BuskeCompressionForce< DIM > Class Template Reference

#include <BuskeCompressionForce.hpp>

Inheritance diagram for BuskeCompressionForce< DIM >:

Collaboration diagram for BuskeCompressionForce< DIM >:

Public Member Functions
	BuskeCompressionForce ()
double	GetCompressionEnergyParameter ()
void	SetCompressionEnergyParameter (double compressionEnergyParameter)
void	AddForceContribution (AbstractCellPopulation< DIM > &rCellPopulation)
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

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

Private Attributes
double	mCompressionEnergyParameter

Friends
class	TestForcesNotForRelease
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class BuskeCompressionForce< DIM >

A force law employed by Buske et al (2011) in their overlapping spheres model of the intestinal crypt (doi:10.1371/journal.pcbi.1001045).

Length is scaled by natural length.

Todo:

does this mean natural radius of a cell? If so at what age? (#1764) Time is in hours.

This class specifically calculates the compression force which forms part of equation (A6) in the Buske paper.

Definition at line 55 of file BuskeCompressionForce.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

BuskeCompressionForce< DIM >::BuskeCompressionForce

(

)

Constructor.

Definition at line 40 of file BuskeCompressionForce.cpp.

Member Function Documentation

template<unsigned DIM>

void BuskeCompressionForce< DIM >::AddForceContribution

(

AbstractCellPopulation< DIM > &

rCellPopulation

)

Overridden AddForceContribution() method.

Parameters

rCellPopulation

a cell population object

Target volume of the cell

Todo:

Doesn't say in the Buske paper how they calculate this, so we need to look at this to be sure it's what we want (#1764)

Definition at line 59 of file BuskeCompressionForce.cpp.

References Node< SPACE_DIM >::AddAppliedForceContribution(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode(), Node< SPACE_DIM >::GetRadius(), BuskeCompressionForce< DIM >::mCompressionEnergyParameter, and Node< SPACE_DIM >::rGetLocation().

template<unsigned DIM>

double BuskeCompressionForce< DIM >::GetCompressionEnergyParameter

(

)

Returns

mCompressionEnergyParameter.

Definition at line 47 of file BuskeCompressionForce.cpp.

References BuskeCompressionForce< DIM >::mCompressionEnergyParameter.

template<unsigned DIM>

void BuskeCompressionForce< 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 142 of file BuskeCompressionForce.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, BuskeCompressionForce< DIM >::mCompressionEnergyParameter, and AbstractForce< ELEMENT_DIM, SPACE_DIM >::OutputForceParameters().

template<unsigned DIM>

template<class Archive >

void BuskeCompressionForce< 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 69 of file BuskeCompressionForce.hpp.

References BuskeCompressionForce< DIM >::mCompressionEnergyParameter.

template<unsigned DIM>

void BuskeCompressionForce< DIM >::SetCompressionEnergyParameter

(

double

compressionEnergyParameter

)

Set mCompressionEnergyParameter.

Parameters

compressionEnergyParameter

the new value of mCompressionEnergyParameter

Definition at line 53 of file BuskeCompressionForce.cpp.

References BuskeCompressionForce< DIM >::mCompressionEnergyParameter.

Member Data Documentation

template<unsigned DIM>

double BuskeCompressionForce< DIM >::mCompressionEnergyParameter

private

Returns

Compression energy parameter.

Represented by the parameter K in the model by Buske et al (2011) in their off-lattice model of the intestinal crypt (doi:10.1371/journal.pcbi.1001045).

Note: K is the bulk modulus of the spheres.

Definition at line 84 of file BuskeCompressionForce.hpp.

Referenced by BuskeCompressionForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::GetCompressionEnergyParameter(), BuskeCompressionForce< DIM >::OutputForceParameters(), BuskeCompressionForce< DIM >::serialize(), and BuskeCompressionForce< DIM >::SetCompressionEnergyParameter().

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

• cell_based/src/population/forces/BuskeCompressionForce.hpp
• cell_based/src/population/forces/BuskeCompressionForce.cpp