#include <NodeBasedCellPopulation.hpp>

Inheritance diagram for NodeBasedCellPopulation< DIM >:

Collaboration diagram for NodeBasedCellPopulation< DIM >:

Public Member Functions
void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)

	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)

	NodeBasedCellPopulation (NodesOnlyMesh< DIM > &rMesh)

virtual	~NodeBasedCellPopulation ()

NodesOnlyMesh< DIM > &	rGetMesh ()

const NodesOnlyMesh< DIM > &	rGetMesh () const

virtual TetrahedralMesh< DIM, DIM > *	GetTetrahedralMeshForPdeModifier ()

unsigned	GetNumNodes ()

virtual CellPtr	GetCellUsingLocationIndex (unsigned index)

Node< DIM > *	GetNode (unsigned index)

unsigned	RemoveDeadCells ()

void	Clear ()

void	Update (bool hasHadBirthsOrDeaths=true)

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

void	OutputCellPopulationParameters (out_stream &rParamsFile)

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

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

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

double	GetMechanicsCutOffLength ()

bool	GetUseVariableRadii ()

void	SetUseVariableRadii (bool useVariableRadii=true)

void	SetLoadBalanceMesh (bool loadBalanceMesh)

void	SetLoadBalanceFrequency (unsigned loadBalanceFrequency)

double	GetWidth (const unsigned &rDimension)

c_vector< double, DIM >	GetSizeOfCellPopulation ()

std::set< unsigned >	GetNodesWithinNeighbourhoodRadius (unsigned index, double neighbourhoodRadius)

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

virtual CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell)

double	GetVolumeOfCell (CellPtr pCell)

void	SendCellsToNeighbourProcesses ()

void	NonBlockingSendCellsToNeighbourProcesses ()

void	GetReceivedCells ()

std::pair< CellPtr, Node< DIM > * >	GetCellNodePair (unsigned nodeIndex)

void	AddReceivedCells ()

virtual void	UpdateCellProcessLocation ()

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

c_vector< double, ELEMENT_DIM >	GetLocationOfCellCentre (CellPtr pCell)

Node< ELEMENT_DIM > *	GetNodeCorrespondingToCell (CellPtr pCell)

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

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

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

virtual double	GetDampingConstant (unsigned nodeIndex)

virtual bool	IsGhostNode (unsigned index)

virtual bool	IsParticle (unsigned index)

double	GetMeinekeDivisionSeparation ()

void	SetMeinekeDivisionSeparation (double divisionSeparation)

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

void	SetCentreBasedDivisionRule (boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, ELEMENT_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)

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

void	SetDampingConstantNormal (double dampingConstantNormal)

void	SetDampingConstantMutant (double dampingConstantMutant)

void	SetAbsoluteMovementThreshold (double absoluteMovementThreshold)

double	GetAbsoluteMovementThreshold ()

double	GetDampingConstantNormal ()

double	GetDampingConstantMutant ()

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

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

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

AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

std::list< CellPtr > &	rGetCells ()

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

std::vector< unsigned >	GetCellMutationStateCount ()

std::vector< unsigned >	GetCellProliferativeTypeCount ()

std::vector< unsigned >	GetCellCyclePhaseCount ()

unsigned	GetNumRealCells ()

unsigned	GetNumAllCells ()

void	SetCellAncestorsToLocationIndices ()

std::set< unsigned >	GetCellAncestors ()

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	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

void	CloseWritersFiles ()

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

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

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

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

void	OutputCellPopulationInfo (out_stream &rParamsFile)

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

bool	GetOutputResultsForChasteVisualizer ()

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	UpdateParticlesAfterReMesh (NodeMap &rMap)

virtual void	Validate ()

Protected Member Functions inherited from AbstractCentreBasedCellPopulation< DIM >
	AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_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
NodesOnlyMesh< DIM > *	mpNodesOnlyMesh

Protected Attributes inherited from AbstractCentreBasedCellPopulation< DIM >
double	mMeinekeDivisionSeparation

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

boost::shared_ptr < AbstractCentreBasedDivisionRule < ELEMENT_DIM, ELEMENT_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

