FarhadifarForce< DIM > Class Template Reference

#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 ()
double	GetTargetAreaParameter ()
void	SetAreaElasticityParameter (double areaElasticityParameter)
void	SetPerimeterContractilityParameter (double perimeterContractilityParameter)
void	SetLineTensionParameter (double lineTensionParameter)
void	SetBoundaryLineTensionParameter (double boundaryLineTensionParameter)
void	SetTargetAreaParameter (double targetAreaParameter)
void	OutputForceParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractForce< DIM >
	AbstractForce ()
virtual	~AbstractForce ()
virtual void	AddForceContribution (AbstractCellPopulation< ELEMENT_DIM, SPACE_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
double	mTargetAreaParameter

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

FarhadifarForce()

template<unsigned DIM>

FarhadifarForce< DIM >::FarhadifarForce

(

)

Constructor.

Definition at line 39 of file FarhadifarForce.cpp.

~FarhadifarForce()

template<unsigned DIM>

FarhadifarForce< DIM >::~FarhadifarForce ( )

virtual

Destructor.

Definition at line 50 of file FarhadifarForce.cpp.

Member Function Documentation

AddForceContribution()

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 55 of file FarhadifarForce.cpp.

References Node< SPACE_DIM >::AddAppliedForceContribution(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), EXCEPTION, VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), VertexBasedCellPopulation< DIM >::GetElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexBasedCellPopulation< DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), MutableElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocalIndex(), VertexBasedCellPopulation< DIM >::GetNumElements(), VertexBasedCellPopulation< DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), Node< SPACE_DIM >::rGetContainingElementIndices(), and VertexBasedCellPopulation< DIM >::rGetMesh().

GetAreaElasticityParameter()

template<unsigned DIM>

double FarhadifarForce< DIM >::GetAreaElasticityParameter

(

)

Returns

mAreaElasticityParameter

Definition at line 206 of file FarhadifarForce.cpp.

GetBoundaryLineTensionParameter()

template<unsigned DIM>

double FarhadifarForce< DIM >::GetBoundaryLineTensionParameter

(

)

Returns

mBoundaryLineTensionParameter

Definition at line 224 of file FarhadifarForce.cpp.

GetLineTensionParameter() [1/2]

template<unsigned DIM>

double FarhadifarForce< DIM >::GetLineTensionParameter

(

)

Returns

mLineTensionParameter

Definition at line 218 of file FarhadifarForce.cpp.

GetLineTensionParameter() [2/2]

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.

Reimplemented in PlanarPolarisedFarhadifarForce< DIM >.

Definition at line 175 of file FarhadifarForce.cpp.

References Node< SPACE_DIM >::rGetContainingElementIndices().

GetPerimeterContractilityParameter()

template<unsigned DIM>

double FarhadifarForce< DIM >::GetPerimeterContractilityParameter

(

)

Returns

mPerimeterContractilityParameter

Definition at line 212 of file FarhadifarForce.cpp.

GetTargetAreaParameter()

template<unsigned DIM>

double FarhadifarForce< DIM >::GetTargetAreaParameter

(

)

Returns

mTargetAreaParameter

Definition at line 230 of file FarhadifarForce.cpp.

OutputForceParameters()

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 >.

Reimplemented in PlanarPolarisedFarhadifarForce< DIM >.

Definition at line 266 of file FarhadifarForce.cpp.

References AbstractForce< ELEMENT_DIM, SPACE_DIM >::OutputForceParameters().

Referenced by PlanarPolarisedFarhadifarForce< DIM >::OutputForceParameters().

serialize()

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, FarhadifarForce< DIM >::mPerimeterContractilityParameter, and FarhadifarForce< DIM >::mTargetAreaParameter.

SetAreaElasticityParameter()

template<unsigned DIM>

void FarhadifarForce< DIM >::SetAreaElasticityParameter

(

double

areaElasticityParameter

)

Set mAreaElasticityParameter.

Parameters

areaElasticityParameter

the new value of mAreaElasticityParameter

Definition at line 236 of file FarhadifarForce.cpp.

SetBoundaryLineTensionParameter()

template<unsigned DIM>

void FarhadifarForce< DIM >::SetBoundaryLineTensionParameter

(

double

boundaryLineTensionParameter

)

Set mBoundaryLineTensionParameter.

Parameters

boundaryLineTensionParameter

the new value of mBoundaryLineTensionParameter

Definition at line 254 of file FarhadifarForce.cpp.

SetLineTensionParameter()

template<unsigned DIM>

void FarhadifarForce< DIM >::SetLineTensionParameter

(

double

lineTensionParameter

)

Set mLineTensionParameter.

Parameters

lineTensionParameter

the new value of mLineTensionParameter

Definition at line 248 of file FarhadifarForce.cpp.

SetPerimeterContractilityParameter()

template<unsigned DIM>

void FarhadifarForce< DIM >::SetPerimeterContractilityParameter

(

double

perimeterContractilityParameter

)

Set mPerimeterContractilityParameter.

Parameters

perimeterContractilityParameter

the new value of perimterContractilityParameter

Definition at line 242 of file FarhadifarForce.cpp.

SetTargetAreaParameter()

template<unsigned DIM>

void FarhadifarForce< DIM >::SetTargetAreaParameter

(

double

targetAreaParameter

)

Set mTargetAreaParameter.

Parameters

targetAreaParameter

the new value of mTargetAreaParameter

Definition at line 260 of file FarhadifarForce.cpp.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Definition at line 61 of file FarhadifarForce.hpp.

TestForces

template<unsigned DIM>

friend class TestForces

friend

Definition at line 57 of file FarhadifarForce.hpp.

Member Data Documentation

mAreaElasticityParameter

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 85 of file FarhadifarForce.hpp.

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

mBoundaryLineTensionParameter

template<unsigned DIM>

double FarhadifarForce< DIM >::mBoundaryLineTensionParameter

protected

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

Definition at line 100 of file FarhadifarForce.hpp.

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

mLineTensionParameter

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 95 of file FarhadifarForce.hpp.

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

mPerimeterContractilityParameter

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 90 of file FarhadifarForce.hpp.

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

mTargetAreaParameter

template<unsigned DIM>

double FarhadifarForce< DIM >::mTargetAreaParameter

protected

The target area. This term corresponds to A_0 in Farhadifar's paper.

Note: If a subclass of AbstractTargetAreaModifier is present in the cell-based simulation, then we use the CellData item "target area" stored in each Cell in the force calculation instead of this parameter value.

Definition at line 109 of file FarhadifarForce.hpp.

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

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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