#include <FarhadifarForce.hpp>

Inheritance diagram for FarhadifarForce< DIM >:

Collaboration diagram for FarhadifarForce< DIM >:

Public Member Functions
	FarhadifarForce ()

virtual	~FarhadifarForce ()

virtual void	AddForceContribution (AbstractCellPopulation< DIM > &rCellPopulation)

virtual double	GetLineTensionParameter (Node< DIM > pNodeA, Node< DIM > pNodeB, VertexBasedCellPopulation< DIM > &rVertexCellPopulation)

double	GetAreaElasticityParameter ()

double	GetPerimeterContractilityParameter ()

double	GetLineTensionParameter ()

double	GetBoundaryLineTensionParameter ()

void	SetAreaElasticityParameter (double areaElasticityParameter)

void	SetPerimeterContractilityParameter (double perimeterContractilityParameter)

void	SetLineTensionParameter (double lineTensionParameter)

void	SetBoundaryLineTensionParameter (double boundaryLineTensionParameter)

void	OutputForceParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractForce< DIM >
	AbstractForce ()

virtual	~AbstractForce ()

virtual void	AddForceContribution (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation)=0

void	OutputForceInfo (out_stream &rParamsFile)

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Attributes
double	mAreaElasticityParameter

double	mPerimeterContractilityParameter

double	mLineTensionParameter

double	mBoundaryLineTensionParameter

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	TestForces

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class FarhadifarForce< DIM >

A force class for use in Vertex-based simulations. This force is based on the Energy function proposed by Farhadifar et al in Curr. Biol., 2007, 17, 2095-2104.

Definition at line 55 of file FarhadifarForce.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

FarhadifarForce< DIM >::FarhadifarForce ( )

Constructor.

Definition at line 39 of file FarhadifarForce.cpp.

template<unsigned DIM>

FarhadifarForce< DIM >::~FarhadifarForce ( )

virtual

Destructor.

Definition at line 49 of file FarhadifarForce.cpp.

Member Function Documentation

template<unsigned DIM>

void FarhadifarForce< DIM >::AddForceContribution ( AbstractCellPopulation< DIM > & rCellPopulation )

virtual

Overridden AddForceContribution() method.

Calculates the force on each node in the vertex-based cell population based on the energy function Farhadifar's model.

Parameters

rCellPopulation reference to the cell population

Todo:: : check whether this line influences profiling tests - if so, we should remove it.

Definition at line 54 of file FarhadifarForce.cpp.

template<unsigned DIM>

double FarhadifarForce< DIM >::GetAreaElasticityParameter ( )

Returns: mAreaElasticityParameter

Definition at line 200 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mAreaElasticityParameter.

Referenced by FarhadifarForce< DIM >::AddForceContribution().

template<unsigned DIM>

double FarhadifarForce< DIM >::GetBoundaryLineTensionParameter ( )

Returns: mBoundaryLineTensionParameter

Definition at line 218 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mBoundaryLineTensionParameter.

Referenced by FarhadifarForce< DIM >::GetLineTensionParameter().

template<unsigned DIM>

double FarhadifarForce< DIM >::GetLineTensionParameter	(	Node< DIM > *	pNodeA,
		Node< DIM > *	pNodeB,
		VertexBasedCellPopulation< DIM > &	rVertexCellPopulation
	)

virtual

Get the line tension parameter for the edge between two given nodes.

Parameters

pNodeA	one node
pNodeB	the other node
rVertexCellPopulation	reference to the cell population

Returns: the line tension parameter for this edge.

Definition at line 169 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::GetBoundaryLineTensionParameter(), FarhadifarForce< DIM >::GetLineTensionParameter(), and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned DIM>

double FarhadifarForce< DIM >::GetLineTensionParameter ( )

Returns: mLineTensionParameter

Definition at line 212 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mLineTensionParameter.

Referenced by FarhadifarForce< DIM >::AddForceContribution(), and FarhadifarForce< DIM >::GetLineTensionParameter().

template<unsigned DIM>

double FarhadifarForce< DIM >::GetPerimeterContractilityParameter ( )

Returns: mPerimeterContractilityParameter

Definition at line 206 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mPerimeterContractilityParameter.

Referenced by FarhadifarForce< DIM >::AddForceContribution().

template<unsigned DIM>

void FarhadifarForce< DIM >::OutputForceParameters ( out_stream & rParamsFile )

virtual

Overridden OutputForceParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractForce< DIM >.