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

unsigned	AddNode (Node< DIM > *pNewNode)

void	AddMovedCell (CellPtr pCell, boost::shared_ptr< Node< DIM > > pNode)

void	DeleteMovedCell (unsigned index)

void	RefreshHaloCells ()

void	AddNodeAndCellToSendRight (unsigned nodeIndex)

void	AddNodeAndCellToSendLeft (unsigned nodeIndex)

void	AddCellsToSendRight (std::vector< unsigned > &cellLocationIndices)

void	AddCellsToSendLeft (std::vector< unsigned > &cellLocationIndices)

void	AddReceivedHaloCells ()

void	AddHaloCell (CellPtr pCell, boost::shared_ptr< Node< DIM > > pNode)

void	UpdateMapsAfterRemesh (NodeMap &map)

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

Private Attributes
c_vector< double, DIM >	mMinSpatialPositions

c_vector< double, DIM >	mMaxSpatialPositions

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

bool	mDeleteMesh

bool	mUseVariableRadii

std::vector< std::pair < CellPtr, Node< DIM > * > >	mCellsToSendRight

std::vector< std::pair < CellPtr, Node< DIM > * > >	mCellsToSendLeft

boost::shared_ptr< std::vector < std::pair< CellPtr, Node < DIM > * > > >	mpCellsRecvRight

boost::shared_ptr< std::vector < std::pair< CellPtr, Node < DIM > * > > >	mpCellsRecvLeft

ObjectCommunicator < std::vector< std::pair < CellPtr, Node< DIM > * > > >	mRightCommunicator

ObjectCommunicator < std::vector< std::pair < CellPtr, Node< DIM > * > > >	mLeftCommunicator

std::vector< CellPtr >	mHaloCells

std::map< unsigned, CellPtr >	mLocationHaloCellMap

std::map< CellPtr, unsigned >	mHaloCellLocationMap

bool	mLoadBalanceMesh

unsigned	mLoadBalanceFrequency

Static Private Attributes
static const unsigned	mCellCommunicationTag = 123

Friends
class	TestNodeBasedCellPopulation

class	TestNodeBasedCellPopulationParallelMethods

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class NodeBasedCellPopulation< DIM >

A NodeBasedCellPopulation is a CellPopulation consisting of only nodes in space with associated cells. There are no elements and no mesh.

Definition at line 52 of file NodeBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation	(	NodesOnlyMesh< DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`,
		bool	validate = `true`
	)

Default constructor.

Note that the cell population will take responsibility for freeing the memory used by the nodes.

Parameters

rMesh	a mutable nodes-only mesh
rCells	a vector of cells
locationIndices	an optional vector of location indices that correspond to real cells
deleteMesh	whether to delete nodes-only mesh in destructor
validate	whether to call Validate() in the constructor or not

Definition at line 41 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation ( NodesOnlyMesh< DIM > & rMesh )

Constructor for use by the de-serializer.

Parameters

rMesh a mutable nodes-only mesh

Definition at line 61 of file NodeBasedCellPopulation.cpp.

References NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

template<unsigned DIM>

NodeBasedCellPopulation< DIM >::~NodeBasedCellPopulation ( )

virtual

Destructor.

Frees all our node memory.

Definition at line 72 of file NodeBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

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

virtual

A virtual method to accept a cell writer so it can write data from this object to file.

Parameters

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

Definition at line 317 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

A virtual method to accept a cell population count writer so it can write data from this object to file.

Parameters

pPopulationCountWriter the population count writer.

Definition at line 311 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

A virtual method to accept a cell population writer so it can write data from this object to file.

Parameters

pPopulationWriter the population writer.

Definition at line 305 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Overridden AddCell() method.

Add a new cell to the cell population and update the vector of cell radii in the NodesOnlyMesh.

Parameters

pNewCell	the cell to add
pParentCell	pointer to a parent cell - this is required for node-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)

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 698 of file NodeBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), Node< SPACE_DIM >::GetRadius(), and Node< SPACE_DIM >::SetRadius().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddCellsToSendLeft ( std::vector< unsigned > & cellLocationIndices )

private

Add a collection of cells to send left

Parameters

cellLocationIndices the list of location indices of cells to send.

Definition at line 935 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddCellsToSendRight ( std::vector< unsigned > & cellLocationIndices )

private

Add a collection of cells to send right

Parameters

cellLocationIndices the list of location indices of cells to send.

Definition at line 924 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddHaloCell	(	CellPtr	pCell,
		boost::shared_ptr< Node< DIM > >	pNode
	)

private

Add a single halo cell with its node to the halo structures on this process.

Parameters

pCell	the cell to add.
pNode	the node to add.

