VolumeConstraintPottsUpdateRule< DIM > Class Template Reference

#include <VolumeConstraintPottsUpdateRule.hpp>

Inherits AbstractPottsUpdateRule< DIM >.

Collaboration diagram for VolumeConstraintPottsUpdateRule< DIM >:
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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

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 48 of file VolumeConstraintPottsUpdateRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
VolumeConstraintPottsUpdateRule< DIM >::VolumeConstraintPottsUpdateRule (  )  [inline]

Constructor.

Todo:
Default values don't apply in 3D.

Definition at line 32 of file VolumeConstraintPottsUpdateRule.cpp.

template<unsigned DIM>
VolumeConstraintPottsUpdateRule< DIM >::~VolumeConstraintPottsUpdateRule (  )  [inline]

Destructor.

Definition at line 41 of file VolumeConstraintPottsUpdateRule.cpp.

Member Function Documentation

template<unsigned DIM>
double VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution ( unsigned  currentNodeIndex,
unsigned  targetNodeIndex,
PottsBasedCellPopulation< DIM > &  rCellPopulation 
) [inline, 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 46 of file VolumeConstraintPottsUpdateRule.cpp.

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

template<unsigned DIM>
double VolumeConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter (  )  [inline]
Returns:
mDeformationEnergyParameter

Definition at line 95 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

template<unsigned DIM>
double VolumeConstraintPottsUpdateRule< DIM >::GetMatureCellTargetVolume (  )  const [inline]
Returns:
mMatureCellTargetVolume

Definition at line 107 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume.

template<unsigned DIM>
void VolumeConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters ( out_stream &  rParamsFile  )  [inline, virtual]

Overridden OutputUpdateRuleParameters() method.

Parameters:
rParamsFile the file stream to which the parameters are output

Implements AbstractPottsUpdateRule< DIM >.

Definition at line 120 of file VolumeConstraintPottsUpdateRule.cpp.

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

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 70 of file VolumeConstraintPottsUpdateRule.hpp.

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

template<unsigned DIM>
void VolumeConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter ( double  deformationEnergyParameter  )  [inline]

Set mDeformationEnergyParameter.

Parameters:
deformationEnergyParameter the new value of mDeformationEnergyParameter

Definition at line 101 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

template<unsigned DIM>
void VolumeConstraintPottsUpdateRule< DIM >::SetMatureCellTargetVolume ( double  matureCellTargetVolume  )  [inline]

Set mMatureCellTargetVolume.

Parameters:
matureCellTargetVolume the new value of mMatureCellTargetVolume

Definition at line 113 of file VolumeConstraintPottsUpdateRule.cpp.

References VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume.

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractPottsUpdateRule< DIM >.

Definition at line 68 of file VolumeConstraintPottsUpdateRule.hpp.

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 59 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 66 of file VolumeConstraintPottsUpdateRule.hpp.

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

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