AdhesionPottsUpdateRule< DIM > Class Template Reference

#include <AdhesionPottsUpdateRule.hpp>

Inheritance diagram for AdhesionPottsUpdateRule< DIM >:

Collaboration diagram for AdhesionPottsUpdateRule< DIM >:

Public Member Functions
	AdhesionPottsUpdateRule ()
virtual	~AdhesionPottsUpdateRule ()
double	EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)
virtual double	GetCellCellAdhesionEnergy (CellPtr pCellA, CellPtr pCellB)
virtual double	GetCellBoundaryAdhesionEnergy (CellPtr pCell)
double	GetCellCellAdhesionEnergyParameter ()
double	GetCellBoundaryAdhesionEnergyParameter ()
void	SetCellCellAdhesionEnergyParameter (double cellCellAdhesionEnergyEnergyParameter)
void	SetCellBoundaryAdhesionEnergyParameter (double cellBoundaryAdhesionEnergyParameter)
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	mCellCellAdhesionEnergyParameter
double	mCellBoundaryAdhesionEnergyParameter

Friends
class	TestPottsUpdateRules
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AdhesionPottsUpdateRule< DIM >

An adhesion update rule for use in cell-based simulations using the cellular Potts model.

Definition at line 50 of file AdhesionPottsUpdateRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AdhesionPottsUpdateRule< DIM >::AdhesionPottsUpdateRule

(

)

Constructor.

Definition at line 39 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

AdhesionPottsUpdateRule< DIM >::~AdhesionPottsUpdateRule ( )

virtual

Destructor.

Definition at line 47 of file AdhesionPottsUpdateRule.cpp.

Member Function Documentation

template<unsigned DIM>

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

virtual

Overridden EvaluateHamiltonianContribution() method

Uses sum_adjacentsites (1-delta(spin(i),spin(j))) gamma(spin(i),spin(j))

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

Before the move, we have a negative contribution (H_0) to the Hamiltonian if: the target node and neighbouring node are NOT contained in the same Potts element; the neighbouring node is contained in a Potts element, but the target node is not; or the target node is contained in a Potts element, but the neighbouring node is not.

After the move, we have a positive contribution (H_1) to the Hamiltonian if: the current node and neighbouring node are contained in different Potts elements; the neighbouring node is contained in a Potts element, but the current node is not; or the current node is contained in a Potts element, but the neighbouring node is not.

Implements AbstractPottsUpdateRule< DIM >.

Definition at line 52 of file AdhesionPottsUpdateRule.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), PottsBasedCellPopulation< DIM >::GetNode(), and PottsBasedCellPopulation< DIM >::rGetMesh().

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy ( CellPtr  pCell )

virtual

Method to calculate the specific interaction between cell and medium can be overridden in child classes to implement differential adhesion .etc.

Parameters

pCell

pointer to the cell

Returns

Cell boundary interaction adhesion energy for the cell

Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.

Definition at line 161 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter

(

)

Returns

mCellBoundaryAdhesionEnergyParameter

Definition at line 173 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy ( CellPtr  pCellA, CellPtr  pCellB  )

virtual

Method to calculate the specific interaction between 2 cells can be overridden in child classes to implement differential adhesion .etc.

Parameters

pCellA	pointer to the 1st cell
pCellB	pointer to the 2nd cell

Returns

The cell cell interaction adhesion energy between the two cells

Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.

Definition at line 155 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter

(

)

Returns

mCellCellAdhesionEnergyParameter

Definition at line 167 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

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

virtual

Overridden OutputUpdateRuleParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractPottsUpdateRule< DIM >.

Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.

Definition at line 191 of file AdhesionPottsUpdateRule.cpp.

References AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

template<unsigned DIM>

template<class Archive >

void AdhesionPottsUpdateRule< 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 79 of file AdhesionPottsUpdateRule.hpp.

References AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter, and AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter.

template<unsigned DIM>

void AdhesionPottsUpdateRule< DIM >::SetCellBoundaryAdhesionEnergyParameter

(

double

cellBoundaryAdhesionEnergyParameter

)

Set mCellBoundaryAdhesionEnergyParameter.

Parameters

cellBoundaryAdhesionEnergyParameter

the new value of mCellBoundaryAdhesionEnergyParameter

Definition at line 185 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

void AdhesionPottsUpdateRule< DIM >::SetCellCellAdhesionEnergyParameter

(

double

cellCellAdhesionEnergyEnergyParameter

)

Set mCellCellAdhesionEnergyParameter.

Parameters

cellCellAdhesionEnergyEnergyParameter

the new value of mCellCellAdhesionEnergyParameter

Definition at line 179 of file AdhesionPottsUpdateRule.cpp.

Member Data Documentation

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter

private

Cell-boundary adhesion energy parameter. Set to the default value 0.2 in the constructor.

Todo:

provide units

Definition at line 68 of file AdhesionPottsUpdateRule.hpp.

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

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter

private

Cell-cell adhesion energy parameter. Set to the default value 0.1 in the constructor.

Todo:

provide units

Definition at line 61 of file AdhesionPottsUpdateRule.hpp.

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

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

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