#include <VertexBasedCellPopulation.hpp>

Inheritance diagram for VertexBasedCellPopulation< SPACE_DIM >:

Collaboration diagram for VertexBasedCellPopulation< SPACE_DIM >:

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

	VertexBasedCellPopulation (MutableVertexMesh< DIM, DIM > &rMesh)

virtual	~VertexBasedCellPopulation ()

double	GetDampingConstant (unsigned nodeIndex)

MutableVertexMesh< DIM, DIM > &	rGetMesh ()

const MutableVertexMesh< DIM, DIM > &	rGetMesh () const

VertexElement< DIM, DIM > *	GetElement (unsigned elementIndex)

unsigned	GetNumElements ()

unsigned	GetNumNodes ()

c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)

Node< DIM > *	GetNode (unsigned index)

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

unsigned	AddNode (Node< DIM > *pNewNode)

virtual void	CheckForStepSizeException (unsigned nodeIndex, c_vector< double, DIM > &rDisplacement, double dt)

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

VertexElement< DIM, DIM > *	GetElementCorrespondingToCell (CellPtr pCell)

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

unsigned	RemoveDeadCells ()

bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)

void	Update (bool hasHadBirthsOrDeaths=true)

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

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)

unsigned	GetRosetteRankOfCell (CellPtr pCell)

double	GetVolumeOfCell (CellPtr pCell)

std::vector< c_vector< double, DIM > >	GetLocationsOfT2Swaps ()

std::vector< unsigned >	GetCellIdsOfT2Swaps ()

void	AddLocationOfT2Swap (c_vector< double, DIM > locationOfT2Swap)

void	AddCellIdOfT2Swap (unsigned idOfT2Swap)

void	ClearLocationsAndCellIdsOfT2Swaps ()

bool	GetOutputCellRearrangementLocations ()

void	SetOutputCellRearrangementLocations (bool outputCellRearrangementLocations)

void	OutputCellPopulationParameters (out_stream &rParamsFile)

double	GetWidth (const unsigned &rDimension)

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

virtual TetrahedralMesh< DIM, DIM > *	GetTetrahedralMeshForPdeModifier ()

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

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

boost::shared_ptr < AbstractVertexBasedDivisionRule < DIM > >	GetVertexBasedDivisionRule ()

void	SetVertexBasedDivisionRule (boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > pVertexBasedDivisionRule)

virtual double	GetDefaultTimeStep ()

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

virtual void	SimulationSetupHook (AbstractCellBasedSimulation< DIM, DIM > *pSimulation)

bool	GetRestrictVertexMovementBoolean ()

void	SetRestrictVertexMovementBoolean (bool restrictVertexMovement)

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

virtual unsigned	AddNode (Node< ELEMENT_DIM > *pNewNode)=0

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

virtual void	UpdateNodeLocations (double dt)

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

void	SetDampingConstantNormal (double dampingConstantNormal)

void	SetDampingConstantMutant (double dampingConstantMutant)

void	SetAbsoluteMovementThreshold (double absoluteMovementThreshold)

double	GetAbsoluteMovementThreshold ()

double	GetDampingConstantNormal ()

double	GetDampingConstantMutant ()

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

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

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

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

std::list< CellPtr > &	rGetCells ()

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

c_vector< double, SPACE_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

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 ()

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)

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

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

void	Validate ()

Private Attributes
bool	mDeleteMesh

MutableVertexMesh< DIM, DIM > *	mpMutableVertexMesh

bool	mOutputCellRearrangementLocations

boost::shared_ptr < AbstractVertexBasedDivisionRule < DIM > >	mpVertexBasedDivisionRule

std::vector< c_vector< double, DIM > >	mLocationsOfT2Swaps

std::vector< unsigned >	mCellIdsOfT2Swaps

bool	mRestrictVertexMovement

Friends
class	TestVertexBasedDivisionRules

class	boost::serialization::access

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

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

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Attributes inherited from AbstractOffLatticeCellPopulation< DIM >
double	mDampingConstantNormal

double	mDampingConstantMutant

double	mAbsoluteMovementThreshold

Protected Attributes inherited from AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
std::map< unsigned, std::set < CellPtr > >	mLocationCellMap

std::map< Cell *, unsigned >	mCellLocationMap

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	mrMesh

std::list< CellPtr >	mCells

c_vector< double, SPACE_DIM >	mCentroid

out_stream	mpVtkMetaFile

boost::shared_ptr < CellPropertyRegistry >	mpCellPropertyRegistry

bool	mOutputResultsForChasteVisualizer

std::vector< boost::shared_ptr < AbstractCellWriter < ELEMENT_DIM, SPACE_DIM > > >	mCellWriters

std::vector< boost::shared_ptr < AbstractCellPopulationWriter < ELEMENT_DIM, SPACE_DIM > > >	mCellPopulationWriters

std::vector< boost::shared_ptr < AbstractCellPopulationCountWriter < ELEMENT_DIM, SPACE_DIM > > >	mCellPopulationCountWriters

Detailed Description

template<unsigned SPACE_DIM>
class VertexBasedCellPopulation< SPACE_DIM >

A facade class encapsulating a vertex-based cell population.

Contains a group of cells and maintains the associations between CellPtrs and elements in the MutableVertexMesh.

Definition at line 47 of file FixedVertexBasedDivisionRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation	(	MutableVertexMesh< DIM, 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 VertexElement in the mesh.

Parameters

rMesh	reference to a
rCells	reference to a vector of CellPtrs
deleteMesh	set to true if you want the cell population to free the mesh memory on destruction
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 52 of file VertexBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mCells, VertexBasedCellPopulation< SPACE_DIM >::mpMutableVertexMesh, VertexBasedCellPopulation< SPACE_DIM >::mpVertexBasedDivisionRule, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mrMesh, and VertexBasedCellPopulation< SPACE_DIM >::Validate().

template<unsigned DIM>

VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation ( MutableVertexMesh< DIM, DIM > & rMesh )

Constructor for use by boost serialization ONLY!

Parameters

rMesh a vertex mesh.

Definition at line 81 of file VertexBasedCellPopulation.cpp.

References VertexBasedCellPopulation< SPACE_DIM >::mpMutableVertexMesh, and AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::mrMesh.

template<unsigned DIM>

VertexBasedCellPopulation< DIM >::~VertexBasedCellPopulation ( )

virtual

Destructor, which frees any memory allocated by the constructor.

Definition at line 91 of file VertexBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

void VertexBasedCellPopulation< 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 362 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< 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 356 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< 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 350 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

CellPtr VertexBasedCellPopulation< 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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 202 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::AddCellIdOfT2Swap ( unsigned idOfT2Swap )

Add ID of T2 Swap.

Parameters

idOfT2Swap ID of the cell undergoing a T2 swap

Definition at line 579 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::AddLocationOfT2Swap ( c_vector< double, DIM > locationOfT2Swap )

Add location of T2 Swap.

Parameters

locationOfT2Swap Location of the T2 swap

Definition at line 573 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::AddNode ( Node< DIM > * pNewNode )

Overridden AddNode() method.

Add a new node to the cell population.

Parameters

pNewNode pointer to the new node

Returns: global index of new node in cell population

Definition at line 178 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::CheckForStepSizeException	(	unsigned	nodeIndex,
		c_vector< double, 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

Definition at line 260 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::ClearLocationsAndCellIdsOfT2Swaps ( )

Clear the locations and IDs of cells undergoing T2 Swaps.

Definition at line 585 of file VertexBasedCellPopulation.cpp.

Referenced by VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

double VertexBasedCellPopulation< 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.

Todo:: Work out a better way to do the nodes not associated with cells

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 759 of file VertexBasedCellPopulation.cpp.

References Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned DIM>

std::vector< unsigned > VertexBasedCellPopulation< DIM >::GetCellIdsOfT2Swaps ( )

Return all IDs of cells undergoing T2 swaps since the last sampling time step.

Returns: mLocationsOfT2Swaps

Definition at line 567 of file VertexBasedCellPopulation.cpp.

Referenced by VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

double VertexBasedCellPopulation< DIM >::GetDampingConstant ( unsigned nodeIndex )

virtual

Overridden GetDampingConstant() method.

