VolumeConstraintPottsUpdateRule< DIM > Class Template Reference

#include <VolumeConstraintPottsUpdateRule.hpp>

Inheritance diagram for VolumeConstraintPottsUpdateRule< DIM >:

Collaboration diagram for VolumeConstraintPottsUpdateRule< DIM >:

Public Member Functions
	VolumeConstraintPottsUpdateRule ()
	~VolumeConstraintPottsUpdateRule ()
double	EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)
double	GetDeformationEnergyParameter ()
void	SetDeformationEnergyParameter (double deformationEnergyParameter)
double	GetMatureCellTargetVolume () const
void	SetMatureCellTargetVolume (double matureCellTargetVolume)
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	mMatureCellTargetVolume

Friends
class	TestPottsUpdateRules
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class VolumeConstraintPottsUpdateRule< 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 VolumeConstraintPottsUpdateRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VolumeConstraintPottsUpdateRule< DIM >::VolumeConstraintPottsUpdateRule

(

)

Constructor.

Todo:

Default values don't apply in 3D.

Definition at line 39 of file VolumeConstraintPottsUpdateRule.cpp.

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

template<unsigned DIM>

VolumeConstraintPottsUpdateRule< DIM >::~VolumeConstraintPottsUpdateRule

(

)

Destructor.

Definition at line 48 of file VolumeConstraintPottsUpdateRule.cpp.

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

Member Function Documentation

template<unsigned DIM>

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

virtual

Overridden EvaluateHamiltonianContribution() method

Uses sum_elements alpha (V_i - V_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 VolumeConstraintPottsUpdateRule.cpp.

References EXCEPTION, PottsBasedCellPopulation< DIM >::GetNode(), VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume, and PottsBasedCellPopulation< DIM >::rGetMesh().

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

template<unsigned DIM>

double VolumeConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter

(

)

Returns

mDeformationEnergyParameter

Definition at line 102 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

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

template<unsigned DIM>

double VolumeConstraintPottsUpdateRule< DIM >::GetMatureCellTargetVolume

(

)

const

Returns

mMatureCellTargetVolume

Definition at line 114 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume.

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

template<unsigned DIM>

void VolumeConstraintPottsUpdateRule< 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 127 of file VolumeConstraintPottsUpdateRule.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume, and AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

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

template<unsigned DIM>

template<class Archive >

void VolumeConstraintPottsUpdateRule< 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 81 of file VolumeConstraintPottsUpdateRule.hpp.

References VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), EXPORT_TEMPLATE_CLASS_SAME_DIMS, VolumeConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter(), VolumeConstraintPottsUpdateRule< DIM >::GetMatureCellTargetVolume(), VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume, VolumeConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), VolumeConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter(), VolumeConstraintPottsUpdateRule< DIM >::SetMatureCellTargetVolume(), VolumeConstraintPottsUpdateRule< DIM >::VolumeConstraintPottsUpdateRule(), and VolumeConstraintPottsUpdateRule< DIM >::~VolumeConstraintPottsUpdateRule().

template<unsigned DIM>

void VolumeConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter

(

double

deformationEnergyParameter

)

Set mDeformationEnergyParameter.

Parameters

deformationEnergyParameter

the new value of mDeformationEnergyParameter

Definition at line 108 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

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

template<unsigned DIM>

void VolumeConstraintPottsUpdateRule< DIM >::SetMatureCellTargetVolume

(

double

matureCellTargetVolume

)

Set mMatureCellTargetVolume.

Parameters

matureCellTargetVolume

the new value of mMatureCellTargetVolume

Definition at line 120 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume.

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

Member Data Documentation

template<unsigned DIM>

double VolumeConstraintPottsUpdateRule< 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 VolumeConstraintPottsUpdateRule.hpp.

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

template<unsigned DIM>

double VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume

private

Non-dimensional target volume of a mature (fully-grown) cell, given in number of lattice sites. Set to the default value 16 in the constructor.

Definition at line 70 of file VolumeConstraintPottsUpdateRule.hpp.

Referenced by VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), VolumeConstraintPottsUpdateRule< DIM >::GetMatureCellTargetVolume(), VolumeConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), VolumeConstraintPottsUpdateRule< DIM >::serialize(), and VolumeConstraintPottsUpdateRule< DIM >::SetMatureCellTargetVolume().

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

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