasedCellPopulation (PottsMesh< DIM > &rMesh)

virtual	~PottsBasedCellPopulation ()

PottsMesh< DIM > &	rGetMesh ()

const PottsMesh< DIM > &	rGetMesh () const

virtual TetrahedralMesh< DIM, DIM > *	GetTetrahedralMeshForPdeModifier ()

PottsElement< DIM > *	GetElement (unsigned elementIndex)

unsigned	GetNumElements ()

Node< DIM > *	GetNode (unsigned index)

unsigned	GetNumNodes ()

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

c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)

PottsElement< DIM > *	GetElementCorrespondingToCell (CellPtr pCell)

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

unsigned	RemoveDeadCells ()

void	UpdateCellLocations (double dt)

bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)

void	Update (bool hasHadBirthsOrDeaths=true)

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

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

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

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

virtual void	AcceptPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< DIM, DIM > > pPopulationEventWriter)

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

double	GetVolumeOfCell (CellPtr pCell)

double	GetWidth (const unsigned &rDimension)

void	OutputCellPopulationParameters (out_stream &rParamsFile)

void	SetTemperature (double temperature)

double	GetTemperature ()

void	SetNumSweepsPerTimestep (unsigned numSweepsPerTimestep)

unsigned	GetNumSweepsPerTimestep ()

void	CreateElementTessellation ()

VertexMesh< DIM, DIM > *	GetElementTessellation ()

void	CreateMutableMesh ()

MutableMesh< DIM, DIM > *	GetMutableMesh ()

virtual void	AddUpdateRule (boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule)

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

Public Member Functions inherited from AbstractOnLatticeCellPopulation< DIM >
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)

virtual	~AbstractOnLatticeCellPopulation ()

bool	GetUpdateNodesInRandomOrder ()

void	SetUpdateNodesInRandomOrder (bool updateNodesInRandomOrder)

void	SetIterateRandomlyOverUpdateRuleCollection (bool iterateRandomly)

bool	GetIterateRandomlyOverUpdateRuleCollection ()

void	SetNode (unsigned index, ChastePoint< DIM > &rNewLocation)

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

virtual double	GetDefaultTimeStep ()

virtual void	RemoveAllUpdateRules ()

virtual const std::vector< boost::shared_ptr< AbstractUpdateRule< DIM > > >	GetUpdateRuleCollection () const

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

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

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

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

std::list< CellPtr > &	rGetCells ()

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

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

std::vector< unsigned >	GetCellMutationStateCount ()

std::vector< unsigned >	GetCellProliferativeTypeCount ()

std::vector< unsigned >	GetCellCyclePhaseCount ()

unsigned	GetNumRealCells ()

unsigned	GetNumAllCells ()

void	SetCellAncestorsToLocationIndices ()

std::set< unsigned >	GetCellAncestors ()

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 std::set< std::pair< unsigned, unsigned > >	GetNeighbouringEdgeIndices (CellPtr pCell, unsigned pEdgeIndex)

c_vector< double, SPACE_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

virtual void	CloseWritersFiles ()

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	AcceptPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationEventWriter)=0

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

std::vector< std::string >	GetDivisionsInformation ()

void	AddDivisionInformation (std::string divisionInformation)

void	ClearDivisionsInformation ()

std::vector< std::string >	GetRemovalsInformation ()

void	AddRemovalInformation (std::string removalInformation)

void	ClearRemovalsInformation ()

void	GenerateRemovalInformation (CellPtr pCell, std::string killerInfo)

void	KillCell (CellPtr pCell, std::string killerInfo)

void	StartApoptosisOnCell (CellPtr pCell, std::string killerInfo)

void	OutputCellPopulationInfo (out_stream &rParamsFile)

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

bool	GetOutputResultsForChasteVisualizer ()

void	AddPopulationWriter ()

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

void	AddCellWriter ()

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

void	AddCellPopulationCountWriter ()

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

void	AddCellPopulationEventWriter ()

void	AddCellPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationEventWriter)

bool	HasWriter () const

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, SPACE_DIM >	GetSizeOfCellPopulation ()

virtual bool	IsRoomToDivide (CellPtr pCell)

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

Iterator	Begin ()

Iterator	End ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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

void	Validate ()

