SurfaceAreaConstraintPottsUpdateRule< DIM > Class Template Reference

#include <SurfaceAreaConstraintPottsUpdateRule.hpp>

Inherits AbstractPottsUpdateRule< DIM >.

Collaboration diagram for SurfaceAreaConstraintPottsUpdateRule< DIM >:
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List of all members.

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)

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 (  )  [inline]

Constructor.

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

Definition at line 39 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

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

Destructor.

Definition at line 48 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

Member Function Documentation

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

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

Definition at line 176 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

template<unsigned DIM>
double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea (  )  const [inline]
Returns:
mMatureCellTargetSurfaceArea

Definition at line 188 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.

template<unsigned DIM>
void SurfaceAreaConstraintPottsUpdateRule< 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 201 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.

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

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.

Reimplemented from AbstractPottsUpdateRule< DIM >.

Definition at line 82 of file SurfaceAreaConstraintPottsUpdateRule.hpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.

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

Set mDeformationEnergyParameter.

Parameters:
deformationEnergyParameter the new value of mDeformationEnergyParameter

Definition at line 182 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.

template<unsigned DIM>
void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea ( double  matureCellTargetSurfaceArea  )  [inline]

Set mMatureCellTargetSurfaceArea.

Parameters:
matureCellTargetSurfaceArea the new value of mMatureCellTargetSurfaceArea

Definition at line 194 of file SurfaceAreaConstraintPottsUpdateRule.cpp.

References SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractPottsUpdateRule< DIM >.

Definition at line 73 of file SurfaceAreaConstraintPottsUpdateRule.hpp.

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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