AbstractOnLatticeCellPopulation< DIM > Class Template Reference

#include <AbstractOnLatticeCellPopulation.hpp>

Inherited by CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Collaboration diagram for AbstractOnLatticeCellPopulation< DIM >:

Public Member Functions
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)
virtual	~AbstractOnLatticeCellPopulation ()
virtual void	UpdateCellLocations (double dt)=0
bool	GetUpdateNodesInRandomOrder ()
void	SetUpdateNodesInRandomOrder (bool updateNodesInRandomOrder)
void	SetIterateRandomlyOverUpdateRuleCollection (bool iterateRandomly)
bool	GetIterateRandomlyOverUpdateRuleCollection ()
void	SetNode (unsigned index, ChastePoint< DIM > &rNewLocation)
std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)
virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)
Protected Member Functions
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh)
Protected Attributes
bool	mDeleteMesh
bool	mUpdateNodesInRandomOrder
bool	mIterateRandomlyOverUpdateRuleCollection
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 AbstractOnLatticeCellPopulation< DIM >

An abstract class for on-lattice cell populations.

Definition at line 48 of file AbstractOnLatticeCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation ( AbstractMesh< DIM, DIM > & rMesh ) [inline, protected]

Constructor that just takes in a mesh.

Parameters:

rMesh

the mesh for the cell population.

Definition at line 57 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation	(	AbstractMesh< DIM, DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`
	)			`[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
	deleteMesh	set to true if you want the cell population to free the mesh memory on destruction (defaults to false)

Definition at line 39 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractCellPopulation< DIM >::AddCellUsingLocationIndex(), and AbstractCellPopulation< DIM >::mCells.

template<unsigned DIM>

AbstractOnLatticeCellPopulation< DIM >::~AbstractOnLatticeCellPopulation ( ) [inline, virtual]

Destructor.

Definition at line 66 of file AbstractOnLatticeCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::GetIterateRandomlyOverUpdateRuleCollection ( ) [inline]

Returns:: mIterateRandomlyOverUpdateRuleCollection.

Definition at line 89 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection.

template<unsigned DIM>

std::set< unsigned > AbstractOnLatticeCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned index ) [inline, virtual]

Overridden GetNeighbouringNodeIndices() method.

This method currently returns an exception as the two types of neighbourhood (Moore and Von Neumann) are defined in the PottsMesh.

Parameters:

index

the node index

Returns:: the set of neighbouring node indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 101 of file AbstractOnLatticeCellPopulation.cpp.

References EXCEPTION.

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::GetUpdateNodesInRandomOrder ( ) [inline]

Get whether we update nodes in a random order.

Returns:: mUpdateNodesInRandomOrder

Definition at line 71 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.

template<unsigned DIM>

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

Outputs CellPopulation parameters to file

Parameters:

rParamsFile

the file stream to which the parameters are output

Implements AbstractCellPopulation< DIM >.

Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Definition at line 109 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection, and AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.

template<unsigned DIM>

template<class Archive >

void AbstractOnLatticeCellPopulation< 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 CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Definition at line 61 of file AbstractOnLatticeCellPopulation.hpp.

References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection, and AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::SetIterateRandomlyOverUpdateRuleCollection ( bool iterateRandomly ) [inline]

Set mIterateRandomlyOverUpdateRuleCollection.

Parameters:

iterateRandomly

whether to iterate randomly over mUpdateRuleCollection

Definition at line 83 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection.

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::SetNode	(	unsigned	index,
		ChastePoint< DIM > &	rNewLocation
	)			`[inline]`

Overridden SetNode() method.

This method throws an exception if called on a subclass of AbstractOnLatticeCellPopulation, since in such classes the lattice is assumed to be fixed.

Parameters:

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

Definition at line 95 of file AbstractOnLatticeCellPopulation.cpp.

References EXCEPTION.

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::SetUpdateNodesInRandomOrder ( bool updateNodesInRandomOrder ) [inline]

Get whether we update nodes in a random order.

Parameters:

updateNodesInRandomOrder

Whether to update nodes in a random order.

Definition at line 77 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder.

template<unsigned DIM>

virtual void AbstractOnLatticeCellPopulation< DIM >::UpdateCellLocations ( double dt ) [pure virtual]

Update cell locations over the course of a time step of specified length.

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

Parameters:

dt

time step

Implemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCellPopulation< DIM >.

Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Definition at line 53 of file AbstractOnLatticeCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::mDeleteMesh [protected]

Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.

Definition at line 74 of file AbstractOnLatticeCellPopulation.hpp.

Referenced by CaBasedCellPopulation< DIM >::~CaBasedCellPopulation(), and PottsBasedCellPopulation< DIM >::~PottsBasedCellPopulation().

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection [protected]

Whether to iterate randomly over mUpdateRuleCollection when updating cell locations. Initialized to false in the constructor.

Definition at line 86 of file AbstractOnLatticeCellPopulation.hpp.

Referenced by AbstractOnLatticeCellPopulation< DIM >::GetIterateRandomlyOverUpdateRuleCollection(), AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractOnLatticeCellPopulation< DIM >::serialize(), AbstractOnLatticeCellPopulation< DIM >::SetIterateRandomlyOverUpdateRuleCollection(), and PottsBasedCellPopulation< DIM >::UpdateCellLocations().

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder [protected]

Whether to update nodes in random order. Initialized to true in the constructor.

Definition at line 80 of file AbstractOnLatticeCellPopulation.hpp.

Referenced by AbstractOnLatticeCellPopulation< DIM >::GetUpdateNodesInRandomOrder(), AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractOnLatticeCellPopulation< DIM >::serialize(), AbstractOnLatticeCellPopulation< DIM >::SetUpdateNodesInRandomOrder(), and PottsBasedCellPopulation< DIM >::UpdateCellLocations().

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

cell_based/src/population/AbstractOnLatticeCellPopulation.hpp
cell_based/src/population/AbstractOnLatticeCellPopulation.cpp

AbstractOnLatticeCellPopulation< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractOnLatticeCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractOnLatticeCellPopulation< DIM >