AbstractOffLatticeCellPopulation< DIM > Class Template Reference

#include <AbstractOffLatticeCellPopulation.hpp>

Inherited by AbstractCentreBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Collaboration diagram for AbstractOffLatticeCellPopulation< DIM >:

Public Member Functions
	AbstractOffLatticeCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
virtual unsigned	AddNode (Node< DIM > *pNewNode)=0
virtual void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)=0
virtual void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)=0
virtual double	GetDampingConstant (unsigned nodeIndex)=0
void	SetDampingConstantNormal (double dampingConstantNormal)
void	SetDampingConstantMutant (double dampingConstantMutant)
double	GetDampingConstantNormal ()
double	GetDampingConstantMutant ()
virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)
Protected Member Functions
	AbstractOffLatticeCellPopulation ()
Protected Attributes
double	mDampingConstantNormal
double	mDampingConstantMutant
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AbstractOffLatticeCellPopulation< DIM >

An abstract facade class encapsulating an off-lattice (centre- or vertex-based) cell population.

Definition at line 42 of file AbstractOffLatticeCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractOffLatticeCellPopulation< DIM >::AbstractOffLatticeCellPopulation ( ) [inline, protected]

Constructor for use by archiving only.

Definition at line 41 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned DIM>

AbstractOffLatticeCellPopulation< DIM >::AbstractOffLatticeCellPopulation	(	std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`
	)			`[inline]`

Default constructor.

Parameters:

	rCells	a vector of cells
	locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 32 of file AbstractOffLatticeCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

virtual unsigned AbstractOffLatticeCellPopulation< DIM >::AddNode ( Node< DIM > * pNewNode ) [pure virtual]

Add a new node to the cell population.

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

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in cell population.

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

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

template<unsigned DIM>

virtual double AbstractOffLatticeCellPopulation< DIM >::GetDampingConstant ( unsigned nodeIndex ) [pure virtual]

Get the damping constant for this node - ie d in drdt = F/d.

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

Parameters:

nodeIndex

the global index of this node

Returns:: the damping constant at the node.

Implemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>

double AbstractOffLatticeCellPopulation< DIM >::GetDampingConstantMutant ( ) [inline]

Returns:: mDampingConstantMutant

Definition at line 67 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< DIM >::mDampingConstantMutant.

Referenced by VertexBasedCellPopulation< DIM >::GetDampingConstant(), and AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant().

template<unsigned DIM>

double AbstractOffLatticeCellPopulation< DIM >::GetDampingConstantNormal ( ) [inline]

Returns:: mDampingConstantNormal

Definition at line 61 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< DIM >::mDampingConstantNormal.

Referenced by VertexBasedCellPopulation< DIM >::GetDampingConstant(), AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant(), and MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions().

template<unsigned DIM>

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

Overridden OutputCellPopulationParameters() method.

Parameters:

rParamsFile

the file stream to which the parameters are output

Implements AbstractCellPopulation< DIM >.

Reimplemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 73 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< DIM >::mDampingConstantMutant, and AbstractOffLatticeCellPopulation< DIM >::mDampingConstantNormal.

template<unsigned DIM>

template<class Archive >

void AbstractOffLatticeCellPopulation< 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 AbstractCellPopulation< DIM >.

Reimplemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 55 of file AbstractOffLatticeCellPopulation.hpp.

References AbstractOffLatticeCellPopulation< DIM >::mDampingConstantMutant, and AbstractOffLatticeCellPopulation< DIM >::mDampingConstantNormal.

template<unsigned DIM>

void AbstractOffLatticeCellPopulation< DIM >::SetDampingConstantMutant ( double dampingConstantMutant ) [inline]

Set mDampingConstantMutant.

Parameters:

dampingConstantMutant

the new value of mDampingConstantMutant

Definition at line 54 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< DIM >::mDampingConstantMutant.

template<unsigned DIM>

void AbstractOffLatticeCellPopulation< DIM >::SetDampingConstantNormal ( double dampingConstantNormal ) [inline]

Set mDampingConstantNormal.

Parameters:

dampingConstantNormal

the new value of mDampingConstantNormal

Definition at line 47 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< DIM >::mDampingConstantNormal.

template<unsigned DIM>

virtual void AbstractOffLatticeCellPopulation< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)			`[pure virtual]`

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

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

Parameters:

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

Implements AbstractCellPopulation< DIM >.

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

Referenced by AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned DIM>

virtual void AbstractOffLatticeCellPopulation< DIM >::UpdateNodeLocations	(	const std::vector< c_vector< double, DIM > > &	rNodeForces,
		double	dt
	)			`[pure virtual]`

Update the location of each node in the cell population given a vector of forces on nodes and a time step over which to integrate the equations of motion.

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

Parameters:

	rNodeForces	forces on nodes
	dt	time step

Implemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, and VertexBasedCellPopulation< DIM >.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCellPopulation< DIM >.

Reimplemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 47 of file AbstractOffLatticeCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

double AbstractOffLatticeCellPopulation< DIM >::mDampingConstantMutant [protected]

Damping constant for mutant cells has units of kg s^-1.

Definition at line 75 of file AbstractOffLatticeCellPopulation.hpp.

Referenced by AbstractOffLatticeCellPopulation< DIM >::GetDampingConstantMutant(), AbstractOffLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractOffLatticeCellPopulation< DIM >::serialize(), and AbstractOffLatticeCellPopulation< DIM >::SetDampingConstantMutant().

template<unsigned DIM>

double AbstractOffLatticeCellPopulation< DIM >::mDampingConstantNormal [protected]

Damping constant for normal cells has units of kg s^-1 Represented by the parameter eta in the model by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 70 of file AbstractOffLatticeCellPopulation.hpp.

Referenced by AbstractOffLatticeCellPopulation< DIM >::GetDampingConstantNormal(), AbstractOffLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractOffLatticeCellPopulation< DIM >::serialize(), and AbstractOffLatticeCellPopulation< DIM >::SetDampingConstantNormal().

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

cell_based/src/population/AbstractOffLatticeCellPopulation.hpp
cell_based/src/population/AbstractOffLatticeCellPopulation.cpp

AbstractOffLatticeCellPopulation< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractOffLatticeCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractOffLatticeCellPopulation< DIM >