#include <MeshBasedCellPopulationWithGhostNodes.hpp>

Inheritance diagram for MeshBasedCellPopulationWithGhostNodes< DIM >:

Collaboration diagram for MeshBasedCellPopulationWithGhostNodes< DIM >:

Public Member Functions
	MeshBasedCellPopulationWithGhostNodes (MutableMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, double ghostSpringStiffness=15.0)

	MeshBasedCellPopulationWithGhostNodes (MutableMesh< DIM, DIM > &rMesh, double ghostSpringStiffness=15.0)

virtual	~MeshBasedCellPopulationWithGhostNodes ()

virtual TetrahedralMesh< DIM, DIM > *	GetTetrahedralMeshForPdeModifier ()

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

void	ApplyGhostForces ()

std::vector< bool > &	rGetGhostNodes ()

bool	IsGhostNode (unsigned index)

std::set< unsigned >	GetGhostNodeIndices ()

void	UpdateGhostNodesAfterReMesh (NodeMap &rMap)

c_vector< double, DIM >	CalculateForceBetweenGhostNodes (const unsigned &rNodeAGlobalIndex, const unsigned &rNodeBGlobalIndex)

CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell)

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

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

void	OutputCellPopulationParameters (out_stream &rParamsFile)

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

	MeshBasedCellPopulation (MutableMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh)

virtual	~MeshBasedCellPopulation ()

MutableMesh< ELEMENT_DIM, ELEMENT_DIM > &	rGetMesh ()

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

bool	UseAreaBasedDampingConstant ()

unsigned	AddNode (Node< ELEMENT_DIM > *pNewNode)

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

double	GetDampingConstant (unsigned nodeIndex)

void	SetAreaBasedDampingConstant (bool useAreaBasedDampingConstant)

virtual unsigned	RemoveDeadCells ()

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

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

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

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

virtual void	Update (bool hasHadBirthsOrDeaths=true)

void	TessellateIfNeeded ()

void	DivideLongSprings (double springDivisionThreshold)

Node< ELEMENT_DIM > *	GetNode (unsigned index)

unsigned	GetNumNodes ()

double	GetVolumeOfCell (CellPtr pCell)

void	CreateVoronoiTessellation ()

VertexMesh< ELEMENT_DIM, ELEMENT_DIM > *	GetVoronoiTessellation ()

double	GetVolumeOfVoronoiElement (unsigned index)

double	GetSurfaceAreaOfVoronoiElement (unsigned index)

double	GetVoronoiEdgeLength (unsigned index1, unsigned index2)

double	GetWidth (const unsigned &rDimension)

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

SpringIterator	SpringsBegin ()

SpringIterator	SpringsEnd ()

void	CheckCellPointers ()

double	GetAreaBasedDampingConstantParameter ()

void	SetAreaBasedDampingConstantParameter (double areaBasedDampingConstantParameter)

std::vector< std::pair< Node< ELEMENT_DIM > , Node< ELEMENT_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)

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)

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

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

virtual bool	IsParticle (unsigned index)

double	GetMeinekeDivisionSeparation ()

void	SetMeinekeDivisionSeparation (double divisionSeparation)

boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > >	GetCentreBasedDivisionRule ()

void	SetCentreBasedDivisionRule (boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > pCentreBasedDivisionRule)

virtual double	GetDefaultTimeStep ()

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 >())

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

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

virtual void	UpdateNodeLocations (double dt)

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 ()

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

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)

virtual bool	IsCellAttachedToLocationIndex (unsigned index)

void	SetCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	AddCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)

void	MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index)

unsigned	GetLocationIndexUsingCell (CellPtr pCell)

boost::shared_ptr< CellPropertyRegistry >	GetCellPropertyRegistry ()

void	SetDefaultCellMutationStateAndProliferativeTypeOrdering ()

c_vector< double, SPACE_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

void	CloseWritersFiles ()

virtual void	AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)=0

virtual void	AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter)=0

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

void	OutputCellPopulationInfo (out_stream &rParamsFile)

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

bool	GetOutputResultsForChasteVisualizer ()

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	AcceptCellWritersAcrossPopulation ()

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

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)

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

void	SetGhostNodes (const std::set< unsigned > &rGhostNodeIndices)

void	Validate ()

Private Attributes
std::vector< bool >	mIsGhostNode

double	mGhostSpringStiffness

Friends
class	TestMeshBasedCellPopulationWithGhostNodes

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from MeshBasedCellPopulation< DIM >
VertexMesh< ELEMENT_DIM, ELEMENT_DIM > *	mpVoronoiTessellation

MutableMesh< ELEMENT_DIM, ELEMENT_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< ELEMENT_DIM > , Node< ELEMENT_DIM > > >	mNodePairs

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

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

boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > >	mpCentreBasedDivisionRule

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

Detailed Description

template<unsigned DIM>
class MeshBasedCellPopulationWithGhostNodes< DIM >

A facade class encapsulating a mesh-based cell population with ghost nodes.

If simulating a crypt with a mesh-based cell population, the mesh should be surrounded by at least one layer of ghost nodes. These are nodes which do not correspond to a cell, but are necessary for remeshing (because the remesher tries to create a convex hull of the set of nodes) and visualization purposes. The MeshBasedCellPopulationWithGhostNodes class deals with these ghost nodes, hiding the 'ghost nodes' concept from the OffLatticeSimulation class, so the latter only ever deals with real cells.

Definition at line 56 of file MeshBasedCellPopulationWithGhostNodes.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes	(	MutableMesh< DIM, DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`,
		double	ghostSpringStiffness = `15.0`
	)

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

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
ghostSpringStiffness	spring stiffness used to move the ghost nodes defaults to 15.0.

Definition at line 40 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulation< DIM >::GetNode(), MeshBasedCellPopulation< DIM >::GetNumNodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode, MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::Validate().

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

template<unsigned DIM>

MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes	(	MutableMesh< DIM, DIM > &	rMesh,
		double	ghostSpringStiffness = `15.0`
	)

Constructor for use by the de-serializer.

Parameters

rMesh	a mutable tetrahedral mesh.
ghostSpringStiffness	spring stiffness used to move the ghost nodes defaults to 15.0.

Definition at line 80 of file MeshBasedCellPopulationWithGhostNodes.cpp.

template<unsigned DIM>

MeshBasedCellPopulationWithGhostNodes< DIM >::~MeshBasedCellPopulationWithGhostNodes ( )

virtual

Empty destructor so archiving works with static libraries.

Definition at line 88 of file MeshBasedCellPopulationWithGhostNodes.cpp.

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

Member Function Documentation

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::AcceptCellWritersAcrossPopulation ( )

protectedvirtual

Overridden method

Calls AcceptCellWriter across the whole population, iterating in an appropriate way to skip ghost nodes.

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 253 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulation< DIM >::AcceptCellWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), MeshBasedCellPopulationWithGhostNodes< DIM >::IsGhostNode(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, and MeshBasedCellPopulation< DIM >::rGetMesh().

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

template<unsigned DIM>

CellPtr MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell	(	CellPtr	pNewCell,
		CellPtr	pParentCell
	)

virtual

Overridden AddCell() method.

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

Parameters

pNewCell	the cell to add
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 MeshBasedCellPopulation< DIM >.

Definition at line 160 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< DIM >::GetNumNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

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

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::ApplyGhostForces ( )

Applies the appropriate force to each ghost node in the population. Called by AbstractNumericalMethod.

Definition at line 274 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd(), MeshBasedCellPopulation< DIM >::GetNumNodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

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

template<unsigned DIM>

c_vector< double, DIM > MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes	(	const unsigned &	rNodeAGlobalIndex,
		const unsigned &	rNodeBGlobalIndex
	)

This method is used to calculate the force between GHOST nodes.

