#include <AbstractOffLatticeCellPopulation.hpp>

Inheritance diagram for AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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 (const std::vector< c_vector< double, SPACE_DIM > > &rNodeForces, double dt)=0
virtual double	GetDampingConstant (unsigned nodeIndex)=0
void	SetDampingConstantNormal (double dampingConstantNormal)
void	SetDampingConstantMutant (double dampingConstantMutant)
void	SetAbsoluteMovementThreshold (double absoluteMovementThreshold)
double	GetAbsoluteMovementThreshold ()
double	GetDampingConstantNormal ()
double	GetDampingConstantMutant ()
virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)
Protected Member Functions
	AbstractOffLatticeCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
Protected Attributes
double	mDampingConstantNormal
double	mDampingConstantMutant
double	mAbsoluteMovementThreshold
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 AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >

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

Definition at line 49 of file AbstractOffLatticeCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractOffLatticeCellPopulation ( 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 50 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractOffLatticeCellPopulation	(	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 AbstractOffLatticeCellPopulation.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual unsigned AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddNode ( Node< SPACE_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< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAbsoluteMovementThreshold ( )

Returns:: mAbsoluteMovementThreshold

Definition at line 88 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_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< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodePositions().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantMutant ( )

Returns:: mDampingConstantMutant

Definition at line 82 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantNormal ( )

Returns:: mDampingConstantNormal

Definition at line 76 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Overridden OutputCellPopulationParameters() method.

Parameters:

rParamsFile the file stream to which the parameters are output

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 94 of file AbstractOffLatticeCellPopulation.cpp.

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

Referenced by VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void AbstractOffLatticeCellPopulation< 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 AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 62 of file AbstractOffLatticeCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAbsoluteMovementThreshold ( double absoluteMovementThreshold )

Set mAbsoluteMovementThreshold.

Parameters:

absoluteMovementThreshold the new value of mAbsoluteMovementThreshold

Definition at line 70 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantMutant ( double dampingConstantMutant )

Set mDampingConstantMutant.

Parameters:

dampingConstantMutant the new value of mDampingConstantMutant

Definition at line 63 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantNormal ( double dampingConstantNormal )

Set mDampingConstantNormal.

Parameters:

dampingConstantNormal the new value of mDampingConstantNormal

Definition at line 56 of file AbstractOffLatticeCellPopulation.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< SPACE_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< ELEMENT_DIM, SPACE_DIM >.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations	(	const std::vector< c_vector< double, SPACE_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< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Referenced by OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodePositions().

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 AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Definition at line 54 of file AbstractOffLatticeCellPopulation.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAbsoluteMovementThreshold [protected]

The absolute distance which a cell is permitted to move in one time-step. Movement beyond this threshold will trigger UpdateNodeLocations to throw an exception

Definition at line 89 of file AbstractOffLatticeCellPopulation.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantMutant [protected]

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

Definition at line 82 of file AbstractOffLatticeCellPopulation.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_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 77 of file AbstractOffLatticeCellPopulation.hpp.

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

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

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