MeshBasedCellPopulation< DIM > Class Template Reference

#include <MeshBasedCellPopulation.hpp>

Inherits AbstractCentreBasedCellPopulation< DIM >.

Inherited by MeshBasedCellPopulationWithGhostNodes< DIM >.

Collaboration diagram for MeshBasedCellPopulation< DIM >:

Classes
class	SpringIterator
Public Member Functions
	MeshBasedCellPopulation (MutableMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)
	MeshBasedCellPopulation (MutableMesh< DIM, DIM > &rMesh)
	~MeshBasedCellPopulation ()
MutableMesh< DIM, DIM > &	rGetMesh ()
const MutableMesh< DIM, DIM > &	rGetMesh () const
bool	UseAreaBasedDampingConstant ()
void	SetOutputVoronoiData (bool outputVoronoiData)
unsigned	AddNode (Node< DIM > *pNewNode)
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)
double	GetDampingConstant (unsigned nodeIndex)
void	SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)
virtual unsigned	RemoveDeadCells ()
virtual CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)
void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
void	CloseOutputFiles ()
void	WriteResultsToFiles ()
virtual void	Update (bool hasHadBirthsOrDeaths=true)
void	TessellateIfNeeded ()
Node< DIM > *	GetNode (unsigned index)
unsigned	GetNumNodes ()
virtual void	WriteVtkResultsToFile ()
void	WriteVoronoiResultsToFile ()
void	WriteCellPopulationVolumeResultsToFile ()
void	WriteCellVolumeResultsToFile ()
void	CreateVoronoiTessellation ()
VertexMesh< DIM, 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 ()
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)
double	GetAreaBasedDampingConstantParameter ()
void	SetAreaBasedDampingConstantParameter (double areaBasedDampingConstantParameter)
bool	GetOutputVoronoiData ()
bool	GetOutputCellPopulationVolumes ()
void	SetOutputCellPopulationVolumes (bool outputCellPopulationVolumes)
void	OutputCellPopulationParameters (out_stream &rParamsFile)
void	SetWriteVtkAsPoints (bool writeVtkAsPoints)
bool	GetWriteVtkAsPoints ()
std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)
template<>
void	CreateVoronoiTessellation ()
Protected Member Functions
virtual void	UpdateGhostNodesAfterReMesh (NodeMap &rMap)
virtual void	Validate ()
Protected Attributes
MutableMesh< DIM, DIM > &	mrMesh
VertexMesh< DIM, DIM > *	mpVoronoiTessellation
bool	mDeleteMesh
std::set< std::pair< CellPtr, CellPtr > >	mMarkedSprings
out_stream	mpVizElementsFile
out_stream	mpVoronoiFile
out_stream	mpCellPopulationVolumesFile
bool	mUseAreaBasedDampingConstant
double	mAreaBasedDampingConstantParameter
bool	mOutputVoronoiData
bool	mOutputCellPopulationVolumes
bool	mWriteVtkAsPoints
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 DIM>
class MeshBasedCellPopulation< 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 52 of file MeshBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

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 40 of file MeshBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractCellPopulation< DIM >::mCells, MeshBasedCellPopulation< DIM >::mrMesh, and MeshBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

MeshBasedCellPopulation< DIM >::MeshBasedCellPopulation ( MutableMesh< DIM, DIM > & rMesh ) [inline]

Constructor for use by the de-serializer.

Parameters:

rMesh

a mutable tetrahedral mesh.

Definition at line 65 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mDeleteMesh, and MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

template<unsigned DIM>

MeshBasedCellPopulation< DIM >::~MeshBasedCellPopulation ( ) [inline]

Destructor.

Definition at line 73 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mDeleteMesh, MeshBasedCellPopulation< DIM >::mpVoronoiTessellation, and MeshBasedCellPopulation< DIM >::mrMesh.

Member Function Documentation

template<unsigned DIM>

CellPtr MeshBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell
	)			`[inline, 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< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 359 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::CreateCellPair(), and MeshBasedCellPopulation< DIM >::MarkSpring().

template<unsigned DIM>

unsigned MeshBasedCellPopulation< DIM >::AddNode ( Node< DIM > * pNewNode ) [inline, 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< DIM >.

Definition at line 97 of file MeshBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and MeshBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::CheckCellPointers ( ) [inline]

Helper method for use in debugging.

Definition at line 1015 of file MeshBasedCellPopulation.cpp.

References AbstractCellCycleModel::GetCell(), AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, and MeshBasedCellPopulation< DIM >::mMarkedSprings.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::CloseOutputFiles ( ) [inline, virtual]

Overridden CloseOutputFiles() method.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 399 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes, MeshBasedCellPopulation< DIM >::mOutputVoronoiData, MeshBasedCellPopulation< DIM >::mpCellPopulationVolumesFile, MeshBasedCellPopulation< DIM >::mpVizElementsFile, and MeshBasedCellPopulation< DIM >::mpVoronoiFile.

template<unsigned DIM>

std::pair< CellPtr, CellPtr > MeshBasedCellPopulation< DIM >::CreateCellPair	(	CellPtr	pCell1,
		CellPtr	pCell2
	)			`[inline]`

Helper method that returns a set of pointers to two given Cells. Used by the spring marking routines. Elements in the returned pair are ordered by cell ID number - the cell in the pair will have a smaller ID.

Parameters:

	pCell1	a Cell
	pCell2	a Cell

Definition at line 1094 of file MeshBasedCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< DIM >::AddCell(), CryptProjectionForce::CalculateForceBetweenNodes(), and GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::CreateOutputFiles	(	const std::string &	rDirectory,
		bool	cleanOutputDirectory
	)			`[inline, virtual]`

Overridden CreateOutputFiles() method.

Parameters:

	rDirectory	pathname of the output directory, relative to where Chaste output is stored
	cleanOutputDirectory	whether to delete the contents of the output directory prior to output file creation

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 381 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes, MeshBasedCellPopulation< DIM >::mOutputVoronoiData, MeshBasedCellPopulation< DIM >::mpCellPopulationVolumesFile, MeshBasedCellPopulation< DIM >::mpVizElementsFile, MeshBasedCellPopulation< DIM >::mpVoronoiFile, and OutputFileHandler::OpenOutputFile().

template<>

void MeshBasedCellPopulation< 3 >::CreateVoronoiTessellation ( ) [inline]

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 957 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mpVoronoiTessellation, and MeshBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::CreateVoronoiTessellation ( )

Create a Voronoi tessellation of the mesh.

Referenced by VolumeTrackedOffLatticeSimulation< DIM >::PostSolve(), and MeshBasedCellPopulation< DIM >::TessellateIfNeeded().

template<unsigned DIM>

double MeshBasedCellPopulation< DIM >::GetAreaBasedDampingConstantParameter ( ) [inline]

Returns:: mAreaBasedDampingConstantParameter

Definition at line 1142 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mAreaBasedDampingConstantParameter.

template<unsigned DIM>

double MeshBasedCellPopulation< DIM >::GetDampingConstant ( unsigned nodeIndex ) [inline, 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)/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< DIM >.

Definition at line 109 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::GetVolumeOfVoronoiElement(), MeshBasedCellPopulation< DIM >::mAreaBasedDampingConstantParameter, and MeshBasedCellPopulation< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

std::set< unsigned > MeshBasedCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned index ) [inline, virtual]

Overridden GetNeighbouringNodeIndices() method.

Parameters:

index

the node index

Returns:: the set of neighbouring node indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 1199 of file MeshBasedCellPopulation.cpp.

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

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), and DiscreteSystemForceCalculator::GetSamplingAngles().

template<unsigned DIM>

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

Overridden GetNode() method.

Parameters:

index

global index of the specified Node

Returns:: pointer to the Node with given index.

Implements AbstractCellPopulation< DIM >.

Definition at line 342 of file MeshBasedCellPopulation.cpp.

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

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes(), MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MeshBasedCellPopulation< DIM >::WriteResultsToFiles(), and MeshBasedCellPopulation< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

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

Overridden GetNumNodes() method.

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

Implements AbstractCellPopulation< DIM >.

Definition at line 348 of file MeshBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), and MeshBasedCellPopulation< DIM >::mrMesh.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell(), DiscreteSystemForceCalculator::CalculateExtremalNormalForces(), MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes(), CellwiseDataGradient< DIM >::SetupGradients(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostNodesAfterReMesh(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::GetOutputCellPopulationVolumes ( ) [inline]

Returns:: mOutputCellPopulationVolumes

Definition at line 1167 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes.

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::GetOutputVoronoiData ( ) [inline]

Returns:: mOutputVoronoiData

Definition at line 1155 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mOutputVoronoiData.

template<unsigned DIM>

double MeshBasedCellPopulation< DIM >::GetSurfaceAreaOfVoronoiElement ( unsigned index ) [inline]

Get 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 990 of file MeshBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(), and MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

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

template<unsigned DIM>

double MeshBasedCellPopulation< DIM >::GetVolumeOfVoronoiElement ( unsigned index ) [inline]

Get 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.

