#include <MeshBasedCellPopulation.hpp>

Inheritance diagram for MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Classes
class	SpringIterator

Public Member Functions
	MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)

	MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

virtual	~MeshBasedCellPopulation ()

MutableMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

const MutableMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh () const

bool	UseAreaBasedDampingConstant ()

unsigned	AddNode (Node< SPACE_DIM > *pNewNode)

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

double	GetDampingConstant (unsigned nodeIndex)

void	SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

virtual unsigned	RemoveDeadCells ()

virtual CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, SPACE_DIM > &rCellDivisionVector, CellPtr pParentCell)

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

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

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

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

virtual void	Update (bool hasHadBirthsOrDeaths=true)

void	TessellateIfNeeded ()

void	DivideLongSprings (double springDivisionThreshold)

Node< SPACE_DIM > *	GetNode (unsigned index)

unsigned	GetNumNodes ()

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

double	GetVolumeOfCell (CellPtr pCell)

void	CreateVoronoiTessellation ()

VertexMesh< ELEMENT_DIM, SPACE_DIM > *	GetVoronoiTessellation ()

double	GetVolumeOfVoronoiElement (unsigned index)

double	GetSurfaceAreaOfVoronoiElement (unsigned index)

double	GetVoronoiEdgeLength (unsigned index1, unsigned index2)

double	GetWidth (const unsigned &rDimension)

SpringIterator	SpringsBegin ()

SpringIterator	SpringsEnd ()

void	CheckCellPointers ()

double	GetAreaBasedDampingConstantParameter ()

void	SetAreaBasedDampingConstantParameter (double areaBasedDampingConstantParameter)

std::vector< std::pair< Node < SPACE_DIM > , Node < SPACE_DIM > > > &	rGetNodePairs ()

void	OutputCellPopulationParameters (out_stream &rParamsFile)

void	SetWriteVtkAsPoints (bool writeVtkAsPoints)

bool	GetWriteVtkAsPoints ()

void	SetOutputMeshInVtk (bool outputMeshInVtk)

bool	GetOutputMeshInVtk ()

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

void	CalculateRestLengths ()

double	GetRestLength (unsigned indexA, unsigned indexB)

void	SetRestLength (unsigned indexA, unsigned indexB, double restLength)

template<>
void	CreateVoronoiTessellation ()

template<>
void	CreateVoronoiTessellation ()

template<>
void	CreateVoronoiTessellation ()

template<>
void	CreateVoronoiTessellation ()

template<>
void	CreateVoronoiTessellation ()

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

c_vector< double, SPACE_DIM >	GetLocationOfCellCentre (CellPtr pCell)

Node< SPACE_DIM > *	GetNodeCorrespondingToCell (CellPtr pCell)

std::pair< CellPtr, CellPtr >	CreateCellPair (CellPtr pCell1, CellPtr pCell2)

bool	IsMarkedSpring (const std::pair< CellPtr, CellPtr > &rCellPair)

void	MarkSpring (std::pair< CellPtr, CellPtr > &rCellPair)

void	UnmarkSpring (std::pair< CellPtr, CellPtr > &rCellPair)

bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)

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

virtual void	UpdateNodeLocations (double dt)

virtual bool	IsGhostNode (unsigned index)

virtual bool	IsParticle (unsigned index)

double	GetMeinekeDivisionSeparation ()

void	SetMeinekeDivisionSeparation (double divisionSeparation)

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

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 ()

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)

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 ()

void	OutputCellPopulationInfo (out_stream &rParamsFile)

bool	GetOutputResultsForChasteVisualizer ()

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

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

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

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

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

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

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

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, SPACE_DIM >	GetSizeOfCellPopulation ()

virtual bool	IsRoomToDivide (CellPtr pCell)

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

Iterator	Begin ()

Iterator	End ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
virtual void	UpdateGhostNodesAfterReMesh (NodeMap &rMap)

virtual void	Validate ()

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

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Member Functions inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_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)

Protected Attributes
VertexMesh< ELEMENT_DIM, SPACE_DIM > *	mpVoronoiTessellation

MutableMesh< ELEMENT_DIM, SPACE_DIM > *	mpMutableMesh

bool	mDeleteMesh

std::map< std::pair< unsigned, unsigned >, double >	mSpringRestLengths

bool	mUseAreaBasedDampingConstant

double	mAreaBasedDampingConstantParameter

bool	mWriteVtkAsPoints

bool	mOutputMeshInVtk

bool	mHasVariableRestLength

std::vector< std::pair< Node < SPACE_DIM > , Node < SPACE_DIM > > >	mNodePairs

Protected Attributes inherited from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >
double	mMeinekeDivisionSeparation

std::set< std::pair< CellPtr, CellPtr > >	mMarkedSprings

Protected Attributes inherited from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_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

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

Friends
class	TestMeshBasedCellPopulation

class	boost::serialization::access

Detailed Description

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

A facade class encapsulating a mesh-based 'cell population'.

Contains a group of cells and maintains the associations between cells and nodes in the mesh.

Definition at line 57 of file MeshBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation	(	MutableMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`,
		bool	validate = `true`
	)

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

There must be precisely 1 cell for each node of the mesh.

Parameters

rMesh	a mutable tetrahedral mesh
rCells	cells corresponding to the nodes of the mesh
locationIndices	an optional vector of location indices that correspond to real cells
deleteMesh	set to true if you want the cell population to free the mesh memory on destruction
validate	whether to validate the cell population

Definition at line 61 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation ( MutableMesh< ELEMENT_DIM, SPACE_DIM > & rMesh )

Constructor for use by the de-serializer.

Parameters

rMesh a mutable tetrahedral mesh.

Definition at line 94 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::~MeshBasedCellPopulation ( )

virtual

Destructor.

Definition at line 103 of file MeshBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWriter	(	boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_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.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 592 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_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.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 586 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_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.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 580 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CellPtr MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, SPACE_DIM > &	rCellDivisionVector,
		CellPtr	pParentCell
	)

virtual

Overridden AddCell() method.

Add a new cell to the cell population and update mIsGhostNode.

Parameters

pNewCell	the cell to add
rCellDivisionVector	the position in space at which to put it
pParentCell	pointer to a parent cell - this is required for mesh-based cell populations

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

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 533 of file MeshBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

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

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 127 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths ( )

Populate mSpringRestLengths by looping over all springs and calculating the current length

Definition at line 1208 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), Node< SPACE_DIM >::GetIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers ( )

Helper method for use in debugging.

Definition at line 1057 of file MeshBasedCellPopulation.cpp.

References AbstractCellCycleModel::GetCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMarkedSprings, and UNUSED_OPT.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation ( )

Create a Voronoi tessellation of the mesh.

Referenced by VolumeTrackingModifier< DIM >::UpdateCellData(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<>

void MeshBasedCellPopulation< 2, 3 >::CreateVoronoiTessellation ( )

Can't tessellate 2d meshes in 3d space yet.

Definition at line 965 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<>

void MeshBasedCellPopulation< 3 >::CreateVoronoiTessellation ( )

The cylindrical mesh is only defined in 2D, hence there is a separate definition for this method in 3D, which doesn't have the capability of dealing with periodic boundaries in 3D. This is

Todo:: #1374.

Definition at line 977 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<>

void MeshBasedCellPopulation< 1, 1 >::CreateVoronoiTessellation ( )

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 988 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<>

void MeshBasedCellPopulation< 1, 2 >::CreateVoronoiTessellation ( )

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 999 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<>

void MeshBasedCellPopulation< 1, 3 >::CreateVoronoiTessellation ( )

The VoronoiTessellation class is only defined in 2D or 3D, hence there are two definitions to this method (one templated and one not).

Definition at line 1010 of file MeshBasedCellPopulation.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings ( double springDivisionThreshold )

Divides springs longer than the given threshold

Parameters

springDivisionThreshold a given threshold

Definition at line 450 of file MeshBasedCellPopulation.cpp.

References CellPropertyCollection::RemoveProperty(), and UNSIGNED_UNSET.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter ( )

Returns: mAreaBasedDampingConstantParameter

Definition at line 1137 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Overridden GetDampingConstant() method that includes the case of a cell-area-based damping constant.

Parameters

nodeIndex the global index of this node

Returns: the damping constant for the given Cell.

We use a linear dependence of the form

new_damping_const = old_damping_const * (d0+d1*A)

where d0, d1 are parameters, A is the cell's area, and old_damping_const is the damping constant if not using mUseAreaBasedDampingConstant

Compute the parameter d1 such that d0+A*d1=1, where A is the equilibrium area of a cell (this is equal to sqrt(3.0)/4, which is a third of the area of a regular hexagon of edge length 1)

The cell area should not be too large - the next assertion is to avoid getting an infinite cell area, which may occur if area-based viscosity is chosen in the absence of ghost nodes.

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 139 of file MeshBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > MeshBasedCellPopulation< ELEMENT_DIM, SPACE_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 1179 of file MeshBasedCellPopulation.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), DiscreteSystemForceCalculator::GetSamplingAngles(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode ( unsigned index )

virtual

Overridden GetNode() method.

Parameters

index global index of the specified Node

Returns: pointer to the Node with given index.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 516 of file MeshBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( )

virtual

Overridden GetNumNodes() method.