Definition at line 248 of file FarhadifarForce.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, FarhadifarForce< DIM >::mAreaElasticityParameter, FarhadifarForce< DIM >::mBoundaryLineTensionParameter, FarhadifarForce< DIM >::mLineTensionParameter, FarhadifarForce< DIM >::mPerimeterContractilityParameter, and AbstractForce< ELEMENT_DIM, SPACE_DIM >::OutputForceParameters().

template<unsigned DIM>

template<class Archive >

void FarhadifarForce< 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 70 of file FarhadifarForce.hpp.

References FarhadifarForce< DIM >::mAreaElasticityParameter, FarhadifarForce< DIM >::mBoundaryLineTensionParameter, FarhadifarForce< DIM >::mLineTensionParameter, and FarhadifarForce< DIM >::mPerimeterContractilityParameter.

template<unsigned DIM>

void FarhadifarForce< DIM >::SetAreaElasticityParameter ( double areaElasticityParameter )

Set mAreaElasticityParameter.

Parameters

areaElasticityParameter the new value of mAreaElasticityParameter

Definition at line 224 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mAreaElasticityParameter.

template<unsigned DIM>

void FarhadifarForce< DIM >::SetBoundaryLineTensionParameter ( double boundaryLineTensionParameter )

Set mBoundaryLineTensionParameter.

Parameters

boundaryLineTensionParameter the new value of mBoundaryLineTensionParameter

Definition at line 242 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mBoundaryLineTensionParameter.

template<unsigned DIM>

void FarhadifarForce< DIM >::SetLineTensionParameter ( double lineTensionParameter )

Set mLineTensionParameter.

Parameters

lineTensionParameter the new value of mLineTensionParameter

Definition at line 236 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mLineTensionParameter.

template<unsigned DIM>

void FarhadifarForce< DIM >::SetPerimeterContractilityParameter ( double perimeterContractilityParameter )

Set mPerimeterContractilityParameter.

Parameters

perimeterContractilityParameter the new value of perimterContractilityParameter

Definition at line 230 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mPerimeterContractilityParameter.

Member Data Documentation

template<unsigned DIM>

double FarhadifarForce< DIM >::mAreaElasticityParameter

protected

The strength of the area term in the model. Corresponds to K_alpha in Farhadifar's paper.

Definition at line 84 of file FarhadifarForce.hpp.

Referenced by FarhadifarForce< DIM >::GetAreaElasticityParameter(), FarhadifarForce< DIM >::OutputForceParameters(), FarhadifarForce< DIM >::serialize(), and FarhadifarForce< DIM >::SetAreaElasticityParameter().

template<unsigned DIM>

double FarhadifarForce< DIM >::mBoundaryLineTensionParameter

protected

The strength of the line tension at the boundary. This term does correspond to Lambda_{i,j} in Farhadifar's paper.

Definition at line 99 of file FarhadifarForce.hpp.

Referenced by FarhadifarForce< DIM >::GetBoundaryLineTensionParameter(), FarhadifarForce< DIM >::OutputForceParameters(), FarhadifarForce< DIM >::serialize(), and FarhadifarForce< DIM >::SetBoundaryLineTensionParameter().

template<unsigned DIM>

double FarhadifarForce< DIM >::mLineTensionParameter

protected

The strength of the line tension term in the model. Lambda_{i,j} in Farhadifar's paper.

Definition at line 94 of file FarhadifarForce.hpp.

Referenced by FarhadifarForce< DIM >::GetLineTensionParameter(), FarhadifarForce< DIM >::OutputForceParameters(), FarhadifarForce< DIM >::serialize(), and FarhadifarForce< DIM >::SetLineTensionParameter().

template<unsigned DIM>

double FarhadifarForce< DIM >::mPerimeterContractilityParameter

protected

The strength of the perimeter term in the model. Corresponds to Gamma_alpha in Farhadifar's paper.

Definition at line 89 of file FarhadifarForce.hpp.

Referenced by FarhadifarForce< DIM >::GetPerimeterContractilityParameter(), FarhadifarForce< DIM >::OutputForceParameters(), FarhadifarForce< DIM >::serialize(), and FarhadifarForce< DIM >::SetPerimeterContractilityParameter().

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

cell_based/src/population/forces/FarhadifarForce.hpp
cell_based/src/population/forces/FarhadifarForce.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class FarhadifarForce< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class FarhadifarForce< DIM >