Parameters:

index

a node global index

Definition at line 982 of file MeshBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(), and MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

Referenced by MeshBasedCellPopulation< DIM >::GetDampingConstant(), and VolumeTrackedOffLatticeSimulation< DIM >::PostSolve().

template<unsigned DIM>

double MeshBasedCellPopulation< DIM >::GetVoronoiEdgeLength	(	unsigned	index1,
		unsigned	index2
	)			`[inline]`

Get 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 998 of file MeshBasedCellPopulation.cpp.

References EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(), and MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

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

template<unsigned DIM>

VertexMesh< DIM, DIM > * MeshBasedCellPopulation< DIM >::GetVoronoiTessellation ( ) [inline]

Get a reference to mpVoronoiTessellation.

Definition at line 975 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

template<unsigned DIM>

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

Overridden GetWidth() method.

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

Parameters:

rDimension

a dimension (0,1 or 2)

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

Implements AbstractCellPopulation< DIM >.

Definition at line 1191 of file MeshBasedCellPopulation.cpp.

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

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::GetWriteVtkAsPoints ( ) [inline]

Returns:: mWriteVtkAsPoints.

Definition at line 840 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mWriteVtkAsPoints.

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::IsMarkedSpring ( const std::pair< CellPtr, CellPtr > & rCellPair ) [inline]

Parameters:

rCellPair

a set of pointers to Cells

Returns:: whether the spring between two given cells is marked.

Definition at line 1115 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mMarkedSprings.

Referenced by CryptProjectionForce::CalculateForceBetweenNodes(), and GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::MarkSpring ( std::pair< CellPtr, CellPtr > & rCellPair ) [inline]

Mark the spring between the given cells.

Parameters:

rCellPair

a set of pointers to Cells

Definition at line 1124 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mMarkedSprings.

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

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs CellPopulation parameters to file

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 1179 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mAreaBasedDampingConstantParameter, MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes, MeshBasedCellPopulation< DIM >::mOutputVoronoiData, and MeshBasedCellPopulation< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

unsigned MeshBasedCellPopulation< DIM >::RemoveDeadCells ( ) [inline, 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< DIM >.

Definition at line 184 of file MeshBasedCellPopulation.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, MeshBasedCellPopulation< DIM >::mMarkedSprings, and MeshBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

const MutableMesh< DIM, DIM > & MeshBasedCellPopulation< DIM >::rGetMesh ( ) const [inline]

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

Definition at line 178 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mrMesh.

template<unsigned DIM>

MutableMesh< DIM, DIM > & MeshBasedCellPopulation< DIM >::rGetMesh ( ) [inline]

Returns:: reference to mrMesh.

Definition at line 172 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mrMesh.

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), DiscreteSystemForceCalculator::GetSamplingAngles(), CellwiseDataGradient< DIM >::SetupGradients(), and DiscreteSystemForceCalculator::WriteResultsToFile().

template<unsigned DIM>

template<class Archive >

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

Serialize the object and its member variables.

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

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

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 70 of file MeshBasedCellPopulation.hpp.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::SetAreaBasedDampingConstant ( bool useAreaBasedDampingConstant ) [inline]

Set method for mUseAreaBasedDampingConstant.

Parameters:

useAreaBasedDampingConstant

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

Definition at line 90 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::SetAreaBasedDampingConstantParameter ( double areaBasedDampingConstantParameter ) [inline]

Set mAreaBasedDampingConstantParameter.

Parameters:

areaBasedDampingConstantParameter

the new value of mAreaBasedDampingConstantParameter

Definition at line 1148 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mAreaBasedDampingConstantParameter.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)			`[inline, 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< DIM >.

Definition at line 103 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mrMesh, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::SetOutputCellPopulationVolumes ( bool outputCellPopulationVolumes ) [inline]

Set mOutputCellPopulationVolumes.

Parameters:

outputCellPopulationVolumes

the new value of mOutputCellPopulationVolumes

Definition at line 1173 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::SetOutputVoronoiData ( bool outputVoronoiData ) [inline]

Set method for mOutputVoronoiData.

Parameters:

outputVoronoiData

whether to output cell area and perimeter information

Definition at line 1161 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mOutputVoronoiData.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::SetWriteVtkAsPoints ( bool writeVtkAsPoints ) [inline]

Set mWriteVtkAsPoints.