Parameters

nodeIndex the global index of this node

Returns: the average damping constant of the cells surrounding the node.

Implements AbstractOffLatticeCellPopulation< DIM >.

Definition at line 100 of file VertexBasedCellPopulation.cpp.

References EXCEPTION, and SimulationTime::Instance().

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

template<unsigned DIM>

double VertexBasedCellPopulation< 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 0.002 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, ELEMENT_DIM >.

Definition at line 809 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

VertexElement< DIM, DIM > * VertexBasedCellPopulation< DIM >::GetElement ( unsigned elementIndex )

Get a particular VertexElement.

Parameters

elementIndex the global index of the VertexElement

Returns: a pointer to the VertexElement.

Definition at line 147 of file VertexBasedCellPopulation.cpp.

Referenced by FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), and CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

VertexElement< DIM, DIM > * VertexBasedCellPopulation< 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 190 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

c_vector< double, DIM > VertexBasedCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr pCell )

virtual

Overridden GetLocationOfCellCentre() method.

Find the centre of mass of a given cell (assuming uniform density). Note that, as there is no guarantee of convexity, this may lie outside the VertexElement corresponding to the cell.

Parameters

pCell a cell in the population

Returns: the location of the centre of mass of the element corresponding to this cell.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 159 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

std::vector< c_vector< double, DIM > > VertexBasedCellPopulation< DIM >::GetLocationsOfT2Swaps ( )

Return all locations of T2 swaps since the last sampling time step.

Returns: mLocationsOfT2Swaps

Definition at line 561 of file VertexBasedCellPopulation.cpp.

Referenced by VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

std::set< unsigned > VertexBasedCellPopulation< 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, ELEMENT_DIM >.

Definition at line 171 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Overridden GetNeighbouringNodeIndices() method.

Parameters

index the node index

Returns: the set of neighbouring node indices.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 543 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Overridden GetNode() method.

Parameters

index global index of the specified node

Returns: a pointer to the node.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 165 of file VertexBasedCellPopulation.cpp.

Referenced by WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), and NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::GetNumElements ( )

Returns: the number of VertexElements in the cell population.

Definition at line 196 of file VertexBasedCellPopulation.cpp.

Referenced by FarhadifarForce< DIM >::AddForceContribution(), and NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::GetNumNodes ( )

virtual

Overridden GetNumNodes() method.

Returns: the number of nodes in the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 153 of file VertexBasedCellPopulation.cpp.

Referenced by FarhadifarForce< DIM >::AddForceContribution(), and NagaiHondaForce< DIM >::AddForceContribution().

template<unsigned DIM>

bool VertexBasedCellPopulation< DIM >::GetOutputCellRearrangementLocations ( )

Returns: mOutputCellRearrangementLocations

Definition at line 505 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

bool VertexBasedCellPopulation< DIM >::GetRestrictVertexMovementBoolean ( )

Get the value of the mRestrictVertexMovement boolean.

Returns: True if vertex movement is restricted at each timestep.

Definition at line 832 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

unsigned VertexBasedCellPopulation< DIM >::GetRosetteRankOfCell ( CellPtr pCell )

Get the "rosette rank" of a cell.

This is defined as the maximum number of cells shared by any node in the cell's corresponding element.

Parameters

pCell boost shared pointer to a cell

Returns: rosette rank via associated mesh element

Definition at line 368 of file VertexBasedCellPopulation.cpp.

Referenced by CellRosetteRankWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput().

template<unsigned DIM>

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

virtual

Overridden GetTetrahedralMeshForPdeModifier() method.

Returns: a pointer to a tetrahedral mesh using the nodes in the VertexMesh as well as an additional node at the centre of each VertexElement. At present, this method only works in 2D.

This method is called by AbstractGrowingDomainPdeModifier.

Todo:: will the nodes in mpMutableVertexMesh always have indices 0,1,2,...? (#2221)

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 592 of file VertexBasedCellPopulation.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), OutputFileHandler::GetOutputDirectoryFullPath(), Node< SPACE_DIM >::IsBoundaryNode(), PetscTools::IsSequential(), Node< SPACE_DIM >::rGetLocation(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading().

template<unsigned DIM>

boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > VertexBasedCellPopulation< DIM >::GetVertexBasedDivisionRule ( )

Returns: The Vertex division rule that is currently being used.

