#include <ImmersedBoundaryCellPopulation.hpp>

Inheritance diagram for ImmersedBoundaryCellPopulation< DIM >:

Collaboration diagram for ImmersedBoundaryCellPopulation< DIM >:

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

	ImmersedBoundaryCellPopulation (ImmersedBoundaryMesh< DIM, DIM > &rMesh)

virtual	~ImmersedBoundaryCellPopulation ()

double	GetDampingConstant (unsigned nodeIndex)

ImmersedBoundaryMesh< DIM, DIM > &	rGetMesh ()

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

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

ImmersedBoundaryElement< DIM - 1, DIM > *	GetLamina (unsigned laminaIndex)

unsigned	GetNumElements ()

unsigned	GetNumLaminas ()

unsigned	GetNumNodes ()

void	SetInteractionDistance (double newDistance)

double	GetInteractionDistance () const

void	SetReMeshFrequency (unsigned newFrequency)

unsigned	GetReMeshFrequency () const

void	SetThrowsStepSizeException (bool throws)

bool	ThrowsStepSizeException () const

double	GetIntrinsicSpacing () const

void	SetCellRearrangementThreshold (double newThreshold)

double	GetCellRearrangementThreshold () const

c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)

Node< DIM > *	GetNode (unsigned index)

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

unsigned	AddNode (Node< DIM > *pNewNode)

void	UpdateNodeLocations (double dt)

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

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

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)

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< AbstractImmersedBoundaryDivisionRule< DIM > >	GetImmersedBoundaryDivisionRule ()

void	SetImmersedBoundaryDivisionRule (boost::shared_ptr< AbstractImmersedBoundaryDivisionRule< DIM > > pImmersedBoundaryDivisionRule)

bool	DoesPopulationHaveActiveSources () const

bool	IsCellOnBoundary (CellPtr pCell)

void	SetIfPopulationHasActiveSources (bool hasActiveSources)

void	SetOutputNodeRegionToVtk (bool outputNodeRegionsToVtk)

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

virtual double	GetDefaultTimeStep ()

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

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

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

virtual void	CheckForStepSizeException (unsigned nodeIndex, c_vector< double, SPACE_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, SPACE_DIM >
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

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

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

std::list< CellPtr > &	rGetCells ()

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	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	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 ()

template<template< unsigned, unsigned > class T>
void	AddPopulationWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellPopulationCountWriter ()

template<template< unsigned, unsigned > class T>
void	AddCellPopulationEventWriter ()

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

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

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

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

template<template< unsigned, unsigned > class T>
bool	HasWriter () const

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, SPACE_DIM >	GetSizeOfCellPopulation ()

virtual bool	IsRoomToDivide (CellPtr pCell)

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

Iterator	Begin ()

Iterator	End ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Private Member Functions
virtual void	WriteVtkResultsToFile (const std::string &rDirectory)

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

double	Delta1D (double dist, double spacing)

double	CalculateIntrinsicCellSize ()

void	Validate ()

Private Attributes
bool	mDeleteMesh

ImmersedBoundaryMesh< DIM, DIM > *	mpImmersedBoundaryMesh

boost::shared_ptr< AbstractImmersedBoundaryDivisionRule< DIM > >	mpImmersedBoundaryDivisionRule

double	mIntrinsicSpacing

bool	mPopulationHasActiveSources

bool	mOutputNodeRegionToVtk

double	mInteractionDistance

unsigned	mReMeshFrequency

bool	mThrowStepSizeException

double	mCellRearrangementThreshold

Friends
class	TestImmersedBoundaryDivisionRules

class	TestImmersedBoundaryCellPopulation

class	boost::serialization::access

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

Protected Member Functions inherited from AbstractCellPopulation< ELEMENT_DIM, SPACE_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, SPACE_DIM >
std::map< unsigned, std::set< CellPtr > >	mLocationCellMap

std::map< Cell *, unsigned >	mCellLocationMap

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	mrMesh

std::list< CellPtr >	mCells

c_vector< double, SPACE_DIM >	mCentroid

out_stream	mpVtkMetaFile

boost::shared_ptr< CellPropertyRegistry >	mpCellPropertyRegistry

bool	mOutputResultsForChasteVisualizer

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

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

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

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 ImmersedBoundaryCellPopulation< DIM >

A facade class encapsulating an immersed boundary cell population.

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

Definition at line 57 of file ImmersedBoundaryCellPopulation.hpp.

Constructor & Destructor Documentation

◆ ImmersedBoundaryCellPopulation() [1/2]

template<unsigned DIM>

ImmersedBoundaryCellPopulation< DIM >::ImmersedBoundaryCellPopulation	(	ImmersedBoundaryMesh< 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 ImmersedBoundaryElement in the mesh.

Parameters

rMesh	reference to an immersed boundary mesh. Each element in the mesh will correspond to a cell.
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 49 of file ImmersedBoundaryCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), ImmersedBoundaryCellPopulation< DIM >::CalculateIntrinsicCellSize(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, ImmersedBoundaryCellPopulation< DIM >::mInteractionDistance, ImmersedBoundaryCellPopulation< DIM >::mpImmersedBoundaryDivisionRule, ImmersedBoundaryCellPopulation< DIM >::mpImmersedBoundaryMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::SetElementDivisionSpacing(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::SetNeighbourDist(), and ImmersedBoundaryCellPopulation< DIM >::Validate().

◆ ImmersedBoundaryCellPopulation() [2/2]

template<unsigned DIM>

ImmersedBoundaryCellPopulation< DIM >::ImmersedBoundaryCellPopulation ( ImmersedBoundaryMesh< DIM, DIM > & rMesh )

Constructor for use by boost serialization ONLY!

Parameters

rMesh an immersed boundary mesh.

Definition at line 93 of file ImmersedBoundaryCellPopulation.cpp.

References ImmersedBoundaryCellPopulation< DIM >::mpImmersedBoundaryMesh, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

◆ ~ImmersedBoundaryCellPopulation()

template<unsigned DIM>

ImmersedBoundaryCellPopulation< DIM >::~ImmersedBoundaryCellPopulation ( )

virtual

Destructor, which frees any memory allocated by the constructor.

Definition at line 108 of file ImmersedBoundaryCellPopulation.cpp.

Member Function Documentation

◆ AcceptCellWriter()

template<unsigned DIM>

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

virtual

Overridden AcceptCellWriter() method.

Parameters

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

Definition at line 626 of file ImmersedBoundaryCellPopulation.cpp.

◆ AcceptPopulationCountWriter()

template<unsigned DIM>

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

virtual

Overridden AcceptPopulationCountWriter() method.

Parameters

pPopulationCountWriter the population count writer.

Definition at line 619 of file ImmersedBoundaryCellPopulation.cpp.

◆ AcceptPopulationEventWriter()

template<unsigned DIM>

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

virtual

Overridden AcceptPopulationWriter() method.

Parameters

pPopulationEventWriter the population event writer.

Definition at line 612 of file ImmersedBoundaryCellPopulation.cpp.

◆ AcceptPopulationWriter()

template<unsigned DIM>

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

virtual

Overridden AcceptPopulationWriter() method.

Parameters

pPopulationWriter the population writer.

Definition at line 605 of file ImmersedBoundaryCellPopulation.cpp.

◆ AddCell()

template<unsigned DIM>

CellPtr ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 277 of file ImmersedBoundaryCellPopulation.cpp.

◆ AddNode()

template<unsigned DIM>

unsigned ImmersedBoundaryCellPopulation< 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 242 of file ImmersedBoundaryCellPopulation.cpp.

◆ CalculateIntrinsicCellSize()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< DIM >::CalculateIntrinsicCellSize ( )

private

Helper method for the constructor. Calculate an intrinsic length scale based on the size of elements in the mesh.

Returns: computed intrinsic length scale

Definition at line 117 of file ImmersedBoundaryCellPopulation.cpp.

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

◆ CheckForStepSizeException()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< 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 578 of file ImmersedBoundaryCellPopulation.cpp.