Definition at line 976 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddMovedCell	(	CellPtr	pCell,
		boost::shared_ptr< Node< DIM > >	pNode
	)

private

Add a moved cell to this process along with its node.

Parameters

pCell	the pointer to the cell that is to be added.
pNode	the pointer to the node that is to be added.

Definition at line 720 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

private

Overridden AddNode() method.

Add a new node to the cell population.

Parameters

pNewNode pointer to the new node

Returns: global index of new node in cell population

Definition at line 258 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendLeft ( unsigned nodeIndex )

private

Add the node and cell with index nodeIndex to the list of cells to send to the process left.

Parameters

nodeIndex the index of the node and cell to send.

Definition at line 832 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddNodeAndCellToSendRight ( unsigned nodeIndex )

private

Add the node and cell with index nodeIndex to the list of cells to send to the process right.

Parameters

nodeIndex the index of the node and cell to send.

Definition at line 824 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddReceivedCells ( )

Add the contents of mpCellsRecvRight and mpCellsRecvLeft to the local population.

Definition at line 840 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), and PetscTools::AmTopMost().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::AddReceivedHaloCells ( )

private

Add halo cells to the halo structure on this process.

Definition at line 946 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), and PetscTools::AmTopMost().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::Clear ( )

Reset the member variables mNodePairs and mpBoxCollection in the underlying mesh.

Definition at line 113 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::DeleteMovedCell ( unsigned index )

private

Delete a cell and its associated node that have moved off this process.

Parameters

index the location of the cell to be deleted

Definition at line 733 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

std::pair< CellPtr, Node< DIM > * > NodeBasedCellPopulation< DIM >::GetCellNodePair ( unsigned nodeIndex )

Helper method to find and pack up nodes and cells together

Parameters

nodeIndex the global index of the node.

Returns: the pair.

Definition at line 812 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

CellPtr NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex ( unsigned index )

virtual

Overridden method from AbstractCellPopulation so that we can access halo cells through this method.

Parameters

index the global index of the node assocaited with a cell

Returns: the (set of) cells to which the node is attached.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 270 of file NodeBasedCellPopulation.cpp.

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

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

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetMechanicsCutOffLength ( )

Returns: the maximum interaction distance between cells, defined in NodesOnlyMesh.

Definition at line 323 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Overridden GetNeighbouringNodeIndices() method.

Not that this method only returns node indices for cells that are strictly touching each other.

Parameters

index the node index

Returns: the set of neighbouring node indices.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 429 of file NodeBasedCellPopulation.cpp.

References EXCEPTION, Node< SPACE_DIM >::GetNeighboursSetUp(), Node< SPACE_DIM >::GetRadius(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetNeighbours().

Referenced by BuskeCompressionForce< DIM >::AddForceContribution(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned DIM>

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

virtual

Overridden GetNode() method.

Parameters

index global index of the specified node

Returns: a pointer to the node with a given index.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 137 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

std::set< unsigned > NodeBasedCellPopulation< DIM >::GetNodesWithinNeighbourhoodRadius	(	unsigned	index,
		double	neighbourhoodRadius
	)

Method to return nodes within a given radius of a node. Note this is independent of cell radius and returns all nodes within a given radius.

Parameters

index	the node index
neighbourhoodRadius	the radius to find neighbours in. Note must be less than the MaximumInteractionDistance in the NodesOnlyMesh

Returns: the set of neighbouring node indices within neighbourhoodRadius of the specified node.

Definition at line 373 of file NodeBasedCellPopulation.cpp.

References EXCEPTION, Node< SPACE_DIM >::GetNeighboursSetUp(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetNeighbours().

template<unsigned DIM>

unsigned NodeBasedCellPopulation< DIM >::GetNumNodes ( )

virtual

Returns: the number of nodes in the cell population.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 264 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::GetReceivedCells ( )

Obtain proper cell/node pair objects from a previous call to NonBlockingSendCellsToNeighbourProcesses();

Definition at line 799 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), and PetscTools::AmTopMost().

template<unsigned DIM>

c_vector< double, DIM > NodeBasedCellPopulation< DIM >::GetSizeOfCellPopulation ( )

Overridden GetSizeOfCellPopulation to work in parallel.

Returns: the size of the cell population.

Definition at line 359 of file NodeBasedCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation(), and PetscTools::GetWorld().

template<unsigned DIM>

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

virtual

Overridden GetTetrahedralMeshForPdeModifier() method.

Returns: a pointer to a tetrahedral mesh whose nodes match those of the NodesOnlyMesh.

This method is called by AbstractGrowingDomainPdeModifier.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 94 of file NodeBasedCellPopulation.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), and PetscTools::IsSequential().

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::GetUseVariableRadii ( )

Returns: mUseVariableRadii

Definition at line 329 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Overridden GetVolumeOfCell() method.

Parameters

pCell boost shared pointer to a cell

Returns: volume via associated mesh node

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 495 of file NodeBasedCellPopulation.cpp.

References Node< SPACE_DIM >::GetRadius(), and Node< SPACE_DIM >::rGetLocation().

template<unsigned DIM>

double NodeBasedCellPopulation< DIM >::GetWidth ( const unsigned & rDimension )

virtual

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the cell population by computing the maximum distance between any nodes in this dimension.

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 353 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses ( )

Send the contents of mCellsToSendRight/Left to neighbouring processes using asynchronous communication. mpCellsRecvLeft/Right will not be updated until the equivalent GetReceivedCells() is called.

Definition at line 771 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::GetMyRank(), and SmallPow().

template<unsigned DIM>

void NodeBasedCellPopulation< 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< DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >, and NodeBasedCellPopulationWithBuskeUpdate< DIM >.

Definition at line 295 of file NodeBasedCellPopulation.cpp.

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

Referenced by NodeBasedCellPopulationWithBuskeUpdate< DIM >::OutputCellPopulationParameters(), and NodeBasedCellPopulationWithParticles< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::RefreshHaloCells ( )

private

Send and receive halo nodes with neighbours and populate memory structures to store them

Definition at line 906 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

unsigned NodeBasedCellPopulation< DIM >::RemoveDeadCells ( )

virtual

Remove all cells labelled as dead.

Note that after calling this method the cell population will be in an inconsistent state until the equivalent of a 'remesh' is performed! So don't try iterating over cells or anything like that.

Returns: number of cells removed

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 227 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh ( )

Returns: reference to mrMesh.

Definition at line 82 of file NodeBasedCellPopulation.cpp.

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

template<unsigned DIM>

const NodesOnlyMesh< DIM > & NodeBasedCellPopulation< DIM >::rGetMesh ( ) const

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

Definition at line 88 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

std::vector< std::pair< Node< DIM > *, Node< DIM > * > > & NodeBasedCellPopulation< DIM >::rGetNodePairs ( )

virtual

Overridden rGetNodePairs method

Returns: Node pairs for force calculation.

Implements AbstractCentreBasedCellPopulation< DIM >.

Definition at line 289 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses ( )

Send the contents of mCellsToSendRight/Left to neighbouring processes and receive from them into mpCellsRecvRight/Left.

Definition at line 754 of file NodeBasedCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), and PetscTools::GetMyRank().

template<unsigned DIM>

template<class Archive >

void NodeBasedCellPopulation< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Note that serialization of the nodes is handled by load/save_construct_data, so we don't actually have to do anything here except delegate to the base class.

Parameters

archive	the archive
version	the current version of this class

Definition at line 127 of file NodeBasedCellPopulation.hpp.

References NodeBasedCellPopulation< DIM >::mUseVariableRadii, and NodeBasedCellPopulation< DIM >::Validate().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetLoadBalanceFrequency ( unsigned loadBalanceFrequency )

Set the freqeuncy, in number of time steps, with which the underlying mesh should be load balanced.

Parameters

loadBalanceFrequency the frequency for load balancing.

Definition at line 347 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetLoadBalanceMesh ( bool loadBalanceMesh )

Set whether to carry out the dynamic load balance algorithm on this mesh when it is updated

Parameters

loadBalanceMesh whether to do dynamic load balancing.

Definition at line 341 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)

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

Definition at line 143 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::SetUseVariableRadii ( bool useVariableRadii = true )

Set mUseVariableRadii.

Parameters

useVariableRadii the new value of mUseVariableRadii

Definition at line 335 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

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

virtual

Remove nodes that have been marked as deleted and update the node cell map.

Parameters

hasHadBirthsOrDeaths whether cell population has had Births Or Deaths

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 149 of file NodeBasedCellPopulation.cpp.

References PetscTools::Barrier(), and SimulationTime::Instance().

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

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::UpdateCellProcessLocation ( )

virtual

Update which process each cell is owned by.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 866 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh ( NodeMap & map )

private

Update the map between nodes and cells after a call to remesh.

