AdhesionPottsUpdateRule< DIM > Class Template Reference

#include <AdhesionPottsUpdateRule.hpp>

Inherits AbstractPottsUpdateRule< DIM >.

Inherited by DifferentialAdhesionPottsUpdateRule< 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)
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 ( ) [inline]

Constructor.

Definition at line 39 of file AdhesionPottsUpdateRule.cpp.

template<unsigned DIM>

AdhesionPottsUpdateRule< DIM >::~AdhesionPottsUpdateRule ( ) [inline, 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
	)			`[inline, 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, AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy(), AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy(), AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), PottsBasedCellPopulation< DIM >::GetNode(), and PottsBasedCellPopulation< DIM >::rGetMesh().

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy ( CellPtr pCell ) [inline, 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 162 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter().

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

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter ( ) [inline]

Returns:: mCellBoundaryAdhesionEnergyParameter

Definition at line 174 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy(), and AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy().

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy	(	CellPtr	pCellA,
		CellPtr	pCellB
	)			`[inline, 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 156 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter().

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

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter ( ) [inline]

Returns:: mCellCellAdhesionEnergyParameter

Definition at line 168 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy(), and AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy().

template<unsigned DIM>

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

Overridden OutputUpdateRuleParameters() method.

Parameters:

rParamsFile

the file stream to which the parameters are output

Implements AbstractPottsUpdateRule< DIM >.

Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.

Definition at line 192 of file AdhesionPottsUpdateRule.cpp.

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

template<unsigned DIM>

template<class Archive >

void AdhesionPottsUpdateRule< 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 >.

Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.

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 ) [inline]

Set mCellBoundaryAdhesionEnergyParameter.

Parameters:

cellBoundaryAdhesionEnergyParameter

the new value of mCellBoundaryAdhesionEnergyParameter

Definition at line 186 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter.

template<unsigned DIM>

void AdhesionPottsUpdateRule< DIM >::SetCellCellAdhesionEnergyParameter ( double cellCellAdhesionEnergyEnergyParameter ) [inline]

Set mCellCellAdhesionEnergyParameter.

Parameters:

cellCellAdhesionEnergyEnergyParameter

the new value of mCellCellAdhesionEnergyParameter

Definition at line 180 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractPottsUpdateRule< DIM >.

Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.

Definition at line 70 of file AdhesionPottsUpdateRule.hpp.

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 >::GetCellBoundaryAdhesionEnergyParameter(), AdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), AdhesionPottsUpdateRule< DIM >::serialize(), and AdhesionPottsUpdateRule< DIM >::SetCellBoundaryAdhesionEnergyParameter().

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 >::GetCellCellAdhesionEnergyParameter(), AdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), AdhesionPottsUpdateRule< DIM >::serialize(), and AdhesionPottsUpdateRule< DIM >::SetCellCellAdhesionEnergyParameter().

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

AdhesionPottsUpdateRule< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class AdhesionPottsUpdateRule< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AdhesionPottsUpdateRule< DIM >