◆ Delta1D()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< DIM >::Delta1D	(	double	dist,
		double	spacing
	)

private

Helper method. Calculate the discrete delta approximation based on distance and grid spacing.

Parameters

dist	distance between the two points
spacing	the grid spacing

Returns: computed Delta1D value

Definition at line 517 of file ImmersedBoundaryCellPopulation.cpp.

◆ DoesPopulationHaveActiveSources()

template<unsigned DIM>

bool ImmersedBoundaryCellPopulation< DIM >::DoesPopulationHaveActiveSources ( ) const

Returns: mPopulationHasActiveSources whether the population has active fluid sources

Definition at line 1083 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetCellDataItemAtPdeNode()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 1018 of file ImmersedBoundaryCellPopulation.cpp.

References Node< SPACE_DIM >::rGetContainingElementIndices().

◆ GetCellRearrangementThreshold()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< DIM >::GetCellRearrangementThreshold ( ) const

Returns: mCellRearrangementThreshold.

Definition at line 211 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetDampingConstant()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< 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 132 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetDefaultTimeStep()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 1109 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetElement()

template<unsigned DIM>

ImmersedBoundaryElement< DIM, DIM > * ImmersedBoundaryCellPopulation< DIM >::GetElement ( unsigned elementIndex )

Get a particular ImmersedBoundaryElement.

Parameters

elementIndex the global index of the ImmersedBoundaryElement

Returns: a pointer to the ImmersedBoundaryElement.

Definition at line 150 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by AbstractImmersedBoundaryForce< DIM >::AddNormalNoiseToNodes(), and CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

◆ GetElementCorrespondingToCell()

template<unsigned DIM>

ImmersedBoundaryElement< DIM, DIM > * ImmersedBoundaryCellPopulation< 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 258 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetImmersedBoundaryDivisionRule()

template<unsigned DIM>

boost::shared_ptr< AbstractImmersedBoundaryDivisionRule< DIM > > ImmersedBoundaryCellPopulation< DIM >::GetImmersedBoundaryDivisionRule ( )

Returns: The division rule that is currently being used.

Definition at line 1070 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetInteractionDistance()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< DIM >::GetInteractionDistance ( ) const

Returns: the cell-cell interaction distance.

Definition at line 187 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by ImmersedBoundaryKinematicFeedbackForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearDifferentialAdhesionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), and ImmersedBoundaryMorseInteractionForce< DIM >::AddImmersedBoundaryForceContribution().

◆ GetIntrinsicSpacing()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< DIM >::GetIntrinsicSpacing ( ) const

Returns: the intrinsic node spacing

Definition at line 229 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by ImmersedBoundaryKinematicFeedbackForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearDifferentialAdhesionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearMembraneForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryMorseInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), and ImmersedBoundaryMorseMembraneForce< DIM >::AddImmersedBoundaryForceContribution().

◆ GetLamina()

template<unsigned DIM>

ImmersedBoundaryElement< DIM - 1, DIM > * ImmersedBoundaryCellPopulation< DIM >::GetLamina ( unsigned laminaIndex )

Get a particular ImmersedBoundaryElement representing a lamina. A lamina is a reduced-dimension element. For a 2d simulation, a lamina element is a line. For a 3d simulation, a lamina element is a surface.

Parameters

laminaIndex the global index of the lamina

Returns: a pointer to the lamina.

Definition at line 156 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by AbstractImmersedBoundaryForce< DIM >::AddNormalNoiseToNodes().

◆ GetLocationOfCellCentre()

template<unsigned DIM>

c_vector< double, DIM > ImmersedBoundaryCellPopulation< 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 ImmersedBoundaryElement 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, SPACE_DIM >.

Definition at line 168 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetNeighbouringLocationIndices()

template<unsigned DIM>

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

virtual

Overridden GetNeighbouringLocationIndices() method. Given a cell, returns the set of location indices corresponding to neighbouring cells. At least once per timestep, UpdateCellCentroids() should be called before this function.