Parameters:

writeVtkAsPoints

whether to write cells as points in VTK

Definition at line 834 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mWriteVtkAsPoints.

template<unsigned DIM>

MeshBasedCellPopulation< DIM >::SpringIterator MeshBasedCellPopulation< DIM >::SpringsBegin ( ) [inline]

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

Definition at line 922 of file MeshBasedCellPopulation.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), and MeshBasedCellPopulation< DIM >::mrMesh.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), AbstractTwoBodyInteractionForce< DIM >::AddForceContribution(), and DeltaNotchOffLatticeSimulation< DIM >::PostSolve().

template<unsigned DIM>

MeshBasedCellPopulation< DIM >::SpringIterator MeshBasedCellPopulation< DIM >::SpringsEnd ( ) [inline]

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

Definition at line 928 of file MeshBasedCellPopulation.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd(), and MeshBasedCellPopulation< DIM >::mrMesh.

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), AbstractTwoBodyInteractionForce< DIM >::AddForceContribution(), and DeltaNotchOffLatticeSimulation< DIM >::PostSolve().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::TessellateIfNeeded ( ) [inline]

Tessellates when required If areas or volumes are needed for mUseAreaBasedDampingConstant or mOutputCellPopulationVolumes or mOutputCellVolumes If Voronoi data is to be output

Definition at line 328 of file MeshBasedCellPopulation.cpp.

References GenericEventHandler< 10, CellBasedEventHandler >::BeginEvent(), MeshBasedCellPopulation< DIM >::CreateVoronoiTessellation(), GenericEventHandler< 10, CellBasedEventHandler >::EndEvent(), MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes, AbstractCellPopulation< DIM >::mOutputCellVolumes, MeshBasedCellPopulation< DIM >::mOutputVoronoiData, and MeshBasedCellPopulation< DIM >::mUseAreaBasedDampingConstant.

Referenced by MeshBasedCellPopulation< DIM >::Update(), and MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::UnmarkSpring ( std::pair< CellPtr, CellPtr > & rCellPair ) [inline]

Stop marking the spring between the given cells.

Parameters:

rCellPair

a set of pointers to Cells

Definition at line 1133 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mMarkedSprings.

Referenced by CryptProjectionForce::CalculateForceBetweenNodes(), and GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [inline, 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

Implements AbstractCellPopulation< DIM >.

Definition at line 241 of file MeshBasedCellPopulation.cpp.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::UpdateGhostNodesAfterReMesh ( NodeMap & rMap ) [inline, protected, virtual]

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 354 of file MeshBasedCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::UseAreaBasedDampingConstant ( ) [inline]

Returns:: mUseAreaBasedDampingConstant.

Definition at line 84 of file MeshBasedCellPopulation.cpp.

References MeshBasedCellPopulation< DIM >::mUseAreaBasedDampingConstant.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::Validate ( ) [inline, protected, virtual]

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

Implements AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 152 of file MeshBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), EXCEPTION, AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), and MeshBasedCellPopulation< DIM >::GetNumNodes().

Referenced by MeshBasedCellPopulation< DIM >::MeshBasedCellPopulation(), MeshBasedCellPopulation< 2 >::serialize(), and MeshBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::WriteCellPopulationVolumeResultsToFile ( ) [inline]

Write the current total area (in 2D) or volume (in 3D) of mrMesh, and of the set of apoptotic cells in the cell population (using mpVoronoiTessellation), to mpCellPopulationVolumesFile.

Definition at line 743 of file MeshBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), SimulationTime::GetTime(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), SimulationTime::Instance(), AbstractCentreBasedCellPopulation< DIM >::IsGhostNode(), AbstractCellPopulation< DIM >::mLocationCellMap, MeshBasedCellPopulation< DIM >::mpCellPopulationVolumesFile, MeshBasedCellPopulation< DIM >::mpVoronoiTessellation, and MeshBasedCellPopulation< DIM >::mrMesh.

Referenced by MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile ( ) [inline, virtual]

Overridden WriteCellVolumeResultsToFile() method.

Implements AbstractCellPopulation< DIM >.

Definition at line 785 of file MeshBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), MeshBasedCellPopulation< DIM >::GetNode(), SimulationTime::GetTime(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), SimulationTime::Instance(), AbstractCentreBasedCellPopulation< DIM >::IsGhostNode(), AbstractCellPopulation< DIM >::mLocationCellMap, AbstractCellPopulation< DIM >::mpCellVolumesFile, and MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::WriteResultsToFiles ( ) [inline, virtual]

Overridden WriteResultsToFiles() method.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 416 of file MeshBasedCellPopulation.cpp.

