#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.

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

template<unsigned DIM>

AdhesionPottsUpdateRule< DIM >::~AdhesionPottsUpdateRule ( )

virtual

Destructor.

Definition at line 47 of file AdhesionPottsUpdateRule.cpp.

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

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

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

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.

References AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter().

Referenced by AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), and AdhesionPottsUpdateRule< DIM >::serialize().

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter ( )

Returns: mCellBoundaryAdhesionEnergyParameter

Definition at line 173 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter.

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

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.

References AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter().

Referenced by AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), and AdhesionPottsUpdateRule< DIM >::serialize().

template<unsigned DIM>

double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter ( )

Returns: mCellCellAdhesionEnergyParameter

Definition at line 167 of file AdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter.

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

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 EXPORT_TEMPLATE_CLASS_SAME_DIMS, AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter, AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter, and AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

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

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.

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.

References AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter.

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

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.

References AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter.

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

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

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class AdhesionPottsUpdateRule< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class AdhesionPottsUpdateRule< DIM >