Parameters

pCell a cell

Returns: the set of neighbouring location indices.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 235 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetNeighbouringNodeIndices()

template<unsigned DIM>

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

virtual

Overridden GetNeighbouringNodeIndices() method.

Parameters

index the node index

Returns: the set of neighbouring node indices.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 831 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetNode()

template<unsigned DIM>

Node< DIM > * ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 174 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetNumElements()

template<unsigned DIM>

unsigned ImmersedBoundaryCellPopulation< DIM >::GetNumElements ( )

Returns: the number of ImmersedBoundaryElements in the cell population.

Definition at line 265 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by AbstractImmersedBoundaryForce< DIM >::AddNormalNoiseToNodes().

◆ GetNumLaminas()

template<unsigned DIM>

unsigned ImmersedBoundaryCellPopulation< DIM >::GetNumLaminas ( )

Returns: the number of ImmersedBoundaryLaminas in the cell population.

Definition at line 271 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by AbstractImmersedBoundaryForce< DIM >::AddNormalNoiseToNodes().

◆ GetNumNodes()

template<unsigned DIM>

unsigned ImmersedBoundaryCellPopulation< DIM >::GetNumNodes ( )

virtual

Overridden GetNumNodes() method.

Returns: the number of nodes in the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 162 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by ImmersedBoundaryKinematicFeedbackForce< DIM >::AddImmersedBoundaryForceContribution().

◆ GetReMeshFrequency()

template<unsigned DIM>

unsigned ImmersedBoundaryCellPopulation< DIM >::GetReMeshFrequency ( ) const

Returns: mReMeshFrequency.

Definition at line 199 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetTetrahedralMeshForPdeModifier()

template<unsigned DIM>

TetrahedralMesh< DIM, DIM > * ImmersedBoundaryCellPopulation< 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.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 838 of file ImmersedBoundaryCellPopulation.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), EXCEPTION, OutputFileHandler::FindFile(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), OutputFileHandler::GetOutputDirectoryFullPath(), PetscTools::IsSequential(), OutputFileHandler::OpenOutputFile(), FileFinder::Remove(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading().

◆ GetVolumeOfCell()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 633 of file ImmersedBoundaryCellPopulation.cpp.

◆ GetWidth()

template<unsigned DIM>

double ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 824 of file ImmersedBoundaryCellPopulation.cpp.

◆ IsCellAssociatedWithADeletedLocation()

template<unsigned DIM>

bool ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 523 of file ImmersedBoundaryCellPopulation.cpp.

◆ IsCellOnBoundary()

template<unsigned DIM>

bool ImmersedBoundaryCellPopulation< DIM >::IsCellOnBoundary ( CellPtr pCell )

Parameters

pCell pointer to a cell

Returns: whether the cell is on the boundary of this population

Definition at line 1089 of file ImmersedBoundaryCellPopulation.cpp.

◆ IsPdeNodeAssociatedWithNonApoptoticCell()

template<unsigned DIM>

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

virtual

Overridden IsPdeNodeAssociatedWithNonApoptoticCell() method.

Parameters

pdeNodeIndex index 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, SPACE_DIM >.

Definition at line 985 of file ImmersedBoundaryCellPopulation.cpp.

◆ OpenWritersFiles()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< 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, SPACE_DIM >.

Definition at line 796 of file ImmersedBoundaryCellPopulation.cpp.

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

◆ OutputCellPopulationParameters()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< 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 811 of file ImmersedBoundaryCellPopulation.cpp.

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

◆ RemoveDeadCells()

template<unsigned DIM>

unsigned ImmersedBoundaryCellPopulation< 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< ELEMENT_DIM, SPACE_DIM >.

Definition at line 302 of file ImmersedBoundaryCellPopulation.cpp.

◆ rGetMesh() [1/2]

template<unsigned DIM>

ImmersedBoundaryMesh< DIM, DIM > & ImmersedBoundaryCellPopulation< DIM >::rGetMesh ( )

Returns: reference to mrMesh.

Definition at line 138 of file ImmersedBoundaryCellPopulation.cpp.

