SurfaceAreaConstraintPottsUpdateRule< DIM > Class Template Reference

#include <SurfaceAreaConstraintPottsUpdateRule.hpp>

Inheritance diagram for SurfaceAreaConstraintPottsUpdateRule< DIM >:

Collaboration diagram for SurfaceAreaConstraintPottsUpdateRule< DIM >:

Public Member Functions
	SurfaceAreaConstraintPottsUpdateRule ()
	~SurfaceAreaConstraintPottsUpdateRule ()
double	EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)
double	GetDeformationEnergyParameter ()
void	SetDeformationEnergyParameter (double deformationEnergyParameter)
double	GetMatureCellTargetSurfaceArea () const
void	SetMatureCellTargetSurfaceArea (double matureCellTargetSurfaceArea)
void	OutputUpdateRuleParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractPottsUpdateRule< DIM >
	AbstractPottsUpdateRule ()
virtual	~AbstractPottsUpdateRule ()
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	mDeformationEnergyParameter
double	mMatureCellTargetSurfaceArea

Friends
class	TestPottsUpdateRules
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class SurfaceAreaConstraintPottsUpdateRule< DIM >

A volume constraint update rule class for use in Potts based simulations.

Note this currently assumes cells don't grow, i.e the target volume is constant for each cell over time.

Definition at line 52 of file SurfaceAreaConstraintPottsUpdateRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

SurfaceAreaConstraintPottsUpdateRule< DIM >::SurfaceAreaConstraintPottsUpdateRule

(

)

Constructor.

Todo:

Default values don't apply in 3D.

Definition at line 39 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

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

template<unsigned DIM>

SurfaceAreaConstraintPottsUpdateRule< DIM >::~SurfaceAreaConstraintPottsUpdateRule

(

)

Destructor.

Definition at line 48 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

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

Member Function Documentation

template<unsigned DIM>

double SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution ( unsigned  currentNodeIndex, unsigned  targetNodeIndex, PottsBasedCellPopulation< DIM > &  rCellPopulation  )

virtual

Overridden EvaluateHamiltonianContribution() method

Uses sum_elements gamma (A_i - A_i^T)^2.

Parameters

currentNodeIndex	The index of the current node/lattice site
targetNodeIndex	The index of the target node/lattice site
rCellPopulation	The cell population

Returns

The difference in the Hamiltonian with the configuration of the target node having the same spin as the current node with the current configuration. i.e H_1-H_0

Implements AbstractPottsUpdateRule< DIM >.

Definition at line 53 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References EXCEPTION, PottsBasedCellPopulation< DIM >::GetNode(), SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea, and PottsBasedCellPopulation< DIM >::rGetMesh().

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

template<unsigned DIM>

double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter

(

)

Returns

mDeformationEnergyParameter

Definition at line 176 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

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

template<unsigned DIM>

double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea

(

)

const

Returns

mMatureCellTargetSurfaceArea

Definition at line 188 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.

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

template<unsigned DIM>

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

virtual

Overridden OutputUpdateRuleParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractPottsUpdateRule< DIM >.

Definition at line 201 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea, and AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

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

template<unsigned DIM>

template<class Archive >

void SurfaceAreaConstraintPottsUpdateRule< 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 82 of file SurfaceAreaConstraintPottsUpdateRule.hpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), EXPORT_TEMPLATE_CLASS_SAME_DIMS, SurfaceAreaConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter(), SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea(), SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea, SurfaceAreaConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), SurfaceAreaConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter(), SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea(), SurfaceAreaConstraintPottsUpdateRule< DIM >::SurfaceAreaConstraintPottsUpdateRule(), and SurfaceAreaConstraintPottsUpdateRule< DIM >::~SurfaceAreaConstraintPottsUpdateRule().

template<unsigned DIM>

void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter

(

double

deformationEnergyParameter

)

Set mDeformationEnergyParameter.

Parameters

deformationEnergyParameter

the new value of mDeformationEnergyParameter

Definition at line 182 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

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

template<unsigned DIM>

void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea

(

double

matureCellTargetSurfaceArea

)

Set mMatureCellTargetSurfaceArea.

Parameters

matureCellTargetSurfaceArea

the new value of mMatureCellTargetSurfaceArea

Definition at line 194 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.

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

Member Data Documentation

template<unsigned DIM>

double SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter

private

Cell deformation energy parameter. Set to the default value 0.5 in the constructor.

Todo:

provide units

Definition at line 63 of file SurfaceAreaConstraintPottsUpdateRule.hpp.

Referenced by SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter(), SurfaceAreaConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize(), and SurfaceAreaConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter().

template<unsigned DIM>

double SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea

private

Todo:

provide units #1829 Non-dimensional target surface area of a mature (fully-grown) cell, given in units of area of lattice site. Set to the default value 16 in the constructor.

Definition at line 71 of file SurfaceAreaConstraintPottsUpdateRule.hpp.

Referenced by SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea(), SurfaceAreaConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize(), and SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea().

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

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