Parameters

map	The node map from ReMesh.

Todo:: we want to make mCellLocationMap private - we need to find a better way of doing this

Definition at line 195 of file NodeBasedCellPopulation.cpp.

References NodeMap::GetNewIndex(), NodeMap::IsDeleted(), and NodeMap::IsIdentityMap().

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::UpdateParticlesAfterReMesh ( NodeMap & rMap )

protectedvirtual

Update mIsParticle if required by a remesh.

Parameters

rMap	A map between node indices before and after remesh

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 284 of file NodeBasedCellPopulation.cpp.

template<unsigned DIM>

void NodeBasedCellPopulation< DIM >::Validate ( )

protectedvirtual

Check consistency of our internal data structures.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 119 of file NodeBasedCellPopulation.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), and SimulationTime::Instance().

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

template<unsigned DIM>

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

privatevirtual

Overridden WriteVtkResultsToFile() method.

Parameters

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

Implements AbstractCentreBasedCellPopulation< DIM >.

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 585 of file NodeBasedCellPopulation.cpp.

References PetscTools::GetMyRank(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), PetscTools::IsSequential(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 116 of file NodeBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

const unsigned NodeBasedCellPopulation< DIM >::mCellCommunicationTag = 123

staticprivate

The tag used to send and recieve cell information

Definition at line 98 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::vector<std::pair<CellPtr, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mCellsToSendLeft

private

The cells to send to the left process

Definition at line 83 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::vector<std::pair<CellPtr, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mCellsToSendRight

private

The cells to send to the right process

Definition at line 80 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mDeleteMesh

private

Whether to delete the nodes-only mesh (taken in one of the constructors, defaults to false).

Definition at line 74 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::map<CellPtr, unsigned> NodeBasedCellPopulation< DIM >::mHaloCellLocationMap

private

Map halo cells back to location indices

Definition at line 107 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::vector<CellPtr> NodeBasedCellPopulation< DIM >::mHaloCells

private

Pointers to halo cells

Definition at line 101 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

ObjectCommunicator<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mLeftCommunicator

private

A communicator to send cells to the left hand process

Definition at line 95 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

unsigned NodeBasedCellPopulation< DIM >::mLoadBalanceFrequency

private

The frequency at which the mesh is rebalanced

Definition at line 113 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mLoadBalanceMesh

private

Whether to load balance the underlying mesh dynamically

Definition at line 110 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::map<unsigned, CellPtr> NodeBasedCellPopulation< DIM >::mLocationHaloCellMap

private

Map location indices back to halo cells

Definition at line 104 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

c_vector<double, DIM> NodeBasedCellPopulation< DIM >::mMaxSpatialPositions

private

Vector of maximal spatial positions in each dimension.

Definition at line 68 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

c_vector<double, DIM> NodeBasedCellPopulation< DIM >::mMinSpatialPositions

private

Vector of minimal spatial positions in each dimension.

Definition at line 65 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

std::vector< std::pair<Node<DIM>*, Node<DIM>* > > NodeBasedCellPopulation< DIM >::mNodePairs

private

Node pairs for force calculations.

Definition at line 71 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mpCellsRecvLeft

private

A pointer to the cells received from the left process

Definition at line 89 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mpCellsRecvRight

private

A shared pointer to the cells received from the right process

Definition at line 86 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

NodesOnlyMesh<DIM>* NodeBasedCellPopulation< DIM >::mpNodesOnlyMesh

protected

Static cast of the mesh from AbstractCellPopulation.

Definition at line 60 of file NodeBasedCellPopulation.hpp.

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

template<unsigned DIM>

ObjectCommunicator<std::vector<std::pair<CellPtr, Node<DIM>* > > > NodeBasedCellPopulation< DIM >::mRightCommunicator

private

A communicator to send cells to the right hand process

Definition at line 92 of file NodeBasedCellPopulation.hpp.

template<unsigned DIM>

bool NodeBasedCellPopulation< DIM >::mUseVariableRadii

private

Whether or not to have cell radii updated from CellData defaults to false.

Definition at line 77 of file NodeBasedCellPopulation.hpp.

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

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

cell_based/src/population/NodeBasedCellPopulation.hpp
cell_based/src/population/NodeBasedCellPopulation.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Detailed Description

template<unsigned DIM> class NodeBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class NodeBasedCellPopulation< DIM >