VolumeConstraintPottsUpdateRule< DIM > Class Template Reference

#include <VolumeConstraintPottsUpdateRule.hpp>

Inheritance diagram for VolumeConstraintPottsUpdateRule< DIM >:

Collaboration diagram for VolumeConstraintPottsUpdateRule< DIM >:

List of all members.

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)
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

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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 55 of file VolumeConstraintPottsUpdateRule.hpp.

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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.

template<unsigned DIM>

VolumeConstraintPottsUpdateRule< DIM >::~VolumeConstraintPottsUpdateRule

(

)

Destructor.

Definition at line 48 of file VolumeConstraintPottsUpdateRule.cpp.

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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(), and PottsBasedCellPopulation< DIM >::rGetMesh().

template<unsigned DIM>

double VolumeConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter

(

)

Returns:

mDeformationEnergyParameter

Definition at line 102 of file VolumeConstraintPottsUpdateRule.cpp.

template<unsigned DIM>

double VolumeConstraintPottsUpdateRule< DIM >::GetMatureCellTargetVolume

(

)

const

Returns:

mMatureCellTargetVolume

Definition at line 114 of file VolumeConstraintPottsUpdateRule.cpp.

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

Implements AbstractPottsUpdateRule< DIM >.

Definition at line 127 of file VolumeConstraintPottsUpdateRule.cpp.

References AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

template<unsigned DIM>

template<class Archive >

void VolumeConstraintPottsUpdateRule< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)		[inline, private]

Serialize the object.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractPottsUpdateRule< DIM >.

Definition at line 77 of file VolumeConstraintPottsUpdateRule.hpp.

References VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume.

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.

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.

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Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractPottsUpdateRule< DIM >.

Definition at line 75 of file VolumeConstraintPottsUpdateRule.hpp.

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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 66 of file VolumeConstraintPottsUpdateRule.hpp.

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

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 73 of file VolumeConstraintPottsUpdateRule.hpp.

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

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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