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

Private Attributes
VertexMesh< DIM, DIM > *	mpElementTessellation

PottsMesh< DIM > *	mpPottsMesh

MutableMesh< DIM, DIM > *	mpMutableMesh

double	mTemperature

unsigned	mNumSweepsPerTimestep

Friends
class	TestPottsBasedCellPopulation

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractOnLatticeCellPopulation< DIM >
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh)

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

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Attributes inherited from AbstractOnLatticeCellPopulation< DIM >
std::vector< boost::shared_ptr< AbstractUpdateRule< DIM > > >	mUpdateRuleCollection

bool	mDeleteMesh

bool	mUpdateNodesInRandomOrder

bool	mIterateRandomlyOverUpdateRuleCollection

Protected Attributes inherited from AbstractCellPopulation< 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

std::vector< boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > >	mCellPopulationEventWriters

std::vector< std::string >	mDivisionsInformation

std::vector< std::string >	mRemovalsInformation

Detailed Description

template<unsigned DIM>
class PottsBasedCellPopulation< DIM >

A facade class encapsulating a cell population under the Cellular Potts Model framework.

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

The code currently requires the PottsMesh object to be fixed, in the sense that no new nodes or elements can be added.

Definition at line 60 of file PottsBasedCellPopulation.hpp.

Constructor & Destructor Documentation

◆ PottsBasedCellPopulation() [1/2]

template<unsigned DIM>

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

Create a new cell population facade from a mesh and collection of cells.

There must be precisely one CellPtr for each PottsElement in the mesh.

Parameters

rMesh	reference to a PottsMesh
rCells	reference to a vector of CellPtrs
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 true)
locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 75 of file PottsBasedCellPopulation.cpp.

References PottsBasedCellPopulation< DIM >::mpPottsMesh, AbstractCellPopulation< DIM >::mrMesh, and PottsBasedCellPopulation< DIM >::Validate().

◆ PottsBasedCellPopulation() [2/2]

template<unsigned DIM>

PottsBasedCellPopulation< DIM >::PottsBasedCellPopulation ( PottsMesh< DIM > & rMesh )

Constructor for use by the de-serializer.

Parameters

rMesh a vertex mesh.

Definition at line 95 of file PottsBasedCellPopulation.cpp.

References PottsBasedCellPopulation< DIM >::mpPottsMesh, and AbstractCellPopulation< DIM >::mrMesh.

◆ ~PottsBasedCellPopulation()

template<unsigned DIM>

PottsBasedCellPopulation< DIM >::~PottsBasedCellPopulation ( )

virtual

Destructor, which frees any memory allocated by the constructor.

Definition at line 106 of file PottsBasedCellPopulation.cpp.

Member Function Documentation

◆ AcceptCellWriter()

template<unsigned DIM>

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

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 are being written.

Definition at line 405 of file PottsBasedCellPopulation.cpp.

◆ AcceptPopulationCountWriter()

template<unsigned DIM>

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

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 393 of file PottsBasedCellPopulation.cpp.

◆ AcceptPopulationEventWriter()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::AcceptPopulationEventWriter ( boost::shared_ptr< AbstractCellPopulationEventWriter< DIM, DIM > > pPopulationEventWriter )

virtual

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

Parameters

pPopulationEventWriter the population event writer.

Definition at line 399 of file PottsBasedCellPopulation.cpp.

◆ AcceptPopulationWriter()

template<unsigned DIM>

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

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 387 of file PottsBasedCellPopulation.cpp.

◆ AddCell()

template<unsigned DIM>

CellPtr PottsBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		CellPtr	pParentCell = `CellPtr()`
	)

virtual

Overridden AddCell() method.

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 (internal of this method uses a copy constructor along the way)

Implements AbstractCellPopulation< DIM >.

Definition at line 194 of file PottsBasedCellPopulation.cpp.

◆ AddUpdateRule()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::AddUpdateRule ( boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule )

virtual

Overridden AddUpdateRule() method.

Parameters

pUpdateRule pointer to an update rule

Implements AbstractOnLatticeCellPopulation< DIM >.

Definition at line 432 of file PottsBasedCellPopulation.cpp.

◆ CreateElementTessellation()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::CreateElementTessellation ( )

Create a Element tessellation of the mesh for use in visualising the mesh.

Todo:: implement this method (#1666)

Definition at line 439 of file PottsBasedCellPopulation.cpp.

◆ CreateMutableMesh()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::CreateMutableMesh ( )

Create a mutable mesh from the nodes of the Potts mesh. Used for solving PDEs

Definition at line 464 of file PottsBasedCellPopulation.cpp.

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

◆ GetCellDataItemAtPdeNode()

template<unsigned DIM>

double PottsBasedCellPopulation< 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< DIM >.

Definition at line 767 of file PottsBasedCellPopulation.cpp.

◆ GetElement()

template<unsigned DIM>

PottsElement< DIM > * PottsBasedCellPopulation< DIM >::GetElement ( unsigned elementIndex )

Get a particular PottsElement.

Parameters

elementIndex the global index of the PottsElement

Returns: a pointer to the PottsElement.

Definition at line 151 of file PottsBasedCellPopulation.cpp.

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

◆ GetElementCorrespondingToCell()

template<unsigned DIM>

PottsElement< DIM > * PottsBasedCellPopulation< DIM >::GetElementCorrespondingToCell ( CellPtr pCell )

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

Parameters

pCell the cell

Returns: pointer to the element.

Definition at line 188 of file PottsBasedCellPopulation.cpp.

◆ GetElementTessellation()

template<unsigned DIM>

VertexMesh< DIM, DIM > * PottsBasedCellPopulation< DIM >::GetElementTessellation ( )

Returns: a reference to mpElementTessellation.

Definition at line 457 of file PottsBasedCellPopulation.cpp.

◆ GetLocationOfCellCentre()

template<unsigned DIM>

c_vector< double, DIM > PottsBasedCellPopulation< 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 centre of mass of the element corresponding to this cell.

Implements AbstractCellPopulation< DIM >.

Definition at line 182 of file PottsBasedCellPopulation.cpp.

◆ GetMutableMesh()

template<unsigned DIM>

MutableMesh< DIM, DIM > * PottsBasedCellPopulation< DIM >::GetMutableMesh ( )

Returns: the Mutable Mesh

Definition at line 480 of file PottsBasedCellPopulation.cpp.

◆ GetNeighbouringLocationIndices()

template<unsigned DIM>

std::set< unsigned > PottsBasedCellPopulation< 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< DIM >.

Definition at line 175 of file PottsBasedCellPopulation.cpp.

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

◆ GetNode()

template<unsigned DIM>

Node< DIM > * PottsBasedCellPopulation< DIM >::GetNode ( unsigned index )

virtual

Overridden GetNode() method.

Parameters

index global index of the specified node

Returns: a pointer to the node.

Implements AbstractCellPopulation< DIM >.

Definition at line 163 of file PottsBasedCellPopulation.cpp.

Referenced by AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), ChemotaxisPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

◆ GetNumElements()

template<unsigned DIM>

unsigned PottsBasedCellPopulation< DIM >::GetNumElements ( )

Returns: the number of PottsElements in the cell population.

Definition at line 157 of file PottsBasedCellPopulation.cpp.

◆ GetNumNodes()

template<unsigned DIM>

unsigned PottsBasedCellPopulation< DIM >::GetNumNodes ( )

virtual

Overridden GetNumNodes() method.

Returns: the number of nodes in the cell population.

Implements AbstractCellPopulation< DIM >.

Definition at line 169 of file PottsBasedCellPopulation.cpp.

◆ GetNumSweepsPerTimestep()

template<unsigned DIM>

unsigned PottsBasedCellPopulation< DIM >::GetNumSweepsPerTimestep ( )

Returns: mNumSweepsPerTimestep

Definition at line 515 of file PottsBasedCellPopulation.cpp.

◆ GetTemperature()

template<unsigned DIM>

double PottsBasedCellPopulation< DIM >::GetTemperature ( )

Returns: mTemperature

Definition at line 503 of file PottsBasedCellPopulation.cpp.

◆ GetTetrahedralMeshForPdeModifier()

template<unsigned DIM>

TetrahedralMesh< DIM, DIM > * PottsBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier ( )

virtual

Overridden GetTetrahedralMeshForPdeModifier() method.

Returns: a pointer to a tetrahedral mesh

This method is called by AbstractGrowingDomainPdeModifier.

Implements AbstractCellPopulation< DIM >.

Definition at line 133 of file PottsBasedCellPopulation.cpp.

◆ GetVolumeOfCell()

template<unsigned DIM>

double PottsBasedCellPopulation< DIM >::GetVolumeOfCell ( CellPtr pCell )

virtual

Overridden GetVolumeOfCell() method.

Parameters

pCell boost shared pointer to a cell

Returns: volume via associated mesh element

Implements AbstractCellPopulation< DIM >.