Parameters

rNodeAGlobalIndex
rNodeBGlobalIndex

Returns: The force exerted on Node A by Node B.

Definition at line 141 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulation< DIM >::GetNode(), MeshBasedCellPopulationWithGhostNodes< DIM >::mGhostSpringStiffness, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::ApplyGhostForces(), and MeshBasedCellPopulationWithGhostNodes< DIM >::serialize().

template<unsigned DIM>

std::set< unsigned > MeshBasedCellPopulationWithGhostNodes< DIM >::GetGhostNodeIndices ( )

Returns: the indices of those nodes that are ghost nodes.

Definition at line 112 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

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

template<unsigned DIM>

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

virtual

Overridden GetNeighbouringLocationIndices() method.

Given a cell, returns the set of location indices corresponding to neighbouring cells.

Parameters

pCell a cell

Returns: the set of neighbouring location indices.

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 230 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), and MeshBasedCellPopulationWithGhostNodes< DIM >::IsGhostNode().

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

template<unsigned DIM>

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

virtual

Overridden GetTetrahedralMeshForPdeModifier() method.

Returns: a shared pointer to mrMesh.

This method is called by AbstractGrowingDomainPdeModifier.

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 93 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References EXCEPTION, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

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

template<unsigned DIM>

bool MeshBasedCellPopulationWithGhostNodes< DIM >::IsGhostNode ( unsigned index )

virtual

Overridden IsGhostNode() method.

Find if a given node is a ghost node. The abstract method always returns false but is overridden in subclasses.

Parameters

index the global index of a specified node

Returns: whether the node is a ghost node

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 106 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::AcceptCellWritersAcrossPopulation(), MeshBasedCellPopulationWithGhostNodes< DIM >::GetNeighbouringLocationIndices(), MeshBasedCellPopulationWithGhostNodes< DIM >::serialize(), and MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< 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 MeshBasedCellPopulation< DIM >.

Definition at line 322 of file MeshBasedCellPopulationWithGhostNodes.cpp.

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

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

template<unsigned DIM>

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

virtual

Outputs CellPopulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 411 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, MeshBasedCellPopulationWithGhostNodes< DIM >::mGhostSpringStiffness, and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

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

template<unsigned DIM>

std::vector< bool > & MeshBasedCellPopulationWithGhostNodes< DIM >::rGetGhostNodes ( )

Returns: mIsGhostNode.

Definition at line 100 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

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

template<unsigned DIM>

template<class Archive >

void MeshBasedCellPopulationWithGhostNodes< 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 85 of file MeshBasedCellPopulationWithGhostNodes.hpp.

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes ( const std::set< unsigned > & rGhostNodeIndices )

private

Set the ghost nodes by taking in a set of which nodes indices are ghost nodes.

Parameters

rGhostNodeIndices set of node indices corresponding to ghost nodes

Definition at line 126 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and MeshBasedCellPopulationWithGhostNodes< DIM >::Validate().

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::serialize().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostNodesAfterReMesh ( NodeMap & rMap )

virtual

Update mIsGhostNode if required by a remesh.

Parameters

rMap	A map between node indices before and after remesh

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 209 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References NodeMap::GetNewIndex(), MeshBasedCellPopulation< DIM >::GetNumNodes(), NodeMap::GetSize(), NodeMap::IsDeleted(), and MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

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

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::Validate ( )

privatevirtual

This is called after a cell population has been constructed to check the user gave consistent instructions. Check consistency of our internal data structures: Each node must have a cell associated with it OR must be a ghost node.

It is called after cells are added or removed from MeshBasedCellPopulation as it is an overridden virtual method.

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 180 of file MeshBasedCellPopulationWithGhostNodes.cpp.

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

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::serialize(), and MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes().

template<unsigned DIM>

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

virtual

Overridden WriteVtkResultsToFile() method.

Parameters

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