DiffusionCaUpdateRule< DIM > Class Template Reference

#include <DiffusionCaUpdateRule.hpp>

Inheritance diagram for DiffusionCaUpdateRule< DIM >:

Collaboration diagram for DiffusionCaUpdateRule< DIM >:

Public Member Functions
	DiffusionCaUpdateRule ()
	~DiffusionCaUpdateRule ()
double	EvaluateProbability (unsigned currentNodeIndex, unsigned targetNodeIndex, CaBasedCellPopulation< DIM > &rCellPopulation, double dt, double deltaX, CellPtr cell)
double	GetDiffusionParameter ()
void	SetDiffusionParameter (double diffusionParameter)
void	OutputUpdateRuleParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractCaUpdateRule< DIM >
	AbstractCaUpdateRule ()
virtual	~AbstractCaUpdateRule ()
Public Member Functions inherited from AbstractUpdateRule< DIM >
	AbstractUpdateRule ()
virtual	~AbstractUpdateRule ()
void	OutputUpdateRuleInfo (out_stream &rParamsFile)
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Private Attributes
double	mDiffusionParameter

Friends
class	TestCaUpdateRules
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class DiffusionCaUpdateRule< DIM >

A diffusion update rule for use in cell-based simulations using the cellular CA model.

The probability of moving to an adjacent lattice site is

D*delta_t/(2*delta_x*delta_x)

Where D is the mDiffusionParameter. delta_t is the timestep. delta_x is the separation of the two lattice sites.

Definition at line 58 of file DiffusionCaUpdateRule.hpp.

Constructor & Destructor Documentation

DiffusionCaUpdateRule()

template<unsigned DIM>

DiffusionCaUpdateRule< DIM >::DiffusionCaUpdateRule

(

)

Constructor.

Definition at line 39 of file DiffusionCaUpdateRule.cpp.

~DiffusionCaUpdateRule()

template<unsigned DIM>

DiffusionCaUpdateRule< DIM >::~DiffusionCaUpdateRule

(

)

Destructor.

Definition at line 46 of file DiffusionCaUpdateRule.cpp.

Member Function Documentation

EvaluateProbability()

template<unsigned DIM>

double DiffusionCaUpdateRule< DIM >::EvaluateProbability ( unsigned  currentNodeIndex, unsigned  targetNodeIndex, CaBasedCellPopulation< DIM > &  rCellPopulation, double  dt, double  deltaX, CellPtr  cell  )

virtual

Calculate the probability of a given move.

Uses random diffusion to each neighbouring node, scaled according to distance.

Parameters

currentNodeIndex	The index of the current node/lattice site
targetNodeIndex	The index of the target node/lattice site
rCellPopulation	The cell population
dt	is the time interval
deltaX	defines the size of the lattice site
cell	a pointer to the cell (needed if more than one cell per lattice site

Returns

The probability of the cell moving from the current node to the target node

Implements AbstractCaUpdateRule< DIM >.

Definition at line 51 of file DiffusionCaUpdateRule.cpp.

References CaBasedCellPopulation< DIM >::GetNode(), Node< SPACE_DIM >::rGetLocation(), and CaBasedCellPopulation< DIM >::rGetMesh().

GetDiffusionParameter()

template<unsigned DIM>

double DiffusionCaUpdateRule< DIM >::GetDiffusionParameter

(

)

Returns

mDiffusionParameter

Definition at line 65 of file DiffusionCaUpdateRule.cpp.

OutputUpdateRuleParameters()

template<unsigned DIM>

void DiffusionCaUpdateRule< DIM >::OutputUpdateRuleParameters ( out_stream &  rParamsFile )

virtual

Overridden OutputUpdateRuleParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractCaUpdateRule< DIM >.

Definition at line 77 of file DiffusionCaUpdateRule.cpp.

References AbstractCaUpdateRule< DIM >::OutputUpdateRuleParameters().

serialize()

template<unsigned DIM>

template<class Archive >

void DiffusionCaUpdateRule< DIM >::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 80 of file DiffusionCaUpdateRule.hpp.

References DiffusionCaUpdateRule< DIM >::mDiffusionParameter.

SetDiffusionParameter()

template<unsigned DIM>

void DiffusionCaUpdateRule< DIM >::SetDiffusionParameter

(

double

diffusionParameter

)

Set mDiffusionParameter.

Parameters

diffusionParameter

the new value of mDiffusionParameter

Definition at line 71 of file DiffusionCaUpdateRule.cpp.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Definition at line 71 of file DiffusionCaUpdateRule.hpp.

TestCaUpdateRules

template<unsigned DIM>

friend class TestCaUpdateRules

friend

Definition at line 60 of file DiffusionCaUpdateRule.hpp.

Member Data Documentation

mDiffusionParameter

template<unsigned DIM>

double DiffusionCaUpdateRule< DIM >::mDiffusionParameter

private

Diffusion parameter for update rule. Set to the default value 0.5 in the constructor.

Todo:

provide units

Definition at line 69 of file DiffusionCaUpdateRule.hpp.

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

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

• cell_based/src/population/update_rules/DiffusionCaUpdateRule.hpp
• cell_based/src/population/update_rules/DiffusionCaUpdateRule.cpp