Definition at line 411 of file PottsBasedCellPopulation.cpp.

◆ GetWidth()

template<unsigned DIM>

double PottsBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension )

virtual

Overridden GetWidth() method.

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

Parameters

rDimension a dimension (0,1 or 2)

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

Implements AbstractCellPopulation< DIM >.

Definition at line 423 of file PottsBasedCellPopulation.cpp.

◆ IsCellAssociatedWithADeletedLocation()

template<unsigned DIM>

bool PottsBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell )

virtual

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters

pCell the cell

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

Implements AbstractCellPopulation< DIM >.

Definition at line 352 of file PottsBasedCellPopulation.cpp.

◆ OpenWritersFiles()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::OpenWritersFiles ( OutputFileHandler & rOutputFileHandler )

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 363 of file PottsBasedCellPopulation.cpp.

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

◆ OutputCellPopulationParameters()

template<unsigned DIM>

void PottsBasedCellPopulation< 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 AbstractOnLatticeCellPopulation< DIM >.

Definition at line 487 of file PottsBasedCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters().

◆ RemoveDeadCells()

template<unsigned DIM>

unsigned PottsBasedCellPopulation< DIM >::RemoveDeadCells ( )

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 212 of file PottsBasedCellPopulation.cpp.

◆ rGetMesh() [1/2]

template<unsigned DIM>

PottsMesh< DIM > & PottsBasedCellPopulation< DIM >::rGetMesh ( )

Returns: reference to mrMesh.

Definition at line 121 of file PottsBasedCellPopulation.cpp.

Referenced by AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

◆ rGetMesh() [2/2]

template<unsigned DIM>

const PottsMesh< DIM > & PottsBasedCellPopulation< DIM >::rGetMesh ( ) const

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

Definition at line 127 of file PottsBasedCellPopulation.cpp.

◆ serialize()

template<unsigned DIM>

template<class Archive >

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

inlineprivate

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

Definition at line 107 of file PottsBasedCellPopulation.hpp.

References PottsBasedCellPopulation< DIM >::mNumSweepsPerTimestep, PottsBasedCellPopulation< DIM >::mpElementTessellation, and PottsBasedCellPopulation< DIM >::mTemperature.

◆ SetNumSweepsPerTimestep()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::SetNumSweepsPerTimestep ( unsigned numSweepsPerTimestep )

Set mNumSweepsPerTimestep.

Parameters

numSweepsPerTimestep the number of MonteCarlo sweeps of the mesh performed each timestep

Definition at line 509 of file PottsBasedCellPopulation.cpp.

◆ SetTemperature()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::SetTemperature ( double temperature )

Set mTemperature.

Parameters

temperature the temperature of the system

Definition at line 497 of file PottsBasedCellPopulation.cpp.

◆ Update()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true )

virtual

Remove the PottsElements which have been marked as deleted, and update the correspondence with CellPtrs.

Parameters

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

Implements AbstractCellPopulation< DIM >.

Definition at line 358 of file PottsBasedCellPopulation.cpp.

◆ UpdateCellLocations()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::UpdateCellLocations ( double dt )

virtual

Overridden UpdateCellLocations() method.

Parameters

dt time step

Todo:: If this causes the element to have no nodes then flag the element and cell to be deleted

Implements AbstractOnLatticeCellPopulation< DIM >.

Definition at line 241 of file PottsBasedCellPopulation.cpp.

References Node< SPACE_DIM >::GetIndex(), Node< SPACE_DIM >::GetNumContainingElements(), RandomNumberGenerator::Instance(), RandomNumberGenerator::randMod(), RandomNumberGenerator::ranf(), Node< SPACE_DIM >::rGetContainingElementIndices(), and RandomNumberGenerator::Shuffle().

◆ Validate()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::Validate ( )

privatevirtual

Check the consistency of internal data structures. Each PottsElement must have a CellPtr associated with it.

Implements AbstractCellPopulation< DIM >.

Definition at line 47 of file PottsBasedCellPopulation.cpp.

References EXCEPTION, and SimulationTime::Instance().

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

◆ WriteResultsToFiles()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::WriteResultsToFiles ( const std::string & rDirectory )

virtual

Overridden WriteResultsToFiles() method.

Parameters

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

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 379 of file PottsBasedCellPopulation.cpp.