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::WriteVoronoiResultsToFile ( ) [inline]

Write the current index and location of each node in mrMesh (including ghost nodes), as well as the area and perimeter (in 2D) or volume and surface area (in 3D) of its corresponding element in mpVoronoiTessellation, to mpVoronoiFile.

Definition at line 709 of file MeshBasedCellPopulation.cpp.

References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), MeshBasedCellPopulation< DIM >::GetNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), SimulationTime::GetTime(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), SimulationTime::Instance(), MeshBasedCellPopulation< DIM >::mpVoronoiFile, and MeshBasedCellPopulation< DIM >::mpVoronoiTessellation.

Referenced by MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

void MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile ( ) [inline, virtual]

Overridden WriteVtkResultsToFile() method.

Implements AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 476 of file MeshBasedCellPopulation.cpp.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 57 of file MeshBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

double MeshBasedCellPopulation< DIM >::mAreaBasedDampingConstantParameter [protected]

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

Definition at line 139 of file MeshBasedCellPopulation.hpp.

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

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::mDeleteMesh [protected]

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

Definition at line 117 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::MeshBasedCellPopulation(), and MeshBasedCellPopulation< DIM >::~MeshBasedCellPopulation().

template<unsigned DIM>

std::set<std::pair<CellPtr,CellPtr> > MeshBasedCellPopulation< DIM >::mMarkedSprings [protected]

Special springs that we want to keep track of for some reason. Currently used to track cells in the process of dividing (which are represented as two cells joined by a shorter spring).

Definition at line 124 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::CheckCellPointers(), MeshBasedCellPopulation< DIM >::IsMarkedSpring(), MeshBasedCellPopulation< DIM >::MarkSpring(), MeshBasedCellPopulation< DIM >::RemoveDeadCells(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< DIM >::UnmarkSpring(), and MeshBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::mOutputCellPopulationVolumes [protected]

Whether to write the cell population volumes (in 3D) or areas (in 2D) to file.

Definition at line 145 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::CloseOutputFiles(), MeshBasedCellPopulation< DIM >::CreateOutputFiles(), MeshBasedCellPopulation< DIM >::GetOutputCellPopulationVolumes(), MeshBasedCellPopulation< DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< DIM >::SetOutputCellPopulationVolumes(), MeshBasedCellPopulation< DIM >::TessellateIfNeeded(), and MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

bool MeshBasedCellPopulation< DIM >::mOutputVoronoiData [protected]

Whether to write cell volume and surface area (in 3D) or area and perimeter (in 2D) information to file.

Definition at line 142 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::CloseOutputFiles(), MeshBasedCellPopulation< DIM >::CreateOutputFiles(), MeshBasedCellPopulation< DIM >::GetOutputVoronoiData(), MeshBasedCellPopulation< DIM >::OutputCellPopulationParameters(), MeshBasedCellPopulation< 2 >::serialize(), MeshBasedCellPopulation< DIM >::SetOutputVoronoiData(), MeshBasedCellPopulation< DIM >::TessellateIfNeeded(), and MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream MeshBasedCellPopulation< DIM >::mpCellPopulationVolumesFile [protected]

Results file for cell population volume (in 3D) or area (in 2D) data.

Definition at line 133 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::CloseOutputFiles(), MeshBasedCellPopulation< DIM >::CreateOutputFiles(), and MeshBasedCellPopulation< DIM >::WriteCellPopulationVolumeResultsToFile().

template<unsigned DIM>

out_stream MeshBasedCellPopulation< DIM >::mpVizElementsFile [protected]

Results file for elements.

Definition at line 127 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::CloseOutputFiles(), MeshBasedCellPopulation< DIM >::CreateOutputFiles(), and MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream MeshBasedCellPopulation< DIM >::mpVoronoiFile [protected]

Results file for Voronoi data.

Definition at line 130 of file MeshBasedCellPopulation.hpp.

Referenced by MeshBasedCellPopulation< DIM >::CloseOutputFiles(), MeshBasedCellPopulation< DIM >::CreateOutputFiles(), and MeshBasedCellPopulation< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

VertexMesh<DIM, DIM>* MeshBasedCellPopulation< 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 111 of file MeshBasedCellPopulation.hpp.