AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractOffLatticeCellPopulation.hpp>

Inherits AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

Inherited by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Collaboration diagram for AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >:
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List of all members.

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 (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  )  [inline, 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>() 
) [inline]

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 >.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetAbsoluteMovementThreshold (  )  [inline]
Returns:
mAbsoluteMovementThreshold

Definition at line 88 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAbsoluteMovementThreshold.

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 >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantMutant (  )  [inline]
Returns:
mDampingConstantMutant

Definition at line 82 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantMutant.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantNormal (  )  [inline]
Returns:
mDampingConstantNormal

Definition at line 76 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantNormal.

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

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

Overridden OutputCellPopulationParameters() method.

Parameters:
rParamsFile the file stream to which the parameters are output

Implements AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >.

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

Definition at line 94 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantMutant, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantNormal.

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 >.

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

Definition at line 62 of file AbstractOffLatticeCellPopulation.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAbsoluteMovementThreshold ( double  absoluteMovementThreshold  )  [inline]

Set mAbsoluteMovementThreshold.

Parameters:
absoluteMovementThreshold the new value of mAbsoluteMovementThreshold

Definition at line 70 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mAbsoluteMovementThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantMutant ( double  dampingConstantMutant  )  [inline]

Set mDampingConstantMutant.

Parameters:
dampingConstantMutant the new value of mDampingConstantMutant

Definition at line 63 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantMutant.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantNormal ( double  dampingConstantNormal  )  [inline]

Set mDampingConstantNormal.

Parameters:
dampingConstantNormal the new value of mDampingConstantNormal

Definition at line 56 of file AbstractOffLatticeCellPopulation.cpp.

References AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDampingConstantNormal.

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 >.

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
virtual void AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations ( 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:
dt time step

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

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 >.

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

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< ELEMENT_DIM, SPACE_DIM >::GetAbsoluteMovementThreshold(), AbstractOffLatticeCellPopulation< DIM >::serialize(), AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetAbsoluteMovementThreshold(), and AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations().

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< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantMutant(), AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), AbstractOffLatticeCellPopulation< DIM >::serialize(), and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantMutant().

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< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantNormal(), AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), AbstractOffLatticeCellPopulation< DIM >::serialize(), and AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDampingConstantNormal().

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