Referenced by ImmersedBoundaryKinematicFeedbackForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearDifferentialAdhesionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearMembraneForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryMorseInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryMorseMembraneForce< DIM >::AddImmersedBoundaryForceContribution(), ShortAxisImmersedBoundaryDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), ImmersedBoundaryLinearMembraneForce< DIM >::CalculateForcesOnElement(), ImmersedBoundaryMorseMembraneForce< DIM >::CalculateForcesOnElement(), ImmersedBoundaryKinematicFeedbackForce< DIM >::UpdatePreviousLocations(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

◆ rGetMesh() [2/2]

template<unsigned DIM>

const ImmersedBoundaryMesh< DIM, DIM > & ImmersedBoundaryCellPopulation< DIM >::rGetMesh ( ) const

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

Definition at line 144 of file ImmersedBoundaryCellPopulation.cpp.

◆ serialize()

template<unsigned DIM>

template<class Archive >

void ImmersedBoundaryCellPopulation< 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 134 of file ImmersedBoundaryCellPopulation.hpp.

References ImmersedBoundaryCellPopulation< DIM >::mCellRearrangementThreshold, ImmersedBoundaryCellPopulation< DIM >::mInteractionDistance, ImmersedBoundaryCellPopulation< DIM >::mpImmersedBoundaryDivisionRule, ImmersedBoundaryCellPopulation< DIM >::mPopulationHasActiveSources, ImmersedBoundaryCellPopulation< DIM >::mReMeshFrequency, and ImmersedBoundaryCellPopulation< DIM >::mThrowStepSizeException.

◆ SetCellRearrangementThreshold()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetCellRearrangementThreshold ( double newThreshold )

Set the maximum distance two nodes should be allowed to move apart from each other in a single step.

Parameters

newThreshold the new cell rearrangement threshold

Definition at line 205 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetIfPopulationHasActiveSources()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetIfPopulationHasActiveSources ( bool hasActiveSources )

Set whether the population has active sources

Parameters

hasActiveSources whether the population has active sources

Definition at line 1095 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetImmersedBoundaryDivisionRule()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetImmersedBoundaryDivisionRule ( boost::shared_ptr< AbstractImmersedBoundaryDivisionRule< DIM > > pImmersedBoundaryDivisionRule )

Set the division rule for this population.

Parameters

pImmersedBoundaryDivisionRule pointer to the new division rule

Definition at line 1076 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetInteractionDistance()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetInteractionDistance ( double newDistance )

Sets the maximum distance over which cell boundary nodes will interact via forces.

Parameters

newDistance the new cell-cell interaction distance.

Definition at line 180 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetNode()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< 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 252 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetOutputNodeRegionToVtk()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetOutputNodeRegionToVtk ( bool outputNodeRegionsToVtk )

Set whether to output node regions to vtk.

Parameters

outputNodeRegionsToVtk whether to output node regions to vtk

Definition at line 1102 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetReMeshFrequency()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetReMeshFrequency ( unsigned newFrequency )

Sets the number of timesteps between each remesh. Remeshing can improve solution quality and prevent divergence, but is an expensive operation.

Parameters

newFrequency the new ReMesh frequency.

Definition at line 193 of file ImmersedBoundaryCellPopulation.cpp.

◆ SetThrowsStepSizeException()

template<unsigned DIM>

void ImmersedBoundaryCellPopulation< DIM >::SetThrowsStepSizeException ( bool throws )

Sets whether an exception will be thrown if nodes move too far within a single timestep.

Parameters

throws whether an exception should be thrown

Definition at line 217 of file ImmersedBoundaryCellPopulation.cpp.

◆ ThrowsStepSizeException()

template<unsigned DIM>

bool ImmersedBoundaryCellPopulation< DIM >::ThrowsStepSizeException ( ) const

Returns: mThrowsStepSizeException.

Definition at line 223 of file ImmersedBoundaryCellPopulation.cpp.

◆ Update()

template<unsigned DIM>

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

virtual

Remove the ImmersedBoundaryElements 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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 529 of file ImmersedBoundaryCellPopulation.cpp.