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

◆ WriteVtkResultsToFile()

template<unsigned DIM>

void PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile ( const std::string & rDirectory )

privatevirtual

Overridden WriteVtkResultsToFile() method.

As a CellIdWriter is added to the population in the overridden method OpenWritersFiles(), distinct cells can be visualized when viewing VTK output of Potts model simulations.

Parameters

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

Implements AbstractCellPopulation< DIM >.

Definition at line 521 of file PottsBasedCellPopulation.cpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Definition at line 94 of file PottsBasedCellPopulation.hpp.

◆ TestPottsBasedCellPopulation

template<unsigned DIM>

friend class TestPottsBasedCellPopulation

friend

Definition at line 62 of file PottsBasedCellPopulation.hpp.

Member Data Documentation

◆ mNumSweepsPerTimestep

template<unsigned DIM>

unsigned PottsBasedCellPopulation< DIM >::mNumSweepsPerTimestep

private

The number of MonteCarlo sweeps of the mesh performed each timestep. Initialised to 1 in the constructor.

Definition at line 92 of file PottsBasedCellPopulation.hpp.

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

◆ mpElementTessellation

template<unsigned DIM>

VertexMesh<DIM,DIM>* PottsBasedCellPopulation< DIM >::mpElementTessellation

private

Pointer to a VertexMesh object that stores the Element tessellation that is used to visualize mrMesh. The tessellation is created by calling CreateElementTessellation() and can be accessed by calling GetElementTessellation().

Definition at line 71 of file PottsBasedCellPopulation.hpp.

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

◆ mpMutableMesh

template<unsigned DIM>

MutableMesh<DIM,DIM>* PottsBasedCellPopulation< DIM >::mpMutableMesh

private

Pointer to a MutableMesh that can be created from the nodes of the PottsMesh in order to solve PDEs on the population.

Definition at line 83 of file PottsBasedCellPopulation.hpp.

◆ mpPottsMesh

template<unsigned DIM>

PottsMesh<DIM>* PottsBasedCellPopulation< DIM >::mpPottsMesh

private

A static cast of the Abstract mesh from `AbstractCellPopulation` for use in this class

Definition at line 77 of file PottsBasedCellPopulation.hpp.

Referenced by PottsBasedCellPopulation< DIM >::PottsBasedCellPopulation(), and PottsBasedCellPopulation< DIM >::PottsBasedCellPopulation().

◆ mTemperature

template<unsigned DIM>

double PottsBasedCellPopulation< DIM >::mTemperature

private

The temperature of the system. Initialized to 0.1 in the constructor.

Definition at line 86 of file PottsBasedCellPopulation.hpp.

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

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

cell_based/src/population/PottsBasedCellPopulation.hpp
cell_based/src/population/PottsBasedCellPopulation.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PottsBasedCellPopulation() [1/2]

◆ PottsBasedCellPopulation() [2/2]

◆ ~PottsBasedCellPopulation()

Member Function Documentation

◆ AcceptCellWriter()

◆ AcceptPopulationCountWriter()

◆ AcceptPopulationEventWriter()

◆ AcceptPopulationWriter()

◆ AddCell()

◆ AddUpdateRule()

◆ CreateElementTessellation()

◆ CreateMutableMesh()

◆ GetCellDataItemAtPdeNode()

◆ GetElement()

◆ GetElementCorrespondingToCell()

◆ GetElementTessellation()

◆ GetLocationOfCellCentre()

◆ GetMutableMesh()

◆ GetNeighbouringLocationIndices()

◆ GetNode()

◆ GetNumElements()

◆ GetNumNodes()

◆ GetNumSweepsPerTimestep()

◆ GetTemperature()

◆ GetTetrahedralMeshForPdeModifier()

◆ GetVolumeOfCell()

◆ GetWidth()

◆ IsCellAssociatedWithADeletedLocation()

◆ OpenWritersFiles()

◆ OutputCellPopulationParameters()

◆ RemoveDeadCells()

◆ rGetMesh() [1/2]

◆ rGetMesh() [2/2]

◆ serialize()

◆ SetNumSweepsPerTimestep()

◆ SetTemperature()

◆ Update()

◆ UpdateCellLocations()

◆ Validate()

◆ WriteResultsToFiles()

◆ WriteVtkResultsToFile()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestPottsBasedCellPopulation

Member Data Documentation

◆ mNumSweepsPerTimestep

◆ mpElementTessellation

◆ mpMutableMesh

◆ mpPottsMesh

◆ mTemperature