Definition at line 549 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Overridden GetVolumeOfCell() method.

Parameters

pCell boost shared pointer to a cell

Returns: volume via associated mesh element

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 380 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

double VertexBasedCellPopulation< 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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 534 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

bool VertexBasedCellPopulation< 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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 282 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

bool VertexBasedCellPopulation< DIM >::IsPdeNodeAssociatedWithNonApoptoticCell ( unsigned pdeNodeIndex )

virtual

Overridden IsPdeNodeAssociatedWithNonApoptoticCell() method.

Parameters

pdeNodeIndex inedx of a node in a tetrahedral mesh for use with a PDE modifier

Returns: if a node, specified by its index in a tetrahedral mesh for use with a PDE modifier, is associated with a non-apoptotic cell. This method can be called by PDE classes.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 727 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< 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< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 475 of file VertexBasedCellPopulation.cpp.

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

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellPopulationParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOffLatticeCellPopulation< DIM >.

Definition at line 517 of file VertexBasedCellPopulation.cpp.

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

template<unsigned DIM>

unsigned VertexBasedCellPopulation< 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

Todo:: (#2489) this should cause an error - we should fix this!

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 225 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

MutableVertexMesh< DIM, DIM > & VertexBasedCellPopulation< DIM >::rGetMesh ( )

Returns: reference to mrMesh.

Definition at line 135 of file VertexBasedCellPopulation.cpp.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), WelikyOsterForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), ShortAxisVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

const MutableVertexMesh< DIM, DIM > & VertexBasedCellPopulation< DIM >::rGetMesh ( ) const

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

Definition at line 141 of file VertexBasedCellPopulation.cpp.

template<unsigned SPACE_DIM>

template<class Archive >

void VertexBasedCellPopulation< SPACE_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 124 of file VertexBasedCellPopulation.hpp.

References VertexBasedCellPopulation< SPACE_DIM >::mOutputCellRearrangementLocations, VertexBasedCellPopulation< SPACE_DIM >::mpVertexBasedDivisionRule, and VertexBasedCellPopulation< SPACE_DIM >::mRestrictVertexMovement.

template<unsigned DIM>

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

Overridden SetNode() method.

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

Parameters

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

Definition at line 184 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::SetOutputCellRearrangementLocations ( bool outputCellRearrangementLocations )

Set mOutputCellRearrangementLocations.

Parameters

outputCellRearrangementLocations the new value of mOutputCellRearrangementLocations

Definition at line 511 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::SetRestrictVertexMovementBoolean ( bool restrictVertexMovement )

Set the value of the mRestrictVertexMovement boolean.

Parameters

restrictVertexMovement whether to restrict vertex movement in this simulation.

Definition at line 838 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::SetVertexBasedDivisionRule ( boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > pVertexBasedDivisionRule )

Set the division rule for this population.

Parameters

pVertexBasedDivisionRule pointer to the new division rule

Definition at line 555 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::SimulationSetupHook ( AbstractCellBasedSimulation< DIM, DIM > * pSimulation )

virtual

Overridden SimulationSetupHook() method.

Hook method to add a T2SwapCellKiller to a simulation object, which is always required in the case of a VertexBasedCellPopulation. This functionality avoids the need for static or dynamic casts to specific cell population types within simulation methods.

Note: In order to inhibit T2 swaps, the user needs to set the threshold for T2 swaps in the MutableVertexMesh object mrMesh to 0, using the SetT2Threshold() method.

Parameters

pSimulation pointer to a cell-based simulation object

Definition at line 824 of file VertexBasedCellPopulation.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AddCellKiller(), and MAKE_PTR_ARGS.

template<unsigned DIM>

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

virtual

Remove the VertexElements which have been marked as deleted, perform any cell rearrangements if required, and update the correspondence with CellPtrs.

Parameters

hasHadBirthsOrDeaths - a bool saying whether cell population has had Births Or Deaths not needed in this cell population class

Todo:: We want to make these maps private, so we need a better way of doing the code below.

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 288 of file VertexBasedCellPopulation.cpp.

References VertexElementMap::GetNewIndex().

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

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::Validate ( )

privatevirtual

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

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 322 of file VertexBasedCellPopulation.cpp.

References EXCEPTION, and SimulationTime::Instance().

Referenced by VertexBasedCellPopulation< SPACE_DIM >::VertexBasedCellPopulation().

template<unsigned DIM>

void VertexBasedCellPopulation< DIM >::WriteDataToVisualizerSetupFile ( out_stream & pVizSetupFile )

virtual

Overridden WriteDataToVisualizerSetupFile() method. Write any data necessary to a visualization setup file. Used by AbstractCellBasedSimulation::WriteVisualizerSetupFile().

Parameters

pVizSetupFile a visualization setup file

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 815 of file VertexBasedCellPopulation.cpp.

template<unsigned DIM>

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

privatevirtual

Overridden WriteVtkResultsToFile() method.

Parameters

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

Implements AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 392 of file VertexBasedCellPopulation.cpp.

References VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().

Friends And Related Function Documentation

template<unsigned SPACE_DIM>

friend class TestVertexBasedDivisionRules

friend

This test uses the private constructor to simplify testing.

Definition at line 65 of file VertexBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned SPACE_DIM>

std::vector< unsigned > VertexBasedCellPopulation< SPACE_DIM >::mCellIdsOfT2Swaps

private

The Ids of cells that have undergone T2 swaps, stored so they can be accessed and output by the cell killer and population writer classes. The Ids are stored until they are cleared by ClearLocationsAndCellIdsOfT2Swaps().

Definition at line 96 of file VertexBasedCellPopulation.hpp.

template<unsigned SPACE_DIM>

bool VertexBasedCellPopulation< SPACE_DIM >::mDeleteMesh

private

Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.

Definition at line 71 of file VertexBasedCellPopulation.hpp.

template<unsigned SPACE_DIM>

std::vector< c_vector<double, DIM> > VertexBasedCellPopulation< SPACE_DIM >::mLocationsOfT2Swaps

private

Locations of T2 swaps (the centre of the removed triangle), stored so they can be accessed and output by the cell killer and population writer classes. The locations are stored until they are cleared by ClearLocationsAndCellIdsOfT2Swaps().

Definition at line 90 of file VertexBasedCellPopulation.hpp.

template<unsigned SPACE_DIM>

bool VertexBasedCellPopulation< SPACE_DIM >::mOutputCellRearrangementLocations

private

Whether to output the locations of T1 swaps and T3 swaps to files. Defaults to true.

Definition at line 80 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< SPACE_DIM >::serialize().

template<unsigned SPACE_DIM>

MutableVertexMesh<DIM, DIM>* VertexBasedCellPopulation< SPACE_DIM >::mpMutableVertexMesh

private

A static cast of the AbstractMesh from AbstractCellPopulation for use in this class

Definition at line 77 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< SPACE_DIM >::VertexBasedCellPopulation().

template<unsigned SPACE_DIM>

boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > VertexBasedCellPopulation< SPACE_DIM >::mpVertexBasedDivisionRule

private

A pointer to a division rule that is used to generate the axis when dividing cells. This is a specialisation for Vertex models.

Definition at line 84 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< SPACE_DIM >::serialize(), and VertexBasedCellPopulation< SPACE_DIM >::VertexBasedCellPopulation().

template<unsigned SPACE_DIM>

bool VertexBasedCellPopulation< SPACE_DIM >::mRestrictVertexMovement

private

Whether to restrict the vertex movement if vertex displacement is larger than the cell rearrangement threshold.

Definition at line 102 of file VertexBasedCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< SPACE_DIM >::serialize().

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

cell_based/src/population/division_rules/FixedVertexBasedDivisionRule.hpp
cell_based/src/population/VertexBasedCellPopulation.hpp
cell_based/src/population/VertexBasedCellPopulation.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned SPACE_DIM> class VertexBasedCellPopulation< SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned SPACE_DIM>
class VertexBasedCellPopulation< SPACE_DIM >