#include <AbstractCentreBasedCellPopulation.hpp>

Inheritance diagram for AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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)
CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, SPACE_DIM > &rCellDivisionVector, 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 void	UpdateNodeLocations (const std::vector< c_vector< double, SPACE_DIM > > &rNodeForces, double dt)
virtual double	GetDampingConstant (unsigned nodeIndex)
virtual void	GenerateCellResultsAndWriteToFiles ()
virtual void	WriteTimeAndNodeResultsToFiles ()
virtual bool	IsGhostNode (unsigned index)
virtual bool	IsParticle (unsigned index)
virtual std::set< std::pair < Node< SPACE_DIM > , Node < SPACE_DIM > > > &	rGetNodePairs ()=0
double	GetMeinekeDivisionSeparation ()
void	SetMeinekeDivisionSeparation (double divisionSeparation)
virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)
Protected Member Functions
	AbstractCentreBasedCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
virtual void	WriteVtkResultsToFile ()=0
Protected Attributes
double	mMeinekeDivisionSeparation
std::set< std::pair< CellPtr, CellPtr > >	mMarkedSprings
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

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

An abstract facade class encapsulating a centre-based cell population, in which each cell corresponds to a Node.

Definition at line 49 of file AbstractCentreBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation ( AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rMesh ) [protected]

Constructor that just takes in a mesh.

Parameters:

rMesh the mesh for the cell population.

Definition at line 48 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation	(	AbstractMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`
	)

Default constructor.

Parameters:

rMesh	a refernce to the mesh underlying the cell population
rCells	a vector of cells
locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 39 of file AbstractCentreBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CellPtr AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, SPACE_DIM > &	rCellDivisionVector,
		CellPtr	pParentCell = `CellPtr()`
	)		`[virtual]`

Add a new cell to the cell population.

Parameters:

pNewCell	the cell to add
rCellDivisionVector	the position in space at which to put it
pParentCell	pointer to a parent cell (if required)

Returns:: address of cell as it appears in the cell list

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 69 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by NodeBasedCellPopulationWithParticles< DIM >::AddCell(), NodeBasedCellPopulation< DIM >::AddCell(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 86 of file AbstractCentreBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GenerateCellResultsAndWriteToFiles ( ) [virtual]

Overridden GenerateCellResultsAndWriteToFiles() method.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 203 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant ( unsigned nodeIndex ) [virtual]

Overridden GetDampingConstant() method.

Get the damping constant for the cell associated with this node, i.e. d in drdt = F/d.

If the cell is wild-type, then the normal damping constant is returned. If the cell has a mutation, then the mutant damping constant is returned.

Note that by default, the normal and mutant damping constants are the same. To alter the damping constant for mutant cells, call the method SetDampingConstantMutant() on the CellPopulation.

Parameters:

nodeIndex the global index of this node

Returns:: the damping constant at the Cell associated with this node

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 177 of file AbstractCentreBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre ( CellPtr pCell ) [virtual]

Overridden GetLocationOfCellCentre() method. Find where a given cell is in space.

Parameters:

pCell the cell

Returns:: the location of the node corresponding to this cell.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 56 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by CryptSimulation1d::CalculateCellDivisionVector(), CryptStatistics::GetCryptSection(), and CryptProjectionStatistics::GetCryptSection().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetMeinekeDivisionSeparation ( )

Returns:: mMeinekeDivisionSeparation

Definition at line 316 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by CryptSimulation1d::CalculateCellDivisionVector(), and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNodeCorrespondingToCell ( CellPtr pCell )

Get a pointer to the node corresponding to a given cell.

Parameters:

pCell the cell

Returns:: address of the node

Definition at line 62 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell ) [virtual]

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters:

pCell the cell

Returns:: whether a given cell is associated with a deleted node.

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 134 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsGhostNode ( unsigned index ) [virtual]

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

Parameters:

index the global index of a specified node

Returns:: whether the node is a ghost node

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >.

Definition at line 191 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator::operator++(), CellwiseDataGradient< DIM >::SetupGradients(), and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodePositions().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Parameters:

rCellPair a set of pointers to Cells

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

Definition at line 107 of file AbstractCentreBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsParticle ( unsigned index ) [virtual]

Find if a given node is a particle. The method always returns false but is overridden in NodeBasedCellPopulationWithParticles.

Parameters:

index the global index of a specified node

Returns:: whether the node is a particle

Reimplemented in NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 197 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Mark the spring between the given cells.

Parameters:

rCellPair a set of pointers to Cells

Definition at line 116 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [virtual]

Overridden OutputCellPopulationParameters() method.

Parameters:

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, NodeBasedCellPopulationWithParticles< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 330 of file AbstractCentreBasedCellPopulation.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual std::set< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > >& AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetNodePairs ( ) [pure virtual]

Method to return the connected nodes in a centre based simulation.

Overridden in sub classes to have correct functionality.

Returns:: Node pairs for force calculation.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::AddForceContribution().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

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

Serialize the object and its member variables.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, NodeBasedCellPopulationWithParticles< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 61 of file AbstractCentreBasedCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetMeinekeDivisionSeparation ( double divisionSeparation )

Set mMeinekeDivisionSeparation.

Parameters:

divisionSeparation the new value of mMeinekeDivisionSeparation

Definition at line 322 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Stop marking the spring between the given cells.

Parameters:

rCellPair a set of pointers to Cells

Definition at line 125 of file AbstractCentreBasedCellPopulation.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations	(	const std::vector< c_vector< double, SPACE_DIM > > &	rNodeForces,
		double	dt
	)		`[virtual]`

Overridden UpdateNodeLocations() method.

Parameters:

rNodeForces	a vector containing the force on each node in the cell population
dt	the time step

Implements AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 140 of file AbstractCentreBasedCellPopulation.cpp.

References EXCEPTION.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteTimeAndNodeResultsToFiles ( ) [virtual]

Overridden WriteTimeAndNodeResultsToFiles() method.

Reimplemented from AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 253 of file AbstractCentreBasedCellPopulation.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::BeginRoundRobin(), PetscTools::EndRoundRobin(), SimulationTime::GetTime(), SimulationTime::Instance(), and OutputFileHandler::OpenOutputFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile ( ) [protected, pure virtual]

Write the current results to mpVtkMetaFile.

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

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithParticles< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

Needed for serialization.

Reimplemented from AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, NodeBasedCellPopulationWithParticles< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 53 of file AbstractCentreBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

std::set<std::pair<CellPtr,CellPtr> > AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_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 80 of file AbstractCentreBasedCellPopulation.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::mMeinekeDivisionSeparation [protected]

Initial separation placement of mother/daughter cells at birth. Has units of cell size at equilibrium rest length

Definition at line 73 of file AbstractCentreBasedCellPopulation.hpp.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::serialize().

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