Returns: the number of nodes in the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 522 of file MeshBasedCellPopulation.cpp.

Referenced by DiscreteSystemForceCalculator::CalculateExtremalNormalForces(), and CellwiseDataGradient< DIM >::SetupGradients().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputMeshInVtk ( )

Returns: mOutputMeshInVtk.

Definition at line 848 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength	(	unsigned	indexA,
		unsigned	indexB
	)

Returns: the rest length for a given spring

Parameters

indexA	index of first node in pair
indexB	index of second node in pair

Definition at line 1236 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), EXCEPTION, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement ( unsigned index )

Returns: the surface area of the element of mpVoronoiTessellation associated with the node with this global index in the Delaunay mesh.

This method should be called instead of calling GetVoronoiTessellation()->GetSurfaceAreaOfElement() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.

Parameters

index a node global index

Definition at line 1032 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_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 766 of file MeshBasedCellPopulation.cpp.

References AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateJacobian(), Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::GetVolume(), NEVER_REACHED, and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement ( unsigned index )

Returns: the volume (or area in 2D, or length in 1D) of the element of mpVoronoiTessellation associated with the node with this global index in the Delaunay mesh.

This method should be called instead of calling GetVoronoiTessellation()->GetVolumeOfElement() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.

Todo:: This method is somewhat redundant following the introduction of the method GetVolumeOfCell() (see #1985).

Parameters

index a node global index

Definition at line 1024 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength	(	unsigned	index1,
		unsigned	index2
	)

Returns: the length of the edge of mpVoronoiTessellation associated with the two nodes with these global indices in the Delaunay mesh.

This method should be called instead of calling GetVoronoiTessellation()->GetEdgeLength() because the global indices of Delaunay nodes and Voronoi elements may not match, e.g. if a node is a ghost node or corresponds to a Voronoi face.

Parameters

index1	a node global index
index2	a node global index

Definition at line 1040 of file MeshBasedCellPopulation.cpp.

References EXCEPTION, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

VertexMesh< ELEMENT_DIM, SPACE_DIM > * MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation ( )

Returns: a reference to mpVoronoiTessellation.

Definition at line 1017 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation.

Referenced by VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_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 1171 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWriteVtkAsPoints ( )

Returns: mWriteVtkAsPoints.

Definition at line 836 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_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 >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 555 of file MeshBasedCellPopulation.cpp.

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

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OpenWritersFiles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Outputs CellPopulation parameters to file

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1158 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells ( )

virtual

Remove all cells that are labelled as dead.

Note that this now calls MutableMesh::DeleteNodePriorToReMesh() and therefore a ReMesh(map) must be called before any element information is used.

Note also that after calling this method the cell population will be in an inconsistent state until Update() is called! 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 219 of file MeshBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh ( )

Returns: reference to mrMesh.

Definition at line 207 of file MeshBasedCellPopulation.cpp.

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), DiscreteSystemForceCalculator::GetSamplingAngles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), CellwiseDataGradient< DIM >::SetupGradients(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and DiscreteSystemForceCalculator::WriteResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const MutableMesh< ELEMENT_DIM, SPACE_DIM > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh ( ) const

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

Definition at line 213 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs ( )

virtual

Overridden rGetNodePairs method which uses the Delaunay triangulatiuon

Returns: Node pairs for force calculation.

Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1150 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs, and NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void MeshBasedCellPopulation< ELEMENT_DIM, 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 75 of file MeshBasedCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstant ( bool useAreaBasedDampingConstant )

Set method for mUseAreaBasedDampingConstant.

Parameters

useAreaBasedDampingConstant whether to use a viscosity that is linear in the cell area, rather than constant

Definition at line 120 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter ( double areaBasedDampingConstantParameter )

Set mAreaBasedDampingConstantParameter.

Parameters

areaBasedDampingConstantParameter the new value of mAreaBasedDampingConstantParameter

Definition at line 1143 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Overridden SetNode() method.

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

Parameters

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

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 133 of file MeshBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputMeshInVtk ( bool outputMeshInVtk )

Set mOutputMeshInVtk.

Parameters

outputMeshInVtk whether to write cells as points in VTK

Definition at line 842 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength	(	unsigned	indexA,
		unsigned	indexB,
		double	restLength
	)

Helper method to modify the rest length of a given spring

Parameters

indexA	index of first node in pair
indexB	index of second node in pair
restLength	the new rest length

Definition at line 1260 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair(), EXCEPTION, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetWriteVtkAsPoints ( bool writeVtkAsPoints )

Set mWriteVtkAsPoints.

Parameters

writeVtkAsPoints whether to write cells as points in VTK

Definition at line 830 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin ( )

Returns: iterator pointing to the first spring in the cell population

Definition at line 930 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd ( )

Returns: iterator pointing to one past the last spring in the cell population

Definition at line 936 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::TessellateIfNeeded ( )

Tessellates when required: if areas or volumes are needed for mUseAreaBasedDampingConstant; if a CellPopulationAreaWriter or CellVolumesWriter has been added to the population; or if Voronoi data are to be output.

Definition at line 433 of file MeshBasedCellPopulation.cpp.

References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), and GenericEventHandler< 11, CellBasedEventHandler >::EndEvent().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update ( bool hasHadBirthsOrDeaths = true )

virtual

Overridden Update(bool hasHadBirthsOrDeaths) method. Fixes up the mappings between cells and nodes.

Parameters

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

Todo:: check if there is a more efficient way of keeping track of node velocity information (#2404)

If node radii are set, then we must keep a record of these, since they will be cleared during the remeshing process. We then restore these attributes to the nodes after calling ReMesh().

At present, we check whether node radii are set by interrogating the radius of the first node in the mesh and asking if it is strictly greater than zero (the default value, as set in the NodeAttributes constructor). Hence, we assume that either ALL node radii are set, or NONE are.

Todo:: There may be a better way of checking if node radii are set (#2694)

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 278 of file MeshBasedCellPopulation.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Node< SPACE_DIM >::rGetContainingElementIndices(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateGhostNodesAfterReMesh ( NodeMap & rMap )

protectedvirtual

Update mIsGhostNode if required by a remesh.

Parameters

rMap	A map between node indices before and after remesh

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 528 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UseAreaBasedDampingConstant ( )

Returns: mUseAreaBasedDampingConstant.

Definition at line 114 of file MeshBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate ( )

protectedvirtual

Check consistency of our internal data structures. Each node must have a cell associated with it.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 187 of file MeshBasedCellPopulation.cpp.

References EXCEPTION, and SimulationTime::Instance().

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< 2 >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_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< ELEMENT_DIM, SPACE_DIM >.

Definition at line 569 of file MeshBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile ( const std::string & rDirectory )

virtual

Overridden WriteVtkResultsToFile() method.

Parameters

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

Implements AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 598 of file MeshBasedCellPopulation.cpp.

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

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 62 of file MeshBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAreaBasedDampingConstantParameter

protected

Non-dimensional parameter d0 for use in area-based damping constant calculations.

Definition at line 134 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAreaBasedDampingConstantParameter(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAreaBasedDampingConstantParameter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDeleteMesh

protected

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

Definition at line 123 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mHasVariableRestLength

protected

Whether springs have variable rest lengths.

Definition at line 143 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::vector< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > > MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mNodePairs

protected

Node pairs for force calculations.

Definition at line 146 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputMeshInVtk

protected

Whether to output the underlying MutableMesh in VTK.

Definition at line 140 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< 2 >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

MutableMesh<ELEMENT_DIM, SPACE_DIM>* MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpMutableMesh

protected

Static cast of the mesh from AbstractCellPopulation

Definition at line 117 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

VertexMesh<ELEMENT_DIM, SPACE_DIM>* MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVoronoiTessellation

protected

Pointer to a VertexMesh object that stores the Voronoi tessellation that is dual to mrMesh. The tessellation is created by calling CreateVoronoiTessellation() and can be accessed by calling GetVoronoiTessellation().

The tessellation can be used to compute the area and perimeter (in 2D) or volume and surface area (in 3D) of the Voronoi element corresponding to each node in the Delaunay mesh (including ghost nodes) by calling the methods GetVolumeOfVoronoiElement() and GetSurfaceAreaOfVoronoiElement() respectively. Each of these methods should be called rather than the relevant method on the VertexMesh. This is because the index of a given Node in mrMesh may not equal the index of the corresponding VertexElement in mpVoronoiTessellation; a map between these indices may be accessed by calling the methods GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex() and GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex() on mpVoronoiTessellation.

Definition at line 114 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< 2 >::CreateVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfVoronoiElement(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiEdgeLength(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< 2 >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::map<std::pair<unsigned,unsigned>, double> MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mSpringRestLengths

protected

Keeps track of the rest lengths of springs if these are being used in the simulation.

Definition at line 128 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mUseAreaBasedDampingConstant

protected

Whether to use a viscosity that is linear in the cell area, rather than constant.

Definition at line 131 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< 2 >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

bool MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mWriteVtkAsPoints

protected

Whether to write cells as points in VTK.

Definition at line 137 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< 2 >::serialize().

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

cell_based/src/population/MeshBasedCellPopulation.hpp
cell_based/src/population/MeshBasedCellPopulation.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

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