Chaste  Release::2017.1
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 ()
 
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
rCellPopulationreference 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 ( )
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
pNodeAone node
pNodeBthe other node
rVertexCellPopulationreference 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 ( )
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
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
archiveThe boost archive.
versionThe 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
areaElasticityParameterthe 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
boundaryLineTensionParameterthe 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
lineTensionParameterthe 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
perimeterContractilityParameterthe 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: