FarhadifarForce< DIM > Class Template Reference

#include <FarhadifarForce.hpp>

Inherits AbstractForce< DIM >.

Collaboration diagram for FarhadifarForce< DIM >:
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List of all members.

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)

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 (  )  [inline]

Constructor.

Definition at line 39 of file FarhadifarForce.cpp.

template<unsigned DIM>
FarhadifarForce< DIM >::~FarhadifarForce (  )  [inline, virtual]

Destructor.

Definition at line 49 of file FarhadifarForce.cpp.

Member Function Documentation

template<unsigned DIM>
void FarhadifarForce< DIM >::AddForceContribution ( AbstractCellPopulation< DIM > &  rCellPopulation  )  [inline, 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.

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

template<unsigned DIM>
double FarhadifarForce< DIM >::GetAreaElasticityParameter (  )  [inline]
Returns:
mAreaElasticityParameter

Definition at line 201 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mAreaElasticityParameter.

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

template<unsigned DIM>
double FarhadifarForce< DIM >::GetBoundaryLineTensionParameter (  )  [inline]
Returns:
mBoundaryLineTensionParameter

Definition at line 219 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mBoundaryLineTensionParameter.

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

template<unsigned DIM>
double FarhadifarForce< DIM >::GetLineTensionParameter (  )  [inline]
Returns:
mLineTensionParameter

Definition at line 213 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mLineTensionParameter.

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

template<unsigned DIM>
double FarhadifarForce< DIM >::GetLineTensionParameter ( Node< DIM > *  pNodeA,
Node< DIM > *  pNodeB,
VertexBasedCellPopulation< DIM > &  rVertexCellPopulation 
) [inline, 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 170 of file FarhadifarForce.cpp.

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

template<unsigned DIM>
double FarhadifarForce< DIM >::GetPerimeterContractilityParameter (  )  [inline]
Returns:
mPerimeterContractilityParameter

Definition at line 207 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mPerimeterContractilityParameter.

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

template<unsigned DIM>
void FarhadifarForce< DIM >::OutputForceParameters ( out_stream &  rParamsFile  )  [inline, virtual]

Overridden OutputForceParameters() method.

Parameters:
rParamsFile the file stream to which the parameters are output

Implements AbstractForce< DIM >.

Definition at line 250 of file FarhadifarForce.cpp.

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

template<unsigned DIM>
template<class Archive >
void FarhadifarForce< 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 AbstractForce< DIM >.

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  )  [inline]

Set mAreaElasticityParameter.

Parameters:
areaElasticityParameter the new value of mAreaElasticityParameter

Definition at line 225 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mAreaElasticityParameter.

template<unsigned DIM>
void FarhadifarForce< DIM >::SetBoundaryLineTensionParameter ( double  boundaryLineTensionParameter  )  [inline]

Set mBoundaryLineTensionParameter.

Parameters:
boundaryLineTensionParameter the new value of mBoundaryLineTensionParameter

Definition at line 243 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mBoundaryLineTensionParameter.

template<unsigned DIM>
void FarhadifarForce< DIM >::SetLineTensionParameter ( double  lineTensionParameter  )  [inline]

Set mLineTensionParameter.

Parameters:
lineTensionParameter the new value of mLineTensionParameter

Definition at line 237 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mLineTensionParameter.

template<unsigned DIM>
void FarhadifarForce< DIM >::SetPerimeterContractilityParameter ( double  perimeterContractilityParameter  )  [inline]

Set mPerimeterContractilityParameter.

Parameters:
perimeterContractilityParameter the new value of perimterContractilityParameter

Definition at line 231 of file FarhadifarForce.cpp.

References FarhadifarForce< DIM >::mPerimeterContractilityParameter.

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractForce< DIM >.

Definition at line 61 of file FarhadifarForce.hpp.

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:
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